1M1A

ligand binding alters the structure and dynamics of nucleosomal dna

• Total interactions analyzed: 45
• Total true interactions: 23
• Strongest Interaction:
  • Chains: E-F
  • Int. Res.: 160
  • Norm. En. per Res.: -5.5849
• Hub Node: A(5)

All Interactions

Chains	Hydro. Bond Ener. (kJ/mol)	Elec. Ener. (kJ/mol)	VDW. Ener. (kJ/mol)	Tot. Stab. Ener. (kJ/mol)	#int. res.	# Short cont.	#Hydr. int.	#VDW pairs	#salt bridges	#Pot. fav. elec. int	#Pot. unfav. elec. int
A-B	-88.5863	-46.449	-712.176	-847.2113	157	43	43	30561	3	60	67
A-C	-8.9337	0.0	-5.9382	-14.872	15	1	0	421	0	3	8
A-E	-36.8066	-119.7697	-162.943	-319.5193	59	5	7	7133	5	25	38
A-G	-51.6976	1.0112	-128.932	-179.6185	71	8	6	6196	0	9	9
A-H	0.0	0.0	-0.1665	-0.1665	8	0	0	63	0	2	0
B-C	0.0	0.0	-0.0289	-0.0289	6	0	0	19	0	2	3
B-D	-28.7962	-16.9726	-139.045	-184.8138	50	9	2	4966	2	18	26
B-G	-28.9895	18.5649	-93.6961	-104.1206	47	2	5	4041	0	0	6
B-H	-11.979	-12.9385	-71.4309	-96.3484	30	3	2	2428	1	5	1
C-D	-117.9515	-21.6759	-727.158	-866.7854	171	39	48	30409	4	47	42
C-E	-22.1166	0.963	-138.559	-159.7126	72	3	5	6283	0	7	8
C-F	-30.5457	11.8585	-86.2098	-104.897	49	3	5	3943	0	0	6
C-G	0.0	-1.786	-26.9586	-28.7447	18	0	0	826	0	8	4
C-H	0.0	2.4635	-9.5952	-7.1317	11	0	0	360	0	0	8
D-E	0.0	0.0	-0.044	-0.044	5	0	0	24	0	2	0
D-F	-21.2852	-18.3171	-61.2593	-100.8616	29	6	2	2240	2	5	1
D-G	0.0	0.3974	-5.5605	-5.1631	13	3	0	335	0	0	8
D-H	0.0	-7.0316	-0.2675	-7.299	9	0	0	68	0	13	9
E-F	-105.9922	-44.0011	-743.594	-893.5873	160	27	44	31767	1	67	74
E-G	0.0	0.0	-0.2634	-0.2634	13	0	0	78	0	3	7
F-G	0.0	0.0	-0.1221	-0.1221	3	0	0	42	0	2	3
F-H	-20.629	-12.5142	-136.955	-170.0983	51	4	2	4785	2	18	26
G-H	-101.8453	-25.1209	-717.869	-844.8352	172	37	48	29936	6	44	39

Interface residues

• A-B: ALA33B, ALA38B, ALA447A, ALA475A, ALA488A, ALA491A, ALA495A, ALA498A, ALA502A, ALA511A, ALA69B, ALA76B, ALA83B, ALA89B, ARG23B, ARG35B, ARG36B, ARG39B, ARG40B, ARG442A, ARG449A, ARG452A, ARG453A, ARG45B, ARG463A, ARG469A, ARG472A, ARG483A, ARG516A, ARG528A, ARG531A, ARG534A, ARG55B, ARG67B, ARG78B, ARG95B, ASN25B, ASN508A, ASN64B, ASP24B, ASP477A, ASP481A, ASP506A, ASP523A, ASP68B, ASP85B, GLN27B, GLN455A, GLN468A, GLN476A, GLN485A, GLN493A, GLN525A, GLU450A, GLU459A, GLU473A, GLU494A, GLU497A, GLU505A, GLU52B, GLU533A, GLU53B, GLU63B, GLU74B, GLY101B, GLY28B, GLY41B, GLY42B, GLY444A, GLY48B, GLY56B, GLY99B, HIS75B, ILE26B, ILE29B, ILE34B, ILE451A, ILE462A, ILE46B, ILE474A, ILE50B, ILE512A, ILE519A, ILE524A, ILE66B, LEU37B, LEU448A, LEU460A, LEU461A, LEU465A, LEU470A, LEU482A, LEU492A, LEU49B, LEU500A, LEU503A, LEU509A, LEU58B, LEU62B, LEU90B, LEU97B, LYS31B, LYS44B, LYS456A, LYS464A, LYS479A, LYS522A, LYS59B, LYS77B, LYS79B, MET490A, MET520A, MET84B, PHE100B, PHE467A, PHE478A, PHE484A, PHE504A, PHE61B, PRO32B, PRO443A, PRO466A, PRO521A, SER457A, SER47B, SER486A, SER487A, SER496A, THR30B, THR445A, THR458A, THR480A, THR507A, THR518A, THR54B, THR71B, THR73B, THR80B, THR82B, THR96B, TYR454A, TYR499A, TYR51B, TYR98B, VAL43B, VAL446A, VAL471A, VAL489A, VAL501A, VAL517A, VAL57B, VAL60B, VAL65B, VAL70B, VAL81B, VAL86B, VAL87B
• A-C: ALA535A, ARG529A, ARG531A, ARG534A, ARG888C, ARG899C, ASN894C, ASN910C, GLN912C, GLU533A, GLU891C, GLY532A, GLY898C, ILE530A, LYS895C
• A-E: ALA502A, ALA511A, ALA514A, ALA527A, ALA702E, ALA711E, ALA714E, ALA727E, ALA735E, ARG516A, ARG528A, ARG529A, ARG531A, ARG534A, ARG716E, ARG728E, ARG729E, ARG731E, ASN508A, ASN708E, ASP506A, ASP523A, ASP706E, ASP723E, CYS510A, CYS710E, GLN525A, GLN725E, GLU505A, GLU705E, GLY532A, GLY732E, HIS513A, HIS713E, ILE512A, ILE519A, ILE524A, ILE530A, ILE712E, ILE719E, ILE724E, ILE730E, LEU503A, LEU509A, LEU526A, LEU703E, LEU709E, LEU726E, LYS515A, LYS522A, LYS715E, LYS722E, MET520A, MET720E, PHE504A, PRO521A, PRO721E, THR507A, THR707E
• A-G: ALA1103G, ALA447A, ALA491A, ALA495A, ALA498A, ALA502A, ALA511A, ARG1081G, ARG1088G, ARG1099G, ARG442A, ARG449A, ARG452A, ARG453A, ARG516A, ARG531A, ASN1110G, ASN508A, GLN1084G, GLN1104G, GLN1112G, GLN455A, GLN493A, GLU450A, GLU459A, GLU494A, GLU497A, GLU505A, GLU533A, GLY1105G, GLY1106G, GLY444A, HIS1082G, HIS513A, ILE1079G, ILE1102G, ILE1111G, ILE451A, ILE512A, ILE519A, LEU1085G, LEU1108G, LEU1115G, LEU1116G, LEU448A, LEU460A, LEU461A, LEU509A, LYS1118G, LYS456A, LYS464A, LYS515A, MET490A, PRO1080G, PRO1109G, PRO1117G, PRO443A, SER1113G, SER457A, SER496A, THR1101G, THR445A, THR458A, THR518A, TYR454A, TYR499A, VAL1100G, VAL1107G, VAL1114G, VAL501A, VAL517A
• A-H: GLU459A, GLU494A, ILE1458H, LEU460A, LYS1454H, LYS464A, MET490A, THR458A
• B-C: ARG67B, ARG92B, ASN64B, GLN93B, LEU896C, LYS895C
• B-D: ALA1274D, ALA1278D, ALA1294D, ALA69B, ALA76B, ALA89B, ARG1269D, ARG1276D, ARG1283D, ARG1289D, ARG1296D, ARG67B, ARG78B, ARG92B, ASN1281D, ASP68B, ASP85B, GLN1292D, GLN93B, GLU1273D, GLU1290D, GLU74B, GLY102B, GLY1301D, HIS1279D, HIS75B, ILE1270D, ILE1286D, ILE1291D, LEU1277D, LEU1297D, LEU1298D, LEU1299D, LYS1282D, LYS77B, LYS91B, MET84B, PRO1300D, SER1288D, THR1285D, THR1287D, THR1293D, THR71B, THR73B, TYR1280D, TYR72B, TYR88B, VAL1295D, VAL70B, VAL87B
• B-G: ALA1103G, ARG1081G, ARG1088G, ARG1099G, ARG39B, ARG40B, ARG45B, ARG95B, ASN1110G, GLN1104G, GLN1112G, GLN93B, GLY1105G, GLY1106G, GLY41B, GLY42B, GLY94B, GLY99B, ILE1062G, ILE1102G, ILE1111G, LEU1083G, LEU1096G, LEU1097G, LEU1108G, LEU1115G, LEU1116G, LEU37B, LEU90B, LEU97B, LYS1118G, LYS44B, LYS91B, PHE100B, PHE61B, PRO1080G, PRO1109G, PRO1117G, SER1113G, THR1101G, THR96B, TYR98B, VAL1087G, VAL1100G, VAL1107G, VAL1114G, VAL43B
• B-H: ALA1455H, ARG1469H, ASN1460H, ASN1464H, ASP1465H, GLU1468H, GLY101B, GLY102B, GLY99B, ILE1458H, LEU97B, LYS1431H, LYS1454H, LYS91B, MET1456H, MET1459H, MET84B, PHE100B, PHE1462H, SER1433H, SER1453H, SER1457H, SER1461H, THR96B, TYR1434H, TYR88B, TYR98B, VAL1463H, VAL1466H, VAL87B
• C-D: ALA1235D, ALA1255D, ALA1271D, ALA1274D, ALA1278D, ALA1294D, ALA1304D, ALA1307D, ALA1314D, ALA1321D, ALA821C, ALA840C, ALA845C, ALA847C, ALA852C, ALA853C, ALA860C, ALA866C, ALA869C, ALA870C, ALA903C, ARG1230D, ARG1269D, ARG1276D, ARG1283D, ARG1289D, ARG1296D, ARG817C, ARG820C, ARG829C, ARG832C, ARG835C, ARG842C, ARG871C, ARG877C, ARG881C, ARG899C, ASN1260D, ASN1264D, ASN838C, ASN868C, ASN894C, ASP1248D, ASP1265D, ASP890C, GLN1244D, GLN1292D, GLN824C, GLN884C, GLN904C, GLU1232D, GLU1268D, GLU1273D, GLU1290D, GLU1302D, GLU1310D, GLU841C, GLU856C, GLU861C, GLU864C, GLU891C, GLU892C, GLY1250D, GLY1272D, GLY1301D, GLY1311D, GLY822C, GLY828C, GLY837C, GLY844C, GLY846C, GLY867C, GLY898C, GLY905C, HIS1246D, HIS1279D, HIS1306D, HIS831C, HIS882C, ILE1236D, ILE1251D, ILE1258D, ILE1270D, ILE1286D, ILE1291D, ILE862C, ILE878C, ILE879C, ILE902C, LEU1242D, LEU1298D, LEU1299D, LEU1303D, LEU823C, LEU833C, LEU834C, LEU851C, LEU855C, LEU858C, LEU863C, LEU865C, LEU883C, LEU893C, LEU896C, LEU897C, LYS1231D, LYS1240D, LYS1243D, LYS1254D, LYS1305D, LYS1313D, LYS1317D, LYS815C, LYS836C, LYS875C, LYS895C, MET1256D, MET1259D, PHE1262D, PHE1267D, PHE825C, PRO1247D, PRO1300D, PRO826C, PRO848C, PRO880C, SER1233D, SER1252D, SER1253D, SER1257D, SER1261D, SER1275D, SER1284D, SER1288D, SER1309D, SER1320D, SER818C, SER819C, THR1249D, THR1285D, THR1287D, THR1293D, THR1312D, THR1316D, THR1319D, THR816C, THR859C, THR876C, THR901C, TYR1234D, TYR1237D, TYR1239D, TYR1318D, TYR839C, TYR850C, TYR857C, VAL1238D, VAL1241D, VAL1245D, VAL1263D, VAL1266D, VAL1295D, VAL1308D, VAL1315D, VAL827C, VAL830C, VAL843C, VAL849C, VAL854C, VAL887C, VAL900C
• C-E: ALA647E, ALA691E, ALA695E, ALA698E, ALA702E, ALA711E, ALA903C, ARG642E, ARG649E, ARG652E, ARG653E, ARG716E, ARG731E, ARG881C, ARG899C, ASN708E, ASN873C, ASN910C, ASP706E, GLN655E, GLN693E, GLN884C, GLN904C, GLN912C, GLU650E, GLU659E, GLU694E, GLU697E, GLU705E, GLU733E, GLY644E, GLY905C, GLY906C, HIS713E, HIS882C, ILE651E, ILE712E, ILE719E, ILE879C, ILE902C, ILE911C, LEU648E, LEU660E, LEU661E, LEU709E, LEU885C, LEU908C, LEU915C, LEU916C, LYS656E, LYS664E, LYS715E, LYS918C, MET690E, PRO643E, PRO880C, PRO909C, PRO917C, SER657E, SER696E, SER913C, THR645E, THR658E, THR718E, THR901C, TYR654E, TYR699E, VAL701E, VAL717E, VAL900C, VAL907C, VAL914C
• C-F: ALA903C, ARG239F, ARG240F, ARG245F, ARG295F, ARG881C, ARG888C, ARG899C, ASN910C, GLN293F, GLN884C, GLN904C, GLN912C, GLY241F, GLY242F, GLY294F, GLY299F, GLY302F, GLY898C, GLY905C, GLY906C, ILE862C, ILE902C, ILE911C, LEU237F, LEU290F, LEU297F, LEU883C, LEU896C, LEU897C, LEU908C, LEU915C, LEU916C, LYS244F, LYS291F, LYS918C, PHE300F, PRO880C, PRO909C, PRO917C, SER913C, THR296F, THR901C, TYR298F, VAL243F, VAL887C, VAL900C, VAL907C, VAL914C
• C-G: ALA1040G, ALA840C, ARG1035G, ARG1042G, ARG1099G, ARG835C, ARG842C, ARG899C, ASN1038G, ASN838C, GLU1041G, GLU841C, GLY1037G, GLY837C, LYS1036G, LYS836C, TYR1039G, TYR839C
• C-H: ARG1476H, ARG1483H, ARG835C, ASN838C, GLY837C, HIS1479H, LYS1482H, LYS836C, SER1475H, SER1484H, TYR839C
• D-E: GLU694E, LEU660E, LYS1254D, MET690E, THR658E
• D-F: ALA1255D, ARG1269D, ASN1260D, ASN1264D, ASP1265D, GLU1268D, GLY299F, GLY301F, GLY302F, ILE1258D, LEU297F, LYS1231D, LYS1254D, LYS291F, MET1256D, MET1259D, MET284F, PHE1262D, PHE1267D, PHE300F, SER1253D, SER1257D, SER1261D, THR296F, TYR288F, TYR298F, VAL1263D, VAL1266D, VAL287F
• D-G: ALA1278D, ARG1035G, ARG1276D, ARG1283D, ASN1038G, GLY1037G, HIS1279D, ILE1286D, LEU1033G, LYS1036G, SER1275D, SER1284D, TYR1039G
• D-H: ARG1276D, ARG1430H, ARG1476H, GLU1268D, GLU1468H, LYS1282D, LYS1431H, TYR1280D, TYR1480H
• E-F: ALA215F, ALA233F, ALA238F, ALA269F, ALA283F, ALA289F, ALA647E, ALA675E, ALA688E, ALA691E, ALA695E, ALA698E, ALA702E, ALA711E, ARG219F, ARG223F, ARG235F, ARG236F, ARG239F, ARG240F, ARG245F, ARG255F, ARG267F, ARG278F, ARG295F, ARG642E, ARG649E, ARG652E, ARG653E, ARG663E, ARG669E, ARG672E, ARG683E, ARG716E, ARG728E, ARG731E, ARG734E, ASN225F, ASN264F, ASN708E, ASP224F, ASP268F, ASP285F, ASP677E, ASP681E, ASP706E, ASP723E, GLN227F, GLN655E, GLN668E, GLN676E, GLN685E, GLN693E, GLN725E, GLU252F, GLU253F, GLU263F, GLU274F, GLU650E, GLU659E, GLU673E, GLU694E, GLU697E, GLU705E, GLU733E, GLY228F, GLY241F, GLY242F, GLY248F, GLY256F, GLY299F, GLY301F, GLY644E, HIS275F, ILE226F, ILE229F, ILE234F, ILE246F, ILE250F, ILE266F, ILE651E, ILE662E, ILE674E, ILE712E, ILE719E, ILE724E, LEU222F, LEU237F, LEU249F, LEU258F, LEU262F, LEU290F, LEU297F, LEU648E, LEU660E, LEU661E, LEU665E, LEU670E, LEU682E, LEU692E, LEU700E, LEU703E, LEU709E, LYS220F, LYS244F, LYS259F, LYS277F, LYS279F, LYS656E, LYS664E, LYS679E, LYS722E, MET284F, MET690E, MET720E, PHE261F, PHE300F, PHE667E, PHE678E, PHE684E, PHE704E, PRO232F, PRO643E, PRO666E, PRO721E, SER247F, SER657E, SER686E, SER687E, SER696E, THR230F, THR254F, THR271F, THR273F, THR280F, THR282F, THR296F, THR645E, THR658E, THR680E, THR707E, THR718E, TYR251F, TYR298F, TYR654E, TYR699E, VAL221F, VAL243F, VAL257F, VAL260F, VAL265F, VAL270F, VAL281F, VAL286F, VAL287F, VAL646E, VAL671E, VAL689E, VAL701E, VAL717E
• E-G: ALA735E, ARG1099G, ARG729E, ARG731E, ARG734E, ASN1094G, ASN1110G, GLN1112G, GLU733E, GLY1098G, GLY732E, ILE730E, LYS1095G
• F-G: ARG267F, ASN264F, LYS1095G
• F-H: ALA1474H, ALA1478H, ALA1494H, ALA269F, ALA276F, ALA289F, ARG1469H, ARG1476H, ARG1483H, ARG1489H, ARG1496H, ARG267F, ARG278F, ARG292F, ASN1481H, ASN264F, ASP268F, ASP285F, GLN1492H, GLN293F, GLU1473H, GLU1490H, GLU274F, GLY1501H, HIS1479H, HIS275F, ILE1470H, ILE1486H, ILE1491H, LEU1477H, LEU1497H, LEU1498H, LEU1499H, LYS1482H, LYS277F, LYS291F, MET284F, PRO1500H, SER1488H, THR1485H, THR1487H, THR1493H, THR271F, THR273F, TYR1480H, TYR272F, TYR288F, VAL1495H, VAL265F, VAL270F, VAL287F
• G-H: ALA1021G, ALA1040G, ALA1045G, ALA1047G, ALA1052G, ALA1053G, ALA1060G, ALA1066G, ALA1069G, ALA1070G, ALA1103G, ALA1435H, ALA1455H, ALA1471H, ALA1474H, ALA1478H, ALA1494H, ALA1504H, ALA1507H, ALA1514H, ALA1521H, ARG1017G, ARG1020G, ARG1029G, ARG1032G, ARG1035G, ARG1042G, ARG1071G, ARG1077G, ARG1081G, ARG1099G, ARG1430H, ARG1469H, ARG1476H, ARG1483H, ARG1489H, ARG1496H, ASN1038G, ASN1068G, ASN1094G, ASN1460H, ASN1464H, ASP1072G, ASP1090G, ASP1448H, ASP1465H, GLN1024G, GLN1084G, GLN1104G, GLN1444H, GLN1492H, GLU1041G, GLU1056G, GLU1061G, GLU1064G, GLU1091G, GLU1092G, GLU1432H, GLU1468H, GLU1473H, GLU1490H, GLU1502H, GLU1510H, GLY1022G, GLY1028G, GLY1037G, GLY1044G, GLY1046G, GLY1067G, GLY1098G, GLY1105G, GLY1450H, GLY1472H, GLY1501H, GLY1511H, HIS1031G, HIS1082G, HIS1446H, HIS1479H, HIS1506H, ILE1062G, ILE1078G, ILE1079G, ILE1102G, ILE1436H, ILE1451H, ILE1458H, ILE1470H, ILE1486H, ILE1491H, LEU1023G, LEU1033G, LEU1034G, LEU1051G, LEU1055G, LEU1058G, LEU1063G, LEU1065G, LEU1083G, LEU1093G, LEU1096G, LEU1097G, LEU1442H, LEU1497H, LEU1498H, LEU1499H, LEU1503H, LYS1015G, LYS1036G, LYS1075G, LYS1095G, LYS1431H, LYS1440H, LYS1443H, LYS1454H, LYS1505H, LYS1513H, LYS1517H, MET1456H, MET1459H, PHE1025G, PHE1462H, PHE1467H, PRO1026G, PRO1048G, PRO1080G, PRO1500H, SER1018G, SER1019G, SER1433H, SER1452H, SER1453H, SER1457H, SER1461H, SER1475H, SER1484H, SER1488H, SER1509H, SER1520H, THR1016G, THR1059G, THR1076G, THR1101G, THR1449H, THR1485H, THR1487H, THR1493H, THR1512H, THR1516H, THR1519H, TYR1039G, TYR1050G, TYR1057G, TYR1434H, TYR1437H, TYR1439H, TYR1518H, VAL1027G, VAL1030G, VAL1043G, VAL1049G, VAL1054G, VAL1087G, VAL1100G, VAL1438H, VAL1441H, VAL1445H, VAL1463H, VAL1466H, VAL1495H, VAL1508H, VAL1515H