Trajectory analysis¶
This example shows how to compute interactions for a trajectory performed using NAMD software for a small protein tyrosine phosphatase LMW-PTP in a complex with inhibitor MES (PDB: 5KQM) and visualize the results using Matplotlib library and VMD program.
In the tutorial, we will use already prepared files for simulation (PDB and DCD file).
Parse trajectory¶
We start by parsing PDB and DCD files, which contain LMW-PTP protein structure (available as tutorial files). PDB file contains the coordinates of protein structure with water and counter ions. DCD file is a binary file that contains a short simulation computed in NAMD package (20 frames). The commands shown below are explained in Trajectory Analysis tutorial.
In [1]: PDBfile = '5kqm_all_sci.pdb'
In [2]: DCDfile = 'NAMD_D2_co100.dcd'
In [3]: atoms = parsePDB(PDBfile)
In [4]: dcd = Trajectory(DCDfile)
In [5]: dcd.link(atoms)
In [6]: dcd.setCoords(atoms)
@> 19321 atoms and 1 coordinate set(s) were parsed in 0.17s.
To compute hydrogen bonds for each frame of the simulation use
calcHydrogenBondsTrajectory() function:
In [7]: calcHydrogenBondsTrajectory(atoms, dcd)
@> Frame: 0
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ARG101 P NH1_1516 <---> ASP98 P OD1_1463 2.0 33.1
@> HSE72 P NE2_1042 <---> ASN15 P OD1_165 2.6 34.8
@> GLN143 P NE2_2192 <---> GLU139 P OE2_2126 2.7 9.2
@> HSE66 P NE2_957 <---> GLU139 P OE1_2125 2.7 6.4
@> ARG40 P N_561 <---> LYS6 P O_37 2.7 17.1
@> ARG58 P N_813 <---> ASP56 P OD1_788 2.7 30.0
@> ALA45 P N_634 <---> ARG75 P O_1097 2.8 35.1
@> ASN53 P ND2_747 <---> GLU50 P OE1_708 2.8 18.2
@> ALA74 P N_1064 <---> ASN53 P O_751 2.8 21.3
@> ASP56 P N_780 <---> ILE16 P O_189 2.8 27.0
@> LYS110 P NZ_1667 <---> THR84 P O_1240 2.8 38.2
@> LEU116 P N_1758 <---> CYS90 P O_1342 2.8 15.0
@> SER103 P N_1546 <---> LEU99 P O_1485 2.8 29.1
@> ASN134 P N_2045 <---> ASP137 P OD2_2091 2.8 22.6
@> PHE152 P N_2321 <---> CYS148 P O_2275 2.8 8.3
@> ASN95 P N_1398 <---> ASP92 P OD1_1368 2.8 12.6
@> LYS6 P N_16 <---> ASN38 P O_536 2.8 25.0
@> ILE77 P N_1115 <---> ALA45 P O_643 2.8 12.2
@> ARG58 P NH2_832 <---> ASP56 P OD2_789 2.8 27.7
@> LEU99 P N_1467 <---> ASN95 P O_1411 2.8 15.5
@> CYS149 P N_2276 <---> CYS145 P O_2224 2.8 9.6
@> GLY52 P N_731 <---> ALA74 P O_1073 2.8 6.6
@> ASP32 P N_435 <---> LYS28 P O_385 2.8 8.8
@> ILE88 P N_1294 <---> LYS112 P O_1704 2.8 17.7
@> GLN143 P N_2180 <---> GLU139 P O_2128 2.8 21.7
@> ARG27 P N_340 <---> GLU23 P O_293 2.8 15.4
@> TYR142 P N_2159 <---> PHE138 P O_2113 2.9 14.2
@> GLY133 P N_2038 <---> PRO130 P O_1995 2.9 25.4
@> PHE26 P N_320 <---> ALA22 P O_278 2.9 4.9
@> ASN15 P ND2_166 <---> SER19 P OG_232 2.9 32.1
@> ARG75 P NH1_1090 <---> ASP81 P OD2_1194 2.9 19.7
@> ARG75 P NH2_1093 <---> ASP42 P OD2_610 2.9 23.5
@> ARG97 P N_1431 <---> GLU93 P O_1386 2.9 22.2
@> ARG65 P NH2_941 <---> GLU139 P OE1_2125 2.9 32.3
@> VAL25 P N_304 <---> ILE21 P O_268 2.9 8.2
@> LEU153 P N_2341 <---> CYS149 P O_2286 2.9 12.5
@> SER7 P N_38 <---> ASP86 P OD2_1270 2.9 39.9
@> ASP86 P N_1261 <---> SER7 P OG_45 2.9 34.7
@> ARG58 P NH2_832 <---> TYR131 P O_2016 2.9 33.1
@> THR46 P N_644 <---> CYS12 P O_130 2.9 36.1
@> GLN144 P N_2197 <---> THR140 P O_2142 2.9 23.3
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.9 12.4
@> LEU89 P N_1313 <---> LEU9 P O_83 2.9 29.5
@> THR31 P N_421 <---> ARG27 P O_363 2.9 24.1
@> CYS90 P N_1332 <---> GLU114 P O_1738 2.9 24.6
..
..
@> ARG40 P NH1_577 <---> THR84 P OG1_1233 2.9 8.4
@> ALA44 P N_624 <---> PHE10 P O_103 2.9 33.2
@> GLU154 P N_2360 <---> ARG150 P O_2310 3.0 22.6
@> VAL8 P N_49 <---> ARG40 P O_584 3.0 25.0
@> SER19 P N_225 <---> CYS12 P SG_127 3.3 8.0
@> PHE82 P N_1197 <---> LYS79 P O_1169 3.4 37.7
@> ASP81 P N_1185 <---> THR78 P OG1_1140 3.5 39.5
@> LYS102 P NZ_1540 <---> ASP98 P OD2_1464 3.5 26.1
@> ARG147 P NH2_2260 <---> GLN124 P OE1_1892 3.5 33.9
@> VAL106 P N_1588 <---> SER103 P O_1556 3.5 34.2
@> Number of detected hydrogen bonds: 124.
@> Frame: 1
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> LYS112 P NZ_1699 <---> GLU114 P OE1_1735 2.5 20.8
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.5 15.6
@> ARG27 P NH2_359 <---> GLU23 P OE2_291 2.5 36.5
@> THR78 P OG1_1140 <---> ASP81 P OD2_1194 2.6 25.2
@> SER7 P OG_45 <---> ASP86 P OD2_1270 2.6 32.3
@> LYS102 P NZ_1540 <---> ASP98 P OD2_1464 2.6 18.6
@> LYS112 P NZ_1699 <---> HSE157 P OT1_2423 2.6 17.8
@> ARG75 P NH2_1093 <---> ASP81 P OD1_1193 2.6 17.6
@> SER118 P OG_1791 <---> LEU115 P O_1757 2.7 25.6
@> ARG58 P NE_826 <---> ASP56 P OD1_788 2.7 6.4
@> GLN124 P N_1881 <---> ASP120 P OD1_1824 2.7 17.2
@> ARG147 P NH1_2257 <---> GLN124 P OE1_1892 2.7 11.8
@> ARG18 P NH1_217 <---> ASP92 P OD2_1369 2.7 14.6
@> ARG75 P NH1_1090 <---> ASP81 P OD2_1194 2.7 23.9
@> TYR87 P OH_1286 <---> HSE157 P OT1_2423 2.7 11.6
@> SER43 P OG_620 <---> GLU23 P OE1_290 2.7 15.2
@> LYS28 P NZ_380 <---> ASP32 P OD1_443 2.7 3.6
@> LYS110 P NZ_1667 <---> ASP86 P OD1_1269 2.7 25.2
@> THR140 P OG1_2135 <---> SER136 P O_2081 2.7 5.2
@> LEU116 P N_1758 <---> CYS90 P O_1342 2.7 24.4
@> THR5 P OG1_8 <---> ASN38 P O_536 2.7 38.6
@> LYS64 P N_900 <---> GLN60 P O_860 2.7 26.8
@> ARG147 P NH1_2257 <---> ASP120 P OD2_1825 2.7 15.2
@> ARG27 P N_340 <---> GLU23 P O_293 2.7 21.9
@> TYR119 P OH_1808 <---> GLU114 P OE1_1735 2.7 15.9
@> ARG18 P NH1_217 <---> ILE127 P O_1954 2.8 16.0
@> SER103 P N_1546 <---> LEU99 P O_1485 2.8 13.6
@> LYS102 P N_1524 <---> ASP98 P O_1466 2.8 15.9
@> ARG58 P NH1_829 <---> GLY133 P O_2044 2.8 31.9
@> ARG75 P NH2_1093 <---> ASP42 P OD2_610 2.8 13.0
@> LYS112 P N_1683 <---> ASP86 P O_1272 2.8 13.2
..
..
@> ILE127 P N_1936 <---> MET91 P O_1359 3.3 29.4
@> ASN104 P N_1557 <---> ASN100 P O_1499 3.4 12.6
@> GLN105 P N_1571 <---> ARG101 P O_1523 3.4 38.7
@> ARG147 P N_2241 <---> GLN143 P O_2196 3.4 10.9
@> ASP56 P N_780 <---> ILE16 P O_189 3.4 25.5
@> ASN95 P N_1398 <---> ASP92 P OD1_1368 3.5 32.5
@> HSE72 P NE2_1042 <---> ASN15 P OD1_165 3.5 7.1
@> VAL106 P N_1588 <---> LYS102 P O_1545 3.5 29.8
@> ILE21 P N_250 <---> CYS17 P O_200 3.5 34.9
@> LEU96 P N_1412 <---> ASP92 P O_1371 3.5 8.7
@> Number of detected hydrogen bonds: 123.
@> Frame: 2
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ARG18 P NH1_217 <---> ASP92 P OD2_1369 2.5 4.9
@> THR31 P OG1_427 <---> ARG27 P O_363 2.5 5.5
@> ARG58 P NH2_832 <---> ASP56 P OD2_789 2.6 8.2
@> LYS112 P NZ_1699 <---> HSE157 P OT1_2423 2.6 19.0
@> ARG75 P NH2_1093 <---> ASP42 P OD2_610 2.6 25.0
@> TYR119 P OH_1808 <---> GLU114 P OE2_1736 2.6 10.3
@> LYS102 P NZ_1540 <---> ASP98 P OD2_1464 2.6 7.9
@> TYR87 P OH_1286 <---> HSE157 P OT1_2423 2.7 14.1
@> LYS64 P N_900 <---> GLN60 P O_860 2.7 4.9
@> SER43 P OG_620 <---> GLU23 P OE1_290 2.7 8.6
@> THR78 P OG1_1140 <---> ASP81 P OD2_1194 2.7 6.5
@> ILE88 P N_1294 <---> LYS112 P O_1704 2.7 25.0
@> SER118 P OG_1791 <---> LEU115 P O_1757 2.7 26.9
@> LYS28 P NZ_380 <---> ASP32 P OD2_444 2.7 13.9
@> THR84 P OG1_1233 <---> GLU80 P O_1184 2.7 13.4
@> LEU89 P N_1313 <---> LEU9 P O_83 2.8 11.8
@> ARG147 P NH1_2257 <---> GLN124 P OE1_1892 2.8 15.1
@> ARG27 P NH2_359 <---> GLU23 P OE2_291 2.8 18.0
@> ILE35 P N_478 <---> VAL30 P O_420 2.8 20.7
@> PHE26 P N_320 <---> ALA22 P O_278 2.8 21.8
@> VAL11 P N_104 <---> LEU89 P O_1331 2.8 10.3
@> VAL25 P N_304 <---> ILE21 P O_268 2.8 9.2
@> SER7 P OG_45 <---> ASP86 P OD2_1270 2.8 29.4
@> HSE72 P NE2_1042 <---> ASN15 P OD1_165 2.8 37.1
@> ASN34 P N_464 <---> THR31 P O_434 2.8 19.7
@> LYS110 P N_1651 <---> PHE82 P O_1216 2.8 9.2
@> LYS110 P NZ_1667 <---> ASP86 P OD1_1269 2.8 13.5
@> ARG58 P NE_826 <---> ASP56 P OD1_788 2.8 8.0
@> ARG75 P NH1_1090 <---> ASP81 P OD2_1194 2.8 14.9
@> VAL8 P N_49 <---> ARG40 P O_584 2.8 19.4
@> ARG18 P NH1_217 <---> ILE127 P O_1954 2.8 7.0
@> LYS155 P N_2375 <---> ALA151 P O_2320 2.8 15.1
@> HSE66 P NE2_957 <---> GLU139 P OE1_2125 2.8 28.9
@> ARG147 P NH1_2257 <---> ASP120 P OD2_1825 2.8 31.7
@> ARG97 P N_1431 <---> GLU93 P O_1386 2.8 15.2
@> LYS123 P N_1859 <---> ASP120 P OD1_1824 2.8 34.0
@> LYS112 P N_1683 <---> ASP86 P O_1272 2.8 10.3
@> ASP86 P N_1261 <---> SER7 P OG_45 2.8 22.0
@> ARG65 P N_922 <---> SER61 P O_871 2.8 24.4
@> ILE127 P N_1936 <---> MET91 P O_1359 2.8 4.1
@> LYS112 P NZ_1699 <---> HSE157 P ND1_2414 2.9 14.0
@> GLY67 P N_963 <---> MET63 P O_899 2.9 38.6
@> SER103 P N_1546 <---> LEU99 P O_1485 2.9 17.1
@> LYS112 P NZ_1699 <---> GLU114 P OE2_1736 2.9 18.1
@> ARG75 P NE_1087 <---> ASP42 P OD2_610 2.9 38.3
@> ALA44 P N_624 <---> PHE10 P O_103 2.9 30.1
@> ILE68 P N_970 <---> MET63 P O_899 2.9 12.9
@> ARG58 P N_813 <---> ASP56 P OD1_788 2.9 21.1
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.9 26.3
@> ALA45 P N_634 <---> ARG75 P O_1097 2.9 27.7
..
..
@> HSE66 P N_946 <---> CYS62 P O_882 2.9 17.6
@> ASP32 P N_435 <---> LYS28 P O_385 3.0 20.4
@> VAL146 P N_2225 <---> TYR142 P O_2179 3.0 20.7
@> VAL106 P N_1588 <---> LYS102 P O_1545 3.0 10.6
@> ARG40 P N_561 <---> LYS6 P O_37 3.4 33.1
@> HSE157 P N_2407 <---> TYR119 P OH_1808 3.4 27.6
@> ARG65 P NH1_938 <---> GLU139 P OE1_2125 3.4 32.0
@> GLU114 P N_1724 <---> ILE88 P O_1312 3.5 13.0
@> ASP92 P N_1360 <---> ASN95 P OD1_1406 3.5 35.4
@> ASN15 P ND2_166 <---> SER43 P OG_620 3.5 33.3
@> Number of detected hydrogen bonds: 113.
..
..
@> Frame: 20
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ARG97 P NE_1444 <---> GLU93 P OE1_1383 2.5 12.5
@> SER19 P OG_232 <---> ASN15 P OD1_165 2.6 31.5
@> ARG27 P NH1_356 <---> GLU23 P OE1_290 2.6 19.1
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.6 21.5
@> GLN122 P NE2_1854 <---> ASP120 P OD2_1825 2.6 39.7
@> SER118 P OG_1791 <---> GLU114 P OE2_1736 2.6 24.5
@> ARG65 P NH1_938 <---> GLU139 P OE1_2125 2.7 6.1
@> ARG65 P NH2_941 <---> ASP135 P OD1_2067 2.7 15.6
@> SER43 P OG_620 <---> GLU23 P OE2_291 2.7 13.9
@> ARG75 P NE_1087 <---> ASP42 P OD1_609 2.7 26.5
@> ARG150 P NE_2300 <---> GLU154 P OE2_2372 2.7 4.9
@> VAL106 P N_1588 <---> LYS102 P O_1545 2.7 16.2
@> LYS28 P N_364 <---> ALA24 P O_303 2.7 38.8
@> HSE157 P NE2_2418 <---> PHE152 P O_2340 2.7 28.5
@> ARG58 P NH2_832 <---> ASP56 P OD2_789 2.7 19.3
@> ARG97 P NH2_1450 <---> GLU93 P OE2_1384 2.7 15.8
@> ARG75 P NH2_1093 <---> ASP42 P OD1_609 2.7 30.5
@> ALA45 P N_634 <---> ARG75 P O_1097 2.7 22.3
@> ARG75 P NH2_1093 <---> ASP81 P OD1_1193 2.7 19.2
@> THR31 P OG1_427 <---> ARG27 P O_363 2.7 13.1
@> ARG150 P NH2_2306 <---> GLU154 P OE1_2371 2.7 8.5
@> ARG75 P NH1_1090 <---> ASP81 P OD2_1194 2.7 14.8
@> GLY67 P N_963 <---> MET63 P O_899 2.7 25.3
@> LEU89 P N_1313 <---> LEU9 P O_83 2.8 18.4
@> ARG101 P NH1_1516 <---> ASP98 P OD2_1464 2.8 11.5
@> ILE77 P N_1115 <---> ALA45 P O_643 2.8 39.9
@> LYS110 P N_1651 <---> PHE82 P O_1216 2.8 32.3
@> LEU29 P N_386 <---> VAL25 P O_319 2.8 5.4
@> ASN100 P N_1486 <---> LEU96 P O_1430 2.8 6.7
@> LYS102 P N_1524 <---> ASP98 P O_1466 2.8 4.9
@> THR78 P OG1_1140 <---> ASP81 P OD2_1194 2.8 10.5
@> VAL8 P N_49 <---> ARG40 P O_584 2.8 16.8
@> GLU154 P N_2360 <---> ARG150 P O_2310 2.8 15.1
@> LYS110 P NZ_1667 <---> ASP86 P OD2_1270 2.8 32.5
@> ARG58 P NE_826 <---> ASP56 P OD1_788 2.8 3.3
@> ILE35 P N_478 <---> VAL30 P O_420 2.8 7.9
@> ARG58 P NH1_829 <---> GLY133 P O_2044 2.8 34.3
@> GLN105 P N_1571 <---> ARG101 P O_1523 2.8 29.9
@> SER7 P N_38 <---> ASP86 P OD1_1269 2.8 10.5
@> ARG101 P NH2_1519 <---> ASP98 P OD1_1463 2.8 17.5
@> GLN143 P N_2180 <---> GLU139 P O_2128 2.8 20.5
@> CYS149 P N_2276 <---> CYS145 P O_2224 2.8 16.0
@> SER103 P OG_1553 <---> LEU99 P O_1485 2.9 21.4
@> ARG18 P NH1_217 <---> ASP92 P OD2_1369 2.9 6.7
@> CYS90 P N_1332 <---> GLU114 P O_1738 2.9 7.9
..
..
@> ALA151 P N_2311 <---> ARG147 P O_2264 3.3 28.5
@> ILE88 P N_1294 <---> LYS112 P O_1704 3.3 8.1
@> CYS12 P N_120 <---> ALA44 P O_633 3.4 24.0
@> GLN124 P NE2_1893 <---> ILE126 P O_1935 3.4 3.3
@> ARG97 P N_1431 <---> GLU93 P O_1386 3.4 28.8
@> SER61 P N_861 <---> TYR57 P O_812 3.4 29.6
@> GLN122 P NE2_1854 <---> ASP120 P OD1_1824 3.5 17.2
@> Number of detected hydrogen bonds: 114.
Similarly, it can be done with other interaction types. Salt bridges
(residues with opposite changes) with calcSaltBridgesTrajectory():
In [8]: calcSaltBridgesTrajectory(atoms, dcd)
@> Frame: 0
@> Calculating salt bridges.
@> GLU139 P OE1_2125_2126 <---> HSE66 P NE2_957 2.8
@> ASP81 P OD1_1193_1194 <---> ARG75 P NH1_1090_1093 2.9
@> ASP32 P OD1_443_444 <---> LYS28 P NZ_380 3.0
@> ASP98 P OD1_1463_1464 <---> ARG101 P NH1_1516_1519 3.1
@> ARG27 P NH1_356_359 <---> GLU23 P OE1_290_291 3.7
@> GLU139 P OE1_2125_2126 <---> ARG65 P NH1_938_941 3.8
@> LYS102 P NZ_1540 <---> ASP98 P OD1_1463_1464 3.9
@> ARG58 P NH1_829_832 <---> ASP56 P OD1_788_789 3.9
@> ARG18 P NH1_217_220 <---> ASP92 P OD1_1368_1369 4.1
@> GLU114 P OE1_1735_1736 <---> LYS112 P NZ_1699 4.1
@> ASP120 P OD1_1824_1825 <---> ARG147 P NH1_2257_2260 4.2
@> ASP86 P OD1_1269_1270 <---> LYS110 P NZ_1667 4.2
@> HSE157 P NE2_2418 <---> GLU114 P OE1_1735_1736 4.4
@> ARG18 P NH1_217_220 <---> ASP129 P OD1_1978_1979 4.6
@> ARG75 P NH1_1090_1093 <---> ASP42 P OD1_609_610 4.6
@> GLU23 P OE1_290_291 <---> HSE72 P NE2_1042 5.0
@> Number of detected salt bridges: 16.
@> Frame: 1
@> Calculating salt bridges.
@> ASP32 P OD1_443_444 <---> LYS28 P NZ_380 2.6
@> ASP81 P OD1_1193_1194 <---> ARG75 P NH1_1090_1093 2.6
@> ASP98 P OD1_1463_1464 <---> ARG101 P NH1_1516_1519 2.8
@> GLU114 P OE1_1735_1736 <---> LYS112 P NZ_1699 3.1
@> HSE157 P NE2_2418 <---> GLU114 P OE1_1735_1736 3.2
@> ASP86 P OD1_1269_1270 <---> LYS110 P NZ_1667 3.3
@> ARG27 P NH1_356_359 <---> GLU23 P OE1_290_291 3.4
@> GLU139 P OE1_2125_2126 <---> ARG65 P NH1_938_941 3.4
@> LYS102 P NZ_1540 <---> ASP98 P OD1_1463_1464 3.5
@> ASP120 P OD1_1824_1825 <---> ARG147 P NH1_2257_2260 3.8
@> ARG58 P NH1_829_832 <---> ASP56 P OD1_788_789 3.8
@> ARG18 P NH1_217_220 <---> ASP92 P OD1_1368_1369 3.8
@> GLU139 P OE1_2125_2126 <---> HSE66 P NE2_957 4.0
@> ARG75 P NH1_1090_1093 <---> ASP42 P OD1_609_610 4.5
@> Number of detected salt bridges: 14.
@> Frame: 2
@> Calculating salt bridges.
@> GLU114 P OE1_1735_1736 <---> LYS112 P NZ_1699 2.6
@> ASP32 P OD1_443_444 <---> LYS28 P NZ_380 2.6
@> GLU139 P OE1_2125_2126 <---> ARG65 P NH1_938_941 2.7
@> ASP81 P OD1_1193_1194 <---> ARG75 P NH1_1090_1093 2.9
@> LYS102 P NZ_1540 <---> ASP98 P OD1_1463_1464 3.1
@> ARG58 P NH1_829_832 <---> ASP56 P OD1_788_789 3.6
@> GLU139 P OE1_2125_2126 <---> HSE66 P NE2_957 3.6
@> ARG18 P NH1_217_220 <---> ASP92 P OD1_1368_1369 3.7
@> ASP86 P OD1_1269_1270 <---> LYS110 P NZ_1667 3.7
@> ASP120 P OD1_1824_1825 <---> ARG147 P NH1_2257_2260 3.8
@> ARG27 P NH1_356_359 <---> GLU23 P OE1_290_291 3.9
@> HSE157 P NE2_2418 <---> GLU114 P OE1_1735_1736 4.2
@> ARG75 P NH1_1090_1093 <---> ASP42 P OD1_609_610 4.3
@> ARG18 P NH1_217_220 <---> ASP129 P OD1_1978_1979 4.6
@> ASP86 P OD1_1269_1270 <---> LYS6 P NZ_32 5.0
@> Number of detected salt bridges: 15.
..
..
@> Frame: 18
@> Calculating salt bridges.
@> ASP81 P OD1_1193_1194 <---> ARG75 P NH1_1090_1093 2.6
@> ASP32 P OD1_443_444 <---> LYS28 P NZ_380 2.7
@> ASP135 P OD1_2067_2068 <---> ARG65 P NH1_938_941 2.8
@> LYS102 P NZ_1540 <---> ASP98 P OD1_1463_1464 3.0
@> GLU23 P OE1_290_291 <---> HSE72 P NE2_1042 3.4
@> ARG27 P NH1_356_359 <---> GLU23 P OE1_290_291 3.6
@> ARG58 P NH1_829_832 <---> ASP56 P OD1_788_789 3.6
@> ASP98 P OD1_1463_1464 <---> ARG101 P NH1_1516_1519 3.9
@> ARG18 P NH1_217_220 <---> ASP92 P OD1_1368_1369 4.2
@> ARG97 P NH1_1447_1450 <---> GLU93 P OE1_1383_1384 4.5
@> ARG150 P NH1_2303_2306 <---> GLU154 P OE1_2371_2372 4.5
@> ARG75 P NH1_1090_1093 <---> ASP42 P OD1_609_610 4.5
@> ARG18 P NH1_217_220 <---> ASP129 P OD1_1978_1979 4.7
@> Number of detected salt bridges: 13.
@> Frame: 19
@> Calculating salt bridges.
@> ASP135 P OD1_2067_2068 <---> ARG65 P NH1_938_941 2.7
@> ASP81 P OD1_1193_1194 <---> ARG75 P NH1_1090_1093 2.9
@> LYS102 P NZ_1540 <---> ASP98 P OD1_1463_1464 3.1
@> ARG27 P NH1_356_359 <---> GLU23 P OE1_290_291 3.3
@> ASP98 P OD1_1463_1464 <---> ARG101 P NH1_1516_1519 3.7
@> ARG58 P NH1_829_832 <---> ASP56 P OD1_788_789 3.7
@> ARG97 P NH1_1447_1450 <---> GLU93 P OE1_1383_1384 3.7
@> ASP86 P OD1_1269_1270 <---> LYS110 P NZ_1667 3.9
@> ARG18 P NH1_217_220 <---> ASP92 P OD1_1368_1369 3.9
@> GLU23 P OE1_290_291 <---> HSE72 P NE2_1042 4.0
@> ARG150 P NH1_2303_2306 <---> GLU154 P OE1_2371_2372 4.2
@> ARG75 P NH1_1090_1093 <---> ASP42 P OD1_609_610 4.6
@> Number of detected salt bridges: 12.
@> Frame: 20
@> Calculating salt bridges.
@> ASP135 P OD1_2067_2068 <---> ARG65 P NH1_938_941 2.5
@> ASP81 P OD1_1193_1194 <---> ARG75 P NH1_1090_1093 2.7
@> ASP98 P OD1_1463_1464 <---> ARG101 P NH1_1516_1519 2.8
@> ASP86 P OD1_1269_1270 <---> LYS110 P NZ_1667 3.4
@> ARG97 P NH1_1447_1450 <---> GLU93 P OE1_1383_1384 3.5
@> ARG150 P NH1_2303_2306 <---> GLU154 P OE1_2371_2372 3.7
@> ARG58 P NH1_829_832 <---> ASP56 P OD1_788_789 3.7
@> GLU139 P OE1_2125_2126 <---> HSE66 P NE2_957 3.9
@> ARG18 P NH1_217_220 <---> ASP92 P OD1_1368_1369 4.0
@> ARG27 P NH1_356_359 <---> GLU23 P OE1_290_291 4.0
@> ARG75 P NH1_1090_1093 <---> ASP42 P OD1_609_610 4.4
@> GLU23 P OE1_290_291 <---> HSE72 P NE2_1042 4.7
@> GLU139 P OE1_2125_2126 <---> ARG65 P NH1_938_941 4.8
@> ARG18 P NH1_217_220 <---> ASP129 P OD1_1978_1979 5.0
@> Number of detected salt bridges: 14.
Repulsive Ionic Bonding using calcRepulsiveIonicBondingTrajectory() for residues with
the same charges:
In [9]: calcRepulsiveIonicBondingTrajectory(atoms, dcd, distA=7)
@> Frame: 0
@> Calculating repulsive ionic bonding.
@> LYS102 P NZ_1540 <---> ARG101 P NH1_1516_1519 4.3
@> Number of detected Repulsive Ionic Bonding interactions: 1.
@> Frame: 1
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 2
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 3
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 4
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 5
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 6
@> Calculating repulsive ionic bonding.
@> LYS102 P NZ_1540 <---> ARG101 P NH1_1516_1519 4.3
@> Number of detected Repulsive Ionic Bonding interactions: 1.
@> Frame: 7
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 8
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 9
@> Calculating repulsive ionic bonding.
@> LYS102 P NZ_1540 <---> ARG101 P NH1_1516_1519 4.3
@> Number of detected Repulsive Ionic Bonding interactions: 1.
@> Frame: 10
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
..
..
@> Frame: 20
@> Calculating repulsive ionic bonding.
@> ARG147 P NH1_2257_2260 <---> LYS123 P NZ_1875 4.5
@> Number of detected Repulsive Ionic Bonding interactions: 1.
Pi-Stacking interactions using calcPiStackingTrajectory():
In [10]: calcPiStackingTrajectory(atoms, dcd, distA=5)
@> Frame: 0
@> Calculating Pi stacking interactions.
@> HSE66 P 953_954_955_957_959 <---> TYR142 P 2166_2167_2169_2171_2174_2176 3.9 162.1
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> TYR119 P 1802_1803_1805_1807_1810_1812 4.4 3.0
@> PHE26 P 327_328_330_332_334_336 <---> TRP39 P 549_550_551_553_555_557 4.8 75.5
@> TYR132 P 2024_2025_2027_2029_2032_2034 <---> TYR131 P 2003_2004_2006_2008_2011_2013 4.9 91.4
@> Number of detected Pi stacking interactions: 4.
@> Frame: 1
@> Calculating Pi stacking interactions.
@> PHE26 P 327_328_330_332_334_336 <---> TRP39 P 549_550_551_553_555_557 4.8 71.0
@> HSE66 P 953_954_955_957_959 <---> TYR142 P 2166_2167_2169_2171_2174_2176 4.8 138.9
@> Number of detected Pi stacking interactions: 2.
@> Frame: 2
@> Calculating Pi stacking interactions.
@> HSE66 P 953_954_955_957_959 <---> TYR142 P 2166_2167_2169_2171_2174_2176 3.6 174.2
@> Number of detected Pi stacking interactions: 1.
@> Frame: 3
@> Calculating Pi stacking interactions.
@> HSE66 P 953_954_955_957_959 <---> TYR142 P 2166_2167_2169_2171_2174_2176 4.1 143.3
@> Number of detected Pi stacking interactions: 1.
@> Frame: 4
@> Calculating Pi stacking interactions.
@> HSE66 P 953_954_955_957_959 <---> TYR142 P 2166_2167_2169_2171_2174_2176 4.3 137.5
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> PHE152 P 2328_2329_2331_2333_2335_2337 5.0 73.7
@> Number of detected Pi stacking interactions: 2.
..
..
@> Frame: 19
@> Calculating Pi stacking interactions.
@> TYR132 P 2024_2025_2027_2029_2032_2034 <---> TYR131 P 2003_2004_2006_2008_2011_2013 4.6 62.2
@> TYR119 P 1802_1803_1805_1807_1810_1812 <---> PHE152 P 2328_2329_2331_2333_2335_2337 4.9 60.8
@> Number of detected Pi stacking interactions: 2.
@> Frame: 20
@> Calculating Pi stacking interactions.
@> TYR119 P 1802_1803_1805_1807_1810_1812 <---> PHE152 P 2328_2329_2331_2333_2335_2337 4.7 125.5
@> HSE66 P 953_954_955_957_959 <---> TYR142 P 2166_2167_2169_2171_2174_2176 4.8 165.0
@> TYR132 P 2024_2025_2027_2029_2032_2034 <---> TYR131 P 2003_2004_2006_2008_2011_2013 4.9 116.3
@> Number of detected Pi stacking interactions: 3.
Pi-Cation interactions using calcPiCationTrajectory():
In [11]: calcPiCationTrajectory(atoms, dcd)
@> Frame: 0
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.7
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.5
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 4.8
@> Number of detected cation-pi interactions: 3.
@> Frame: 1
@> Calculating cation-Pi interactions.
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 3.5
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.9
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.9
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 4.9
@> TYR131 P 2003_2004_2006_2008_2011_2013 <---> ARG58 P NH1_829_832 4.9
@> Number of detected cation-pi interactions: 5.
@> Frame: 2
@> Calculating cation-Pi interactions.
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 2.7
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.1
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.5
@> Number of detected cation-pi interactions: 3.
@> Frame: 3
@> Calculating cation-Pi interactions.
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 2.6
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.6
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 3.8
@> Number of detected cation-pi interactions: 3.
@> Frame: 4
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.9
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.8
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS155 P NZ_2391 4.8
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 4.9
@> Number of detected cation-pi interactions: 4.
..
..
@> Frame: 19
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.9
@> Number of detected cation-pi interactions: 1.
@> Frame: 20
@> Calculating cation-Pi interactions.
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.0
@> Number of detected cation-pi interactions: 1.
Hydrophobic interactions using calcHydrophohicTrajectory():
In [12]: calcHydrophohicTrajectory(atoms, dcd)
@> Frame: 0
@> Hydrophobic Overlaping Areas are computed.
@> Calculating hydrophobic interactions.
@> ALA156 P CB_240114s <---> TYR87 P OH_1286 3.0 22.0
@> ALA24 P CB_29814s <---> MET63 P CE_894 3.3 5.2
@> ILE68 P CG2_97614s <---> MET63 P CE_894 3.3 52.4
@> TYR142 P CZ_217114s <---> VAL146 P CG2_2235 3.5 49.7
@> PHE10 P CD1_9214s <---> ALA22 P CB_273 3.5 31.2
@> LYS6 P CD_2614s <---> TRP39 P CZ2_555 3.5 68.7
@> PHE26 P CE2_33614s <---> VAL30 P CG1_411 3.6 21.1
@> ILE88 P CD_130714s <---> ALA111 P CB_1677 3.6 21.2
@> VAL11 P CG2_11414s <---> ILE88 P CG2_1300 3.6 9.3
@> VAL41 P CG2_59514s <---> PHE26 P CD2_334 3.6 16.6
@> PHE152 P CE1_233114s <---> ALA156 P CB_2401 3.7 17.5
@> LYS79 P CG_115514s <---> VAL106 P CG2_1598 3.7 25.1
@> LEU99 P CD2_148014s <---> ILE77 P CD_1128 3.7 12.0
@> PHE82 P CD1_120514s <---> ILE88 P CD_1307 3.7 17.6
@> LEU116 P CD2_177114s <---> ILE127 P CD_1949 3.7 17.4
@> VAL8 P CG1_5514s <---> PHE26 P CE2_336 3.7 12.1
@> LEU96 P CD1_142114s <---> ILE113 P CG2_1711 3.7 17.0
@> LEU9 P CD2_7814s <---> ILE77 P CD_1128 3.7 15.4
@> LEU89 P CD1_132214s <---> VAL8 P CG2_59 3.8 15.9
@> ILE126 P CD_193014s <---> LEU125 P CD1_1907 3.8 54.2
@> VAL141 P CG1_214914s <---> ILE127 P CG2_1942 3.9 11.5
@> MET91 P SD_135314s <---> ILE127 P CD_1949 3.9 35.9
@> ALA44 P CB_62814s <---> LEU9 P CD1_74 3.9 15.1
@> VAL25 P CG2_31414s <---> TYR142 P CE1_2169 3.9 12.0
@> ILE21 P CG2_25614s <---> MET63 P SD_893 4.0 20.8
@> LEU153 P CD1_235014s <---> TRP39 P NE1_547 4.0 9.4
@> PHE85 P CZ_125314s <---> LEU9 P CD1_74 4.0 32.1
@> ILE35 P CD_49114s <---> TRP39 P NE1_547 4.0 26.0
@> LEU29 P CD1_39514s <---> VAL25 P CG1_310 4.1 19.7
@> ALA74 P CB_106814s <---> ILE16 P CG2_177 4.1 6.7
@> ARG75 P CG_108114s <---> ALA44 P CB_628 4.1 36.2
@> ARG18 P CG_20814s <---> VAL141 P CG1_2149 4.1 20.3
@> LYS102 P CD_153414s <---> ILE77 P CG2_1121 4.1 17.5
@> TYR119 P CE1_180514s <---> LEU89 P CD2_1326 4.1 11.6
@> ARG40 P CG_56814s <---> PHE85 P CE2_1257 4.3 60.9
@> LYS28 P CG_37114s <---> ILE68 P CD_983 4.3 21.8
@> PHE138 P CD2_210814s <---> ILE21 P CD_263 4.3 6.6
@> TYR131 P CE1_200614s <---> ILE16 P CD_184 4.3 8.9
@> ARG58 P CG_82014s <---> PHE138 P CE1_2104 4.5 59.4
@> Number of detected hydrophobic interactions: 39.
@> Frame: 1
@> Hydrophobic Overlaping Areas are computed.
@> Calculating hydrophobic interactions.
@> MET63 P SD_89314s <---> TYR142 P CD1_2167 3.3 26.8
@> ALA24 P CB_29814s <---> MET63 P CE_894 3.4 7.1
@> VAL8 P CG2_5914s <---> PHE10 P CZ_96 3.4 27.8
@> LEU96 P CD1_142114s <---> ILE113 P CG2_1711 3.4 13.3
@> LEU116 P CD1_176714s <---> PHE10 P CE1_94 3.5 13.5
@> PHE82 P CZ_120914s <---> ILE77 P CD_1128 3.6 20.4
@> ILE68 P CD_98314s <---> TYR142 P OH_2172 3.6 27.4
@> PHE26 P CE2_33614s <---> VAL30 P CG1_411 3.6 28.1
@> ALA156 P CB_240114s <---> PHE152 P CD1_2329 3.6 24.5
@> VAL11 P CG2_11414s <---> ILE88 P CG2_1300 3.6 8.6
@> LYS102 P CD_153414s <---> ILE77 P CG2_1121 3.7 18.2
@> LEU99 P CD2_148014s <---> ILE77 P CD_1128 3.7 8.0
@> LEU153 P CD1_235014s <---> VAL30 P CG1_411 3.7 14.5
@> LEU9 P CD2_7814s <---> ILE77 P CD_1128 3.7 16.0
@> TRP39 P CD1_54514s <---> VAL30 P CG1_411 3.7 14.9
@> PHE138 P CD2_210814s <---> ILE21 P CD_263 3.8 15.8
@> TYR119 P OH_180814s <---> ALA156 P CB_2401 3.8 18.6
@> VAL146 P CG2_223514s <---> TYR142 P CZ_2171 3.8 40.5
@> VAL25 P CG2_31414s <---> TYR142 P CD1_2167 3.8 14.3
@> MET91 P CE_135414s <---> LEU116 P CD2_1771 3.8 19.1
@> ILE35 P CD_49114s <---> LEU153 P CD1_2350 3.9 17.2
@> VAL41 P CG2_59514s <---> PHE26 P CD2_334 3.9 21.9
@> ILE127 P CD_194914s <---> LEU116 P CD2_1771 3.9 11.7
@> LEU29 P CD1_39514s <---> VAL25 P CG1_310 3.9 25.1
@> ALA22 P CB_27314s <---> LEU116 P CD2_1771 4.0 7.3
@> ALA111 P CB_167714s <---> ILE88 P CD_1307 4.0 14.9
@> ARG75 P CG_108114s <---> ALA44 P CB_628 4.0 36.8
@> ILE126 P CD_193014s <---> LEU125 P CG_1905 4.0 53.2
@> VAL106 P CG2_159814s <---> PHE82 P CD2_1211 4.0 13.1
@> PHE85 P CZ_125314s <---> LEU9 P CD1_74 4.1 28.5
@> ARG40 P CG_56814s <---> PHE85 P CE2_1257 4.1 50.3
@> TYR87 P CD1_128114s <---> LEU89 P CD2_1326 4.2 14.7
@> LYS28 P CG_37114s <---> ILE68 P CG2_976 4.2 15.9
@> LYS79 P CG_115514s <---> VAL106 P CG2_1598 4.2 20.4
@> ARG18 P CG_20814s <---> VAL141 P CG1_2149 4.3 10.9
@> ARG58 P CG_82014s <---> PHE138 P CD1_2102 4.3 48.8
@> ALA74 P CB_106814s <---> ILE16 P CG2_177 4.4 4.3
@> ARG150 P CG_229414s <---> LEU29 P CD2_399 4.5 22.3
@> Number of detected hydrophobic interactions: 38.
..
..
@> Frame: 20
@> Hydrophobic Overlaping Areas are computed.
@> Calculating hydrophobic interactions.
@> LEU96 P CD1_142114s <---> ILE113 P CG2_1711 3.3 21.1
@> ILE88 P CD_130714s <---> PHE82 P CD2_1211 3.4 25.2
@> VAL11 P CG2_11414s <---> LEU99 P CD1_1476 3.4 11.5
@> MET63 P SD_89314s <---> TYR142 P CE1_2169 3.4 37.7
@> TRP39 P NE1_54714s <---> LEU153 P CD1_2350 3.4 19.2
@> ALA111 P CB_167714s <---> ILE88 P CD_1307 3.5 23.0
@> ILE35 P CD_49114s <---> LEU153 P CD1_2350 3.5 16.4
@> VAL30 P CG1_41114s <---> LEU153 P CD2_2354 3.5 9.8
@> LEU9 P CD2_7814s <---> ILE77 P CD_1128 3.5 17.0
@> PHE10 P CE1_9414s <---> LEU89 P CD1_1322 3.5 25.4
@> TYR119 P CE1_180514s <---> LEU89 P CD2_1326 3.6 18.5
@> ALA24 P CB_29814s <---> MET63 P CE_894 3.6 13.8
@> PHE26 P CZ_33214s <---> LEU153 P CD1_2350 3.6 27.1
@> VAL8 P CG2_5914s <---> LEU89 P CD1_1322 3.6 13.0
@> ALA22 P CB_27314s <---> PHE10 P CD1_92 3.6 29.5
@> MET91 P CE_135414s <---> ALA22 P CB_273 3.7 9.1
@> VAL41 P CG2_59514s <---> PHE26 P CD2_334 3.7 17.5
@> LEU116 P CD2_177114s <---> MET91 P SD_1353 3.7 21.9
@> ALA44 P CB_62814s <---> VAL11 P CG1_110 3.7 34.2
@> LYS6 P CD_2614s <---> TRP39 P CH2_557 3.7 44.8
@> VAL146 P CG2_223514s <---> TYR142 P CE2_2176 3.8 39.4
@> PHE85 P CE1_125114s <---> LEU9 P CD1_74 3.8 31.6
@> ILE21 P CG2_25614s <---> VAL25 P CG2_314 3.8 25.0
@> VAL141 P CG1_214914s <---> ILE21 P CD_263 3.9 13.0
@> ILE68 P CG1_98014s <---> MET63 P CE_894 3.9 37.2
@> PHE152 P CZ_233314s <---> LEU89 P CD1_1322 3.9 18.0
@> ARG18 P CG_20814s <---> VAL141 P CG1_2149 4.0 26.2
@> ARG75 P CG_108114s <---> ALA44 P CB_628 4.2 27.4
@> ILE127 P CD_194914s <---> LEU116 P CD2_1771 4.3 7.9
@> LYS79 P CG_115514s <---> VAL106 P CG2_1598 4.3 15.6
@> LEU29 P CG_39314s <---> VAL25 P CG1_310 4.3 21.7
@> ILE126 P CG1_192714s <---> LEU125 P CG_1905 4.4 55.6
@> Number of detected hydrophobic interactions: 32.
In this particular example you will not have disulfide bonds, but you can
compute it using calcDisulfideBondsTrajectory():
In [13]: calcDisulfideBondsTrajectory(atoms, dcd)
@> Frame: 0
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
@> Frame: 1
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
@> Frame: 2
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
@> Frame: 3
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
@> Frame: 4
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
..
..
Compute all availabe types of interactions¶
First, we instantiate a InteractionsTrajectory instance, which stores all the
information about interactions for protein structure for multiple frames.
With InteractionsTrajectory.calcProteinInteractionsTrajectory(), we can compute all
types of interactions such as hydrogen bonds, salt bridges, repulsive ionic bonding,
Pi-cation, Pi-stacking, and hydrophobic) at once. Be aware that those
computations may take a while, depending on the size of the system and the number
of frames that are stored by the DCD file. Therefore, we recommend saving the
results as a filename file. filename file, here
calcProteinInteractionsTrajectory.pkl, can be reloaded and used with all available
functions and methods.
In [14]: interactionsTrajectory = InteractionsTrajectory('trajectory')
In [15]: interactionsTrajectory.calcProteinInteractionsTrajectory(atoms, dcd,
....: filename='calcProteinInteractionsTrajectory')
....:
@> Frame: 0
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ARG101 P NH1_1516 <---> ASP98 P OD1_1463 2.0 33.1
@> HSE72 P NE2_1042 <---> ASN15 P OD1_165 2.6 34.8
@> GLN143 P NE2_2192 <---> GLU139 P OE2_2126 2.7 9.2
@> HSE66 P NE2_957 <---> GLU139 P OE1_2125 2.7 6.4
@> ARG40 P N_561 <---> LYS6 P O_37 2.7 17.1
@> ARG58 P N_813 <---> ASP56 P OD1_788 2.7 30.0
@> ALA45 P N_634 <---> ARG75 P O_1097 2.8 35.1
@> ASN53 P ND2_747 <---> GLU50 P OE1_708 2.8 18.2
@> ALA74 P N_1064 <---> ASN53 P O_751 2.8 21.3
@> ASP56 P N_780 <---> ILE16 P O_189 2.8 27.0
@> LYS110 P NZ_1667 <---> THR84 P O_1240 2.8 38.2
@> LEU116 P N_1758 <---> CYS90 P O_1342 2.8 15.0
@> SER103 P N_1546 <---> LEU99 P O_1485 2.8 29.1
@> ASN134 P N_2045 <---> ASP137 P OD2_2091 2.8 22.6
@> PHE152 P N_2321 <---> CYS148 P O_2275 2.8 8.3
@> ASN95 P N_1398 <---> ASP92 P OD1_1368 2.8 12.6
@> LYS6 P N_16 <---> ASN38 P O_536 2.8 25.0
@> ILE77 P N_1115 <---> ALA45 P O_643 2.8 12.2
@> ARG58 P NH2_832 <---> ASP56 P OD2_789 2.8 27.7
@> LEU99 P N_1467 <---> ASN95 P O_1411 2.8 15.5
@> CYS149 P N_2276 <---> CYS145 P O_2224 2.8 9.6
@> GLY52 P N_731 <---> ALA74 P O_1073 2.8 6.6
@> ASP32 P N_435 <---> LYS28 P O_385 2.8 8.8
@> ILE88 P N_1294 <---> LYS112 P O_1704 2.8 17.7
@> GLN143 P N_2180 <---> GLU139 P O_2128 2.8 21.7
@> ARG27 P N_340 <---> GLU23 P O_293 2.8 15.4
@> TYR142 P N_2159 <---> PHE138 P O_2113 2.9 14.2
@> GLY133 P N_2038 <---> PRO130 P O_1995 2.9 25.4
@> PHE26 P N_320 <---> ALA22 P O_278 2.9 4.9
@> ASN15 P ND2_166 <---> SER19 P OG_232 2.9 32.1
@> ARG75 P NH1_1090 <---> ASP81 P OD2_1194 2.9 19.7
@> ARG75 P NH2_1093 <---> ASP42 P OD2_610 2.9 23.5
@> ARG97 P N_1431 <---> GLU93 P O_1386 2.9 22.2
@> ARG65 P NH2_941 <---> GLU139 P OE1_2125 2.9 32.3
@> VAL25 P N_304 <---> ILE21 P O_268 2.9 8.2
@> LEU153 P N_2341 <---> CYS149 P O_2286 2.9 12.5
@> SER7 P N_38 <---> ASP86 P OD2_1270 2.9 39.9
@> ASP86 P N_1261 <---> SER7 P OG_45 2.9 34.7
@> ARG58 P NH2_832 <---> TYR131 P O_2016 2.9 33.1
@> THR46 P N_644 <---> CYS12 P O_130 2.9 36.1
@> GLN144 P N_2197 <---> THR140 P O_2142 2.9 23.3
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.9 12.4
@> LEU89 P N_1313 <---> LEU9 P O_83 2.9 29.5
@> THR31 P N_421 <---> ARG27 P O_363 2.9 24.1
@> CYS90 P N_1332 <---> GLU114 P O_1738 2.9 24.6
@> CYS148 P N_2265 <---> GLN144 P O_2213 2.9 9.3
@> GLU23 P N_279 <---> SER19 P O_235 2.9 15.4
@> ILE68 P N_970 <---> MET63 P O_899 2.9 13.0
@> PHE10 P N_84 <---> ASP42 P O_612 2.9 22.8
@> LYS112 P N_1683 <---> ASP86 P O_1272 2.9 10.1
@> SER61 P N_861 <---> TYR57 P O_812 2.9 35.1
@> CYS145 P N_2214 <---> VAL141 P O_2158 2.9 15.9
@> ARG27 P NH2_359 <---> GLU23 P OE2_291 2.9 31.5
@> LYS64 P N_900 <---> GLN60 P O_860 2.9 22.9
@> LEU9 P N_65 <---> TYR87 P O_1293 2.9 16.4
@> ASN38 P N_523 <---> ILE35 P O_496 2.9 29.1
@> VAL11 P N_104 <---> LEU89 P O_1331 2.9 29.7
@> ASN100 P N_1486 <---> LEU96 P O_1430 2.9 10.3
..
..
@> Number of detected hydrogen bonds: 124.
@> Calculating salt bridges.
@> GLU139 P OE1_2125_2126 <---> HSE66 P NE2_957 2.8
@> ASP81 P OD1_1193_1194 <---> ARG75 P NH1_1090_1093 2.9
@> ASP32 P OD1_443_444 <---> LYS28 P NZ_380 3.0
@> ASP98 P OD1_1463_1464 <---> ARG101 P NH1_1516_1519 3.1
@> ARG27 P NH1_356_359 <---> GLU23 P OE1_290_291 3.7
@> GLU139 P OE1_2125_2126 <---> ARG65 P NH1_938_941 3.8
@> LYS102 P NZ_1540 <---> ASP98 P OD1_1463_1464 3.9
@> ARG58 P NH1_829_832 <---> ASP56 P OD1_788_789 3.9
@> ARG18 P NH1_217_220 <---> ASP92 P OD1_1368_1369 4.1
@> GLU114 P OE1_1735_1736 <---> LYS112 P NZ_1699 4.1
@> ASP120 P OD1_1824_1825 <---> ARG147 P NH1_2257_2260 4.2
@> ASP86 P OD1_1269_1270 <---> LYS110 P NZ_1667 4.2
@> HSE157 P NE2_2418 <---> GLU114 P OE1_1735_1736 4.4
@> ARG18 P NH1_217_220 <---> ASP129 P OD1_1978_1979 4.6
@> ARG75 P NH1_1090_1093 <---> ASP42 P OD1_609_610 4.6
@> GLU23 P OE1_290_291 <---> HSE72 P NE2_1042 5.0
@> Number of detected salt bridges: 16.
@> Calculating repulsive ionic bonding.
@> LYS102 P NZ_1540 <---> ARG101 P NH1_1516_1519 4.3
@> Number of detected Repulsive Ionic Bonding interactions: 1.
@> Calculating Pi stacking interactions.
@> HSE66 P 953_954_955_957_959 <---> TYR142 P 2166_2167_2169_2171_2174_2176 3.9 162.1
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> TYR119 P 1802_1803_1805_1807_1810_1812 4.4 3.0
@> PHE26 P 327_328_330_332_334_336 <---> TRP39 P 549_550_551_553_555_557 4.8 75.5
@> TYR132 P 2024_2025_2027_2029_2032_2034 <---> TYR131 P 2003_2004_2006_2008_2011_2013 4.9 91.4
@> Number of detected Pi stacking interactions: 4.
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.7
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.5
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 4.8
@> Number of detected cation-pi interactions: 3.
@> Hydrophobic Overlaping Areas are computed.
@> Calculating hydrophobic interactions.
@> ALA156 P CB_240114s <---> TYR87 P OH_1286 3.0 22.0
@> ALA24 P CB_29814s <---> MET63 P CE_894 3.3 5.2
@> ILE68 P CG2_97614s <---> MET63 P CE_894 3.3 52.4
@> TYR142 P CZ_217114s <---> VAL146 P CG2_2235 3.5 49.7
@> PHE10 P CD1_9214s <---> ALA22 P CB_273 3.5 31.2
@> LYS6 P CD_2614s <---> TRP39 P CZ2_555 3.5 68.7
@> PHE26 P CE2_33614s <---> VAL30 P CG1_411 3.6 21.1
@> ILE88 P CD_130714s <---> ALA111 P CB_1677 3.6 21.2
@> VAL11 P CG2_11414s <---> ILE88 P CG2_1300 3.6 9.3
@> VAL41 P CG2_59514s <---> PHE26 P CD2_334 3.6 16.6
@> PHE152 P CE1_233114s <---> ALA156 P CB_2401 3.7 17.5
@> LYS79 P CG_115514s <---> VAL106 P CG2_1598 3.7 25.1
@> LEU99 P CD2_148014s <---> ILE77 P CD_1128 3.7 12.0
@> PHE82 P CD1_120514s <---> ILE88 P CD_1307 3.7 17.6
@> LEU116 P CD2_177114s <---> ILE127 P CD_1949 3.7 17.4
@> VAL8 P CG1_5514s <---> PHE26 P CE2_336 3.7 12.1
@> LEU96 P CD1_142114s <---> ILE113 P CG2_1711 3.7 17.0
@> LEU9 P CD2_7814s <---> ILE77 P CD_1128 3.7 15.4
@> LEU89 P CD1_132214s <---> VAL8 P CG2_59 3.8 15.9
@> ILE126 P CD_193014s <---> LEU125 P CD1_1907 3.8 54.2
@> VAL141 P CG1_214914s <---> ILE127 P CG2_1942 3.9 11.5
@> MET91 P SD_135314s <---> ILE127 P CD_1949 3.9 35.9
@> ALA44 P CB_62814s <---> LEU9 P CD1_74 3.9 15.1
@> VAL25 P CG2_31414s <---> TYR142 P CE1_2169 3.9 12.0
@> ILE21 P CG2_25614s <---> MET63 P SD_893 4.0 20.8
@> LEU153 P CD1_235014s <---> TRP39 P NE1_547 4.0 9.4
@> PHE85 P CZ_125314s <---> LEU9 P CD1_74 4.0 32.1
@> ILE35 P CD_49114s <---> TRP39 P NE1_547 4.0 26.0
@> LEU29 P CD1_39514s <---> VAL25 P CG1_310 4.1 19.7
@> ALA74 P CB_106814s <---> ILE16 P CG2_177 4.1 6.7
@> ARG75 P CG_108114s <---> ALA44 P CB_628 4.1 36.2
@> ARG18 P CG_20814s <---> VAL141 P CG1_2149 4.1 20.3
@> LYS102 P CD_153414s <---> ILE77 P CG2_1121 4.1 17.5
@> TYR119 P CE1_180514s <---> LEU89 P CD2_1326 4.1 11.6
@> ARG40 P CG_56814s <---> PHE85 P CE2_1257 4.3 60.9
@> LYS28 P CG_37114s <---> ILE68 P CD_983 4.3 21.8
@> PHE138 P CD2_210814s <---> ILE21 P CD_263 4.3 6.6
@> TYR131 P CE1_200614s <---> ILE16 P CD_184 4.3 8.9
@> ARG58 P CG_82014s <---> PHE138 P CE1_2104 4.5 59.4
@> Number of detected hydrophobic interactions: 39.
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
..
..
@> Frame: 20
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ARG97 P NE_1444 <---> GLU93 P OE1_1383 2.5 12.5
@> SER19 P OG_232 <---> ASN15 P OD1_165 2.6 31.5
@> ARG27 P NH1_356 <---> GLU23 P OE1_290 2.6 19.1
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.6 21.5
@> GLN122 P NE2_1854 <---> ASP120 P OD2_1825 2.6 39.7
@> SER118 P OG_1791 <---> GLU114 P OE2_1736 2.6 24.5
@> ARG65 P NH1_938 <---> GLU139 P OE1_2125 2.7 6.1
@> ARG65 P NH2_941 <---> ASP135 P OD1_2067 2.7 15.6
@> SER43 P OG_620 <---> GLU23 P OE2_291 2.7 13.9
@> ARG75 P NE_1087 <---> ASP42 P OD1_609 2.7 26.5
@> ARG150 P NE_2300 <---> GLU154 P OE2_2372 2.7 4.9
@> VAL106 P N_1588 <---> LYS102 P O_1545 2.7 16.2
@> LYS28 P N_364 <---> ALA24 P O_303 2.7 38.8
@> HSE157 P NE2_2418 <---> PHE152 P O_2340 2.7 28.5
@> ARG58 P NH2_832 <---> ASP56 P OD2_789 2.7 19.3
@> ARG97 P NH2_1450 <---> GLU93 P OE2_1384 2.7 15.8
@> ARG75 P NH2_1093 <---> ASP42 P OD1_609 2.7 30.5
@> ALA45 P N_634 <---> ARG75 P O_1097 2.7 22.3
@> ARG75 P NH2_1093 <---> ASP81 P OD1_1193 2.7 19.2
@> THR31 P OG1_427 <---> ARG27 P O_363 2.7 13.1
@> ARG150 P NH2_2306 <---> GLU154 P OE1_2371 2.7 8.5
@> ARG75 P NH1_1090 <---> ASP81 P OD2_1194 2.7 14.8
@> GLY67 P N_963 <---> MET63 P O_899 2.7 25.3
@> LEU89 P N_1313 <---> LEU9 P O_83 2.8 18.4
@> ARG101 P NH1_1516 <---> ASP98 P OD2_1464 2.8 11.5
@> ILE77 P N_1115 <---> ALA45 P O_643 2.8 39.9
@> LYS110 P N_1651 <---> PHE82 P O_1216 2.8 32.3
@> LEU29 P N_386 <---> VAL25 P O_319 2.8 5.4
@> ASN100 P N_1486 <---> LEU96 P O_1430 2.8 6.7
@> LYS102 P N_1524 <---> ASP98 P O_1466 2.8 4.9
@> THR78 P OG1_1140 <---> ASP81 P OD2_1194 2.8 10.5
@> VAL8 P N_49 <---> ARG40 P O_584 2.8 16.8
@> GLU154 P N_2360 <---> ARG150 P O_2310 2.8 15.1
@> LYS110 P NZ_1667 <---> ASP86 P OD2_1270 2.8 32.5
@> ARG58 P NE_826 <---> ASP56 P OD1_788 2.8 3.3
@> ILE35 P N_478 <---> VAL30 P O_420 2.8 7.9
@> ARG58 P NH1_829 <---> GLY133 P O_2044 2.8 34.3
@> GLN105 P N_1571 <---> ARG101 P O_1523 2.8 29.9
@> SER7 P N_38 <---> ASP86 P OD1_1269 2.8 10.5
@> ARG101 P NH2_1519 <---> ASP98 P OD1_1463 2.8 17.5
@> GLN143 P N_2180 <---> GLU139 P O_2128 2.8 20.5
@> CYS149 P N_2276 <---> CYS145 P O_2224 2.8 16.0
@> SER103 P OG_1553 <---> LEU99 P O_1485 2.9 21.4
@> ARG18 P NH1_217 <---> ASP92 P OD2_1369 2.9 6.7
@> CYS90 P N_1332 <---> GLU114 P O_1738 2.9 7.9
@> ARG18 P NH1_217 <---> ILE127 P O_1954 2.9 13.0
@> LYS155 P NZ_2391 <---> TYR119 P O_1815 2.9 27.9
@> ARG150 P N_2287 <---> VAL146 P O_2240 2.9 39.3
@> ARG65 P NH1_938 <---> ASP135 P OD2_2068 2.9 39.2
@> VAL30 P N_405 <---> PHE26 P O_339 2.9 2.0
@> VAL11 P N_104 <---> LEU89 P O_1331 2.9 19.9
@> GLN144 P N_2197 <---> THR140 P O_2142 2.9 16.4
@> LEU116 P N_1758 <---> CYS90 P O_1342 2.9 22.2
@> SER103 P N_1546 <---> LEU99 P O_1485 2.9 35.6
@> ASP56 P N_780 <---> ILE16 P O_189 2.9 5.0
@> GLU139 P N_2114 <---> ASP135 P O_2070 2.9 33.1
@> PHE10 P N_84 <---> ASP42 P O_612 2.9 11.4
@> LYS155 P N_2375 <---> ALA151 P O_2320 2.9 39.0
@> PHE26 P N_320 <---> ALA22 P O_278 2.9 21.1
@> THR140 P N_2129 <---> SER136 P O_2081 3.0 36.4
@> ALA74 P N_1064 <---> ASN53 P O_751 3.0 20.8
@> LYS6 P N_16 <---> ASN38 P O_536 3.0 12.1
@> ARG65 P N_922 <---> SER61 P O_871 3.0 15.7
@> LEU9 P N_65 <---> TYR87 P O_1293 3.0 6.8
..
..
@> Number of detected hydrogen bonds: 114.
@> Calculating salt bridges.
@> ASP135 P OD1_2067_2068 <---> ARG65 P NH1_938_941 2.5
@> ASP81 P OD1_1193_1194 <---> ARG75 P NH1_1090_1093 2.7
@> ASP98 P OD1_1463_1464 <---> ARG101 P NH1_1516_1519 2.8
@> ASP86 P OD1_1269_1270 <---> LYS110 P NZ_1667 3.4
@> ARG97 P NH1_1447_1450 <---> GLU93 P OE1_1383_1384 3.5
@> ARG150 P NH1_2303_2306 <---> GLU154 P OE1_2371_2372 3.7
@> ARG58 P NH1_829_832 <---> ASP56 P OD1_788_789 3.7
@> GLU139 P OE1_2125_2126 <---> HSE66 P NE2_957 3.9
@> ARG18 P NH1_217_220 <---> ASP92 P OD1_1368_1369 4.0
@> ARG27 P NH1_356_359 <---> GLU23 P OE1_290_291 4.0
@> ARG75 P NH1_1090_1093 <---> ASP42 P OD1_609_610 4.4
@> GLU23 P OE1_290_291 <---> HSE72 P NE2_1042 4.7
@> GLU139 P OE1_2125_2126 <---> ARG65 P NH1_938_941 4.8
@> ARG18 P NH1_217_220 <---> ASP129 P OD1_1978_1979 5.0
@> Number of detected salt bridges: 14.
@> Calculating repulsive ionic bonding.
@> ARG147 P NH1_2257_2260 <---> LYS123 P NZ_1875 4.5
@> Number of detected Repulsive Ionic Bonding interactions: 1.
@> Calculating Pi stacking interactions.
@> TYR119 P 1802_1803_1805_1807_1810_1812 <---> PHE152 P 2328_2329_2331_2333_2335_2337 4.7 125.5
@> HSE66 P 953_954_955_957_959 <---> TYR142 P 2166_2167_2169_2171_2174_2176 4.8 165.0
@> TYR132 P 2024_2025_2027_2029_2032_2034 <---> TYR131 P 2003_2004_2006_2008_2011_2013 4.9 116.3
@> Number of detected Pi stacking interactions: 3.
@> Calculating cation-Pi interactions.
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.0
@> Number of detected cation-pi interactions: 1.
@> Hydrophobic Overlaping Areas are computed.
@> Calculating hydrophobic interactions.
@> LEU96 P CD1_142114s <---> ILE113 P CG2_1711 3.3 21.1
@> ILE88 P CD_130714s <---> PHE82 P CD2_1211 3.4 25.2
@> VAL11 P CG2_11414s <---> LEU99 P CD1_1476 3.4 11.5
@> MET63 P SD_89314s <---> TYR142 P CE1_2169 3.4 37.7
@> TRP39 P NE1_54714s <---> LEU153 P CD1_2350 3.4 19.2
@> ALA111 P CB_167714s <---> ILE88 P CD_1307 3.5 23.0
@> ILE35 P CD_49114s <---> LEU153 P CD1_2350 3.5 16.4
@> VAL30 P CG1_41114s <---> LEU153 P CD2_2354 3.5 9.8
@> LEU9 P CD2_7814s <---> ILE77 P CD_1128 3.5 17.0
@> PHE10 P CE1_9414s <---> LEU89 P CD1_1322 3.5 25.4
@> TYR119 P CE1_180514s <---> LEU89 P CD2_1326 3.6 18.5
@> ALA24 P CB_29814s <---> MET63 P CE_894 3.6 13.8
@> PHE26 P CZ_33214s <---> LEU153 P CD1_2350 3.6 27.1
@> VAL8 P CG2_5914s <---> LEU89 P CD1_1322 3.6 13.0
@> ALA22 P CB_27314s <---> PHE10 P CD1_92 3.6 29.5
@> MET91 P CE_135414s <---> ALA22 P CB_273 3.7 9.1
@> VAL41 P CG2_59514s <---> PHE26 P CD2_334 3.7 17.5
@> LEU116 P CD2_177114s <---> MET91 P SD_1353 3.7 21.9
@> ALA44 P CB_62814s <---> VAL11 P CG1_110 3.7 34.2
@> LYS6 P CD_2614s <---> TRP39 P CH2_557 3.7 44.8
@> VAL146 P CG2_223514s <---> TYR142 P CE2_2176 3.8 39.4
@> PHE85 P CE1_125114s <---> LEU9 P CD1_74 3.8 31.6
@> ILE21 P CG2_25614s <---> VAL25 P CG2_314 3.8 25.0
@> VAL141 P CG1_214914s <---> ILE21 P CD_263 3.9 13.0
@> ILE68 P CG1_98014s <---> MET63 P CE_894 3.9 37.2
@> PHE152 P CZ_233314s <---> LEU89 P CD1_1322 3.9 18.0
@> ARG18 P CG_20814s <---> VAL141 P CG1_2149 4.0 26.2
@> ARG75 P CG_108114s <---> ALA44 P CB_628 4.2 27.4
@> ILE127 P CD_194914s <---> LEU116 P CD2_1771 4.3 7.9
@> LYS79 P CG_115514s <---> VAL106 P CG2_1598 4.3 15.6
@> LEU29 P CG_39314s <---> VAL25 P CG1_310 4.3 21.7
@> ILE126 P CG1_192714s <---> LEU125 P CG_1905 4.4 55.6
@> Number of detected hydrophobic interactions: 32.
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
@> File with interactions saved.
The results are displayed on the screen and they can be fetch by
using InteractionsTrajectory.getInteractions() method.
In [16]: interactionsTrajectory.getInteractions()
[[[['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD1_1463', 'P', 1.998, 33.1238],
['HSE72', 'NE2_1042', 'P', 'ASN15', 'OD1_165', 'P', 2.5997, 34.752],
['GLN143', 'NE2_2192', 'P', 'GLU139', 'OE2_2126', 'P', 2.7287, 9.1822],
['HSE66', 'NE2_957', 'P', 'GLU139', 'OE1_2125', 'P', 2.7314, 6.3592],
['ARG40', 'N_561', 'P', 'LYS6', 'O_37', 'P', 2.7479, 17.1499],
['ARG58', 'N_813', 'P', 'ASP56', 'OD1_788', 'P', 2.7499, 29.9737],
['ALA45', 'N_634', 'P', 'ARG75', 'O_1097', 'P', 2.7609, 35.0983],
['ASN53', 'ND2_747', 'P', 'GLU50', 'OE1_708', 'P', 2.7702, 18.2336],
['ALA74', 'N_1064', 'P', 'ASN53', 'O_751', 'P', 2.7782, 21.3375],
['ASP56', 'N_780', 'P', 'ILE16', 'O_189', 'P', 2.7793, 27.0481],
['LYS110', 'NZ_1667', 'P', 'THR84', 'O_1240', 'P', 2.7977, 38.2213],
['LEU116', 'N_1758', 'P', 'CYS90', 'O_1342', 'P', 2.8072, 15.0239],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8075, 29.107],
['ASN134', 'N_2045', 'P', 'ASP137', 'OD2_2091', 'P', 2.8132, 22.562],
['PHE152', 'N_2321', 'P', 'CYS148', 'O_2275', 'P', 2.8141, 8.2562],
['ASN95', 'N_1398', 'P', 'ASP92', 'OD1_1368', 'P', 2.8148, 12.5701],
['LYS6', 'N_16', 'P', 'ASN38', 'O_536', 'P', 2.8178, 25.0306],
['ILE77', 'N_1115', 'P', 'ALA45', 'O_643', 'P', 2.8179, 12.1856],
['ARG58', 'NH2_832', 'P', 'ASP56', 'OD2_789', 'P', 2.8204, 27.6617],
['LEU99', 'N_1467', 'P', 'ASN95', 'O_1411', 'P', 2.8205, 15.4867],
['CYS149', 'N_2276', 'P', 'CYS145', 'O_2224', 'P', 2.8247, 9.5914],
['GLY52', 'N_731', 'P', 'ALA74', 'O_1073', 'P', 2.832, 6.6442],
['ASP32', 'N_435', 'P', 'LYS28', 'O_385', 'P', 2.8357, 8.8318],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8429, 17.7147],
['GLN143', 'N_2180', 'P', 'GLU139', 'O_2128', 'P', 2.8445, 21.6714],
['ARG27', 'N_340', 'P', 'GLU23', 'O_293', 'P', 2.8446, 15.4167],
['TYR142', 'N_2159', 'P', 'PHE138', 'O_2113', 'P', 2.8515, 14.2061],
['GLY133', 'N_2038', 'P', 'PRO130', 'O_1995', 'P', 2.854, 25.4301],
['PHE26', 'N_320', 'P', 'ALA22', 'O_278', 'P', 2.8541, 4.8732],
['ASN15', 'ND2_166', 'P', 'SER19', 'OG_232', 'P', 2.8592, 32.1244],
['ARG75', 'NH1_1090', 'P', 'ASP81', 'OD2_1194', 'P', 2.8632, 19.6664],
['ARG75', 'NH2_1093', 'P', 'ASP42', 'OD2_610', 'P', 2.8649, 23.5083],
['ARG97', 'N_1431', 'P', 'GLU93', 'O_1386', 'P', 2.8654, 22.24],
['ARG65', 'NH2_941', 'P', 'GLU139', 'OE1_2125', 'P', 2.8655, 32.3239],
['VAL25', 'N_304', 'P', 'ILE21', 'O_268', 'P', 2.8666, 8.2255],
['LEU153', 'N_2341', 'P', 'CYS149', 'O_2286', 'P', 2.8707, 12.4931],
['SER7', 'N_38', 'P', 'ASP86', 'OD2_1270', 'P', 2.8732, 39.8839],
['ASP86', 'N_1261', 'P', 'SER7', 'OG_45', 'P', 2.8753, 34.7426],
..
[['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE1_1735', 'P', 2.5487, 20.8176],
['THR78', 'N_1134', 'P', 'ASP81', 'OD2_1194', 'P', 2.5494, 15.6392],
['ARG27', 'NH2_359', 'P', 'GLU23', 'OE2_291', 'P', 2.5496, 36.5043],
['THR78', 'OG1_1140', 'P', 'ASP81', 'OD2_1194', 'P', 2.5756, 25.1514],
['SER7', 'OG_45', 'P', 'ASP86', 'OD2_1270', 'P', 2.5904, 32.2995],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.5963, 18.6089],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.6334, 17.8203],
['ARG75', 'NH2_1093', 'P', 'ASP81', 'OD1_1193', 'P', 2.6367, 17.6426],
['SER118', 'OG_1791', 'P', 'LEU115', 'O_1757', 'P', 2.6547, 25.6442],
['ARG58', 'NE_826', 'P', 'ASP56', 'OD1_788', 'P', 2.6611, 6.4459],
['GLN124', 'N_1881', 'P', 'ASP120', 'OD1_1824', 'P', 2.6666, 17.1571],
['ARG147', 'NH1_2257', 'P', 'GLN124', 'OE1_1892', 'P', 2.6875, 11.8479],
['ARG18', 'NH1_217', 'P', 'ASP92', 'OD2_1369', 'P', 2.6879, 14.5803],
['ARG75', 'NH1_1090', 'P', 'ASP81', 'OD2_1194', 'P', 2.6889, 23.9375],
['TYR87', 'OH_1286', 'P', 'HSE157', 'OT1_2423', 'P', 2.6945, 11.5603],
['SER43', 'OG_620', 'P', 'GLU23', 'OE1_290', 'P', 2.6978, 15.166],
['LYS28', 'NZ_380', 'P', 'ASP32', 'OD1_443', 'P', 2.7003, 3.632],
['LYS110', 'NZ_1667', 'P', 'ASP86', 'OD1_1269', 'P', 2.7025, 25.1511],
['THR140', 'OG1_2135', 'P', 'SER136', 'O_2081', 'P', 2.71, 5.2209],
['LEU116', 'N_1758', 'P', 'CYS90', 'O_1342', 'P', 2.7125, 24.3959],
['THR5', 'OG1_8', 'P', 'ASN38', 'O_536', 'P', 2.7162, 38.6072],
['LYS64', 'N_900', 'P', 'GLN60', 'O_860', 'P', 2.7222, 26.7806],
['ARG147', 'NH1_2257', 'P', 'ASP120', 'OD2_1825', 'P', 2.731, 15.2446],
['ARG27', 'N_340', 'P', 'GLU23', 'O_293', 'P', 2.7341, 21.9432],
['TYR119', 'OH_1808', 'P', 'GLU114', 'OE1_1735', 'P', 2.735, 15.8502],
['ARG18', 'NH1_217', 'P', 'ILE127', 'O_1954', 'P', 2.7501, 16.0113],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.7535, 13.6202],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7626, 15.9446],
['ARG58', 'NH1_829', 'P', 'GLY133', 'O_2044', 'P', 2.7673, 31.8828],
['ARG75', 'NH2_1093', 'P', 'ASP42', 'OD2_610', 'P', 2.7744, 13.0389],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7935, 13.2257],
['GLU23', 'N_279', 'P', 'SER19', 'O_235', 'P', 2.8067, 10.8775],
['SER7', 'N_38', 'P', 'ASP86', 'OD2_1270', 'P', 2.813, 38.9132],
['VAL11', 'N_104', 'P', 'LEU89', 'O_1331', 'P', 2.8182, 13.801],
['PHE26', 'N_320', 'P', 'ALA22', 'O_278', 'P', 2.8212, 18.2267],
['LEU9', 'N_65', 'P', 'TYR87', 'O_1293', 'P', 2.8249, 34.2551],
['ARG65', 'NH2_941', 'P', 'GLU139', 'OE1_2125', 'P', 2.8308, 14.8745],
['ILE68', 'N_970', 'P', 'MET63', 'O_899', 'P', 2.8328, 9.2758],
..
[['ARG18', 'NH1_217', 'P', 'ASP92', 'OD2_1369', 'P', 2.5097, 4.9218],
['THR31', 'OG1_427', 'P', 'ARG27', 'O_363', 'P', 2.5496, 5.4538],
['ARG58', 'NH2_832', 'P', 'ASP56', 'OD2_789', 'P', 2.5525, 8.1856],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.5902, 19.0335],
['ARG75', 'NH2_1093', 'P', 'ASP42', 'OD2_610', 'P', 2.6114, 24.975],
['TYR119', 'OH_1808', 'P', 'GLU114', 'OE2_1736', 'P', 2.6441, 10.2991],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6466, 7.8982],
['TYR87', 'OH_1286', 'P', 'HSE157', 'OT1_2423', 'P', 2.6516, 14.0793],
['LYS64', 'N_900', 'P', 'GLN60', 'O_860', 'P', 2.6643, 4.9246],
['SER43', 'OG_620', 'P', 'GLU23', 'OE1_290', 'P', 2.7024, 8.6062],
['THR78', 'OG1_1140', 'P', 'ASP81', 'OD2_1194', 'P', 2.7158, 6.5273],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7184, 24.9984],
['SER118', 'OG_1791', 'P', 'LEU115', 'O_1757', 'P', 2.7238, 26.9156],
['LYS28', 'NZ_380', 'P', 'ASP32', 'OD2_444', 'P', 2.7274, 13.9298],
['THR84', 'OG1_1233', 'P', 'GLU80', 'O_1184', 'P', 2.7314, 13.4406],
['LEU89', 'N_1313', 'P', 'LEU9', 'O_83', 'P', 2.7581, 11.8493],
['ARG147', 'NH1_2257', 'P', 'GLN124', 'OE1_1892', 'P', 2.7633, 15.0984],
['ARG27', 'NH2_359', 'P', 'GLU23', 'OE2_291', 'P', 2.765, 17.97],
['ILE35', 'N_478', 'P', 'VAL30', 'O_420', 'P', 2.7659, 20.7163],
['PHE26', 'N_320', 'P', 'ALA22', 'O_278', 'P', 2.7663, 21.7712],
['VAL11', 'N_104', 'P', 'LEU89', 'O_1331', 'P', 2.767, 10.3325],
['VAL25', 'N_304', 'P', 'ILE21', 'O_268', 'P', 2.7679, 9.2024],
['SER7', 'OG_45', 'P', 'ASP86', 'OD2_1270', 'P', 2.7682, 29.4143],
['HSE72', 'NE2_1042', 'P', 'ASN15', 'OD1_165', 'P', 2.7756, 37.1399],
['ASN34', 'N_464', 'P', 'THR31', 'O_434', 'P', 2.7794, 19.6803],
['LYS110', 'N_1651', 'P', 'PHE82', 'O_1216', 'P', 2.7863, 9.1814],
['LYS110', 'NZ_1667', 'P', 'ASP86', 'OD1_1269', 'P', 2.7932, 13.508],
['ARG58', 'NE_826', 'P', 'ASP56', 'OD1_788', 'P', 2.8021, 8.0221],
['ARG75', 'NH1_1090', 'P', 'ASP81', 'OD2_1194', 'P', 2.8066, 14.9419],
['VAL8', 'N_49', 'P', 'ARG40', 'O_584', 'P', 2.8114, 19.4027],
['ARG18', 'NH1_217', 'P', 'ILE127', 'O_1954', 'P', 2.8173, 6.9549],
['LYS155', 'N_2375', 'P', 'ALA151', 'O_2320', 'P', 2.8212, 15.1026],
['HSE66', 'NE2_957', 'P', 'GLU139', 'OE1_2125', 'P', 2.8239, 28.9105],
['ARG147', 'NH1_2257', 'P', 'ASP120', 'OD2_1825', 'P', 2.8257, 31.6579],
['ARG97', 'N_1431', 'P', 'GLU93', 'O_1386', 'P', 2.8291, 15.1587],
['LYS123', 'N_1859', 'P', 'ASP120', 'OD1_1824', 'P', 2.8292, 34.0011],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8381, 10.253],
['ASP86', 'N_1261', 'P', 'SER7', 'OG_45', 'P', 2.8406, 22.034],
['ARG65', 'N_922', 'P', 'SER61', 'O_871', 'P', 2.8423, 24.4142],
['ILE127', 'N_1936', 'P', 'MET91', 'O_1359', 'P', 2.8469, 4.126],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'ND1_2414', 'P', 2.8616, 14.018],
['GLY67', 'N_963', 'P', 'MET63', 'O_899', 'P', 2.8626, 38.6183],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8761, 17.0562],
['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE2_1736', 'P', 2.8761, 18.0626],
['ARG75', 'NE_1087', 'P', 'ASP42', 'OD2_610', 'P', 2.8795, 38.3078],
['ALA44', 'N_624', 'P', 'PHE10', 'O_103', 'P', 2.8798, 30.1431],
['ILE68', 'N_970', 'P', 'MET63', 'O_899', 'P', 2.8902, 12.9079],
['ARG58', 'N_813', 'P', 'ASP56', 'OD1_788', 'P', 2.903, 21.0711],
['THR78', 'N_1134', 'P', 'ASP81', 'OD2_1194', 'P', 2.9152, 26.3475],
['ALA45', 'N_634', 'P', 'ARG75', 'O_1097', 'P', 2.9235, 27.7222],
..
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE1_1735', 'P', 2.5321, 12.1754],
['SER7', 'OG_45', 'P', 'ASP86', 'OD2_1270', 'P', 2.5681, 8.2326],
['SER43', 'OG_620', 'P', 'GLU23', 'OE1_290', 'P', 2.5908, 6.4741],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.5911, 17.069],
['ARG58', 'NH2_832', 'P', 'ASP56', 'OD2_789', 'P', 2.6234, 15.5609],
['THR78', 'OG1_1140', 'P', 'ASP81', 'OD2_1194', 'P', 2.6239, 11.6022],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6274, 12.9418],
['ASP32', 'N_435', 'P', 'LYS28', 'O_385', 'P', 2.6388, 5.0129],
['CYS149', 'N_2276', 'P', 'CYS145', 'O_2224', 'P', 2.6571, 20.4048],
['TYR119', 'OH_1808', 'P', 'GLU114', 'OE2_1736', 'P', 2.6666, 5.0368],
['ARG65', 'NH2_941', 'P', 'GLU139', 'OE1_2125', 'P', 2.677, 21.8922],
['ARG18', 'NH2_220', 'P', 'ASP92', 'OD2_1369', 'P', 2.6813, 31.3689],
['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE2_1736', 'P', 2.6844, 12.4337],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.7018, 15.5273],
['LYS64', 'N_900', 'P', 'GLN60', 'O_860', 'P', 2.7094, 34.9749],
['HSE66', 'NE2_957', 'P', 'GLU139', 'OE1_2125', 'P', 2.7146, 21.3402],
['GLY52', 'N_731', 'P', 'ALA74', 'O_1073', 'P', 2.719, 23.3583],
['ARG27', 'NH2_359', 'P', 'GLU23', 'OE2_291', 'P', 2.7207, 8.4795],
['LEU116', 'N_1758', 'P', 'CYS90', 'O_1342', 'P', 2.7283, 14.8893],
['ARG18', 'NH1_217', 'P', 'ASP92', 'OD2_1369', 'P', 2.7353, 26.7201],
['THR31', 'OG1_427', 'P', 'ARG27', 'O_363', 'P', 2.7466, 22.4844],
['ARG18', 'NH1_217', 'P', 'ILE127', 'O_1954', 'P', 2.7489, 16.6396],
['ARG58', 'NH1_829', 'P', 'TYR132', 'O_2037', 'P', 2.7511, 23.6002],
['ARG147', 'NH1_2257', 'P', 'ASP120', 'OD1_1824', 'P', 2.7592, 19.3384],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 2.7625, 21.1367],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7703, 4.1752],
['ARG75', 'NH2_1093', 'P', 'ASP42', 'OD2_610', 'P', 2.7726, 18.0115],
['ARG65', 'NH1_938', 'P', 'GLU139', 'OE1_2125', 'P', 2.7749, 18.9952],
['GLY133', 'N_2038', 'P', 'ASP137', 'OD2_2091', 'P', 2.7764, 32.7458],
['ARG75', 'NH2_1093', 'P', 'ASP81', 'OD1_1193', 'P', 2.7783, 16.8911],
['TYR87', 'OH_1286', 'P', 'HSE157', 'OT2_2424', 'P', 2.7928, 9.9286],
['ILE35', 'N_478', 'P', 'VAL30', 'O_420', 'P', 2.7945, 6.0583],
['LYS28', 'NZ_380', 'P', 'ASP32', 'OD2_444', 'P', 2.7993, 35.4827],
['PHE152', 'N_2321', 'P', 'CYS148', 'O_2275', 'P', 2.8, 5.5477],
['LYS110', 'NZ_1667', 'P', 'ASP86', 'OD1_1269', 'P', 2.8021, 14.2767],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.813, 11.6498],
['GLN60', 'N_844', 'P', 'ASP56', 'O_791', 'P', 2.8156, 25.2584],
['ALA45', 'N_634', 'P', 'ARG75', 'O_1097', 'P', 2.8209, 30.082],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8375, 24.3092],
['ARG150', 'N_2287', 'P', 'VAL146', 'O_2240', 'P', 2.8394, 21.6561],
..
..
[['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.2931, 21.0747],
['ILE88', 'CD_1307', 'P', 'PHE82', 'CD2_1211', 'P', 3.3689, 25.2319],
['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.3771, 11.4804],
['MET63', 'SD_893', 'P', 'TYR142', 'CE1_2169', 'P', 3.3896, 37.7382],
['TRP39', 'NE1_547', 'P', 'LEU153', 'CD1_2350', 'P', 3.4345, 19.2142],
['ALA111', 'CB_1677', 'P', 'ILE88', 'CD_1307', 'P', 3.4669, 22.9943],
['ILE35', 'CD_491', 'P', 'LEU153', 'CD1_2350', 'P', 3.4868, 16.4472],
['VAL30', 'CG1_411', 'P', 'LEU153', 'CD2_2354', 'P', 3.4938, 9.7531],
['LEU9', 'CD2_78', 'P', 'ILE77', 'CD_1128', 'P', 3.5133, 16.9544],
['PHE10', 'CE1_94', 'P', 'LEU89', 'CD1_1322', 'P', 3.5468, 25.3848],
['TYR119', 'CE1_1805', 'P', 'LEU89', 'CD2_1326', 'P', 3.554, 18.5297],
['ALA24', 'CB_298', 'P', 'MET63', 'CE_894', 'P', 3.5859, 13.7697],
['PHE26', 'CZ_332', 'P', 'LEU153', 'CD1_2350', 'P', 3.6118, 27.1048],
['VAL8', 'CG2_59', 'P', 'LEU89', 'CD1_1322', 'P', 3.6199, 12.9537],
['ALA22', 'CB_273', 'P', 'PHE10', 'CD1_92', 'P', 3.6246, 29.4846],
['MET91', 'CE_1354', 'P', 'ALA22', 'CB_273', 'P', 3.6628, 9.0978],
['VAL41', 'CG2_595', 'P', 'PHE26', 'CD2_334', 'P', 3.6792, 17.4783],
['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.6984, 21.9302],
['ALA44', 'CB_628', 'P', 'VAL11', 'CG1_110', 'P', 3.7022, 34.2417],
['LYS6', 'CD_26', 'P', 'TRP39', 'CH2_557', 'P', 3.7135, 44.8],
['VAL146', 'CG2_2235', 'P', 'TYR142', 'CE2_2176', 'P', 3.7622, 39.414],
['PHE85', 'CE1_1251', 'P', 'LEU9', 'CD1_74', 'P', 3.8118, 31.6126],
['ILE21', 'CG2_256', 'P', 'VAL25', 'CG2_314', 'P', 3.825, 25.047],
['VAL141', 'CG1_2149', 'P', 'ILE21', 'CD_263', 'P', 3.8615, 13.036],
['ILE68', 'CG1_980', 'P', 'MET63', 'CE_894', 'P', 3.8698, 37.1931],
['PHE152', 'CZ_2333', 'P', 'LEU89', 'CD1_1322', 'P', 3.9131, 17.9674],
['ARG18', 'CG_208', 'P', 'VAL141', 'CG1_2149', 'P', 3.9881, 26.173],
['ARG75', 'CG_1081', 'P', 'ALA44', 'CB_628', 'P', 4.1878, 27.3996],
['ILE127', 'CD_1949', 'P', 'LEU116', 'CD2_1771', 'P', 4.2643, 7.8575],
['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.2738, 15.6412],
['LEU29', 'CG_393', 'P', 'VAL25', 'CG1_310', 'P', 4.3325, 21.7286],
['ILE126', 'CG1_1927', 'P', 'LEU125', 'CG_1905', 'P', 4.4374, 55.6364]]],
[[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[]]]
Moreover, we can display the evolution of each interaction type during the simulation. There are the following types of plots: hydrogen bonds (blue), salt bridges (yellow), hydrophobic interactions (silver), Pi-stacking (green), Pi-cation (orange), repulsive ionic bonding (red), disulfide bonds(black).
In [17]: interactionsTrajectory.getTimeInteractions()
If the structure is stable, we will not observe a lot of changes in protein structure.
Similar to the single PDB analysis, we have an access to each interaction
type by using: InteractionsTrajectory.getHydrogenBonds() method, etc.
In [18]: interactionsTrajectory.getHydrogenBonds()
[[['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD1_1463', 'P', 1.998, 33.1238],
['HSE72', 'NE2_1042', 'P', 'ASN15', 'OD1_165', 'P', 2.5997, 34.752],
['GLN143', 'NE2_2192', 'P', 'GLU139', 'OE2_2126', 'P', 2.7287, 9.1822],
['HSE66', 'NE2_957', 'P', 'GLU139', 'OE1_2125', 'P', 2.7314, 6.3592],
['ARG40', 'N_561', 'P', 'LYS6', 'O_37', 'P', 2.7479, 17.1499],
['ARG58', 'N_813', 'P', 'ASP56', 'OD1_788', 'P', 2.7499, 29.9737],
['ALA45', 'N_634', 'P', 'ARG75', 'O_1097', 'P', 2.7609, 35.0983],
['ASN53', 'ND2_747', 'P', 'GLU50', 'OE1_708', 'P', 2.7702, 18.2336],
['ALA74', 'N_1064', 'P', 'ASN53', 'O_751', 'P', 2.7782, 21.3375],
['ASP56', 'N_780', 'P', 'ILE16', 'O_189', 'P', 2.7793, 27.0481],
['LYS110', 'NZ_1667', 'P', 'THR84', 'O_1240', 'P', 2.7977, 38.2213],
['LEU116', 'N_1758', 'P', 'CYS90', 'O_1342', 'P', 2.8072, 15.0239],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8075, 29.107],
['ASN134', 'N_2045', 'P', 'ASP137', 'OD2_2091', 'P', 2.8132, 22.562],
['PHE152', 'N_2321', 'P', 'CYS148', 'O_2275', 'P', 2.8141, 8.2562],
['ASN95', 'N_1398', 'P', 'ASP92', 'OD1_1368', 'P', 2.8148, 12.5701],
['LYS6', 'N_16', 'P', 'ASN38', 'O_536', 'P', 2.8178, 25.0306],
['ILE77', 'N_1115', 'P', 'ALA45', 'O_643', 'P', 2.8179, 12.1856],
['ARG58', 'NH2_832', 'P', 'ASP56', 'OD2_789', 'P', 2.8204, 27.6617],
['LEU99', 'N_1467', 'P', 'ASN95', 'O_1411', 'P', 2.8205, 15.4867],
['CYS149', 'N_2276', 'P', 'CYS145', 'O_2224', 'P', 2.8247, 9.5914],
['GLY52', 'N_731', 'P', 'ALA74', 'O_1073', 'P', 2.832, 6.6442],
['ASP32', 'N_435', 'P', 'LYS28', 'O_385', 'P', 2.8357, 8.8318],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8429, 17.7147],
['GLN143', 'N_2180', 'P', 'GLU139', 'O_2128', 'P', 2.8445, 21.6714],
['ARG27', 'N_340', 'P', 'GLU23', 'O_293', 'P', 2.8446, 15.4167],
['TYR142', 'N_2159', 'P', 'PHE138', 'O_2113', 'P', 2.8515, 14.2061],
['GLY133', 'N_2038', 'P', 'PRO130', 'O_1995', 'P', 2.854, 25.4301],
['PHE26', 'N_320', 'P', 'ALA22', 'O_278', 'P', 2.8541, 4.8732],
['ASN15', 'ND2_166', 'P', 'SER19', 'OG_232', 'P', 2.8592, 32.1244],
['ARG75', 'NH1_1090', 'P', 'ASP81', 'OD2_1194', 'P', 2.8632, 19.6664],
['ARG75', 'NH2_1093', 'P', 'ASP42', 'OD2_610', 'P', 2.8649, 23.5083],
['ARG97', 'N_1431', 'P', 'GLU93', 'O_1386', 'P', 2.8654, 22.24],
['ARG65', 'NH2_941', 'P', 'GLU139', 'OE1_2125', 'P', 2.8655, 32.3239],
['VAL25', 'N_304', 'P', 'ILE21', 'O_268', 'P', 2.8666, 8.2255],
['LEU153', 'N_2341', 'P', 'CYS149', 'O_2286', 'P', 2.8707, 12.4931],
['SER7', 'N_38', 'P', 'ASP86', 'OD2_1270', 'P', 2.8732, 39.8839],
['ASP86', 'N_1261', 'P', 'SER7', 'OG_45', 'P', 2.8753, 34.7426],
['ARG58', 'NH2_832', 'P', 'TYR131', 'O_2016', 'P', 2.8815, 33.1098],
['THR46', 'N_644', 'P', 'CYS12', 'O_130', 'P', 2.883, 36.1279],
['GLN144', 'N_2197', 'P', 'THR140', 'O_2142', 'P', 2.8836, 23.2545],
['THR78', 'N_1134', 'P', 'ASP81', 'OD2_1194', 'P', 2.8869, 12.4465],
['LEU89', 'N_1313', 'P', 'LEU9', 'O_83', 'P', 2.8946, 29.5105],
['THR31', 'N_421', 'P', 'ARG27', 'O_363', 'P', 2.896, 24.1287],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8975, 24.576],
['CYS148', 'N_2265', 'P', 'GLN144', 'O_2213', 'P', 2.8976, 9.3165],
['GLU23', 'N_279', 'P', 'SER19', 'O_235', 'P', 2.8979, 15.4146],
['ILE68', 'N_970', 'P', 'MET63', 'O_899', 'P', 2.8986, 12.9903],
['PHE10', 'N_84', 'P', 'ASP42', 'O_612', 'P', 2.9026, 22.751],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.912, 10.1158],
['SER61', 'N_861', 'P', 'TYR57', 'O_812', 'P', 2.9132, 35.1196],
['CYS145', 'N_2214', 'P', 'VAL141', 'O_2158', 'P', 2.9144, 15.8507],
['ARG27', 'NH2_359', 'P', 'GLU23', 'OE2_291', 'P', 2.9199, 31.5487],
['LYS64', 'N_900', 'P', 'GLN60', 'O_860', 'P', 2.9211, 22.8783],
['LEU9', 'N_65', 'P', 'TYR87', 'O_1293', 'P', 2.9229, 16.439],
['ASN38', 'N_523', 'P', 'ILE35', 'O_496', 'P', 2.9255, 29.091],
['VAL11', 'N_104', 'P', 'LEU89', 'O_1331', 'P', 2.9316, 29.7192],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.933, 10.3321],
['GLN124', 'N_1881', 'P', 'ASP120', 'OD2_1825', 'P', 2.9333, 27.4547],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9361, 9.2855],
['GLN76', 'NE2_1110', 'P', 'THR46', 'O_657', 'P', 2.9381, 31.3836],
['ARG40', 'NH1_577', 'P', 'THR84', 'OG1_1233', 'P', 2.9482, 8.3748],
['ALA44', 'N_624', 'P', 'PHE10', 'O_103', 'P', 2.9499, 33.1771],
['GLU154', 'N_2360', 'P', 'ARG150', 'O_2310', 'P', 2.956, 22.5898],
['VAL8', 'N_49', 'P', 'ARG40', 'O_584', 'P', 2.9631, 25.0079],
['MET63', 'N_883', 'P', 'GLY59', 'O_843', 'P', 2.9733, 18.2731],
['GLN60', 'N_844', 'P', 'ASP56', 'O_791', 'P', 2.9795, 35.5229],
['ILE35', 'N_478', 'P', 'VAL30', 'O_420', 'P', 2.9811, 23.5092],
['VAL146', 'N_2225', 'P', 'TYR142', 'O_2179', 'P', 2.9914, 31.4798],
['ARG58', 'NH1_829', 'P', 'TYR131', 'O_2016', 'P', 2.9942, 38.0937],
['ASN53', 'N_738', 'P', 'GLU50', 'O_711', 'P', 2.995, 28.587],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.9952, 32.2712],
['ARG18', 'NH1_217', 'P', 'ILE127', 'O_1954', 'P', 2.9957, 25.9507],
['ARG75', 'N_1074', 'P', 'ASN15', 'OD1_165', 'P', 3.0026, 25.0853],
['GLN144', 'NE2_2209', 'P', 'ILE126', 'O_1935', 'P', 3.0038, 18.2744],
['ASN34', 'N_464', 'P', 'THR31', 'O_434', 'P', 3.0041, 18.2465],
['ASN15', 'ND2_166', 'P', 'SER43', 'OG_620', 'P', 3.0129, 25.6996],
['ARG58', 'NE_826', 'P', 'ASP56', 'OD1_788', 'P', 3.017, 22.2284],
['ARG27', 'NH1_356', 'P', 'GLU23', 'OE2_291', 'P', 3.0175, 36.9342],
['ILE127', 'N_1936', 'P', 'MET91', 'O_1359', 'P', 3.018, 17.5601],
['TYR119', 'OH_1808', 'P', 'HSE157', 'N_2407', 'P', 3.0224, 28.0923],
['HSE157', 'N_2407', 'P', 'TYR119', 'OH_1808', 'P', 3.0224, 19.1804],
['GLU139', 'N_2114', 'P', 'ASP135', 'O_2070', 'P', 3.0245, 27.9246],
['LEU29', 'N_386', 'P', 'VAL25', 'O_319', 'P', 3.0299, 19.1089],
['SER47', 'N_658', 'P', 'LEU13', 'O_149', 'P', 3.0386, 28.8029],
['VAL30', 'N_405', 'P', 'PHE26', 'O_339', 'P', 3.0394, 17.6883],
['GLN105', 'N_1571', 'P', 'LYS102', 'O_1545', 'P', 3.0464, 19.6807],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.051, 21.4045],
['LYS155', 'N_2375', 'P', 'ALA151', 'O_2320', 'P', 3.0555, 21.3244],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.059, 24.1606],
['ASP120', 'N_1816', 'P', 'GLY117', 'O_1783', 'P', 3.0623, 12.666],
['CYS62', 'N_872', 'P', 'ARG58', 'O_836', 'P', 3.0651, 20.443],
['ARG18', 'NH1_217', 'P', 'ASP92', 'OD2_1369', 'P', 3.0679, 4.2778],
['ALA24', 'N_294', 'P', 'PRO20', 'O_249', 'P', 3.0751, 29.9487],
['ARG150', 'N_2287', 'P', 'VAL146', 'O_2240', 'P', 3.078, 12.7022],
['LYS28', 'N_364', 'P', 'ALA24', 'O_303', 'P', 3.0783, 19.9504],
['VAL141', 'N_2143', 'P', 'ASP137', 'O_2093', 'P', 3.081, 18.4811],
['ASP98', 'N_1455', 'P', 'SER94', 'O_1397', 'P', 3.0844, 19.56],
['LEU96', 'N_1412', 'P', 'ASP92', 'O_1371', 'P', 3.085, 36.3254],
['ALA22', 'N_269', 'P', 'ARG18', 'O_224', 'P', 3.088, 21.873],
['ALA151', 'N_2311', 'P', 'ARG147', 'O_2264', 'P', 3.0991, 15.5713],
['GLY67', 'N_963', 'P', 'LYS64', 'O_921', 'P', 3.122, 22.7833],
['ASP42', 'N_601', 'P', 'VAL8', 'O_64', 'P', 3.1331, 35.5671],
['ARG65', 'N_922', 'P', 'SER61', 'O_871', 'P', 3.1339, 23.3682],
['TRP39', 'N_537', 'P', 'SER36', 'O_507', 'P', 3.1343, 15.1775],
['LYS123', 'N_1859', 'P', 'ASP120', 'O_1827', 'P', 3.1375, 18.6589],
['MET91', 'N_1343', 'P', 'ASN95', 'OD1_1406', 'P', 3.1581, 39.0427],
['THR140', 'N_2129', 'P', 'SER136', 'O_2081', 'P', 3.1742, 30.2937],
['PHE85', 'N_1241', 'P', 'ASP81', 'O_1196', 'P', 3.1845, 20.2243],
['ASN15', 'N_157', 'P', 'CYS12', 'SG_127', 'P', 3.2043, 37.4576],
['ALA111', 'N_1673', 'P', 'PHE82', 'O_1216', 'P', 3.2054, 20.58],
['ARG147', 'N_2241', 'P', 'GLN143', 'O_2196', 'P', 3.2416, 12.0678],
['ARG75', 'NH2_1093', 'P', 'ASP81', 'OD1_1193', 'P', 3.2447, 29.3403],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 3.2687, 28.6743],
['ARG147', 'NH1_2257', 'P', 'GLN124', 'OE1_1892', 'P', 3.3008, 29.853],
['PHE138', 'N_2094', 'P', 'ASN134', 'O_2058', 'P', 3.3062, 31.0247],
['SER7', 'OG_45', 'P', 'THR84', 'O_1240', 'P', 3.3227, 35.5231],
['CYS12', 'N_120', 'P', 'ALA44', 'O_633', 'P', 3.3349, 36.1006],
..
..
In [19]: interactionsTrajectory.getSaltBridges()
[[['GLU139', 'OE1_2125_2126', 'P', 'HSE66', 'NE2_957', 'P', 2.8359],
['ASP81', 'OD1_1193_1194', 'P', 'ARG75', 'NH1_1090_1093', 'P', 2.9163],
['ASP32', 'OD1_443_444', 'P', 'LYS28', 'NZ_380', 'P', 3.037],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.0699],
['ARG27', 'NH1_356_359', 'P', 'GLU23', 'OE1_290_291', 'P', 3.7148],
['GLU139', 'OE1_2125_2126', 'P', 'ARG65', 'NH1_938_941', 'P', 3.7799],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.9359],
['ARG58', 'NH1_829_832', 'P', 'ASP56', 'OD1_788_789', 'P', 3.9486],
['ARG18', 'NH1_217_220', 'P', 'ASP92', 'OD1_1368_1369', 'P', 4.0693],
['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 4.0787],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.1543],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 4.1879],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 4.3835],
['ARG18', 'NH1_217_220', 'P', 'ASP129', 'OD1_1978_1979', 'P', 4.5608],
['ARG75', 'NH1_1090_1093', 'P', 'ASP42', 'OD1_609_610', 'P', 4.5612],
['GLU23', 'OE1_290_291', 'P', 'HSE72', 'NE2_1042', 'P', 4.99]],
[['ASP32', 'OD1_443_444', 'P', 'LYS28', 'NZ_380', 'P', 2.5568],
['ASP81', 'OD1_1193_1194', 'P', 'ARG75', 'NH1_1090_1093', 'P', 2.6325],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 2.8263],
['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 3.0552],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 3.2384],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.3269],
['ARG27', 'NH1_356_359', 'P', 'GLU23', 'OE1_290_291', 'P', 3.4115],
['GLU139', 'OE1_2125_2126', 'P', 'ARG65', 'NH1_938_941', 'P', 3.4427],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.5063],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.8015],
['ARG58', 'NH1_829_832', 'P', 'ASP56', 'OD1_788_789', 'P', 3.8017],
['ARG18', 'NH1_217_220', 'P', 'ASP92', 'OD1_1368_1369', 'P', 3.8368],
['GLU139', 'OE1_2125_2126', 'P', 'HSE66', 'NE2_957', 'P', 3.9677],
['ARG75', 'NH1_1090_1093', 'P', 'ASP42', 'OD1_609_610', 'P', 4.5207]],
[['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 2.5925],
['ASP32', 'OD1_443_444', 'P', 'LYS28', 'NZ_380', 'P', 2.5955],
['GLU139', 'OE1_2125_2126', 'P', 'ARG65', 'NH1_938_941', 'P', 2.6677],
['ASP81', 'OD1_1193_1194', 'P', 'ARG75', 'NH1_1090_1093', 'P', 2.945],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.0796],
['ARG58', 'NH1_829_832', 'P', 'ASP56', 'OD1_788_789', 'P', 3.6],
['GLU139', 'OE1_2125_2126', 'P', 'HSE66', 'NE2_957', 'P', 3.6121],
['ARG18', 'NH1_217_220', 'P', 'ASP92', 'OD1_1368_1369', 'P', 3.6951],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.7353],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.8213],
['ARG27', 'NH1_356_359', 'P', 'GLU23', 'OE1_290_291', 'P', 3.897],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 4.2197],
['ARG75', 'NH1_1090_1093', 'P', 'ASP42', 'OD1_609_610', 'P', 4.3401],
['ARG18', 'NH1_217_220', 'P', 'ASP129', 'OD1_1978_1979', 'P', 4.6103],
['ASP86', 'OD1_1269_1270', 'P', 'LYS6', 'NZ_32', 'P', 4.9726]],
[['ASP32', 'OD1_443_444', 'P', 'LYS28', 'NZ_380', 'P', 2.5045],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.8527],
['ASP81', 'OD1_1193_1194', 'P', 'ARG75', 'NH1_1090_1093', 'P', 2.8842],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.2487],
..
..
In [20]: interactionsTrajectory.getHydrophobic()
[[['ALA156', 'CB_2401', 'P', 'TYR87', 'OH_1286', 'P', 3.0459, 21.959],
['ALA24', 'CB_298', 'P', 'MET63', 'CE_894', 'P', 3.3105, 5.1584],
['ILE68', 'CG2_976', 'P', 'MET63', 'CE_894', 'P', 3.3306, 52.4165],
['TYR142', 'CZ_2171', 'P', 'VAL146', 'CG2_2235', 'P', 3.4815, 49.7427],
['PHE10', 'CD1_92', 'P', 'ALA22', 'CB_273', 'P', 3.5334, 31.1973],
['LYS6', 'CD_26', 'P', 'TRP39', 'CZ2_555', 'P', 3.5427, 68.7284],
['PHE26', 'CE2_336', 'P', 'VAL30', 'CG1_411', 'P', 3.5603, 21.127],
['ILE88', 'CD_1307', 'P', 'ALA111', 'CB_1677', 'P', 3.5627, 21.2201],
['VAL11', 'CG2_114', 'P', 'ILE88', 'CG2_1300', 'P', 3.6386, 9.3289],
['VAL41', 'CG2_595', 'P', 'PHE26', 'CD2_334', 'P', 3.6448, 16.55],
['PHE152', 'CE1_2331', 'P', 'ALA156', 'CB_2401', 'P', 3.6594, 17.4765],
['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.6828, 25.1359],
['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.6917, 11.9735],
['PHE82', 'CD1_1205', 'P', 'ILE88', 'CD_1307', 'P', 3.692, 17.6138],
['LEU116', 'CD2_1771', 'P', 'ILE127', 'CD_1949', 'P', 3.7057, 17.4094],
['VAL8', 'CG1_55', 'P', 'PHE26', 'CE2_336', 'P', 3.7106, 12.1392],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.7263, 16.9718],
['LEU9', 'CD2_78', 'P', 'ILE77', 'CD_1128', 'P', 3.745, 15.4175],
['LEU89', 'CD1_1322', 'P', 'VAL8', 'CG2_59', 'P', 3.7672, 15.9262],
['ILE126', 'CD_1930', 'P', 'LEU125', 'CD1_1907', 'P', 3.7885, 54.1512],
['VAL141', 'CG1_2149', 'P', 'ILE127', 'CG2_1942', 'P', 3.8659, 11.4623],
['MET91', 'SD_1353', 'P', 'ILE127', 'CD_1949', 'P', 3.8864, 35.855],
['ALA44', 'CB_628', 'P', 'LEU9', 'CD1_74', 'P', 3.8992, 15.0915],
['VAL25', 'CG2_314', 'P', 'TYR142', 'CE1_2169', 'P', 3.92, 12.0265],
['ILE21', 'CG2_256', 'P', 'MET63', 'SD_893', 'P', 3.9614, 20.7701],
['LEU153', 'CD1_2350', 'P', 'TRP39', 'NE1_547', 'P', 3.967, 9.4118],
['PHE85', 'CZ_1253', 'P', 'LEU9', 'CD1_74', 'P', 4.0119, 32.0573],
['ILE35', 'CD_491', 'P', 'TRP39', 'NE1_547', 'P', 4.0172, 25.9805],
['LEU29', 'CD1_395', 'P', 'VAL25', 'CG1_310', 'P', 4.0642, 19.7098],
['ALA74', 'CB_1068', 'P', 'ILE16', 'CG2_177', 'P', 4.0772, 6.6731],
['ARG75', 'CG_1081', 'P', 'ALA44', 'CB_628', 'P', 4.0853, 36.2109],
['ARG18', 'CG_208', 'P', 'VAL141', 'CG1_2149', 'P', 4.104, 20.3057],
['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.1048, 17.4819],
['TYR119', 'CE1_1805', 'P', 'LEU89', 'CD2_1326', 'P', 4.1435, 11.5628],
['ARG40', 'CG_568', 'P', 'PHE85', 'CE2_1257', 'P', 4.2669, 60.8933],
['LYS28', 'CG_371', 'P', 'ILE68', 'CD_983', 'P', 4.2707, 21.8011],
['PHE138', 'CD2_2108', 'P', 'ILE21', 'CD_263', 'P', 4.3082, 6.5618],
['TYR131', 'CE1_2006', 'P', 'ILE16', 'CD_184', 'P', 4.3352, 8.9118],
['ARG58', 'CG_820', 'P', 'PHE138', 'CE1_2104', 'P', 4.4781, 59.4126]],
[['MET63', 'SD_893', 'P', 'TYR142', 'CD1_2167', 'P', 3.3036, 26.7569],
['ALA24', 'CB_298', 'P', 'MET63', 'CE_894', 'P', 3.3592, 7.0868],
['VAL8', 'CG2_59', 'P', 'PHE10', 'CZ_96', 'P', 3.3808, 27.8216],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.429, 13.2977],
['LEU116', 'CD1_1767', 'P', 'PHE10', 'CE1_94', 'P', 3.549, 13.546],
['PHE82', 'CZ_1209', 'P', 'ILE77', 'CD_1128', 'P', 3.5608, 20.4262],
['ILE68', 'CD_983', 'P', 'TYR142', 'OH_2172', 'P', 3.5692, 27.4475],
['PHE26', 'CE2_336', 'P', 'VAL30', 'CG1_411', 'P', 3.5789, 28.1292],
['ALA156', 'CB_2401', 'P', 'PHE152', 'CD1_2329', 'P', 3.6255, 24.4807],
['VAL11', 'CG2_114', 'P', 'ILE88', 'CG2_1300', 'P', 3.6421, 8.6093],
..
..
In [21]: interactionsTrajectory.getPiCation()
[[['PHE85',
'1248_1249_1251_1253_1255_1257',
'P',
'ARG40',
'NH1_577_580',
'P',
3.6523],
['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.5323],
['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'LYS112',
'NZ_1699',
'P',
4.828]],
[['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'LYS112',
'NZ_1699',
'P',
3.4611],
['PHE85',
'1248_1249_1251_1253_1255_1257',
'P',
'ARG40',
'NH1_577_580',
'P',
3.924],
['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.8561],
['TYR87',
'1280_1281_1283_1285_1288_1290',
'P',
'LYS112',
'NZ_1699',
'P',
4.9287],
['TYR131',
'2003_2004_2006_2008_2011_2013',
'P',
'ARG58',
'NH1_829_832',
'P',
4.9441]],
[['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'LYS112',
'NZ_1699',
'P',
2.693],
['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.0971],
['PHE85',
'1248_1249_1251_1253_1255_1257',
'P',
'ARG40',
'NH1_577_580',
'P',
4.4856]],
[['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'LYS112',
'NZ_1699',
'P',
2.5938],
['PHE85',
'1248_1249_1251_1253_1255_1257',
'P',
'ARG40',
'NH1_577_580',
'P',
3.5816],
['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 3.8296]],
[['PHE85',
'1248_1249_1251_1253_1255_1257',
'P',
'ARG40',
'NH1_577_580',
'P',
3.9363],
['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.7618],
['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'LYS155',
'NZ_2391',
'P',
4.8181],
['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'LYS112',
'NZ_1699',
'P',
4.8867]],
[['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.2935],
['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'LYS112',
'NZ_1699',
'P',
4.3158]],
[['PHE85',
'1248_1249_1251_1253_1255_1257',
'P',
'ARG40',
'NH1_577_580',
'P',
3.8709],
['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.4195],
['PHE138',
'2101_2102_2104_2106_2108_2110',
'P',
'ARG58',
'NH1_829_832',
'P',
4.9708]],
..
..
In [22]: interactionsTrajectory.getPiStacking()
[[['HSE66',
'953_954_955_957_959',
'P',
'TYR142',
'2166_2167_2169_2171_2174_2176',
'P',
3.8882,
162.1245],
['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'TYR119',
'1802_1803_1805_1807_1810_1812',
'P',
4.3605,
3.0063],
['PHE26',
'327_328_330_332_334_336',
'P',
'TRP39',
'549_550_551_553_555_557',
'P',
4.8394,
75.4587],
['TYR132',
'2024_2025_2027_2029_2032_2034',
'P',
'TYR131',
'2003_2004_2006_2008_2011_2013',
'P',
4.8732,
91.4358]],
[['PHE26',
'327_328_330_332_334_336',
'P',
'TRP39',
'549_550_551_553_555_557',
'P',
4.8046,
70.9506],
['HSE66',
'953_954_955_957_959',
'P',
'TYR142',
'2166_2167_2169_2171_2174_2176',
'P',
4.8351,
138.8872]],
[['HSE66',
'953_954_955_957_959',
'P',
'TYR142',
'2166_2167_2169_2171_2174_2176',
'P',
3.6419,
174.2245]],
[['HSE66',
'953_954_955_957_959',
'P',
'TYR142',
'2166_2167_2169_2171_2174_2176',
'P',
4.1376,
143.3286]],
[['HSE66',
'953_954_955_957_959',
'P',
'TYR142',
'2166_2167_2169_2171_2174_2176',
'P',
4.2999,
137.4965],
['TYR87',
'1280_1281_1283_1285_1288_1290',
'P',
'PHE152',
'2328_2329_2331_2333_2335_2337',
'P',
4.9646,
73.7093]],
[['HSE66',
'953_954_955_957_959',
'P',
'TYR142',
'2166_2167_2169_2171_2174_2176',
'P',
4.2623,
158.0688],
..
..
Once we compute interactions, we can also select two that are interesting for
us by using selection or selection and selection2 if we want to
compare two chains of protein structure.
Here, we can display all interactions with residues with numbers between 100
and 106.
In [23]: interactionsTrajectory.getInteractions(selection='resid 100 to 106')
[[['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD1_1463', 'P', 1.998, 33.1238],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8075, 29.107],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.933, 10.3321],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9361, 9.2855],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.9952, 32.2712],
['GLN105', 'N_1571', 'P', 'LYS102', 'O_1545', 'P', 3.0464, 19.6807],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 3.4548, 26.1223],
['VAL106', 'N_1588', 'P', 'SER103', 'O_1556', 'P', 3.4974, 34.2367]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.5963, 18.6089],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.7535, 13.6202],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7626, 15.9446],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.9067, 16.7879],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.0125, 16.6445],
['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD1_1463', 'P', 3.0551, 13.8509],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 3.1649, 39.2608],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.2195, 25.4359],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.3521, 12.6376],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.3904, 38.6896],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.46, 29.7639]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6466, 7.8982],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8761, 17.0562],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9269, 16.8394],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.984, 10.6183],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.101, 38.8603],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.2553, 38.5648]],
[['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.5911, 17.069],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6274, 12.9418],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.7018, 15.5273],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.8801, 16.6129],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.9348, 25.5713],
['GLN105', 'N_1571', 'P', 'LYS102', 'O_1545', 'P', 2.9562, 38.6882],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD1_1463', 'P', 3.1464, 36.9083],
['LYS102', 'NZ_1540', 'P', 'SER47', 'OG_665', 'P', 3.155, 33.2035],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 3.2314, 26.449]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6718, 15.3661],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.6858, 28.5654],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.7479, 25.7898],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7584, 9.5766],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.8029, 24.9678],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD1_1463', 'P', 2.9645, 18.3577],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 3.0085, 24.3135],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.2018, 39.9842],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.2421, 26.211],
['ASN104', 'N_1557', 'P', 'ARG101', 'O_1523', 'P', 3.3623, 38.1443]],
[['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.6595, 13.3173],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.8351, 14.4292],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD1_1463', 'P', 2.8423, 25.7739],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.8761, 36.221],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.9016, 29.2602],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9501, 21.9519],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9534, 4.572],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.9715, 13.2817],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.0385, 28.4861],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.0741, 22.6725],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.0961, 21.9463]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6673, 5.897],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD2_1464', 'P', 2.8621, 21.3715],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.9062, 37.2809],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.9467, 14.2625],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 3.0105, 15.1965],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.1835, 33.0481],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.2504, 29.8412],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.4557, 26.8981]],
[['ARG101', 'NE_1513', 'P', 'ASP98', 'OD1_1463', 'P', 2.6955, 15.9473],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.7336, 13.04],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.7844, 21.0059],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.7921, 34.0413],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 2.8616, 30.9582],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9622, 35.633],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9862, 9.5713],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.992, 28.725],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 3.0439, 38.4803],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.2289, 6.3339],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.3376, 16.6525],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.3409, 32.703]],
[['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.6495, 18.2239],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD1_1463', 'P', 2.675, 14.3671],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.6999, 16.6616],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.7186, 10.5368],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8422, 23.6928],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 2.8537, 21.8508],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.8826, 12.651],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.9711, 26.7601],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.1186, 14.3141],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.2655, 29.3262]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6587, 11.1386],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.7047, 15.6631],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.791, 11.1184],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 2.801, 22.9498],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD2_1464', 'P', 2.9519, 31.5282],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 3.0148, 11.0913],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.3007, 38.2386],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 3.3317, 21.1],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.4041, 33.0264]],
[['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.5558, 15.1737],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD2_1464', 'P', 2.7324, 21.7444],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8949, 31.6832],
['ASN100', 'ND2_1495', 'P', 'LEU96', 'O_1430', 'P', 2.9391, 22.8993],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 3.1202, 21.236],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 3.1673, 16.8727],
['GLN105', 'N_1571', 'P', 'LYS102', 'O_1545', 'P', 3.1973, 19.7715],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.271, 31.13],
['CYS109', 'SG_1647', 'P', 'SER103', 'OG_1553', 'P', 3.3052, 14.7978]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.671, 37.3323],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.739, 34.0943],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD2_1464', 'P', 2.7588, 35.9299],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.8159, 18.3284],
['ASN100', 'ND2_1495', 'P', 'LEU96', 'O_1430', 'P', 2.8621, 29.9939],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.8717, 34.7545],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9076, 6.0046],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.079, 29.8594],
['ASN104', 'N_1557', 'P', 'ARG101', 'O_1523', 'P', 3.4094, 37.1284],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.4107, 38.1571]],
[['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.6803, 15.1718],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.7669, 25.5278],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.8242, 31.1474],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 3.0011, 28.4159],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.0907, 32.962],
['ASN104', 'N_1557', 'P', 'ARG101', 'O_1523', 'P', 3.0944, 31.0232],
['ASN100', 'ND2_1495', 'P', 'LEU96', 'O_1430', 'P', 3.1066, 31.2941],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 3.153, 7.2531],
['ARG101', 'NE_1513', 'P', 'ASP98', 'OD2_1464', 'P', 3.1683, 35.5334]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.5916, 5.2678],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7483, 9.7499],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.7533, 23.1952],
['GLN105', 'NE2_1583', 'P', 'ARG101', 'O_1523', 'P', 2.8947, 9.5954],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9874, 36.0359],
['ASN100', 'ND2_1495', 'P', 'LEU96', 'O_1430', 'P', 2.9944, 17.1267],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.0055, 24.8374],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.0528, 29.1184],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.0686, 20.4109],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.1474, 24.7453]],
[['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.7044, 10.5924],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.7509, 8.0677],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.8112, 11.4161],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.8136, 16.1535],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 2.8215, 39.6551],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.8508, 18.2442],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9434, 34.3129],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.9806, 20.0253],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.1026, 29.4155]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.6685, 15.0847],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.757, 19.0853],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.7715, 5.5688],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.7976, 24.804],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.869, 19.5567],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 2.9269, 20.4698],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.1468, 8.581],
['CYS109', 'SG_1647', 'P', 'SER103', 'OG_1553', 'P', 3.2707, 39.8715],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.2959, 34.2995]],
[['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.6797, 11.1273],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.7404, 22.8181],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.8344, 21.332],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.8389, 18.5308],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8491, 12.329],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 2.9264, 7.5038],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 2.9504, 10.3511],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.0236, 6.9167],
['CYS109', 'SG_1647', 'P', 'SER103', 'OG_1553', 'P', 3.106, 38.5309],
['ASN100', 'ND2_1495', 'P', 'LEU96', 'O_1430', 'P', 3.2461, 4.2582]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.6103, 19.241],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.6343, 15.3945],
['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD2_1464', 'P', 2.6543, 10.2308],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7596, 12.1992],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.7949, 12.7041],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.9188, 34.6284],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9977, 39.8669],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.162, 37.02],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.1719, 26.513],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.2101, 36.7681]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.7558, 29.536],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.7988, 8.8578],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.8421, 28.9541],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.9436, 3.1426],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.0155, 38.3833],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.0202, 2.421],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.2096, 28.1311],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 3.4213, 14.8714]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6129, 19.7326],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.6911, 19.978],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.7089, 22.225],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.7963, 25.158],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8504, 16.7766],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.8915, 21.1984],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.0135, 31.6808],
['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.0372, 20.7935],
['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.0379, 38.205],
['GLN105', 'NE2_1583', 'P', 'ARG101', 'O_1523', 'P', 3.2845, 28.1096],
['CYS109', 'SG_1647', 'P', 'SER103', 'OG_1553', 'P', 3.4421, 25.6483]],
[['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.6793, 16.1937],
['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD2_1464', 'P', 2.7584, 11.5432],
['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.775, 6.6534],
['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7754, 4.8907],
['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 2.8177, 29.9366],
['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.8304, 17.4803],
['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.856, 21.4102],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9243, 35.6267],
['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.0156, 9.3534]],
[['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.0699],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.9359]],
[['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 2.8263],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.5063]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.0796]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.8527],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.5055]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.5251],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.6639]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.784],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7415]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.7833],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.6905]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.118],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.7333]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.9802],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3115]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1925],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3314]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1321],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.377]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.5465],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.1424]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.8662],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7765]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.4575],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7844]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.7106],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2495]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.9739],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3131]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.0533],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.8328]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.2511],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.6196]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.955],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.9277]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1188],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.6654]],
[['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 2.7506]],
[['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2655]],
[],
[],
[],
[],
[],
[['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2903]],
[],
[],
[['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3093]],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.6828, 25.1359],
['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.1048, 17.4819]],
[['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 3.6601, 18.1513],
['VAL106', 'CG2_1598', 'P', 'PHE82', 'CD2_1211', 'P', 4.0401, 13.1367],
['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.2489, 20.4475]],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.9579, 24.0447],
['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 3.993, 10.9852]],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG1_1594', 'P', 3.7771, 25.8417],
['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.2695, 6.7328]],
[['VAL106', 'CG2_1598', 'P', 'PHE82', 'CD2_1211', 'P', 3.7581, 24.2415],
['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.3995, 30.7521]],
[['LYS79', 'CD_1158', 'P', 'VAL106', 'CG2_1598', 'P', 3.9758, 19.5257],
['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.2315, 11.0609]],
[['VAL106', 'CG1_1594', 'P', 'PHE82', 'CG_1204', 'P', 3.8971, 17.973],
['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.0318, 20.1861]],
[['VAL106', 'CG2_1598', 'P', 'PHE82', 'CD2_1211', 'P', 3.9504, 18.2026],
['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.0183, 24.7812],
['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.354, 18.5823]],
[['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.1345, 9.1889],
['LYS79', 'CD_1158', 'P', 'VAL106', 'CG2_1598', 'P', 4.1488, 19.0544]],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.7492, 21.5977]],
[['VAL106', 'CG2_1598', 'P', 'PHE82', 'CD2_1211', 'P', 3.7532, 20.5214],
['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.1843, 21.2188]],
[['LYS79', 'CD_1158', 'P', 'VAL106', 'CG2_1598', 'P', 4.1132, 33.2299],
['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.2545, 30.9532]],
[['VAL106', 'CG1_1594', 'P', 'PHE82', 'CG_1204', 'P', 4.2115, 22.6531],
['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.4451, 30.8638]],
[['LYS102', 'CD_1534', 'P', 'PHE82', 'CE2_1213', 'P', 4.1132, 21.6908],
['VAL106', 'CG2_1598', 'P', 'PHE82', 'CD2_1211', 'P', 4.301, 14.4692]],
[['VAL106', 'CG1_1594', 'P', 'PHE82', 'CD1_1205', 'P', 3.769, 29.2683]],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.7591, 26.6179]],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG1_1594', 'P', 3.7466, 15.362],
['LYS102', 'CD_1534', 'P', 'PHE82', 'CZ_1209', 'P', 4.3692, 20.969]],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.7838, 20.4368],
['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.2006, 12.5337]],
[['LYS102', 'CD_1534', 'P', 'PHE82', 'CZ_1209', 'P', 4.3001, 14.6918]],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.2078, 41.8606],
['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.3141, 10.5395]],
[['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.2738, 15.6412]],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[]]
We can apply the same selection to any type of interaction, for example:
In [24]: interactionsTrajectory.getHydrophobic(selection='chain P and resid 90 to 100')
[[['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.6917, 11.9735],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.7263, 16.9718],
['MET91', 'SD_1353', 'P', 'ILE127', 'CD_1949', 'P', 3.8864, 35.855]],
[['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.429, 13.2977],
['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.6871, 7.95],
['MET91', 'CE_1354', 'P', 'LEU116', 'CD2_1771', 'P', 3.8434, 19.1277]],
[['ILE88', 'CG2_1300', 'P', 'LEU99', 'CD1_1476', 'P', 3.5436, 9.3247],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.57, 23.3065],
['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.6654, 17.4729]],
[['LEU99', 'CD1_1476', 'P', 'ILE88', 'CG2_1300', 'P', 3.5506, 10.5506],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.6132, 25.5246],
['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.6989, 21.7296]],
[['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.681, 13.3699],
['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.7838, 19.4208],
['ILE127', 'CD_1949', 'P', 'MET91', 'SD_1353', 'P', 3.8538, 35.0746],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CD_1718', 'P', 3.993, 32.6427],
['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.3995, 30.7521]],
[['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.4473, 9.6836],
['ILE127', 'CD_1949', 'P', 'MET91', 'SD_1353', 'P', 3.7931, 33.4972],
['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.8599, 15.7656],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG1_1715', 'P', 4.0839, 25.8005]],
[['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.6656, 11.2061],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CD_1718', 'P', 3.7465, 13.9407],
['MET91', 'CE_1354', 'P', 'ALA22', 'CB_273', 'P', 4.1873, 5.8643]],
[['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.577, 21.8565],
['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.7311, 16.6688],
['LEU99', 'CD1_1476', 'P', 'ILE77', 'CD_1128', 'P', 3.7918, 13.9645],
['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.0183, 24.7812]],
[['LEU99', 'CD1_1476', 'P', 'ILE88', 'CG2_1300', 'P', 3.493, 12.0525],
['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.8477, 17.8661],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.9465, 13.0407],
['ARG18', 'CG_208', 'P', 'MET91', 'CG_1350', 'P', 4.4773, 45.2545]],
[['MET91', 'SD_1353', 'P', 'ILE127', 'CD_1949', 'P', 3.6073, 35.8986],
['LEU99', 'CD1_1476', 'P', 'VAL11', 'CG1_110', 'P', 3.8196, 19.5026],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.8266, 8.1345]],
[['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.688, 16.5389],
['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.8303, 12.8658],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.9125, 20.3824],
['ARG18', 'CG_208', 'P', 'MET91', 'CG_1350', 'P', 4.3469, 47.3018]],
[['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.4146, 25.9366],
['LEU99', 'CD2_1480', 'P', 'PHE82', 'CZ_1209', 'P', 3.6458, 17.5698],
['ILE113', 'CG2_1711', 'P', 'LEU99', 'CD1_1476', 'P', 3.7998, 30.7151],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 4.0071, 18.0266],
['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.2545, 30.9532]],
[['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.5757, 19.6775],
['LEU99', 'CD2_1480', 'P', 'ILE88', 'CG2_1300', 'P', 3.8102, 10.1337],
['ILE113', 'CG2_1711', 'P', 'LEU96', 'CG_1419', 'P', 3.8694, 28.8723]],
[['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.5696, 9.6273],
['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.8426, 17.9602]],
[['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.511, 19.586],
['LEU99', 'CD1_1476', 'P', 'VAL11', 'CG2_114', 'P', 3.5732, 10.7329],
['MET91', 'CE_1354', 'P', 'LEU116', 'CD2_1771', 'P', 3.9678, 13.6217]],
[['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.6543, 13.7308],
['ILE113', 'CG2_1711', 'P', 'LEU96', 'CG_1419', 'P', 3.7456, 22.5419],
['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.8152, 17.9895]],
[['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.4849, 12.5888],
['MET91', 'CE_1354', 'P', 'ALA22', 'CB_273', 'P', 3.5767, 9.5877],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.7229, 15.3003],
['ILE127', 'CD_1949', 'P', 'MET91', 'SD_1353', 'P', 4.274, 35.6655]],
[['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.6286, 22.7844],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.6984, 12.3956],
['ALA22', 'CB_273', 'P', 'MET91', 'CE_1354', 'P', 3.7795, 8.4161],
['LEU99', 'CD2_1480', 'P', 'ILE88', 'CG2_1300', 'P', 3.7921, 7.4352]],
[['ILE127', 'CD_1949', 'P', 'MET91', 'SD_1353', 'P', 3.4598, 42.01],
['LEU99', 'CD1_1476', 'P', 'ILE113', 'CG2_1711', 'P', 3.6609, 33.0336],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.7378, 17.5379],
['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.7686, 14.0166]],
[['LEU99', 'CD1_1476', 'P', 'VAL11', 'CG2_114', 'P', 3.518, 18.8799],
['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.5399, 12.2359],
['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.7165, 21.0434]],
[['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.2931, 21.0747],
['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.3771, 11.4804],
['MET91', 'CE_1354', 'P', 'ALA22', 'CB_273', 'P', 3.6628, 9.0978],
['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.6984, 21.9302]]]
In [25]: interactionsTrajectory.getHydrogenBonds(selection='chain P and resid 112 to 115')
[[['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8429, 17.7147],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8975, 24.576],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.912, 10.1158],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.051, 21.4045],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.059, 24.1606],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 3.2687, 28.6743]],
[['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE1_1735', 'P', 2.5487, 20.8176],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.6334, 17.8203],
['SER118', 'OG_1791', 'P', 'LEU115', 'O_1757', 'P', 2.6547, 25.6442],
['TYR119', 'OH_1808', 'P', 'GLU114', 'OE1_1735', 'P', 2.735, 15.8502],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7935, 13.2257],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8946, 17.9316],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.9523, 13.8795],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.0323, 8.8409],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.2094, 37.0837],
['CYS90', 'SG_1339', 'P', 'GLU114', 'O_1738', 'P', 3.2322, 23.7336],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE2_1736', 'P', 3.253, 23.8402]],
[['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.5902, 19.0335],
['TYR119', 'OH_1808', 'P', 'GLU114', 'OE2_1736', 'P', 2.6441, 10.2991],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7184, 24.9984],
['SER118', 'OG_1791', 'P', 'LEU115', 'O_1757', 'P', 2.7238, 26.9156],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8381, 10.253],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'ND1_2414', 'P', 2.8616, 14.018],
['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE2_1736', 'P', 2.8761, 18.0626],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.0416, 27.2343],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 3.195, 38.6534],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.4603, 13.0317]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE1_1735', 'P', 2.5321, 12.1754],
['TYR119', 'OH_1808', 'P', 'GLU114', 'OE2_1736', 'P', 2.6666, 5.0368],
['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE2_1736', 'P', 2.6844, 12.4337],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 2.7625, 21.1367],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7703, 4.1752],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.813, 11.6498],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8375, 24.3092],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'ND1_2414', 'P', 2.8399, 24.5852],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 2.9985, 12.7544]],
[['TYR119', 'OH_1808', 'P', 'GLU114', 'OE2_1736', 'P', 2.6438, 28.5062],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 2.7748, 6.971],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8324, 30.6076],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8567, 3.076],
['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE2_1736', 'P', 2.8677, 22.3219],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.9251, 9.0077],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.0506, 7.4102],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.4475, 19.9922]],
[['TYR119', 'OH_1808', 'P', 'GLU114', 'OE1_1735', 'P', 2.6085, 18.3035],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.7054, 1.3697],
['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE1_1735', 'P', 2.7093, 27.1289],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8128, 18.817],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 3.0762, 12.1723],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.1037, 10.0101],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 3.1356, 19.0662],
['CYS90', 'SG_1339', 'P', 'GLU114', 'O_1738', 'P', 3.3017, 27.3282],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.3047, 11.3911]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.652, 10.3503],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.762, 14.1022],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7884, 21.6503],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.7994, 5.7305],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8628, 30.0771],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 2.9474, 28.4869],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.4304, 27.1097]],
[['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.7778, 28.0614],
['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.7868, 18.8919],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8504, 18.6098],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 2.9351, 15.9934],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.9391, 14.958]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.6858, 23.9752],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8512, 7.2231],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 2.9951, 23.9118],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.0881, 6.5417],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 3.1217, 14.0883],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 3.2069, 19.3312],
['CYS90', 'SG_1339', 'P', 'GLU114', 'O_1738', 'P', 3.2331, 32.7145]],
[['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.6385, 22.7134],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.6967, 1.035],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7267, 17.2895],
['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.8598, 29.0811],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.9766, 16.8905],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.0616, 27.2229],
['CYS90', 'SG_1339', 'P', 'GLU114', 'O_1738', 'P', 3.4089, 25.9472]],
[['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 2.8001, 13.1653],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8336, 11.5184],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8683, 15.5308],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8949, 10.1824],
['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.9677, 16.3497],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.089, 17.9789]],
[['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 2.7045, 11.8564],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8002, 5.9828],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8444, 31.549],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.0718, 34.4381],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 3.3002, 12.0528]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.549, 18.6576],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.7292, 11.3872],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7951, 19.2119],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.861, 9.3445],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 2.8723, 5.3509],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.2056, 13.0868]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.7432, 12.0576],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8455, 10.8341],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8979, 18.8959],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.9513, 25.3055],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.2646, 30.184]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.7509, 33.4365],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7569, 15.9129],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8989, 5.3091],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 3.0521, 14.9906],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.2193, 17.7506]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE1_1735', 'P', 2.9107, 11.3311],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.9279, 24.4459],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.9572, 22.8551],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 3.0531, 39.2571],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.2647, 19.7898]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE1_1735', 'P', 2.7301, 6.4912],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 3.0067, 19.0131],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 3.0515, 32.6929],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 3.0654, 16.9354],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.2584, 28.3632]],
[['SER118', 'OG_1791', 'P', 'LEU115', 'O_1757', 'P', 2.7161, 4.3692],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7665, 15.6553],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.833, 1.7101],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.9604, 20.771],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.1924, 36.5103],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.3101, 22.7426]],
[['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7306, 1.388],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7477, 25.8134],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.7669, 4.8657],
['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.7852, 20.1148]],
[['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8181, 19.759],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8698, 4.299],
['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 3.0671, 23.7084],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.1112, 27.1195],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.1262, 21.7619]],
[['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.6334, 24.4833],
['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8598, 7.853],
['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.0172, 19.6851],
['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.2603, 11.1927],
['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 3.3213, 8.0609]]]
In [26]: interactionsTrajectory.getSaltBridges(selection='chain P and resid 100 to 120')
[[['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.0699],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.9359],
['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 4.0787],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.1543],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 4.1879],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 4.3835]],
[['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 2.8263],
['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 3.0552],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 3.2384],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.3269],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.5063],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.8015]],
[['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 2.5925],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.0796],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.7353],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.8213],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 4.2197]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.8527],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.2487],
['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 3.281],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 3.4289],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.5055],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.7295]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.5251],
['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 2.5476],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 2.8031],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.7693],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.6639]],
[['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 2.5445],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.784],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 2.9545],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.4269],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7415]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.7833],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.7841],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.6393],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.6905],
['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 4.9985]],
[['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 2.7718],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.118],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.7333],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.385]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.9802],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.1049],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3115],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.4854]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1925],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.3668],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3314],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.6386]],
[['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 2.7461],
['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1321],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.377]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.5465],
['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.7315],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.886],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.1424]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.8662],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7765],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 4.9921]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.4575],
['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.6085],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.9194],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.3166],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7844]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.7106],
['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.7026],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.794],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2495]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.9739],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.397],
['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.5529],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.9267],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3131]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.0533],
['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.7951],
['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.8215],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.9526],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.8328]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.2511],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.6196],
['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.9186]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.955],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.9277]],
[['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1188],
['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.6654],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.9234]],
[['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 2.7506],
['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.4341]]]
In [27]: interactionsTrajectory.getRepulsiveIonicBonding(selection='chain P')
[[['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2655]],
[],
[],
[],
[],
[],
[['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2903]],
[],
[],
[['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3093]],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[],
[['ARG147', 'NH1_2257_2260', 'P', 'LYS123', 'NZ_1875', 'P', 4.4846]]]
Change selection criteria for interaction type¶
The interactionsTrajectory.calcProteinInteractionsTrajectory() method computes
interactions using default parameters for interactions. However, it can be
changed according to our needs. To do that, we need to recalculate the
selected types of interactions.
We can do it using the following functions: calcHydrogenBondsTrajectory(),
calcHydrogenBondsTrajectory(), calcSaltBridgesTrajectory(),
calcRepulsiveIonicBondingTrajectory(), calcPiStackingTrajectory(),
calcPiCationTrajectory(), calcHydrophohicTrajectory(), and use
InteractionsTrajectory.setNewHydrogenBondsTrajectory(),
InteractionsTrajectory.setNewSaltBridgesTrajectory(),
InteractionsTrajectory.setNewRepulsiveIonicBondingTrajectory(),
InteractionsTrajectory.setNewPiStackingTrajectory(),
InteractionsTrajectory.setNewPiCationTrajectory(),
InteractionsTrajectory.setNewHydrophohicTrajectory() method to replace it in the main
Instance.
For example:
Repulsive ionic bonding:
In [28]: newRIB = calcRepulsiveIonicBondingTrajectory(atoms, dcd, distA=8)
In [29]: interactionsTrajectory.setNewRepulsiveIonicBondingTrajectory(newRIB)
@> Frame: 0
@> Calculating repulsive ionic bonding.
@> ARG75 P NH1_1090_1093 <---> ARG40 P NH1_577_580 6.7
@> ASP81 P OD1_1193_1194 <---> GLU80 P OE1_1181_1182 7.0
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.6
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 1
@> Calculating repulsive ionic bonding.
@> ARG101 P NH1_1516_1519 <---> LYS102 P NZ_1540 4.5
@> ASP92 P OD1_1368_1369 <---> GLU93 P OE1_1383_1384 7.9
@> Number of detected Repulsive Ionic Bonding interactions: 2.
@> Frame: 2
@> Calculating repulsive ionic bonding.
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 6.8
@> ASP137 P OD1_2090_2091 <---> GLU128 P OE1_1966_1967 7.7
@> ASP81 P OD1_1193_1194 <---> GLU80 P OE1_1181_1182 7.9
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 3
@> Calculating repulsive ionic bonding.
@> GLU80 P OE1_1181_1182 <---> ASP81 P OD1_1193_1194 6.3
@> ASP42 P OD1_609_610 <---> ASP81 P OD1_1193_1194 6.8
@> Number of detected Repulsive Ionic Bonding interactions: 2.
@> Frame: 4
@> Calculating repulsive ionic bonding.
@> ARG101 P NH1_1516_1519 <---> LYS102 P NZ_1540 6.0
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 6.8
@> ARG75 P NH1_1090_1093 <---> ARG40 P NH1_577_580 7.0
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 5
@> Calculating repulsive ionic bonding.
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 6.1
@> ASP42 P OD1_609_610 <---> ASP81 P OD1_1193_1194 6.6
@> LYS79 P NZ_1164 <---> LYS102 P NZ_1540 7.8
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 6
@> Calculating repulsive ionic bonding.
@> ASP42 P OD1_609_610 <---> ASP81 P OD1_1193_1194 6.1
@> LYS112 P NZ_1699 <---> LYS6 P NZ_32 6.4
@> LYS79 P NZ_1164 <---> LYS107 P NZ_1620 7.1
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 7
@> Calculating repulsive ionic bonding.
@> ARG147 P NH1_2257_2260 <---> LYS123 P NZ_1875 4.8
@> ASP42 P OD1_609_610 <---> GLU23 P OE1_290_291 5.9
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 6.4
@> ARG75 P NH1_1090_1093 <---> ARG40 P NH1_577_580 6.9
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 8
@> Calculating repulsive ionic bonding.
@> LYS123 P NZ_1875 <---> ARG147 P NH1_2257_2260 5.1
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.0
@> ASP81 P OD1_1193_1194 <---> GLU80 P OE1_1181_1182 7.2
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 9
@> Calculating repulsive ionic bonding.
@> ARG101 P NH1_1516_1519 <---> LYS102 P NZ_1540 4.3
@> GLU93 P OE1_1383_1384 <---> GLU128 P OE1_1966_1967 6.2
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 6.4
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 10
@> Calculating repulsive ionic bonding.
@> ARG101 P NH1_1516_1519 <---> LYS102 P NZ_1540 4.6
@> LYS123 P NZ_1875 <---> ARG147 P NH1_2257_2260 4.7
@> ASP92 P OD1_1368_1369 <---> GLU128 P OE1_1966_1967 6.4
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.4
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 11
@> Calculating repulsive ionic bonding.
@> ARG101 P NH1_1516_1519 <---> LYS102 P NZ_1540 5.3
@> ASP42 P OD1_609_610 <---> ASP81 P OD1_1193_1194 6.6
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.7
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 12
@> Calculating repulsive ionic bonding.
@> LYS123 P NZ_1875 <---> ARG147 P NH1_2257_2260 5.9
@> ARG75 P NH1_1090_1093 <---> ARG40 P NH1_577_580 6.2
@> ARG150 P NH1_2303_2306 <---> ARG147 P NH1_2257_2260 7.2
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 13
@> Calculating repulsive ionic bonding.
@> ASP42 P OD1_609_610 <---> ASP81 P OD1_1193_1194 6.6
@> ASP129 P OD1_1978_1979 <---> GLU128 P OE1_1966_1967 6.6
@> ARG101 P NH1_1516_1519 <---> LYS102 P NZ_1540 7.8
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.8
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 14
@> Calculating repulsive ionic bonding.
@> LYS123 P NZ_1875 <---> ARG147 P NH1_2257_2260 7.0
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.1
@> ASP81 P OD1_1193_1194 <---> GLU80 P OE1_1181_1182 7.2
@> ASP92 P OD1_1368_1369 <---> GLU128 P OE1_1966_1967 8.0
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 15
@> Calculating repulsive ionic bonding.
@> LYS123 P NZ_1875 <---> ARG147 P NH1_2257_2260 6.5
@> GLU154 P OE1_2371_2372 <---> ASP120 P OD1_1824_1825 6.5
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 6.6
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 16
@> Calculating repulsive ionic bonding.
@> ASP42 P OD1_609_610 <---> GLU23 P OE1_290_291 5.6
@> ARG101 P NH1_1516_1519 <---> LYS102 P NZ_1540 7.1
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.2
@> ASP129 P OD1_1978_1979 <---> GLU128 P OE1_1966_1967 7.2
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 17
@> Calculating repulsive ionic bonding.
@> ARG101 P NH1_1516_1519 <---> LYS102 P NZ_1540 4.9
@> ASP42 P OD1_609_610 <---> ASP81 P OD1_1193_1194 6.5
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.4
@> GLU128 P OE1_1966_1967 <---> ASP129 P OD1_1978_1979 8.0
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 18
@> Calculating repulsive ionic bonding.
@> ASP42 P OD1_609_610 <---> GLU23 P OE1_290_291 5.7
@> ASP135 P OD1_2067_2068 <---> GLU139 P OE1_2125_2126 5.9
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 6.8
@> ASP92 P OD1_1368_1369 <---> GLU128 P OE1_1966_1967 6.8
@> GLU93 P OE1_1383_1384 <---> GLU128 P OE1_1966_1967 7.3
@> Number of detected Repulsive Ionic Bonding interactions: 5.
@> Frame: 19
@> Calculating repulsive ionic bonding.
@> LYS123 P NZ_1875 <---> ARG147 P NH1_2257_2260 5.3
@> GLU139 P OE1_2125_2126 <---> ASP135 P OD1_2067_2068 6.0
@> LYS79 P NZ_1164 <---> LYS107 P NZ_1620 6.1
@> ASP81 P OD1_1193_1194 <---> GLU80 P OE1_1181_1182 7.0
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 20
@> Calculating repulsive ionic bonding.
@> LYS123 P NZ_1875 <---> ARG147 P NH1_2257_2260 4.5
@> ASP135 P OD1_2067_2068 <---> GLU139 P OE1_2125_2126 5.5
@> ASP129 P OD1_1978_1979 <---> ASP92 P OD1_1368_1369 7.1
@> LYS79 P NZ_1164 <---> LYS102 P NZ_1540 7.9
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Repulsive Ionic Bonding are replaced
Pi-cation interactions:
In [30]: newPiCation = calcPiCationTrajectory(atoms, dcd, distA=6)
In [31]: interactionsTrajectory.setNewPiCationTrajectory(newPiCation)
@> Frame: 0
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.7
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.5
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 4.8
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.0
@> TYR131 P 2003_2004_2006_2008_2011_2013 <---> ARG58 P NH1_829_832 5.1
@> Number of detected cation-pi interactions: 5.
@> Frame: 1
@> Calculating cation-Pi interactions.
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 3.5
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.9
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.9
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 4.9
@> TYR131 P 2003_2004_2006_2008_2011_2013 <---> ARG58 P NH1_829_832 4.9
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.7
@> TRP39 P 549_550_551_553_555_557 <---> LYS6 P NZ_32 6.0
@> Number of detected cation-pi interactions: 7.
@> Frame: 2
@> Calculating cation-Pi interactions.
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 2.7
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.1
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.5
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.6
@> Number of detected cation-pi interactions: 4.
@> Frame: 3
@> Calculating cation-Pi interactions.
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 2.6
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.6
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 3.8
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.3
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.3
@> Number of detected cation-pi interactions: 5.
@> Frame: 4
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.9
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.8
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS155 P NZ_2391 4.8
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 4.9
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.3
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.4
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS6 P NZ_32 5.6
@> Number of detected cation-pi interactions: 7.
@> Frame: 5
@> Calculating cation-Pi interactions.
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.3
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 4.3
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 5.2
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.8
@> Number of detected cation-pi interactions: 4.
@> Frame: 6
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.9
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.4
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.0
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 5.0
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS6 P NZ_32 5.3
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.5
@> Number of detected cation-pi interactions: 6.
@> Frame: 7
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.9
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.2
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 4.9
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.7
@> Number of detected cation-pi interactions: 4.
@> Frame: 8
@> Calculating cation-Pi interactions.
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 3.8
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.5
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 5.4
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.6
@> Number of detected cation-pi interactions: 4.
@> Frame: 9
@> Calculating cation-Pi interactions.
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.4
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.8
@> TRP39 P 549_550_551_553_555_557 <---> LYS6 P NZ_32 5.2
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.4
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.5
@> PHE152 P 2328_2329_2331_2333_2335_2337 <---> LYS6 P NZ_32 5.8
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG75 P NH1_1090_1093 5.8
@> Number of detected cation-pi interactions: 7.
@> Frame: 10
@> Calculating cation-Pi interactions.
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.8
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 4.9
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 5.0
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.2
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG75 P NH1_1090_1093 5.9
@> Number of detected cation-pi interactions: 5.
@> Frame: 11
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.1
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS155 P NZ_2391 4.4
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.8
@> TRP39 P 549_550_551_553_555_557 <---> LYS6 P NZ_32 5.4
HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS112 P NZ_1699 5.8
@>
@> Number of detected cation-pi interactions: 5.
@> Frame: 12
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.3
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.4
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.4
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.5
@> HSE72 P 1038_1039_1040_1042_1044 <---> ARG27 P NH1_356_359 5.9
@> Number of detected cation-pi interactions: 5.
@> Frame: 13
@> Calculating cation-Pi interactions.
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 4.4
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.7
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.2
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG75 P NH1_1090_1093 5.8
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS155 P NZ_2391 5.9
@> TRP39 P 549_550_551_553_555_557 <---> LYS6 P NZ_32 6.0
@> Number of detected cation-pi interactions: 6.
@> Frame: 14
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.6
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS6 P NZ_32 5.2
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.3
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 5.6
@> Number of detected cation-pi interactions: 4.
@> Frame: 15
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.4
@> HSE157 P2414_2415_2416_2418_2420_2423_2424 <---> LYS6 P NZ_32 5.1
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.7
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 5.8
@> Number of detected cation-pi interactions: 4.
@> Frame: 16
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 3.8
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS6 P NZ_32 5.4
@> Number of detected cation-pi interactions: 2.
@> Frame: 17
@> Calculating cation-Pi interactions.
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.4
@> TRP39 P 549_550_551_553_555_557 <---> LYS6 P NZ_32 5.6
@> Number of detected cation-pi interactions: 2.
@> Frame: 18
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.5
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.2
@> TRP39 P 549_550_551_553_555_557 <---> LYS6 P NZ_32 5.3
@> TYR87 P 1280_1281_1283_1285_1288_1290 <---> LYS112 P NZ_1699 5.7
@> HSE72 P 1038_1039_1040_1042_1044 <---> ARG27 P NH1_356_359 5.8
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 6.0
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG75 P NH1_1090_1093 6.0
@> Number of detected cation-pi interactions: 7.
@> Frame: 19
@> Calculating cation-Pi interactions.
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 4.9
@> TRP39 P 549_550_551_553_555_557 <---> LYS6 P NZ_32 5.0
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.2
@> HSE66 P 953_954_955_957_959 <---> ARG65 P NH1_938_941 5.9
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG75 P NH1_1090_1093 5.9
@> Number of detected cation-pi interactions: 5.
@> Frame: 20
@> Calculating cation-Pi interactions.
@> PHE138 P 2101_2102_2104_2106_2108_2110 <---> ARG58 P NH1_829_832 5.0
@> TRP39 P 549_550_551_553_555_557 <---> LYS6 P NZ_32 5.6
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG40 P NH1_577_580 5.7
@> PHE85 P 1248_1249_1251_1253_1255_1257 <---> ARG75 P NH1_1090_1093 5.8
@> Number of detected cation-pi interactions: 4.
Pi-Cation interactions are replaced
We can check whether the interactions were replaced. The repulsive ionic
bonding can be found by using getInteractions() and selecting 2
(0 - hydrogen bonds, 1 - salt bridges, 2 - repulsive ionic bonding,
3 - Pi-Stacking, 4 - Pi-Cation, 5 - hydrophobic, 6 - disulfide bonds).
In [32]: interactionsTrajectory.getInteractions()[2]
[[['ARG75', 'NH1_1090_1093', 'P', 'ARG40', 'NH1_577_580', 'P', 6.666],
['ASP81', 'OD1_1193_1194', 'P', 'GLU80', 'OE1_1181_1182', 'P', 6.9843],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.6316]],
[['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 4.5002],
['ASP92', 'OD1_1368_1369', 'P', 'GLU93', 'OE1_1383_1384', 'P', 7.9458]],
[['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.8023],
['ASP137', 'OD1_2090_2091', 'P', 'GLU128', 'OE1_1966_1967', 'P', 7.7429],
['ASP81', 'OD1_1193_1194', 'P', 'GLU80', 'OE1_1181_1182', 'P', 7.9228]],
[['GLU80', 'OE1_1181_1182', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.2655],
['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.8064]],
[['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 6.0034],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.8451],
['ARG75', 'NH1_1090_1093', 'P', 'ARG40', 'NH1_577_580', 'P', 7.0306]],
[['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.1332],
['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.6231],
['LYS79', 'NZ_1164', 'P', 'LYS102', 'NZ_1540', 'P', 7.81]],
[['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.1141],
['LYS112', 'NZ_1699', 'P', 'LYS6', 'NZ_32', 'P', 6.4258],
['LYS79', 'NZ_1164', 'P', 'LYS107', 'NZ_1620', 'P', 7.0898]],
[['ARG147', 'NH1_2257_2260', 'P', 'LYS123', 'NZ_1875', 'P', 4.8418],
['ASP42', 'OD1_609_610', 'P', 'GLU23', 'OE1_290_291', 'P', 5.8605],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.3776],
['ARG75', 'NH1_1090_1093', 'P', 'ARG40', 'NH1_577_580', 'P', 6.9162]],
[['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 5.1095],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.9653],
['ASP81', 'OD1_1193_1194', 'P', 'GLU80', 'OE1_1181_1182', 'P', 7.1885]],
[['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 4.3093],
['GLU93', 'OE1_1383_1384', 'P', 'GLU128', 'OE1_1966_1967', 'P', 6.2251],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.3655]],
[['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 4.6267],
['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.6563],
['ASP92', 'OD1_1368_1369', 'P', 'GLU128', 'OE1_1966_1967', 'P', 6.4486],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.3554]],
[['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 5.2803],
['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.6125],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.7231]],
[['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 5.903],
['ARG75', 'NH1_1090_1093', 'P', 'ARG40', 'NH1_577_580', 'P', 6.2264],
['ARG150', 'NH1_2303_2306', 'P', 'ARG147', 'NH1_2257_2260', 'P', 7.2115]],
[['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.5807],
['ASP129', 'OD1_1978_1979', 'P', 'GLU128', 'OE1_1966_1967', 'P', 6.6156],
['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 7.7691],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.8267]],
[['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 6.9607],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.0793],
['ASP81', 'OD1_1193_1194', 'P', 'GLU80', 'OE1_1181_1182', 'P', 7.1994],
['ASP92', 'OD1_1368_1369', 'P', 'GLU128', 'OE1_1966_1967', 'P', 7.9662]],
[['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 6.4558],
['GLU154', 'OE1_2371_2372', 'P', 'ASP120', 'OD1_1824_1825', 'P', 6.5391],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.6406]],
[['ASP42', 'OD1_609_610', 'P', 'GLU23', 'OE1_290_291', 'P', 5.5599],
['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 7.1302],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.1991],
['ASP129', 'OD1_1978_1979', 'P', 'GLU128', 'OE1_1966_1967', 'P', 7.2499]],
[['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 4.913],
['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.4678],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.3594],
['GLU128', 'OE1_1966_1967', 'P', 'ASP129', 'OD1_1978_1979', 'P', 7.9788]],
[['ASP42', 'OD1_609_610', 'P', 'GLU23', 'OE1_290_291', 'P', 5.6704],
['ASP135', 'OD1_2067_2068', 'P', 'GLU139', 'OE1_2125_2126', 'P', 5.9135],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.7566],
['ASP92', 'OD1_1368_1369', 'P', 'GLU128', 'OE1_1966_1967', 'P', 6.7899],
['GLU93', 'OE1_1383_1384', 'P', 'GLU128', 'OE1_1966_1967', 'P', 7.3464]],
[['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 5.3159],
['GLU139', 'OE1_2125_2126', 'P', 'ASP135', 'OD1_2067_2068', 'P', 6.0087],
['LYS79', 'NZ_1164', 'P', 'LYS107', 'NZ_1620', 'P', 6.0679],
['ASP81', 'OD1_1193_1194', 'P', 'GLU80', 'OE1_1181_1182', 'P', 6.9706]],
[['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.4846],
['ASP135', 'OD1_2067_2068', 'P', 'GLU139', 'OE1_2125_2126', 'P', 5.4686],
['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.0978],
['LYS79', 'NZ_1164', 'P', 'LYS102', 'NZ_1540', 'P', 7.9242]]]
In [33]: interactionsTrajectory.getInteractions()[4]
[[['PHE85',
'1248_1249_1251_1253_1255_1257',
'P',
'ARG40',
'NH1_577_580',
'P',
3.6523],
['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.5323],
['HSE157',
'2414_2415_2416_2418_2420_2423_2424',
'P',
'LYS112',
'NZ_1699',
'P',
4.828],
['PHE138',
'2101_2102_2104_2106_2108_2110',
'P',
'ARG58',
'NH1_829_832',
'P',
5.0448],
['TYR131',
'2003_2004_2006_2008_2011_2013',
'P',
'ARG58',
'NH1_829_832',
'P',
5.0915]],
..
..
Statistics¶
Using calcStatisticsInteractions() function, we can compute the statistics
of interaction in the trajectory, such as the average distance between residues
(usually the center of the mass; details are described in the function which
computes the specific type of interactions), standard deviation for the
distance value and weight. Weight is the number of counts for the whole
trajectory and is divided by the number of frames in the dcd file. Weight equal to 1
corresponds to the contact that was main the whole time of the simulation.
Note that weight can be >1 when multiple contacts are present between the same
residues.
For example:
In [34]: interactions = interactionsTrajectory.getPiCation()
In [35]: calcStatisticsInteractions(interactions)
@> Statistics for PHE85P-ARG40P:
@> Average [Ang.]: 4.385379791259766
@> Standard deviation [Ang.]: 0.5366479754447937
@> Weight: 0.952381
@> Energy [RT]: -4.51
@> Statistics for HIS66P-ARG65P:
@> Average [Ang.]: 4.717772006988525
@> Standard deviation [Ang.]: 0.6487299799919128
@> Weight: 0.857143
@> Energy [RT]: -3.24
@> Statistics for HIS157P-LYS112P:
@> Average [Ang.]: 4.388020038604736
@> Standard deviation [Ang.]: 1.0506110191345215
@> Weight: 0.47619
@> Energy [RT]: -2.14
@> Statistics for PHE138P-ARG58P:
@> Average [Ang.]: 5.318399906158447
@> Standard deviation [Ang.]: 0.24265700578689575
@> Weight: 0.809524
@> Energy [RT]: -4.51
@> Statistics for TYR87P-LYS112P:
@> Average [Ang.]: 5.441559791564941
@> Standard deviation [Ang.]: 0.25401198863983154
@> Weight: 0.47619
@> Energy [RT]: -2.64
@> Statistics for TRP39P-LYS6P:
@> Average [Ang.]: 5.522061824798584
@> Standard deviation [Ang.]: 0.31886300444602966
@> Weight: 0.380952
@> Energy [RT]: -3.12
@> Statistics for PHE85P-ARG75P:
@> Average [Ang.]: 5.877999782562256
@> Standard deviation [Ang.]: 0.06788399815559387
@> Weight: 0.285714
@> Energy [RT]: -4.51
In [36]: calcStatisticsInteractions(interactionsTrajectory.getHydrogenBonds())
@> Statistics for ARG101P-ASP98P:
@> Average [Ang.]: 2.793931
@> Standard deviation [Ang.]: 0.205527
@> Weight: 1.52381
@> Energy [RT]: -3.92
@> Statistics for HIS72P-ASN15P:
@> Average [Ang.]: 2.989283
@> Standard deviation [Ang.]: 0.270697
@> Weight: 0.285714
@> Energy [RT]: -3.05
@> Statistics for GLN143P-GLU139P:
@> Average [Ang.]: 3.051633
@> Standard deviation [Ang.]: 0.20753
@> Weight: 1.285714
@> Energy [RT]: -3.45
@> Statistics for HIS66P-GLU139P:
@> Average [Ang.]: 2.900411
@> Standard deviation [Ang.]: 0.169455
@> Weight: 0.428571
@> Energy [RT]: -3.15
@> Statistics for ARG40P-LYS6P:
@> Average [Ang.]: 3.055475
@> Standard deviation [Ang.]: 0.213814
@> Weight: 0.380952
@> Energy [RT]: -2.11
@> Statistics for ARG58P-ASP56P:
@> Average [Ang.]: 2.827481
@> Standard deviation [Ang.]: 0.171087
@> Weight: 2.952381
@> Energy [RT]: -3.92
@> Statistics for ALA45P-ARG75P:
@> Average [Ang.]: 2.840721
@> Standard deviation [Ang.]: 0.105565
@> Weight: 0.904762
@> Energy [RT]: -3.26
@> Statistics for ASN53P-GLU50P:
@> Average [Ang.]: 2.980214
@> Standard deviation [Ang.]: 0.147229
@> Weight: 0.333333
@> Energy [RT]: -2.43
@> Statistics for ALA74P-ASN53P:
@> Average [Ang.]: 2.98522
@> Standard deviation [Ang.]: 0.148331
@> Weight: 0.952381
@> Energy [RT]: -2.06
@> Statistics for ASP56P-ILE16P:
@> Average [Ang.]: 3.085957
@> Standard deviation [Ang.]: 0.21134
@> Weight: 0.666667
@> Energy [RT]: -3.46
@> Statistics for LYS110P-THR84P:
@> Average [Ang.]: 2.774475
@> Standard deviation [Ang.]: 0.080304
@> Weight: 0.380952
@> Energy [RT]: -1.64
@> Statistics for LEU116P-CYS90P:
@> Average [Ang.]: 2.887425
@> Standard deviation [Ang.]: 0.118768
@> Weight: 0.952381
@> Energy [RT]: -6.13
@> Statistics for SER103P-LEU99P:
@> Average [Ang.]: 2.897324
@> Standard deviation [Ang.]: 0.17182
@> Weight: 1.380952
@> Energy [RT]: -4.12
@> Statistics for ASN134P-ASP137P:
@> Average [Ang.]: 2.917242
@> Standard deviation [Ang.]: 0.160488
@> Weight: 0.904762
@> Energy [RT]: -2.5
@> Statistics for PHE152P-CYS148P:
@> Average [Ang.]: 2.956784
@> Standard deviation [Ang.]: 0.160039
@> Weight: 0.904762
@> Energy [RT]: -4.81
@> Statistics for ASN95P-ASP92P:
@> Average [Ang.]: 3.061373
@> Standard deviation [Ang.]: 0.215848
@> Weight: 0.714286
@> Energy [RT]: -2.5
@> Statistics for LYS6P-ASN38P:
@> Average [Ang.]: 3.006786
@> Standard deviation [Ang.]: 0.154497
@> Weight: 0.333333
@> Energy [RT]: -1.63
@> Statistics for ILE77P-ALA45P:
@> Average [Ang.]: 2.819429
@> Standard deviation [Ang.]: 0.092538
@> Weight: 0.666667
@> Energy [RT]: -4.45
@> Statistics for LEU99P-ASN95P:
@> Average [Ang.]: 3.027242
@> Standard deviation [Ang.]: 0.19744
@> Weight: 0.904762
@> Energy [RT]: -3.94
..
..
For better visualization of the results, we can use
showInteractionsGraph(), which displays results as a graph with
residue-residue pairs of interactions. The intensity of the color of the
lines connecting two residues corresponds to the number of counts. Darker
lines are assigned to the most frequent appearance of interaction. The
distance between pairs corresponds to the average distance across
all the frames. Moreover, ovals with residue names are color-coded: acidic
residues: red, basic: blue, polar: green, non-polar: silver, and
proline: pink. The same function can be applied to ensemble PDB (more
examples can be found there).
We will also change the region of protein structure, which we would like to
analyze from residue 1 to 100.
In [37]: statistics = calcStatisticsInteractions(interactionsTrajectory.getHydrogenBonds(selection='resid 5 to 100'))
In [38]: showInteractionsGraph(statistics, code='1-letter', cutoff=0.5)
@> Statistics for ARG101P-ASP98P:
@> Average [Ang.]: 2.793931
@> Standard deviation [Ang.]: 0.205527
@> Weight: 1.52381
@> Energy [RT]: -3.92
@> Statistics for HIS72P-ASN15P:
@> Average [Ang.]: 2.989283
@> Standard deviation [Ang.]: 0.270697
@> Weight: 0.285714
@> Energy [RT]: -3.05
@> Statistics for HIS66P-GLU139P:
@> Average [Ang.]: 2.900411
@> Standard deviation [Ang.]: 0.169455
@> Weight: 0.428571
@> Energy [RT]: -3.15
@> Statistics for ARG40P-LYS6P:
@> Average [Ang.]: 3.055475
@> Standard deviation [Ang.]: 0.213814
@> Weight: 0.380952
@> Energy [RT]: -2.11
@> Statistics for ARG58P-ASP56P:
@> Average [Ang.]: 2.827481
@> Standard deviation [Ang.]: 0.171087
@> Weight: 2.952381
@> Energy [RT]: -3.92
@> Statistics for ALA45P-ARG75P:
@> Average [Ang.]: 2.840721
@> Standard deviation [Ang.]: 0.105565
@> Weight: 0.904762
@> Energy [RT]: -3.26
@> Statistics for ASN53P-GLU50P:
@> Average [Ang.]: 2.980214
@> Standard deviation [Ang.]: 0.147229
@> Weight: 0.333333
@> Energy [RT]: -2.43
@> Statistics for ALA74P-ASN53P:
@> Average [Ang.]: 2.98522
@> Standard deviation [Ang.]: 0.148331
@> Weight: 0.952381
@> Energy [RT]: -2.06
..
..
We can also use the showInteractionsHist() function to display the
results as a bar plot (clip define how many pair we would like to display).
In [39]: showInteractionsHist(statistics, clip=20)
Compare two independent frames¶
With this analysis, we can also compare interactions between frames. Below, we
will compute hydrogen bonds for frame 0 and frame 18 and we will compare
them using the compareInteractions() function. That function will be helpful
in checking the difference between interactions. The results will be saved
as diff_fr0_vsfr18.dat file.
Let’s check the interactions for the initail frame in our trajectory:
In [40]: frame0 = dcd.getFrame(0)
In [41]: at0 = frame0.getAtoms()
In [42]: hb0 = calcHydrogenBonds(at0.select('protein'))
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ARG101 P NH1_1516 <---> ASP98 P OD1_1463 2.0 33.1
@> HSE72 P NE2_1042 <---> ASN15 P OD1_165 2.6 34.8
@> GLN143 P NE2_2192 <---> GLU139 P OE2_2126 2.7 9.2
@> HSE66 P NE2_957 <---> GLU139 P OE1_2125 2.7 6.4
@> ARG40 P N_561 <---> LYS6 P O_37 2.7 17.1
@> ARG58 P N_813 <---> ASP56 P OD1_788 2.7 30.0
@> ALA45 P N_634 <---> ARG75 P O_1097 2.8 35.1
@> ASN53 P ND2_747 <---> GLU50 P OE1_708 2.8 18.2
@> ALA74 P N_1064 <---> ASN53 P O_751 2.8 21.3
@> ASP56 P N_780 <---> ILE16 P O_189 2.8 27.0
@> LYS110 P NZ_1667 <---> THR84 P O_1240 2.8 38.2
@> LEU116 P N_1758 <---> CYS90 P O_1342 2.8 15.0
@> SER103 P N_1546 <---> LEU99 P O_1485 2.8 29.1
@> ASN134 P N_2045 <---> ASP137 P OD2_2091 2.8 22.6
@> PHE152 P N_2321 <---> CYS148 P O_2275 2.8 8.3
@> ASN95 P N_1398 <---> ASP92 P OD1_1368 2.8 12.6
@> LYS6 P N_16 <---> ASN38 P O_536 2.8 25.0
@> ILE77 P N_1115 <---> ALA45 P O_643 2.8 12.2
@> ARG58 P NH2_832 <---> ASP56 P OD2_789 2.8 27.7
@> LEU99 P N_1467 <---> ASN95 P O_1411 2.8 15.5
@> CYS149 P N_2276 <---> CYS145 P O_2224 2.8 9.6
@> GLY52 P N_731 <---> ALA74 P O_1073 2.8 6.6
@> ASP32 P N_435 <---> LYS28 P O_385 2.8 8.8
@> ILE88 P N_1294 <---> LYS112 P O_1704 2.8 17.7
@> GLN143 P N_2180 <---> GLU139 P O_2128 2.8 21.7
@> ARG27 P N_340 <---> GLU23 P O_293 2.8 15.4
@> TYR142 P N_2159 <---> PHE138 P O_2113 2.9 14.2
@> GLY133 P N_2038 <---> PRO130 P O_1995 2.9 25.4
@> PHE26 P N_320 <---> ALA22 P O_278 2.9 4.9
@> ASN15 P ND2_166 <---> SER19 P OG_232 2.9 32.1
@> ARG75 P NH1_1090 <---> ASP81 P OD2_1194 2.9 19.7
@> ARG75 P NH2_1093 <---> ASP42 P OD2_610 2.9 23.5
@> ARG97 P N_1431 <---> GLU93 P O_1386 2.9 22.2
@> ARG65 P NH2_941 <---> GLU139 P OE1_2125 2.9 32.3
@> VAL25 P N_304 <---> ILE21 P O_268 2.9 8.2
@> LEU153 P N_2341 <---> CYS149 P O_2286 2.9 12.5
@> SER7 P N_38 <---> ASP86 P OD2_1270 2.9 39.9
@> ASP86 P N_1261 <---> SER7 P OG_45 2.9 34.7
@> ARG58 P NH2_832 <---> TYR131 P O_2016 2.9 33.1
@> THR46 P N_644 <---> CYS12 P O_130 2.9 36.1
@> GLN144 P N_2197 <---> THR140 P O_2142 2.9 23.3
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.9 12.4
@> LEU89 P N_1313 <---> LEU9 P O_83 2.9 29.5
@> THR31 P N_421 <---> ARG27 P O_363 2.9 24.1
@> CYS90 P N_1332 <---> GLU114 P O_1738 2.9 24.6
@> CYS148 P N_2265 <---> GLN144 P O_2213 2.9 9.3
@> GLU23 P N_279 <---> SER19 P O_235 2.9 15.4
@> ILE68 P N_970 <---> MET63 P O_899 2.9 13.0
@> PHE10 P N_84 <---> ASP42 P O_612 2.9 22.8
@> LYS112 P N_1683 <---> ASP86 P O_1272 2.9 10.1
@> SER61 P N_861 <---> TYR57 P O_812 2.9 35.1
@> CYS145 P N_2214 <---> VAL141 P O_2158 2.9 15.9
@> ARG27 P NH2_359 <---> GLU23 P OE2_291 2.9 31.5
@> LYS64 P N_900 <---> GLN60 P O_860 2.9 22.9
@> LEU9 P N_65 <---> TYR87 P O_1293 2.9 16.4
@> ASN38 P N_523 <---> ILE35 P O_496 2.9 29.1
@> VAL11 P N_104 <---> LEU89 P O_1331 2.9 29.7
@> ASN100 P N_1486 <---> LEU96 P O_1430 2.9 10.3
@> GLN124 P N_1881 <---> ASP120 P OD2_1825 2.9 27.5
@> LYS102 P N_1524 <---> ASP98 P O_1466 2.9 9.3
@> GLN76 P NE2_1110 <---> THR46 P O_657 2.9 31.4
@> ARG40 P NH1_577 <---> THR84 P OG1_1233 2.9 8.4
@> ALA44 P N_624 <---> PHE10 P O_103 2.9 33.2
@> GLU154 P N_2360 <---> ARG150 P O_2310 3.0 22.6
@> VAL8 P N_49 <---> ARG40 P O_584 3.0 25.0
@> MET63 P N_883 <---> GLY59 P O_843 3.0 18.3
@> GLN60 P N_844 <---> ASP56 P O_791 3.0 35.5
@> ILE35 P N_478 <---> VAL30 P O_420 3.0 23.5
@> VAL146 P N_2225 <---> TYR142 P O_2179 3.0 31.5
@> ARG58 P NH1_829 <---> TYR131 P O_2016 3.0 38.1
@> ASN53 P N_738 <---> GLU50 P O_711 3.0 28.6
@> ARG101 P N_1500 <---> ARG97 P O_1454 3.0 32.3
@> ARG18 P NH1_217 <---> ILE127 P O_1954 3.0 26.0
@> ARG75 P N_1074 <---> ASN15 P OD1_165 3.0 25.1
@> GLN144 P NE2_2209 <---> ILE126 P O_1935 3.0 18.3
@> ASN34 P N_464 <---> THR31 P O_434 3.0 18.2
@> ASN15 P ND2_166 <---> SER43 P OG_620 3.0 25.7
@> ARG58 P NE_826 <---> ASP56 P OD1_788 3.0 22.2
@> ARG27 P NH1_356 <---> GLU23 P OE2_291 3.0 36.9
@> ILE127 P N_1936 <---> MET91 P O_1359 3.0 17.6
@> TYR119 P OH_1808 <---> HSE157 P N_2407 3.0 28.1
@> HSE157 P N_2407 <---> TYR119 P OH_1808 3.0 19.2
@> GLU139 P N_2114 <---> ASP135 P O_2070 3.0 27.9
@> LEU29 P N_386 <---> VAL25 P O_319 3.0 19.1
@> SER47 P N_658 <---> LEU13 P O_149 3.0 28.8
@> VAL30 P N_405 <---> PHE26 P O_339 3.0 17.7
@> GLN105 P N_1571 <---> LYS102 P O_1545 3.0 19.7
@> SER118 P N_1784 <---> LEU115 P O_1757 3.1 21.4
@> LYS155 P N_2375 <---> ALA151 P O_2320 3.1 21.3
@> GLU114 P N_1724 <---> ILE88 P O_1312 3.1 24.2
@> ASP120 P N_1816 <---> GLY117 P O_1783 3.1 12.7
@> CYS62 P N_872 <---> ARG58 P O_836 3.1 20.4
@> ARG18 P NH1_217 <---> ASP92 P OD2_1369 3.1 4.3
@> ALA24 P N_294 <---> PRO20 P O_249 3.1 29.9
@> ARG150 P N_2287 <---> VAL146 P O_2240 3.1 12.7
@> LYS28 P N_364 <---> ALA24 P O_303 3.1 20.0
@> VAL141 P N_2143 <---> ASP137 P O_2093 3.1 18.5
@> ASP98 P N_1455 <---> SER94 P O_1397 3.1 19.6
@> LEU96 P N_1412 <---> ASP92 P O_1371 3.1 36.3
@> ALA22 P N_269 <---> ARG18 P O_224 3.1 21.9
@> ALA151 P N_2311 <---> ARG147 P O_2264 3.1 15.6
@> GLY67 P N_963 <---> LYS64 P O_921 3.1 22.8
@> ASP42 P N_601 <---> VAL8 P O_64 3.1 35.6
@> ARG65 P N_922 <---> SER61 P O_871 3.1 23.4
@> TRP39 P N_537 <---> SER36 P O_507 3.1 15.2
@> LYS123 P N_1859 <---> ASP120 P O_1827 3.1 18.7
@> MET91 P N_1343 <---> ASN95 P OD1_1406 3.2 39.0
@> THR140 P N_2129 <---> SER136 P O_2081 3.2 30.3
@> PHE85 P N_1241 <---> ASP81 P O_1196 3.2 20.2
@> ASN15 P N_157 <---> CYS12 P SG_127 3.2 37.5
@> ALA111 P N_1673 <---> PHE82 P O_1216 3.2 20.6
@> ARG147 P N_2241 <---> GLN143 P O_2196 3.2 12.1
@> ARG75 P NH2_1093 <---> ASP81 P OD1_1193 3.2 29.3
@> LYS112 P NZ_1699 <---> HSE157 P OT2_2424 3.3 28.7
@> ARG147 P NH1_2257 <---> GLN124 P OE1_1892 3.3 29.9
@> PHE138 P N_2094 <---> ASN134 P O_2058 3.3 31.0
@> SER7 P OG_45 <---> THR84 P O_1240 3.3 35.5
@> CYS12 P N_120 <---> ALA44 P O_633 3.3 36.1
@> SER19 P N_225 <---> CYS12 P SG_127 3.3 8.0
@> PHE82 P N_1197 <---> LYS79 P O_1169 3.4 37.7
@> ASP81 P N_1185 <---> THR78 P OG1_1140 3.5 39.5
@> LYS102 P NZ_1540 <---> ASP98 P OD2_1464 3.5 26.1
@> ARG147 P NH2_2260 <---> GLN124 P OE1_1892 3.5 33.9
@> VAL106 P N_1588 <---> SER103 P O_1556 3.5 34.2
@> Number of detected hydrogen bonds: 124.
Let’s check the interactions for frame number 18 in our trajectory:
In [43]: frame18 = dcd.getFrame(18)
In [44]: at18 = frame18.getAtoms()
In [45]: hb18 = calcHydrogenBonds(at18.select('protein'))
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ARG75 P NH2_1093 <---> ASP81 P OD1_1193 2.6 18.5
@> ARG58 P NH2_832 <---> ASP56 P OD2_789 2.6 21.5
@> ARG27 P NH2_359 <---> GLU23 P OE2_291 2.7 18.4
@> LYS28 P NZ_380 <---> ASP32 P OD2_444 2.7 25.9
@> ARG150 P NE_2300 <---> GLU154 P OE1_2371 2.7 22.4
@> ARG18 P NH1_217 <---> ASP92 P OD2_1369 2.7 25.9
@> ARG75 P NE_1087 <---> ASP42 P OD1_609 2.7 16.1
@> ARG58 P NE_826 <---> ASP56 P OD1_788 2.7 2.1
@> SER19 P OG_232 <---> ASN15 P OD1_165 2.7 8.1
@> ILE88 P N_1294 <---> LYS112 P O_1704 2.7 1.4
@> VAL8 P N_49 <---> ARG40 P O_584 2.7 11.5
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.7 28.1
@> ASN134 P N_2045 <---> ASP137 P OD1_2090 2.7 12.5
@> LYS155 P NZ_2391 <---> HSE157 P OT2_2424 2.7 38.9
@> LYS112 P N_1683 <---> ASP86 P O_1272 2.7 25.8
@> CYS145 P N_2214 <---> VAL141 P O_2158 2.7 13.7
@> LYS102 P NZ_1540 <---> ASP98 P OD1_1463 2.8 29.5
@> GLN143 P N_2180 <---> GLU139 P O_2128 2.8 21.3
@> LEU29 P N_386 <---> VAL25 P O_319 2.8 16.9
@> THR84 P OG1_1233 <---> GLU80 P O_1184 2.8 10.5
@> CYS90 P N_1332 <---> GLU114 P O_1738 2.8 4.9
@> THR31 P OG1_427 <---> ARG27 P O_363 2.8 21.2
@> ASP98 P N_1455 <---> SER94 P O_1397 2.8 6.1
@> SER43 P OG_620 <---> GLU23 P OE1_290 2.8 13.9
@> LYS110 P N_1651 <---> PHE82 P O_1216 2.8 36.4
@> SER118 P OG_1791 <---> GLU114 P OE2_1736 2.8 20.1
@> ARG65 P NH1_938 <---> ASP135 P OD2_2068 2.8 12.3
@> LYS64 P N_900 <---> GLN60 P O_860 2.8 3.3
@> ARG101 P NH2_1519 <---> ASP98 P OD2_1464 2.8 8.9
@> ARG75 P NH1_1090 <---> ASP81 P OD2_1194 2.8 25.1
@> ARG65 P N_922 <---> SER61 P O_871 2.8 24.3
@> ARG58 P NH1_829 <---> GLY133 P O_2044 2.8 34.0
@> ILE127 P N_1936 <---> MET91 P O_1359 2.8 22.3
@> THR78 P OG1_1140 <---> ASP81 P OD2_1194 2.8 12.4
@> THR84 P N_1227 <---> GLU80 P O_1184 2.8 10.8
@> GLN33 P N_447 <---> LEU29 P O_404 2.8 6.2
@> SER7 P N_38 <---> ASP86 P OD1_1269 2.8 25.3
@> ASP32 P N_435 <---> LYS28 P O_385 2.8 16.9
@> ASP86 P N_1261 <---> SER7 P O_48 2.8 35.1
@> LYS102 P N_1524 <---> ASP98 P O_1466 2.8 29.0
@> ASP42 P N_601 <---> VAL8 P O_64 2.9 25.5
@> SER61 P N_861 <---> TYR57 P O_812 2.9 32.8
@> CYS149 P N_2276 <---> CYS145 P O_2224 2.9 2.6
@> VAL146 P N_2225 <---> TYR142 P O_2179 2.9 9.7
@> GLN60 P N_844 <---> ASP56 P O_791 2.9 25.1
@> LYS155 P N_2375 <---> ARG150 P O_2310 2.9 13.4
@> ALA74 P N_1064 <---> ASN53 P O_751 2.9 16.2
@> TYR87 P N_1273 <---> SER7 P O_48 2.9 18.2
@> GLN144 P N_2197 <---> THR140 P O_2142 2.9 16.3
@> LEU89 P N_1313 <---> LEU9 P O_83 2.9 28.6
@> ARG101 P N_1500 <---> ARG97 P O_1454 2.9 3.1
@> CYS12 P SG_127 <---> SER19 P OG_232 3.0 35.8
@> ASN53 P ND2_747 <---> GLU50 P OE2_709 3.0 21.4
@> ALA45 P N_634 <---> ARG75 P O_1097 3.0 11.5
@> ASP56 P N_780 <---> ILE16 P O_189 3.0 15.2
@> ARG58 P N_813 <---> ASP56 P OD1_788 3.0 14.2
@> ILE77 P N_1115 <---> ALA45 P O_643 3.0 12.8
@> GLY67 P N_963 <---> MET63 P O_899 3.0 16.3
@> ARG18 P NH1_217 <---> ILE127 P O_1954 3.0 33.1
@> ARG75 P NH1_1090 <---> ASP81 P OD1_1193 3.0 39.7
@> THR140 P N_2129 <---> SER136 P O_2081 3.0 18.5
@> LEU153 P N_2341 <---> CYS149 P O_2286 3.0 12.0
@> ASN104 P N_1557 <---> ASN100 P O_1499 3.0 38.4
@> CYS62 P N_872 <---> ARG58 P O_836 3.0 39.7
@> VAL11 P N_104 <---> LEU89 P O_1331 3.0 15.4
@> VAL106 P N_1588 <---> LYS102 P O_1545 3.0 2.4
@> ALA151 P N_2311 <---> ARG147 P O_2264 3.0 21.7
@> ARG40 P N_561 <---> LYS6 P O_37 3.0 33.0
@> LEU9 P N_65 <---> TYR87 P O_1293 3.0 39.7
@> ARG27 P N_340 <---> GLU23 P O_293 3.0 17.9
@> ASN95 P ND2_1407 <---> THR46 P OG1_650 3.0 38.8
@> ARG27 P NH2_359 <---> VAL41 P O_600 3.0 32.9
@> LEU99 P N_1467 <---> ASN95 P O_1411 3.0 21.7
@> GLU154 P N_2360 <---> ARG150 P O_2310 3.0 37.1
@> ALA111 P N_1673 <---> PHE82 P O_1216 3.0 18.4
@> ARG150 P NH2_2306 <---> GLU154 P OE1_2371 3.0 31.0
@> VAL25 P N_304 <---> ILE21 P O_268 3.0 10.3
@> ASN15 P ND2_166 <---> SER43 P OG_620 3.1 18.8
@> MET63 P N_883 <---> GLY59 P O_843 3.1 15.7
@> VAL30 P N_405 <---> PHE26 P O_339 3.1 6.2
@> ARG150 P N_2287 <---> VAL146 P O_2240 3.1 30.1
@> PHE138 P N_2094 <---> ASN134 P O_2058 3.1 10.8
@> VAL141 P N_2143 <---> ASP137 P O_2093 3.1 10.8
@> PHE10 P N_84 <---> ASP42 P O_612 3.1 17.6
@> CYS148 P N_2265 <---> GLN144 P O_2213 3.1 23.2
@> PHE26 P N_320 <---> ALA22 P O_278 3.1 9.0
@> GLN76 P NE2_1110 <---> THR46 P O_657 3.1 11.9
@> LEU116 P N_1758 <---> CYS90 P O_1342 3.2 18.5
@> GLU23 P N_279 <---> SER19 P O_235 3.2 2.4
@> ALA44 P N_624 <---> PHE10 P O_103 3.2 38.7
@> ARG65 P NH2_941 <---> ASP135 P OD1_2067 3.2 19.6
@> ASN34 P N_464 <---> THR31 P O_434 3.2 38.6
@> ARG97 P N_1431 <---> GLU93 P O_1386 3.2 17.8
@> ALA22 P N_269 <---> ARG18 P O_224 3.2 11.6
@> GLN105 P N_1571 <---> ARG101 P O_1523 3.2 28.1
@> LYS6 P N_16 <---> ASN38 P O_536 3.2 31.6
@> ASN95 P N_1398 <---> ASP92 P OD1_1368 3.2 11.6
@> CYS145 P SG_2221 <---> VAL141 P O_2158 3.3 30.4
@> HSE66 P N_946 <---> CYS62 P O_882 3.3 14.7
@> ARG147 P N_2241 <---> GLN143 P O_2196 3.3 26.0
@> TYR142 P N_2159 <---> PHE138 P O_2113 3.3 11.5
@> TRP39 P N_537 <---> ILE35 P O_496 3.4 35.3
@> GLN124 P N_1881 <---> GLN144 P OE1_2208 3.4 35.9
@> CYS12 P N_120 <---> ALA44 P O_633 3.4 35.7
@> SER103 P OG_1553 <---> LEU99 P O_1485 3.4 14.9
@> PHE85 P N_1241 <---> ASP81 P O_1196 3.4 24.1
@> SER19 P N_225 <---> CYS12 P SG_127 3.5 7.6
@> Number of detected hydrogen bonds: 107.
And compare them using compareInteractions(). We will obtain
information on which interactions are newly maintained, which are stable,
and which ones were lost.
In [46]: compareInteractions(hb0, hb18, filename='diff_fr0_vsfr18.dat')
@> Which interactions disappeared: 23
@> TYR87P <---> SER7P
@> SER43P <---> GLU23P
@> ASN104P <---> ASN100P
@> LYS155P <---> HSE157P
@> ARG150P <---> GLU154P
@> ASN95P <---> THR46P
@> LYS110P <---> PHE82P
@> SER19P <---> ASN15P
@> LYS155P <---> ARG150P
@> SER118P <---> GLU114P
@> GLY67P <---> MET63P
@> ARG65P <---> ASP135P
@> TRP39P <---> ILE35P
@> THR84P <---> GLU80P
@> HSE66P <---> CYS62P
@> GLN105P <---> ARG101P
@> CYS12P <---> SER19P
@> ARG58P <---> GLY133P
@> VAL106P <---> LYS102P
@> LYS28P <---> ASP32P
@> GLN124P <---> GLN144P
@> ARG27P <---> VAL41P
@> GLN33P <---> LEU29P
Which interactions appeared: 41
@> SER118P <---> LEU115P
@> GLY67P <---> LYS64P
@> GLU139P <---> ASP135P
@> ARG75P <---> ASN15P
@> PHE82P <---> LYS79P
@> ARG147P <---> GLN124P
@> GLY52P <---> ALA74P
@> ASP81P <---> THR78P
@> GLN144P <---> ILE126P
@> ASN38P <---> ILE35P
@> SER47P <---> LEU13P
@> ARG58P <---> TYR131P
@> LYS155P <---> ALA151P
@> MET91P <---> ASN95P
@> PHE152P <---> CYS148P
@> LYS28P <---> ALA24P
@> ASN100P <---> LEU96P
@> VAL106P <---> SER103P
@> SER7P <---> THR84P
@> ALA24P <---> PRO20P
@> HSE66P <---> GLU139P
@> GLU114P <---> ILE88P
@> LEU96P <---> ASP92P
@> GLN105P <---> LYS102P
@> LYS123P <---> ASP120P
@> GLY133P <---> PRO130P
@> TYR119P <---> HSE157P
@> ASN15P <---> SER19P
@> ILE35P <---> VAL30P
@> ARG65P <---> GLU139P
@> HSE157P <---> TYR119P
@> ASP120P <---> GLY117P
@> ARG40P <---> THR84P
@> ILE68P <---> MET63P
@> ASN15P <---> CYS12P
@> HSE72P <---> ASN15P
@> LYS110P <---> THR84P
@> GLN124P <---> ASP120P
@> TRP39P <---> SER36P
@> THR46P <---> CYS12P
@> LYS112P <---> HSE157P
@> Which interactions are the same: 73
@> GLN60P <---> ASP56P
@> ARG150P <---> VAL146P
@> ARG101P <---> ASP98P
@> ILE77P <---> ALA45P
@> VAL11P <---> LEU89P
@> SER61P <---> TYR57P
@> ARG18P <---> ASP92P
@> ALA22P <---> ARG18P
@> THR31P <---> ARG27P
@> ALA44P <---> PHE10P
@> LEU153P <---> CYS149P
@> ARG58P <---> ASP56P
@> ALA111P <---> PHE82P
@> CYS62P <---> ARG58P
@> VAL146P <---> TYR142P
@> GLU23P <---> SER19P
@> ARG27P <---> GLU23P
@> CYS149P <---> CYS145P
@> LYS64P <---> GLN60P
@> VAL8P <---> ARG40P
@> ARG40P <---> LYS6P
@> ARG65P <---> SER61P
@> ASP32P <---> LYS28P
@> ILE88P <---> LYS112P
@> ALA45P <---> ARG75P
@> PHE26P <---> ALA22P
@> ASN95P <---> ASP92P
@> VAL30P <---> PHE26P
@> THR140P <---> SER136P
@> LEU89P <---> LEU9P
@> SER103P <---> LEU99P
@> LEU116P <---> CYS90P
@> PHE10P <---> ASP42P
@> ASN15P <---> SER43P
@> TYR142P <---> PHE138P
@> ASN34P <---> THR31P
@> ASN134P <---> ASP137P
@> LEU99P <---> ASN95P
@> ASP98P <---> SER94P
@> GLN144P <---> THR140P
@> ARG97P <---> GLU93P
@> GLN76P <---> THR46P
@> LYS6P <---> ASN38P
@> ARG75P <---> ASP81P
@> ASN53P <---> GLU50P
@> THR78P <---> ASP81P
@> VAL141P <---> ASP137P
@> SER19P <---> CYS12P
@> GLN143P <---> GLU139P
@> LEU29P <---> VAL25P
@> ALA151P <---> ARG147P
@> GLU154P <---> ARG150P
@> ALA74P <---> ASN53P
@> CYS148P <---> GLN144P
@> SER7P <---> ASP86P
@> LYS102P <---> ASP98P
@> MET63P <---> GLY59P
@> ASP56P <---> ILE16P
@> PHE138P <---> ASN134P
@> CYS90P <---> GLU114P
@> ASP42P <---> VAL8P
@> CYS145P <---> VAL141P
@> ARG147P <---> GLN143P
@> PHE85P <---> ASP81P
@> VAL25P <---> ILE21P
@> LEU9P <---> TYR87P
@> ASP86P <---> SER7P
@> ARG101P <---> ARG97P
@> ILE127P <---> MET91P
@> LYS112P <---> ASP86P
@> CYS12P <---> ALA44P
@> ARG75P <---> ASP42P
@> ARG18P <---> ILE127P
We can also all the tools that are shown for single PDB analysis in this
tutorial. For example, we can compute all interactions for frame0 and
frame18 and display the interactions:
In [47]: interactions0 = Interactions()
In [48]: interactions0.calcProteinInteractions(at0)
In [49]: matrix0 = interactions0.buildInteractionMatrix()
In [50]: interactions0.showCumulativeInteractionTypes()
@> Calculating interaction matrix
@> Calculating interaction matrix
@> Calculating interaction matrix
@> Calculating interaction matrix
@> Calculating interaction matrix
@> Calculating interaction matrix
@> Calculating interaction matrix
In [51]: interactions18 = Interactions()
In [52]: interactions18.calcProteinInteractions(at18)
In [53]: matrix18 = interactions18.buildInteractionMatrix()
@> Calculating interations.
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ARG75 P NH2_1093 <---> ASP81 P OD1_1193 2.6 18.5
@> ARG58 P NH2_832 <---> ASP56 P OD2_789 2.6 21.5
@> ARG27 P NH2_359 <---> GLU23 P OE2_291 2.7 18.4
@> LYS28 P NZ_380 <---> ASP32 P OD2_444 2.7 25.9
@> ARG150 P NE_2300 <---> GLU154 P OE1_2371 2.7 22.4
@> ARG18 P NH1_217 <---> ASP92 P OD2_1369 2.7 25.9
@> ARG75 P NE_1087 <---> ASP42 P OD1_609 2.7 16.1
@> ARG58 P NE_826 <---> ASP56 P OD1_788 2.7 2.1
@> SER19 P OG_232 <---> ASN15 P OD1_165 2.7 8.1
@> ILE88 P N_1294 <---> LYS112 P O_1704 2.7 1.4
@> VAL8 P N_49 <---> ARG40 P O_584 2.7 11.5
@> THR78 P N_1134 <---> ASP81 P OD2_1194 2.7 28.1
@> ASN134 P N_2045 <---> ASP137 P OD1_2090 2.7 12.5
@> LYS155 P NZ_2391 <---> HSE157 P OT2_2424 2.7 38.9
@> LYS112 P N_1683 <---> ASP86 P O_1272 2.7 25.8
In [54]: interactions18.showCumulativeInteractionTypes()
@> Calculating interaction matrix
@> Calculating interaction matrix
@> Calculating interaction matrix
@> Calculating interaction matrix
@> Calculating interaction matrix
@> Calculating interaction matrix
@> Calculating interaction matrix
Parse previously saved data¶
To upload and further use the interactions data use
InteractionsTrajectory.parseInteractions() function:
In [55]: interactionsTrajectory2 = InteractionsTrajectory('5kqm_import')
In [56]: interactionsTrajectory2.parseInteractions('calcProteinInteractionsTrajectory.pkl')
[[[['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD1_1463', 'P', 1.998, 33.1238],
['HSE72', 'NE2_1042', 'P', 'ASN15', 'OD1_165', 'P', 2.5997, 34.752],
['GLN143', 'NE2_2192', 'P', 'GLU139', 'OE2_2126', 'P', 2.7287, 9.1822],
['HSE66', 'NE2_957', 'P', 'GLU139', 'OE1_2125', 'P', 2.7314, 6.3592],
['ARG40', 'N_561', 'P', 'LYS6', 'O_37', 'P', 2.7479, 17.1499],
['ARG58', 'N_813', 'P', 'ASP56', 'OD1_788', 'P', 2.7499, 29.9737],
['ALA45', 'N_634', 'P', 'ARG75', 'O_1097', 'P', 2.7609, 35.0983],
['ASN53', 'ND2_747', 'P', 'GLU50', 'OE1_708', 'P', 2.7702, 18.2336],
['ALA74', 'N_1064', 'P', 'ASN53', 'O_751', 'P', 2.7782, 21.3375],
['ASP56', 'N_780', 'P', 'ILE16', 'O_189', 'P', 2.7793, 27.0481],
['LYS110', 'NZ_1667', 'P', 'THR84', 'O_1240', 'P', 2.7977, 38.2213],
['LEU116', 'N_1758', 'P', 'CYS90', 'O_1342', 'P', 2.8072, 15.0239],
['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8075, 29.107],
['ASN134', 'N_2045', 'P', 'ASP137', 'OD2_2091', 'P', 2.8132, 22.562],
['PHE152', 'N_2321', 'P', 'CYS148', 'O_2275', 'P', 2.8141, 8.2562],
['ASN95', 'N_1398', 'P', 'ASP92', 'OD1_1368', 'P', 2.8148, 12.5701],
['LYS6', 'N_16', 'P', 'ASN38', 'O_536', 'P', 2.8178, 25.0306],
['ILE77', 'N_1115', 'P', 'ALA45', 'O_643', 'P', 2.8179, 12.1856],
['ARG58', 'NH2_832', 'P', 'ASP56', 'OD2_789', 'P', 2.8204, 27.6617],
['LEU99', 'N_1467', 'P', 'ASN95', 'O_1411', 'P', 2.8205, 15.4867],
['CYS149', 'N_2276', 'P', 'CYS145', 'O_2224', 'P', 2.8247, 9.5914],
['GLY52', 'N_731', 'P', 'ALA74', 'O_1073', 'P', 2.832, 6.6442],
['ASP32', 'N_435', 'P', 'LYS28', 'O_385', 'P', 2.8357, 8.8318],
..
..
After uploading, we have access to all data, for example:
In [57]: interactionsTrajectory2.getHydrophohic()
[[['ALA156', 'CB_2401', 'P', 'TYR87', 'OH_1286', 'P', 3.0459, 21.959],
['ALA24', 'CB_298', 'P', 'MET63', 'CE_894', 'P', 3.3105, 5.1584],
['ILE68', 'CG2_976', 'P', 'MET63', 'CE_894', 'P', 3.3306, 52.4165],
['TYR142', 'CZ_2171', 'P', 'VAL146', 'CG2_2235', 'P', 3.4815, 49.7427],
['PHE10', 'CD1_92', 'P', 'ALA22', 'CB_273', 'P', 3.5334, 31.1973],
['LYS6', 'CD_26', 'P', 'TRP39', 'CZ2_555', 'P', 3.5427, 68.7284],
['PHE26', 'CE2_336', 'P', 'VAL30', 'CG1_411', 'P', 3.5603, 21.127],
['ILE88', 'CD_1307', 'P', 'ALA111', 'CB_1677', 'P', 3.5627, 21.2201],
['VAL11', 'CG2_114', 'P', 'ILE88', 'CG2_1300', 'P', 3.6386, 9.3289],
['VAL41', 'CG2_595', 'P', 'PHE26', 'CD2_334', 'P', 3.6448, 16.55],
['PHE152', 'CE1_2331', 'P', 'ALA156', 'CB_2401', 'P', 3.6594, 17.4765],
['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.6828, 25.1359],
['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.6917, 11.9735],
['PHE82', 'CD1_1205', 'P', 'ILE88', 'CD_1307', 'P', 3.692, 17.6138],
['LEU116', 'CD2_1771', 'P', 'ILE127', 'CD_1949', 'P', 3.7057, 17.4094],
..
..
In [58]: calcStatisticsInteractions(interactionsTrajectory2.getHydrogenBonds())
@> Statistics for ARG101P-ASP98P:
@> Average [Ang.]: 2.793931
@> Standard deviation [Ang.]: 0.205527
@> Weight: 1.52381
@> Energy [RT]: -3.92
@> Statistics for HIS72P-ASN15P:
@> Average [Ang.]: 2.989283
@> Standard deviation [Ang.]: 0.270697
@> Weight: 0.285714
@> Energy [RT]: -3.05
@> Statistics for GLN143P-GLU139P:
@> Average [Ang.]: 3.051633
@> Standard deviation [Ang.]: 0.20753
@> Weight: 1.285714
@> Energy [RT]: -3.45
@> Statistics for HIS66P-GLU139P:
@> Average [Ang.]: 2.900411
@> Standard deviation [Ang.]: 0.169455
@> Weight: 0.428571
@> Energy [RT]: -3.15
@> Statistics for ARG40P-LYS6P:
@> Average [Ang.]: 3.055475
@> Standard deviation [Ang.]: 0.213814
@> Weight: 0.380952
@> Energy [RT]: -2.11
@> Statistics for ARG58P-ASP56P:
@> Average [Ang.]: 2.827481
@> Standard deviation [Ang.]: 0.171087
@> Weight: 2.952381
@> Energy [RT]: -3.92
..
..
In [59]: interactionsTrajectory2.getTimeInteractions()
