3JUY

crystal structure of a 3b3 variant, a broadly neutralizing hiv-1 scfv antibody

• Total interactions analyzed: 15
• Total true interactions: 10
• Strongest Interaction:
  • Chains: B-A
  • Int. Res.: 59
  • Norm. En. per Res.: -2.8944
• Hub Node: B(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
B-A	-7.388	11.7206	-175.1	-170.7674	59	13	1	5870	0	22	13
B-C	-8.1659	13.0244	-155.184	-150.3254	57	7	1	5265	0	22	13
B-E	0.0	0.0	-84.0956	-84.0956	69	4	5	4397	0	3	10
B-F	0.0	0.0	-0.004	-0.004	5	0	0	3	0	0	1
B-D	-4.5253	-12.2005	-23.3103	-40.0361	28	0	0	1068	0	5	3
A-C	-10.0616	10.582	-144.913	-144.3926	55	7	1	5095	0	22	13
A-E	0.0	0.0	-0.5525	-0.5525	6	0	0	83	0	2	1
A-D	0.0	0.0	-2.3421	-2.3421	12	0	0	161	0	1	0
E-F	0.0	-11.5374	-11.9557	-23.4931	12	0	0	473	2	2	0
F-D	-8.6926	14.275	-147.831	-142.2486	56	7	0	5255	0	22	13

Interface residues

• B-A: ALA16B, ALA236A, ALA62B, ALA89B, ARG28A, ARG67B, ARG84B, ARG87B, ASN111A, ASN52A, ASN55A, ASN57A, ASP105A, ASP106A, ASP66B, GLN65B, GLU101A, GLU59A, GLU59B, GLU82B, GLY100A, GLY103A, GLY128B, GLY129B, GLY130B, GLY131B, GLY15B, GLY56A, HIS31A, LEU83B, LEU86B, LYS19B, LYS58A, LYS58B, LYS63B, MET81B, PHE32A, PHE60B, PHE64B, PHE70B, PRO108A, PRO53A, SER107A, SER17B, SER30A, SER61B, SER85B, THR33A, THR69B, THR71B, TRP102A, TRP104A, TRP50A, TYR109A, TYR112A, TYR54A, VAL18B, VAL68B, VAL99A
• B-C: ALA16C, ALA236B, ALA62C, ALA89C, ARG28B, ARG67C, ARG84C, ARG87C, ASN111B, ASN52B, ASN55B, ASN57B, ASP106B, ASP66C, GLN65C, GLU101B, GLU59B, GLU59C, GLU82C, GLY100B, GLY103B, GLY15C, GLY56B, HIS31B, ILE51B, LEU83C, LEU86C, LYS19C, LYS58B, LYS58C, LYS63C, MET81C, PHE32B, PHE60C, PHE64C, PHE70C, PRO108B, PRO53B, SER107B, SER17C, SER30B, SER61C, SER85C, SER88C, THR33B, THR69C, THR71C, TRP102B, TRP104B, TRP50B, TYR109B, TYR112B, TYR239B, TYR54B, VAL18C, VAL68C, VAL99B
• B-E: ALA186B, ALA40B, ALA40E, ALA89E, ALA92B, ALA92E, ALA9B, ALA9E, ARG87E, GLN185B, GLN185E, GLN39E, GLN43B, GLN43E, GLN6B, GLU10B, GLU10E, GLU248E, GLY120B, GLY128B, GLY129B, GLY130B, GLY131B, GLY184B, GLY184E, GLY42B, GLY42E, GLY8B, GLY8E, HIS181E, ILE124B, ILE124E, LYS119B, LYS119E, LYS12B, LYS12E, LYS182B, LYS182E, LYS246E, PRO14B, PRO14E, PRO183B, PRO183E, PRO41B, PRO41E, SER126B, SER126E, SER127B, SER127E, SER7B, SER88B, SER88E, THR121B, THR121E, THR122B, THR122E, THR91B, THR91E, TYR94B, TYR95B, VAL11B, VAL11E, VAL123B, VAL123E, VAL125B, VAL125E, VAL5B, VAL93B, VAL93E
• B-F: ALA16F, GLN23B, GLU82F, SER17F, SER75B
• B-D: ALA76B, ALA76D, ALA79B, ARG28D, ASN77B, ASN77D, ASP73B, ASP73D, CYS22B, GLN23B, GLN23D, GLU10B, GLU82B, HIS31D, LYS12B, LYS19B, MET81B, PHE29D, SER21B, SER30D, SER75B, SER75D, SER7B, THR71B, THR74D, THR78B, TYR80B, VAL20B
• A-C: ALA16A, ALA236C, ALA62A, ALA89A, ARG28C, ARG67A, ARG84A, ARG87A, ASN111C, ASN52C, ASN55C, ASN57C, ASP106C, ASP66A, GLN65A, GLU101C, GLU59A, GLU59C, GLU82A, GLY100C, GLY103C, GLY15A, GLY56C, HIS31C, ILE51C, LEU83A, LEU86A, LYS19A, LYS58A, LYS58C, LYS63A, MET81A, PHE32C, PHE60A, PHE64A, PHE70A, PRO108C, PRO53C, SER107C, SER17A, SER30C, SER61A, SER85A, THR33C, THR69A, THR71A, TRP102C, TRP104C, TRP50C, TYR109C, TYR112C, TYR54C, VAL18A, VAL68A, VAL99C
• A-E: ARG249E, ASP105A, GLU248E, LYS246E, PHE226E, TRP104A
• A-D: ALA76A, ARG28A, ASP73A, GLN23D, GLN3D, GLN6D, LYS119D, SER75A, SER7D, THR74A, TYR80D, VAL5D
• E-F: ALA16E, ALA72F, ALA76F, ASN77F, ASP73F, GLY15E, LYS13E, PRO14E, SER75F, THR74F, THR78F, TYR80F
• F-D: ALA16F, ALA236D, ALA62F, ALA89F, ARG28D, ARG67F, ARG84F, ARG87F, ASN111D, ASN52D, ASN55D, ASN57D, ASP106D, ASP66F, GLN65F, GLU101D, GLU59D, GLU59F, GLU82F, GLY100D, GLY103D, GLY15F, GLY56D, HIS31D, ILE51D, LEU83F, LEU86F, LYS19F, LYS58D, LYS58F, LYS63F, MET81F, PHE32D, PHE60F, PHE64F, PHE70F, PRO108D, PRO53D, SER107D, SER17F, SER30D, SER61F, SER85F, SER88F, THR33D, THR69F, THR71F, TRP102D, TRP104D, TRP50D, TYR109D, TYR112D, TYR54D, VAL18F, VAL68F, VAL99D