2VI6

crystal structure of the nanog homeodomain

• Total interactions analyzed: 28
• Total true interactions: 13
• Strongest Interaction:
  • Chains: C-H
  • Int. Res.: 42
  • Norm. En. per Res.: -1.8327
• Hub Node: C(4)

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	0.0	0.0	-0.5453	-0.5453	2	0	0	63	0	0	0
A-C	0.0	9.3632	-32.4514	-23.0882	18	4	0	1266	0	0	11
A-G	-3.883	0.0	-61.3006	-65.1836	41	7	3	3389	0	6	7
B-C	-5.7887	-2.9807	-59.4809	-68.2503	43	1	2	3489	0	5	2
C-D	0.0	0.0	-0.0055	-0.0055	2	0	0	4	0	0	0
C-F	0.0	0.0	-4.2902	-4.2902	13	0	1	524	0	0	0
C-G	-13.5272	-16.9155	1329.3	1298.8573	50	13	0	4992	0	14	24
C-H	-3.3581	0.0	-73.6166	-76.9747	42	3	4	3670	0	6	6
D-E	-14.2735	-17.6099	1415.32	1383.4365	50	18	0	4639	1	14	25
D-F	0.0	0.0	-54.3038	-54.3038	40	3	2	3080	0	6	7
E-F	-4.5902	9.9185	-36.2944	-30.966	17	7	0	1391	0	0	11
F-H	0.0	-2.6718	-13.0494	-15.7212	22	1	1	1297	0	2	0
G-H	0.0	18.631	-38.2127	-19.5817	19	7	0	1676	0	0	14

Interface residues

• A-B: GLN10B, LYS57A
• A-C: ARG53A, ARG58C, ASN51A, CYS56A, CYS56C, GLN50A, GLN60A, GLN60C, LYS24A, LYS55C, LYS57A, LYS57C, MET54A, MET54C, THR47A, TRP59A, TRP59C, TYR25A
• A-G: ALA11G, ALA15G, ARG19A, ARG19G, ARG53A, ARG58A, ASN39G, ASP18G, CYS14G, GLN10G, GLN12G, GLN23A, GLN29A, GLN30A, GLN50A, GLN60A, ILE37G, LEU13G, LEU16G, LEU26A, LEU28A, LEU34G, LEU38G, LEU40G, LYS22A, LYS22G, LYS24A, LYS46A, LYS57A, MET31A, MET54A, PHE49A, PHE8G, SER27A, SER35G, SER36G, SER9G, TRP59A, TYR25A, TYR42A, VAL7G
• B-C: ALA11B, ALA15B, ARG19B, ARG53C, ARG58C, ASN39B, ASP18B, CYS14B, GLN10B, GLN12B, GLN23B, GLN23C, GLN29C, GLN30B, GLN30C, GLN50C, GLN60C, GLU33B, ILE37B, LEU13B, LEU16B, LEU26B, LEU26C, LEU28C, LEU34B, LEU38B, LEU40B, LYS22B, LYS24C, LYS46C, LYS57C, MET31C, MET54C, PHE49C, PHE8B, SER27C, SER35B, SER36B, SER9B, THR47C, TRP59C, TYR25C, TYR42C
• C-D: GLN10D, THR6C
• C-F: GLN10C, GLN29F, GLN32F, GLU33F, LEU13C, LEU28F, LYS46F, PHE8C, SER36F, SER9C, THR6C, TYR42F, VAL7C
• C-G: ALA11C, ALA11G, ALA15C, ALA15G, ARG19C, ARG19G, ARG58C, ARG58G, ASP18C, ASP18G, CYS14C, CYS14G, CYS56C, CYS56G, GLN10C, GLN10G, GLN12C, GLN12G, GLN21C, GLN21G, GLN23G, GLN52C, GLN52G, LEU13C, LEU13G, LEU16C, LEU16G, LEU34C, LEU34G, LEU38C, LEU38G, LYS17C, LYS17G, LYS22C, LYS22G, LYS24C, LYS24G, LYS55C, LYS55G, LYS57C, LYS57G, MET54C, MET54G, PHE20C, PHE20G, SER9C, TRP48C, TRP48G, TRP59C, TRP59G
• C-H: ALA11C, ALA15C, ARG19C, ARG19H, ARG53H, ARG58H, ASN39C, ASP18C, CYS14C, GLN10C, GLN12C, GLN23H, GLN29H, GLN30H, GLN44C, GLN50H, GLN60H, ILE37C, LEU13C, LEU16C, LEU26H, LEU28H, LEU34C, LEU38C, LEU40C, LYS22C, LYS22H, LYS24H, LYS46H, MET31H, MET54H, PHE49H, PHE8C, SER27H, SER35C, SER36C, SER9C, THR6C, TRP59H, TYR25H, TYR42H, VAL7C
• D-E: ALA11D, ALA11E, ALA15D, ALA15E, ARG19D, ARG19E, ARG53D, ARG58D, ARG58E, ASP18D, ASP18E, CYS14D, CYS14E, CYS56D, CYS56E, GLN10D, GLN10E, GLN12D, GLN12E, GLN21D, GLN21E, GLN23D, GLN23E, GLN52D, GLN52E, ILE37D, LEU13D, LEU13E, LEU16D, LEU16E, LEU34D, LEU38D, LEU38E, LYS17D, LYS17E, LYS22D, LYS22E, LYS24D, LYS24E, LYS55D, LYS55E, LYS57D, LYS57E, MET54D, PHE20D, PHE20E, TRP48D, TRP48E, TRP59D, TRP59E
• D-F: ALA11D, ALA15D, ARG19D, ARG19F, ARG53F, ARG58F, ASN39D, ASP18D, CYS14D, GLN10D, GLN12D, GLN23F, GLN29F, GLN30F, GLN50F, GLN60F, ILE37D, LEU13D, LEU16D, LEU26F, LEU28F, LEU34D, LEU38D, LEU40D, LYS22D, LYS22F, LYS24F, LYS46F, LYS57F, MET31F, PHE49F, PHE8D, SER27F, SER35D, SER36D, SER9D, TRP59F, TYR25F, TYR42F, VAL7D
• E-F: ARG53F, ARG58E, ASN51F, CYS56E, CYS56F, GLN50F, GLN60E, GLN60F, LYS55E, LYS57E, LYS57F, MET54E, MET54F, THR47F, TRP59E, TRP59F, TYR25F
• F-H: ASN39F, GLN29H, GLN32F, GLN32H, GLN44F, GLN44H, GLU33H, ILE37F, LEU28H, LEU40F, LYS43F, LYS43H, LYS46H, SER35F, SER35H, SER36F, SER36H, SER41F, SER41H, THR6F, TYR42F, TYR42H
• G-H: ARG53H, ARG58G, ASN51H, CYS56G, CYS56H, GLN50H, GLN60G, GLN60H, LYS24H, LYS46H, LYS55G, LYS57G, LYS57H, MET54G, MET54H, PHE49H, TRP59G, TRP59H, TYR25H