3DNO

molecular structure for the hiv-1 gp120 trimer in the cd4- bound state

• Total interactions analyzed: 36
• Total true interactions: 9
• Strongest Interaction:
  • Chains: A-C
  • Int. Res.: 67
  • Norm. En. per Res.: -4.8219
• Hub Node: A(2)

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	-39.177	0.0	358.988	319.811	99	28	3	12790	0	8	4
A-C	-43.8621	1.612	-280.82	-323.0701	67	16	3	10513	0	22	19
B-C	-420.6773	-57.0093	385.676	-92.0107	238	96	32	44122	5	45	40
D-E	-39.1431	0.0	362.654	323.5109	99	28	3	12790	0	8	4
D-F	-43.8394	1.6152	-280.725	-322.9492	67	16	3	10515	0	22	18
E-F	-426.6988	-57.0131	372.745	-110.967	238	94	32	44120	5	45	40
G-H	-39.0552	0.0	362.758	323.7028	99	28	3	12792	0	8	4
G-I	-43.7739	1.6053	-280.837	-323.0055	67	16	3	10516	0	22	18
H-I	-428.8606	-57.0	382.684	-103.1766	238	94	32	44123	5	45	40

Interface residues

• A-B: ALA204B, ALA219B, ALA224B, ARG252B, ARG273B, ASN234B, ASN241B, ASN276B, ASN377B, ASN92A, ASN94A, ASP107A, ASP113A, ASP99A, CYS119A, CYS205B, CYS218B, CYS228B, CYS239B, CYS247B, CYS378B, GLN103A, GLN114A, GLN203B, GLU106A, GLU211B, GLU381B, GLU91A, GLY235B, GLY237B, GLY379B, GLY380B, HIS105A, HIS216B, HIS249B, ILE108A, ILE109A, ILE201B, ILE213B, ILE215B, ILE225B, ILE251B, ILE272B, ILE284B, ILE285B, LEU111A, LEU116A, LEU122A, LEU226B, LYS117A, LYS121A, LYS207B, LYS227B, LYS282B, LYS97A, MET100A, MET104A, MET95A, PHE210B, PHE223B, PHE233B, PHE277B, PHE376B, PHE382B, PHE93A, PRO118A, PRO124A, PRO206B, PRO212B, PRO214B, PRO220B, PRO238B, PRO253B, SER115A, SER199B, SER209B, SER243B, SER256B, SER274B, THR123A, THR198B, THR202B, THR236B, THR240B, THR244B, THR248B, THR283B, THR90A, TRP112A, TRP96A, TYR217B, VAL120A, VAL200B, VAL208B, VAL242B, VAL254B, VAL255B, VAL275B, VAL286B
• A-C: ALA433C, ALA436C, ARG476C, ARG480C, ASN425C, ASN478C, ASN92A, ASN94A, ASN98A, ASP107A, ASP113A, ASP474C, ASP477C, ASP99A, CYS119A, GLN103A, GLN114A, GLN422C, GLN428C, GLU102A, GLU106A, GLU482C, GLU91A, GLY431C, GLY473C, HIS105A, ILE108A, ILE109A, ILE423C, ILE424C, LEU111A, LEU116A, LEU122A, LEU453C, LEU483C, LYS117A, LYS121A, LYS429C, LYS432C, LYS485C, LYS487C, LYS97A, MET100A, MET104A, MET426C, MET434C, MET475C, MET95A, PHE93A, PRO118A, PRO124A, SER110A, SER115A, SER481C, THR123A, TRP112A, TRP427C, TRP479C, TRP96A, TYR435C, TYR484C, TYR486C, VAL101A, VAL120A, VAL430C, VAL488C, VAL489C
• B-C: ALA204B, ALA219B, ALA221B, ALA224B, ALA266B, ALA281B, ALA299B, ALA336B, ALA346B, ALA433C, ALA436C, ARG252B, ARG273B, ARG335B, ARG350B, ARG419C, ARG444C, ARG456C, ARG469C, ARG476C, ARG480C, ASN229B, ASN230B, ASN234B, ASN262B, ASN276B, ASN280B, ASN289B, ASN295B, ASN332B, ASN339B, ASN340B, ASN356B, ASN377B, ASN386B, ASN392B, ASN425C, ASN448C, ASN460C, ASN462C, ASN463C, ASN478C, ASP279B, ASP368B, ASP412C, ASP457C, ASP474C, ASP477C, CYS205B, CYS218B, CYS228B, CYS239B, CYS247B, CYS296B, CYS331B, CYS378B, CYS385B, CYS418C, CYS445C, GLN203B, GLN258B, GLN287B, GLN352B, GLN363B, GLN389B, GLN422C, GLN428C, GLN442C, GLU267B, GLU293B, GLU351B, GLU370B, GLU381B, GLU464C, GLU466C, GLU482C, GLU492C, GLY222B, GLY235B, GLY250B, GLY263B, GLY298B, GLY329B, GLY354B, GLY366B, GLY367B, GLY379B, GLY380B, GLY410C, GLY431C, GLY441C, GLY451C, GLY458C, GLY459C, GLY471C, GLY472C, GLY473C, HIS216B, HIS249B, HIS330B, HIS374B, ILE201B, ILE215B, ILE225B, ILE251B, ILE272B, ILE284B, ILE285B, ILE294B, ILE333B, ILE345B, ILE359B, ILE360B, ILE371B, ILE414C, ILE420C, ILE423C, ILE424C, ILE439C, ILE443C, ILE449C, ILE467C, ILE491C, LEU226B, LEU259B, LEU260B, LEU261B, LEU265B, LEU288B, LEU342B, LEU349B, LEU390B, LEU416C, LEU452C, LEU453C, LEU454C, LEU483C, LYS207B, LYS227B, LYS231B, LYS282B, LYS337B, LYS348B, LYS357B, LYS362B, LYS421C, LYS429C, LYS432C, LYS485C, LYS487C, LYS490C, MET426C, MET434C, MET475C, PHE210B, PHE223B, PHE233B, PHE277B, PHE361B, PHE376B, PHE382B, PHE383B, PHE391B, PHE396B, PHE468C, PRO206B, PRO212B, PRO220B, PRO253B, PRO369B, PRO417C, PRO437C, PRO438C, PRO470C, SER199B, SER209B, SER243B, SER256B, SER264B, SER274B, SER291B, SER334B, SER364B, SER365B, SER375B, SER387B, SER393B, SER411C, SER440C, SER446C, SER447C, SER461C, SER465C, SER481C, THR198B, THR202B, THR232B, THR236B, THR244B, THR248B, THR257B, THR278B, THR283B, THR290B, THR297B, THR341B, THR358B, THR373B, THR388B, THR394B, THR413C, THR415C, THR450C, THR455C, TRP338B, TRP395B, TRP427C, TRP479C, TYR217B, TYR384B, TYR435C, TYR484C, TYR486C, VAL200B, VAL208B, VAL242B, VAL245B, VAL254B, VAL255B, VAL270B, VAL271B, VAL275B, VAL286B, VAL292B, VAL372B, VAL430C, VAL488C, VAL489C
• D-E: ALA204E, ALA219E, ALA224E, ARG252E, ARG273E, ASN234E, ASN241E, ASN276E, ASN377E, ASN92D, ASN94D, ASP107D, ASP113D, ASP99D, CYS119D, CYS205E, CYS218E, CYS228E, CYS239E, CYS247E, CYS378E, GLN103D, GLN114D, GLN203E, GLU106D, GLU211E, GLU381E, GLU91D, GLY235E, GLY237E, GLY379E, GLY380E, HIS105D, HIS216E, HIS249E, ILE108D, ILE109D, ILE201E, ILE213E, ILE215E, ILE225E, ILE251E, ILE272E, ILE284E, ILE285E, LEU111D, LEU116D, LEU122D, LEU226E, LYS117D, LYS121D, LYS207E, LYS227E, LYS282E, LYS97D, MET100D, MET104D, MET95D, PHE210E, PHE223E, PHE233E, PHE277E, PHE376E, PHE382E, PHE93D, PRO118D, PRO124D, PRO206E, PRO212E, PRO214E, PRO220E, PRO238E, PRO253E, SER115D, SER199E, SER209E, SER243E, SER256E, SER274E, THR123D, THR198E, THR202E, THR236E, THR240E, THR244E, THR248E, THR283E, THR90D, TRP112D, TRP96D, TYR217E, VAL120D, VAL200E, VAL208E, VAL242E, VAL254E, VAL255E, VAL275E, VAL286E
• D-F: ALA433F, ALA436F, ARG476F, ARG480F, ASN425F, ASN478F, ASN92D, ASN94D, ASN98D, ASP107D, ASP113D, ASP474F, ASP477F, ASP99D, CYS119D, GLN103D, GLN114D, GLN422F, GLN428F, GLU102D, GLU106D, GLU482F, GLU91D, GLY431F, GLY473F, HIS105D, ILE108D, ILE109D, ILE423F, ILE424F, LEU111D, LEU116D, LEU122D, LEU453F, LEU483F, LYS117D, LYS121D, LYS429F, LYS432F, LYS485F, LYS487F, LYS97D, MET100D, MET104D, MET426F, MET434F, MET475F, MET95D, PHE93D, PRO118D, PRO124D, SER110D, SER115D, SER481F, THR123D, TRP112D, TRP427F, TRP479F, TRP96D, TYR435F, TYR484F, TYR486F, VAL101D, VAL120D, VAL430F, VAL488F, VAL489F
• E-F: ALA204E, ALA219E, ALA221E, ALA224E, ALA266E, ALA281E, ALA299E, ALA336E, ALA346E, ALA433F, ALA436F, ARG252E, ARG273E, ARG335E, ARG350E, ARG419F, ARG444F, ARG456F, ARG469F, ARG476F, ARG480F, ASN229E, ASN230E, ASN234E, ASN262E, ASN276E, ASN280E, ASN289E, ASN295E, ASN332E, ASN339E, ASN340E, ASN356E, ASN377E, ASN386E, ASN392E, ASN425F, ASN448F, ASN460F, ASN462F, ASN463F, ASN478F, ASP279E, ASP368E, ASP412F, ASP457F, ASP474F, ASP477F, CYS205E, CYS218E, CYS228E, CYS239E, CYS247E, CYS296E, CYS331E, CYS378E, CYS385E, CYS418F, CYS445F, GLN203E, GLN258E, GLN287E, GLN352E, GLN363E, GLN389E, GLN422F, GLN428F, GLN442F, GLU267E, GLU293E, GLU351E, GLU370E, GLU381E, GLU464F, GLU466F, GLU482F, GLU492F, GLY222E, GLY235E, GLY250E, GLY263E, GLY298E, GLY329E, GLY354E, GLY366E, GLY367E, GLY379E, GLY380E, GLY410F, GLY431F, GLY441F, GLY451F, GLY458F, GLY459F, GLY471F, GLY472F, GLY473F, HIS216E, HIS249E, HIS330E, HIS374E, ILE201E, ILE215E, ILE225E, ILE251E, ILE272E, ILE284E, ILE285E, ILE294E, ILE333E, ILE345E, ILE359E, ILE360E, ILE371E, ILE414F, ILE420F, ILE423F, ILE424F, ILE439F, ILE443F, ILE449F, ILE467F, ILE491F, LEU226E, LEU259E, LEU260E, LEU261E, LEU265E, LEU288E, LEU342E, LEU349E, LEU390E, LEU416F, LEU452F, LEU453F, LEU454F, LEU483F, LYS207E, LYS227E, LYS231E, LYS282E, LYS337E, LYS348E, LYS357E, LYS362E, LYS421F, LYS429F, LYS432F, LYS485F, LYS487F, LYS490F, MET426F, MET434F, MET475F, PHE210E, PHE223E, PHE233E, PHE277E, PHE361E, PHE376E, PHE382E, PHE383E, PHE391E, PHE396E, PHE468F, PRO206E, PRO212E, PRO220E, PRO253E, PRO369E, PRO417F, PRO437F, PRO438F, PRO470F, SER199E, SER209E, SER243E, SER256E, SER264E, SER274E, SER291E, SER334E, SER364E, SER365E, SER375E, SER387E, SER393E, SER411F, SER440F, SER446F, SER447F, SER461F, SER465F, SER481F, THR198E, THR202E, THR232E, THR236E, THR244E, THR248E, THR257E, THR278E, THR283E, THR290E, THR297E, THR341E, THR358E, THR373E, THR388E, THR394E, THR413F, THR415F, THR450F, THR455F, TRP338E, TRP395E, TRP427F, TRP479F, TYR217E, TYR384E, TYR435F, TYR484F, TYR486F, VAL200E, VAL208E, VAL242E, VAL245E, VAL254E, VAL255E, VAL270E, VAL271E, VAL275E, VAL286E, VAL292E, VAL372E, VAL430F, VAL488F, VAL489F
• G-H: ALA204H, ALA219H, ALA224H, ARG252H, ARG273H, ASN234H, ASN241H, ASN276H, ASN377H, ASN92G, ASN94G, ASP107G, ASP113G, ASP99G, CYS119G, CYS205H, CYS218H, CYS228H, CYS239H, CYS247H, CYS378H, GLN103G, GLN114G, GLN203H, GLU106G, GLU211H, GLU381H, GLU91G, GLY235H, GLY237H, GLY379H, GLY380H, HIS105G, HIS216H, HIS249H, ILE108G, ILE109G, ILE201H, ILE213H, ILE215H, ILE225H, ILE251H, ILE272H, ILE284H, ILE285H, LEU111G, LEU116G, LEU122G, LEU226H, LYS117G, LYS121G, LYS207H, LYS227H, LYS282H, LYS97G, MET100G, MET104G, MET95G, PHE210H, PHE223H, PHE233H, PHE277H, PHE376H, PHE382H, PHE93G, PRO118G, PRO124G, PRO206H, PRO212H, PRO214H, PRO220H, PRO238H, PRO253H, SER115G, SER199H, SER209H, SER243H, SER256H, SER274H, THR123G, THR198H, THR202H, THR236H, THR240H, THR244H, THR248H, THR283H, THR90G, TRP112G, TRP96G, TYR217H, VAL120G, VAL200H, VAL208H, VAL242H, VAL254H, VAL255H, VAL275H, VAL286H
• G-I: ALA433I, ALA436I, ARG476I, ARG480I, ASN425I, ASN478I, ASN92G, ASN94G, ASN98G, ASP107G, ASP113G, ASP474I, ASP477I, ASP99G, CYS119G, GLN103G, GLN114G, GLN422I, GLN428I, GLU102G, GLU106G, GLU482I, GLU91G, GLY431I, GLY473I, HIS105G, ILE108G, ILE109G, ILE423I, ILE424I, LEU111G, LEU116G, LEU122G, LEU453I, LEU483I, LYS117G, LYS121G, LYS429I, LYS432I, LYS485I, LYS487I, LYS97G, MET100G, MET104G, MET426I, MET434I, MET475I, MET95G, PHE93G, PRO118G, PRO124G, SER110G, SER115G, SER481I, THR123G, TRP112G, TRP427I, TRP479I, TRP96G, TYR435I, TYR484I, TYR486I, VAL101G, VAL120G, VAL430I, VAL488I, VAL489I
• H-I: ALA204H, ALA219H, ALA221H, ALA224H, ALA266H, ALA281H, ALA299H, ALA336H, ALA346H, ALA433I, ALA436I, ARG252H, ARG273H, ARG335H, ARG350H, ARG419I, ARG444I, ARG456I, ARG469I, ARG476I, ARG480I, ASN229H, ASN230H, ASN234H, ASN262H, ASN276H, ASN280H, ASN289H, ASN295H, ASN332H, ASN339H, ASN340H, ASN356H, ASN377H, ASN386H, ASN392H, ASN425I, ASN448I, ASN460I, ASN462I, ASN463I, ASN478I, ASP279H, ASP368H, ASP412I, ASP457I, ASP474I, ASP477I, CYS205H, CYS218H, CYS228H, CYS239H, CYS247H, CYS296H, CYS331H, CYS378H, CYS385H, CYS418I, CYS445I, GLN203H, GLN258H, GLN287H, GLN352H, GLN363H, GLN389H, GLN422I, GLN428I, GLN442I, GLU267H, GLU293H, GLU351H, GLU370H, GLU381H, GLU464I, GLU466I, GLU482I, GLU492I, GLY222H, GLY235H, GLY250H, GLY263H, GLY298H, GLY329H, GLY354H, GLY366H, GLY367H, GLY379H, GLY380H, GLY410I, GLY431I, GLY441I, GLY451I, GLY458I, GLY459I, GLY471I, GLY472I, GLY473I, HIS216H, HIS249H, HIS330H, HIS374H, ILE201H, ILE215H, ILE225H, ILE251H, ILE272H, ILE284H, ILE285H, ILE294H, ILE333H, ILE345H, ILE359H, ILE360H, ILE371H, ILE414I, ILE420I, ILE423I, ILE424I, ILE439I, ILE443I, ILE449I, ILE467I, ILE491I, LEU226H, LEU259H, LEU260H, LEU261H, LEU265H, LEU288H, LEU342H, LEU349H, LEU390H, LEU416I, LEU452I, LEU453I, LEU454I, LEU483I, LYS207H, LYS227H, LYS231H, LYS282H, LYS337H, LYS348H, LYS357H, LYS362H, LYS421I, LYS429I, LYS432I, LYS485I, LYS487I, LYS490I, MET426I, MET434I, MET475I, PHE210H, PHE223H, PHE233H, PHE277H, PHE361H, PHE376H, PHE382H, PHE383H, PHE391H, PHE396H, PHE468I, PRO206H, PRO212H, PRO220H, PRO253H, PRO369H, PRO417I, PRO437I, PRO438I, PRO470I, SER199H, SER209H, SER243H, SER256H, SER264H, SER274H, SER291H, SER334H, SER364H, SER365H, SER375H, SER387H, SER393H, SER411I, SER440I, SER446I, SER447I, SER461I, SER465I, SER481I, THR198H, THR202H, THR232H, THR236H, THR244H, THR248H, THR257H, THR278H, THR283H, THR290H, THR297H, THR341H, THR358H, THR373H, THR388H, THR394H, THR413I, THR415I, THR450I, THR455I, TRP338H, TRP395H, TRP427I, TRP479I, TYR217H, TYR384H, TYR435I, TYR484I, TYR486I, VAL200H, VAL208H, VAL242H, VAL245H, VAL254H, VAL255H, VAL270H, VAL271H, VAL275H, VAL286H, VAL292H, VAL372H, VAL430I, VAL488I, VAL489I