2Q9I

crystal structure of d-dimer from human fibrin complexed with met-his- arg-pro-tyr-amide.

• Total interactions analyzed: 45
• Total true interactions: 11
• Strongest Interaction:
  • Chains: C-S
  • Int. Res.: 50
  • Norm. En. per Res.: -4.2098
• 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	-65.029	-110.8378	294.705	118.8382	142	74	15	20381	7	61	58
A-C	-7.5096	-10.8506	604.134	585.7738	78	27	8	7338	3	23	13
B-C	-83.9041	-42.0945	264.239	138.2404	189	45	19	20636	6	41	44
B-M	-39.3778	-24.5868	-139.882	-203.8466	52	18	0	5318	3	15	14
C-F	0.0	17.4796	-84.6561	-67.1765	65	1	1	4061	0	20	18
C-S	-26.6292	-56.0832	-127.778	-210.4904	50	15	0	4659	4	18	16
D-E	-59.0013	-97.034	285.177	129.1418	127	40	11	18068	5	58	52
D-F	-4.4346	-6.2799	655.116	644.4015	61	11	3	5044	1	16	9
E-F	-99.6208	-42.8048	286.786	144.3604	175	51	18	19097	4	38	36
E-N	-29.7704	-26.1334	-128.214	-184.1178	52	11	0	4903	3	15	14
F-T	-33.3895	-12.6087	-91.4131	-137.4113	48	17	0	4509	3	19	16

Interface residues

• A-B: ALA142A, ALA168A, ALA170A, ALA188B, ALA190A, ALA427B, ARG141A, ARG149A, ARG159A, ARG162A, ARG166B, ARG167A, ARG169B, ARG171A, ARG176B, ARG194B, ARG255B, ARG264B, ARG415B, ASN139A, ASN158B, ASN160B, ASN164B, ASN174B, ASN275B, ASP146A, ASP153A, ASP155A, ASP174A, ASP177A, ASP180A, ASP185B, ASP192A, ASP257B, ASP261B, ASP425B, ASP433B, CYS161A, CYS165A, CYS193B, CYS197B, GLN134A, GLN137A, GLN143A, GLN180B, GLN181A, GLN182A, GLN184A, GLN187A, GLN189B, GLN256B, GLN421B, GLU151A, GLU172A, GLU179A, GLU183B, GLU186A, GLU191B, GLU291B, GLY163A, GLY258B, GLY263B, GLY274B, GLY290B, GLY414B, GLY419B, GLY430B, GLY434B, HIS132A, HIS429B, ILE127A, ILE133A, ILE154A, ILE156A, ILE158A, ILE161B, ILE171B, ILE179B, ILE189A, LEU135A, LEU136A, LEU144A, LEU150A, LEU165B, LEU168B, LEU169A, LEU172B, LEU175A, LEU175B, LEU182B, LEU185A, LYS129A, LYS138A, LYS148A, LYS157A, LYS176A, LYS178B, LYS181B, LYS183A, LYS191A, LYS428B, MET147A, MET190B, MET426B, PHE262B, PRO162B, PRO196B, SER159B, SER160A, SER164A, SER166A, SER170B, SER177B, SER184B, SER187B, SER259B, SER446B, THR163B, THR195B, THR198B, THR278B, THR423B, THR431B, TRP317B, TRP418B, TRP424B, TYR178A, TYR192B, TYR416B, TYR417B, TYR422B, VAL126A, VAL130A, VAL140A, VAL145A, VAL152A, VAL167B, VAL173A, VAL186B, VAL188A, VAL260B, VAL435B
• A-C: ALA129C, ALA133C, ALA142A, ALA168A, ARG108C, ARG141A, ARG149A, ARG159A, ARG162A, ARG171A, ASN115C, ASN117C, ASN118C, ASN123C, ASN139A, ASP104C, ASP146A, ASP153A, ASP155A, CYS135C, CYS139C, CYS161A, CYS165A, GLN111C, GLN119C, GLN130C, GLN131A, GLN134C, GLN136C, GLN137A, GLN143A, GLU112C, GLU126C, GLU128A, GLU132C, GLU137C, GLU151A, GLY163A, HIS103C, HIS132A, ILE107C, ILE113C, ILE121C, ILE133A, ILE154A, ILE156A, ILE158A, LEU110C, LEU124C, LEU131C, LEU135A, LEU136A, LEU144A, LEU150A, LEU169A, LYS120C, LYS125C, LYS127C, LYS129A, LYS138A, LYS140C, LYS148A, LYS157A, MET147A, PRO138C, SER105C, SER106C, SER116C, SER160A, SER164A, THR102C, TYR109C, TYR114C, VAL122C, VAL126A, VAL128C, VAL130A, VAL140A
• B-C: ALA129C, ALA133C, ALA188B, ALA277B, ARG108C, ARG166B, ARG169B, ARG176B, ARG194B, ARG216B, ARG237B, ARG264B, ARG415B, ASN115C, ASN117C, ASN118C, ASN123C, ASN174B, ASN175C, ASN202B, ASN207C, ASN230C, ASN275B, ASN279B, ASN284B, ASP104C, ASP141C, ASP147C, ASP185B, ASP199C, ASP203C, ASP230B, ASP261B, CYS135C, CYS139C, CYS193B, CYS197B, CYS201B, CYS286B, GLN111C, GLN119C, GLN130C, GLN134C, GLN136C, GLN144C, GLN176C, GLN177C, GLN180B, GLN189B, GLN195C, GLN210C, GLN228B, GLU112C, GLU126C, GLU132C, GLU137C, GLU173B, GLU183B, GLU191B, GLU213B, GLU213C, GLU220B, GLU223B, GLU225C, GLU291B, GLY200C, GLY208B, GLY214C, GLY216C, GLY218B, GLY219B, GLY222C, GLY229C, GLY263B, GLY272B, GLY274B, GLY287B, GLY290B, HIS103C, HIS146C, HIS217C, ILE107C, ILE113C, ILE121C, ILE145C, ILE171B, ILE179B, ILE203B, ILE209C, ILE214B, ILE215B, ILE227B, ILE233C, LEU110C, LEU124C, LEU131C, LEU165B, LEU166C, LEU168B, LEU172B, LEU175B, LEU179C, LEU182B, LEU198C, LEU218C, LEU226B, LEU228C, LYS120C, LYS125C, LYS127C, LYS140C, LYS170C, LYS178B, LYS181B, LYS205C, LYS206C, LYS209B, LYS212C, LYS217B, LYS232C, LYS234B, LYS265B, LYS283B, LYS428B, MET190B, MET224B, PHE168C, PHE178C, PHE194C, PHE215C, PHE226C, PHE262B, PHE273B, PRO138C, PRO162B, PRO196B, PRO204B, PRO220C, PRO229B, PRO235B, PRO268B, SER105C, SER106C, SER116C, SER159B, SER170B, SER177B, SER184B, SER187B, SER200B, SER201C, SER207B, SER219C, SER231B, SER232B, SER259B, THR142C, THR163B, THR195B, THR198B, THR221B, THR221C, THR223C, THR224C, THR278B, TRP227C, TYR109C, TYR114C, TYR181C, TYR192B, TYR211C, TYR225B, TYR236B, TYR285B, TYR292B, TYR378B, VAL122C, VAL128C, VAL143C, VAL167B, VAL180C, VAL186B, VAL199B, VAL202C, VAL205B, VAL206B, VAL233B, VAL260B, VAL276B
• B-M: ALA357B, ALA409B, ALA410B, ARG365B, ARG3M, ARG406B, ASN364B, ASN405B, ASN411B, ASN439B, ASP383B, ASP398B, ASP432B, ASP433B, CYS394B, CYS407B, GLN359B, GLN393B, GLU363B, GLU397B, GLY356B, GLY362B, GLY384B, GLY399B, GLY430B, GLY434B, HIS2M, HIS370B, HIS408B, HIS429B, LEU360B, LEU386B, LYS392B, LYS396B, MET1M, MET361B, MET367B, MET438B, PRO4M, SER395B, SER443B, THR366B, THR368B, THR387B, THR431B, TRP385B, TRP424B, TRP444B, TYR404B, TYR422B, TYR5M, VAL436B
• C-F: ALA241C, ALA263C, ALA271C, ALA279C, ALA279F, ARG275C, ARG275F, ASN308C, ASN308F, ASN390C, ASP272C, ASP272F, ASP288C, ASP291C, ASP291F, ASP298F, ASP301F, ASP320F, GLN311C, GLN311F, GLU270C, GLU323F, GLY268C, GLY309C, GLY309F, HIS307C, HIS307F, ILE242C, LEU276C, LEU276F, LEU392C, LYS266C, LYS266F, LYS273C, LYS302C, LYS302F, LYS321C, LYS321F, LYS338F, MET264C, MET264F, MET310C, MET310F, PHE281C, PHE281F, PHE290C, PHE303C, PHE303F, PHE304F, PHE389C, PHE389F, PRO243C, PRO269C, PRO299F, SER300F, SER306C, SER306F, THR238C, THR277C, THR277F, THR393C, TYR278C, TYR278F, TYR280C, TYR280F
• C-S: ALA327C, ALA341C, ALA370C, ARG375C, ARG3S, ASN325C, ASN337C, ASN361C, ASN365C, ASP294C, ASP297C, ASP298C, ASP301C, ASP320C, ASP330C, ASP364C, CYS326C, CYS339C, GLN329C, GLU323C, GLU328C, GLY1S, GLY296C, GLY324C, GLY331C, GLY342C, GLY362C, GLY366C, HIS2S, HIS307C, HIS340C, HIS343C, ILE368C, LYS302C, LYS321C, LYS338C, MET336C, PHE293C, PHE295C, PHE303C, PHE304C, PHE322C, PRO299C, PRO360C, PRO4S, SER300C, THR305C, TRP376C, TYR354C, TYR363C
• D-E: ALA142D, ALA168D, ALA170D, ALA188E, ALA427E, ARG141D, ARG149D, ARG159D, ARG162D, ARG166E, ARG167D, ARG169E, ARG171D, ARG176E, ARG194E, ARG255E, ARG264E, ARG415E, ASN139D, ASN164E, ASN174E, ASN275E, ASP146D, ASP153D, ASP155D, ASP174D, ASP177D, ASP180D, ASP185E, ASP257E, ASP261E, ASP425E, ASP433E, CYS161D, CYS165D, CYS193E, CYS197E, GLN137D, GLN143D, GLN180E, GLN181D, GLN182D, GLN184D, GLN187D, GLN189E, GLN256E, GLN421E, GLU151D, GLU172D, GLU173E, GLU179D, GLU183E, GLU186D, GLU191E, GLU291E, GLY163D, GLY258E, GLY263E, GLY274E, GLY290E, GLY414E, GLY419E, GLY430E, GLY434E, HIS429E, ILE154D, ILE156D, ILE158D, ILE171E, ILE179E, LEU136D, LEU144D, LEU150D, LEU165E, LEU168E, LEU169D, LEU172E, LEU175D, LEU175E, LEU182E, LEU185D, LYS138D, LYS148D, LYS157D, LYS176D, LYS178E, LYS181E, LYS183D, LYS428E, MET147D, MET190E, MET426E, PHE262E, PRO196E, SER160D, SER164D, SER166D, SER170E, SER177E, SER184E, SER187E, SER259E, SER446E, THR195E, THR198E, THR278E, THR423E, THR431E, TRP317E, TRP418E, TRP424E, TRP444E, TYR178D, TYR192E, TYR416E, TYR417E, TYR422E, VAL140D, VAL145D, VAL152D, VAL167E, VAL173D, VAL186E, VAL188D, VAL199E, VAL260E, VAL435E
• D-F: ALA129F, ALA133F, ALA142D, ARG141D, ARG149D, ARG159D, ARG162D, ARG167D, ARG171D, ASN115F, ASN117F, ASN118F, ASN123F, ASN139D, ASP146D, ASP153D, CYS135F, CYS139F, CYS161D, CYS165D, GLN111F, GLN119F, GLN130F, GLN134F, GLN136F, GLN137D, GLN143D, GLU126F, GLU132F, GLU137F, GLU151D, GLY163D, ILE113F, ILE121F, ILE154D, ILE158D, LEU110F, LEU124F, LEU131F, LEU136D, LEU144D, LEU150D, LEU169D, LEU185D, LYS120F, LYS125F, LYS127F, LYS138D, LYS140F, LYS148D, LYS157D, MET147D, PRO138F, SER160D, SER164D, SER166D, TYR114F, TYR178D, VAL122F, VAL128F, VAL140D
• E-F: ALA129F, ALA133F, ALA188E, ALA277E, ARG166E, ARG169E, ARG176E, ARG194E, ARG216E, ARG237E, ARG264E, ARG415E, ASN115F, ASN117F, ASN118F, ASN123F, ASN174E, ASN175F, ASN202E, ASN207F, ASN230F, ASN275E, ASN279E, ASN284E, ASP141F, ASP147F, ASP185E, ASP199F, ASP203F, ASP230E, ASP261E, CYS135F, CYS139F, CYS193E, CYS197E, CYS201E, CYS286E, GLN111F, GLN119F, GLN130F, GLN134F, GLN136F, GLN144F, GLN176F, GLN177F, GLN180E, GLN189E, GLN195F, GLN210F, GLN228E, GLU112F, GLU126F, GLU132F, GLU137F, GLU173E, GLU183E, GLU191E, GLU213E, GLU213F, GLU220E, GLU223E, GLU225F, GLU231F, GLU291E, GLY208E, GLY214F, GLY216F, GLY218E, GLY219E, GLY222F, GLY229F, GLY263E, GLY272E, GLY274E, GLY287E, HIS146F, HIS217F, ILE113F, ILE121F, ILE145F, ILE171E, ILE179E, ILE203E, ILE209F, ILE214E, ILE215E, ILE227E, LEU110F, LEU124F, LEU131F, LEU166F, LEU168E, LEU172E, LEU175E, LEU179F, LEU182E, LEU198F, LEU218F, LEU226E, LEU228F, LYS120F, LYS125F, LYS127F, LYS140F, LYS170F, LYS178E, LYS181E, LYS206F, LYS209E, LYS212F, LYS217E, LYS232F, LYS234E, LYS265E, LYS283E, LYS428E, MET190E, MET224E, PHE168F, PHE178F, PHE194F, PHE215F, PHE226F, PHE262E, PHE273E, PRO138F, PRO196E, PRO204E, PRO220F, PRO229E, PRO235E, PRO268E, SER116F, SER177E, SER184E, SER187E, SER200E, SER201F, SER207E, SER219F, SER231E, SER232E, SER259E, THR142F, THR195E, THR198E, THR221E, THR221F, THR223F, THR224F, THR278E, TRP227F, TYR109F, TYR114F, TYR167F, TYR181F, TYR192E, TYR211F, TYR225E, TYR236E, TYR285E, TYR292E, TYR378E, VAL122F, VAL128F, VAL143F, VAL180F, VAL186E, VAL199E, VAL202F, VAL205E, VAL206E, VAL233E, VAL260E, VAL276E
• E-N: ALA357E, ALA409E, ALA410E, ARG365E, ARG391E, ARG3N, ARG406E, ASN364E, ASN405E, ASN411E, ASN439E, ASP383E, ASP398E, ASP432E, ASP433E, CYS394E, CYS407E, GLN359E, GLN393E, GLU363E, GLU397E, GLY356E, GLY384E, GLY399E, GLY430E, GLY442E, HIS2N, HIS370E, HIS408E, HIS429E, LEU360E, LEU386E, LYS392E, LYS396E, MET1N, MET361E, MET367E, MET438E, PRO4N, SER395E, SER443E, THR366E, THR368E, THR387E, THR431E, TRP385E, TRP424E, TRP444E, TYR404E, TYR422E, TYR5N, VAL436E
• F-T: ALA327F, ALA341F, ALA370F, ARG375F, ARG3T, ASN325F, ASN337F, ASN361F, ASN365F, ASP294F, ASP297F, ASP298F, ASP301F, ASP320F, ASP330F, ASP364F, CYS326F, CYS339F, GLN329F, GLU323F, GLU328F, GLY1T, GLY296F, GLY324F, GLY331F, GLY342F, GLY362F, GLY366F, HIS2T, HIS307F, HIS340F, HIS343F, ILE368F, LYS302F, LYS321F, LYS338F, MET336F, PHE293F, PHE295F, PHE304F, PHE322F, PRO360F, PRO4T, SER300F, THR305F, TRP376F, TYR354F, TYR363F