3GIS

crystal structure of na-free thrombin in complex with thrombomodulin

• Total interactions analyzed: 36
• Total true interactions: 21
• Strongest Interaction:
  • Chains: B-Y
  • Int. Res.: 21
  • Norm. En. per Res.: -5.6157
• Hub Node: B(6)

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	-110.7882	-71.8295	222.292	39.6743	118	42	4	20318	9	46	36
A-E	0.0	0.0	-0.0003	-0.0003	2	0	0	1	0	0	0
A-F	0.0	-9.045	-1.5305	-10.5755	7	0	0	208	0	2	5
A-Y	0.0	0.0	-0.0165	-0.0165	5	0	0	12	0	1	0
B-D	-10.4357	19.504	-25.0107	-15.9424	22	3	0	1294	0	9	9
B-E	-5.0437	1.0974	-7.7125	-11.6589	15	5	0	799	0	4	3
B-F	0.0	0.0	-0.9343	-0.9343	10	0	0	166	0	6	4
B-X	-72.8837	-51.9914	-177.301	-302.1761	78	9	2	7075	1	39	20
B-Y	-7.8216	-62.1943	-47.9144	-117.9303	21	5	0	1873	5	8	5
B-Z	0.0	0.0	-0.044	-0.044	7	0	0	22	0	4	1
C-D	-117.5756	-66.3712	236.184	52.2372	118	37	4	19952	9	45	37
C-X	0.0	-14.6628	-6.3457	-21.0085	18	1	0	375	2	6	3
D-X	-8.2792	-49.4878	-47.918	-105.685	44	10	2	2595	3	16	14
D-Y	-65.5904	-42.2895	-180.346	-288.2259	79	11	2	7612	2	39	22
D-Z	0.0	0.0	-0.0078	-0.0078	2	0	0	10	0	1	0
E-F	-130.1072	-62.1806	225.274	32.9862	116	43	4	19959	8	47	37
F-X	0.0	0.0	-0.0324	-0.0324	9	0	0	15	0	4	1
F-Z	-75.0627	-58.9526	-177.623	-311.6383	76	12	2	7122	1	39	20
X-Y	0.0	0.0	-0.028	-0.028	6	0	0	11	0	1	9
X-Z	-55.6303	-18.8237	-143.221	-217.6751	56	7	5	5263	1	3	17
Y-Z	0.0	0.0	-1.78	-1.78	7	0	0	181	0	0	3

Interface residues

• A-B: ALA113B, ALA132B, ALA1A, ALA22B, ARG126B, ARG137B, ARG14A, ARG1A, ARG206B, ARG4A, ARG50B, ASN159B, ASN1A, ASN204B, ASN205B, ASP116B, ASP125B, ASP14A, ASP1A, ASP21B, ASP243B, ASP49B, CYS122B, CYS1A, GLN131B, GLN1A, GLN209B, GLN239B, GLN244B, GLU13A, GLU14A, GLU1A, GLU23B, GLU247B, GLU8A, GLY133B, GLY136B, GLY14A, GLY1A, GLY246B, GLY25B, GLY2A, HIS119B, ILE118B, ILE14A, ILE162B, ILE238B, ILE242B, ILE24B, ILE47B, LEU105B, LEU123B, LEU129B, LEU12A, LEU130B, LEU14A, LEU160B, LEU3A, LEU46B, LEU53B, LEU6A, LYS107B, LYS10A, LYS135B, LYS14A, LYS186B, LYS202B, LYS235B, LYS236B, LYS240B, LYS9A, MET201B, MET210B, MET26B, PHE114B, PHE199B, PHE1A, PHE204B, PHE232B, PHE245B, PHE7A, PRO111B, PRO120B, PRO124B, PRO161B, PRO1A, PRO204B, PRO28B, PRO5A, SER115B, SER11A, SER129B, SER14A, SER1A, SER203B, SER20B, SER27B, SER48B, THR128B, THR14A, THR1A, TRP207B, TRP29B, TRP51B, TYR117B, TYR134B, TYR14A, TYR184B, TYR1A, TYR208B, VAL112B, VAL121B, VAL138B, VAL157B, VAL158B, VAL200B, VAL241B, VAL52B
• A-E: ARG1E, THR1A
• A-F: ARG1A, GLN244F, GLU86F, LYS107F, LYS87F, THR1A, TYR89F
• A-Y: GLU374Y, LEU6A, LYS10A, PHE419Y, PRO401Y
• B-D: ARG67B, ARG73D, ARG75B, ARG75D, ARG77B, ARG77D, ASN78B, ASP21B, GLU77B, GLU77D, GLU80B, LYS149D, PRO152D, SER153B, SER153D, SER72B, SER72D, THR74B, THR74D, TYR76B, TYR76D, VAL154D
• B-E: ARG1E, ASN1E, ASP243B, GLN244B, GLU247B, GLU86B, GLY246B, ILE242B, LYS107B, LYS87B, PHE245B, THR1E, TRP51B, TYR89B, VAL241B
• B-F: ARG50F, ASP243B, ASP243F, GLN244B, GLN244F, GLU247B, GLU86F, LYS107F, LYS110B, LYS110F
• B-X: ALA113B, ALA397X, ALA405X, ARG35B, ARG67B, ARG73B, ARG75B, ARG77B, ASN429X, ASN439X, ASN62B, ASN78B, ASP398X, ASP400X, ASP416X, ASP417X, ASP423X, ASP425X, ASP461X, CYS399X, CYS407X, CYS409X, CYS421X, CYS427X, CYS433X, CYS462X, GLN151B, GLN38B, GLU39B, GLU408X, GLU411X, GLU426X, GLU428X, GLU77B, GLU80B, GLY412X, GLY418X, GLY430X, GLY431X, GLY459X, ILE414X, ILE420X, ILE424X, ILE68B, ILE79B, ILE82B, LEU388X, LEU40B, LEU415X, LEU65B, LYS109B, LYS110B, LYS36B, LYS70B, LYS81B, MET32B, MET84B, PHE34B, PHE419X, PHE432X, PHE444X, PRO111B, PRO37B, PRO410X, SER153B, SER36B, SER406X, SER434X, SER72B, SER83B, THR393X, THR422X, THR460X, THR74B, TYR413X, TYR76B, VAL112B, VAL66B
• B-Y: ALA394Y, ARG75B, ARG77B, ASN78B, ASP116B, ASP416Y, ASP417Y, CYS421Y, GLU77B, GLU80B, GLY25B, GLY418Y, HIS71B, ILE24B, ILE420Y, ILE79B, LEU415Y, PHE419Y, THR422Y, TYR117B, TYR76B
• B-Z: ALA113B, ASP463Z, LYS110B, LYS81B, PRO111B, PRO450Z, SER434Z
• C-D: ALA113D, ALA132D, ALA1C, ALA22D, ARG126D, ARG137D, ARG14C, ARG1C, ARG206D, ARG4C, ARG50D, ASN159D, ASN1C, ASN204D, ASN205D, ASP116D, ASP125D, ASP14C, ASP1C, ASP21D, ASP243D, ASP49D, CYS122D, CYS1C, GLN131D, GLN1C, GLN209D, GLN239D, GLN244D, GLU13C, GLU14C, GLU1C, GLU23D, GLU8C, GLY133D, GLY136D, GLY14C, GLY1C, GLY246D, GLY25D, GLY2C, HIS119D, ILE118D, ILE14C, ILE162D, ILE238D, ILE242D, ILE24D, ILE47D, LEU105D, LEU123D, LEU129D, LEU12C, LEU130D, LEU14C, LEU160D, LEU3C, LEU46D, LEU53D, LEU6C, LYS107D, LYS10C, LYS135D, LYS14C, LYS186D, LYS202D, LYS235D, LYS236D, LYS240D, LYS9C, MET201D, MET210D, MET26D, PHE114D, PHE199D, PHE1C, PHE204D, PHE232D, PHE245D, PHE7C, PRO111D, PRO120D, PRO124D, PRO161D, PRO1C, PRO204D, PRO28D, PRO5C, SER115D, SER11C, SER129D, SER14C, SER1C, SER203D, SER20D, SER27D, SER48D, THR128D, THR14C, THR1C, TRP207D, TRP237D, TRP29D, TRP51D, TYR117D, TYR134D, TYR14C, TYR184D, TYR1C, TYR208D, VAL112D, VAL121D, VAL138D, VAL157D, VAL158D, VAL200D, VAL241D, VAL52D
• C-X: ALA394X, ALA397X, ALA405X, ASP400X, CYS395X, CYS399X, GLN392X, GLU374X, GLY375X, GLY418X, LEU12C, LEU6C, LYS10C, LYS14C, PHE419X, PHE7C, PRO396X, PRO401X
• D-X: ALA22D, ALA394X, ALA397X, ARG73D, ARG75D, ARG77D, ASN391X, ASN439X, ASN78D, ASP116D, ASP21D, ASP416X, ASP417X, ASP423X, ASP425X, CYS395X, CYS421X, GLN156D, GLN392X, GLU23D, GLU428X, GLU77D, GLU80D, GLY25D, GLY418X, HIS71D, ILE24D, ILE414X, ILE420X, ILE424X, ILE79D, LEU155D, PHE419X, PRO152D, PRO396X, SER115D, SER153D, SER20D, SER72D, THR393X, THR422X, TYR117D, TYR76D, VAL154D
• D-Y: ALA113D, ALA394Y, ALA397Y, ALA405Y, ARG35D, ARG67D, ARG73D, ARG75D, ARG77D, ASN429Y, ASN439Y, ASN78D, ASP398Y, ASP400Y, ASP416Y, ASP417Y, ASP423Y, ASP425Y, ASP461Y, ASP463Y, CYS399Y, CYS407Y, CYS409Y, CYS421Y, CYS427Y, CYS433Y, CYS462Y, GLN38D, GLU39D, GLU408Y, GLU411Y, GLU426Y, GLU428Y, GLU77D, GLU80D, GLY412Y, GLY418Y, GLY430Y, GLY431Y, GLY435Y, GLY459Y, ILE414Y, ILE420Y, ILE424Y, ILE68D, ILE79D, ILE82D, LEU108D, LEU40D, LEU415Y, LEU65D, LYS109D, LYS110D, LYS149D, LYS36D, LYS70D, LYS81D, MET32D, MET84D, PHE34D, PHE419Y, PHE432Y, PHE444Y, PRO111D, PRO37D, PRO410Y, SER36D, SER406Y, SER434Y, SER72D, SER83D, THR393Y, THR422Y, THR460Y, THR74D, TYR413Y, TYR76D, VAL112D, VAL66D
• D-Z: ARG77D, SER452Z
• E-F: ALA132F, ALA1E, ALA22F, ARG126F, ARG137F, ARG14E, ARG1E, ARG206F, ARG4E, ARG50F, ASN159F, ASN1E, ASN204F, ASN205F, ASP116F, ASP125F, ASP14E, ASP1E, ASP21F, ASP243F, ASP49F, CYS122F, CYS1E, GLN131F, GLN1E, GLN209F, GLN239F, GLN244F, GLU13E, GLU14E, GLU1E, GLU23F, GLU8E, GLY133F, GLY136F, GLY14E, GLY1E, GLY25F, GLY2E, HIS119F, ILE118F, ILE14E, ILE162F, ILE238F, ILE242F, ILE24F, ILE47F, LEU105F, LEU123F, LEU129F, LEU12E, LEU130F, LEU14E, LEU160F, LEU3E, LEU46F, LEU53F, LEU6E, LYS107F, LYS10E, LYS135F, LYS14E, LYS186F, LYS202F, LYS235F, LYS236F, LYS240F, LYS9E, MET201F, MET210F, MET26F, PHE114F, PHE199F, PHE1E, PHE204F, PHE232F, PHE7E, PRO111F, PRO120F, PRO124F, PRO161F, PRO1E, PRO204F, PRO28F, PRO5E, SER115F, SER11E, SER129F, SER14E, SER1E, SER203F, SER20F, SER27F, SER48F, THR128F, THR139F, THR14E, THR1E, TRP207F, TRP237F, TRP29F, TRP51F, TYR117F, TYR134F, TYR14E, TYR184F, TYR1E, TYR208F, VAL112F, VAL121F, VAL138F, VAL157F, VAL158F, VAL200F, VAL241F, VAL52F
• F-X: ALA113F, ALA453X, ASN78F, ASP463X, LYS110F, LYS81F, PRO111F, PRO450X, SER434X
• F-Z: ALA113F, ALA397Z, ALA405Z, ARG35F, ARG67F, ARG73F, ARG75F, ARG77F, ASN429Z, ASN439Z, ASN62F, ASN78F, ASP398Z, ASP400Z, ASP416Z, ASP417Z, ASP423Z, ASP425Z, ASP461Z, CYS399Z, CYS407Z, CYS409Z, CYS421Z, CYS427Z, CYS433Z, CYS462Z, GLN151F, GLN38F, GLU39F, GLU408Z, GLU411Z, GLU426Z, GLU428Z, GLU77F, GLU80F, GLY412Z, GLY418Z, GLY430Z, GLY431Z, ILE414Z, ILE420Z, ILE424Z, ILE68F, ILE79F, ILE82F, LEU388Z, LEU40F, LEU415Z, LEU65F, LYS109F, LYS110F, LYS36F, LYS70F, LYS81F, MET32F, MET84F, PHE34F, PHE419Z, PHE432Z, PRO111F, PRO37F, PRO410Z, SER153F, SER36F, SER406Z, SER434Z, SER72F, SER83F, THR393Z, THR403Z, THR422Z, THR74F, TYR413Z, TYR76F, VAL112F, VAL66F
• X-Y: ALA394Y, ASP416X, ASP417Y, GLU428X, ILE420Y, THR422X
• X-Z: ALA453X, ALA453Z, ALA455X, ALA455Z, ASN429X, ASN429Z, ASN439X, ASN439Z, ASP425X, ASP425Z, ASP451X, ASP451Z, ASP461X, ASP461Z, ASP463X, ASP463Z, CYS427X, CYS427Z, CYS433X, CYS433Z, CYS437X, CYS437Z, CYS446X, CYS446Z, CYS448X, CYS448Z, CYS462X, CYS462Z, GLU426X, GLU426Z, GLU428X, GLU428Z, GLU445X, GLU445Z, GLY430X, GLY430Z, GLY431X, GLY431Z, GLY435X, GLY435Z, GLY449X, GLY449Z, HIS438X, HIS438Z, ILE447X, ILE447Z, LEU454X, LEU454Z, PRO450X, PRO450Z, SER434X, SER434Z, SER452X, SER452Z, VAL436X, VAL436Z
• Y-Z: ALA394Y, ALA453Z, ASP451Z, GLN392Y, SER452Z, THR393Y, THR422Y