3KUY

dna stretching in the nucleosome facilitates alkylation by an intercalating antitumor agent

• Total interactions analyzed: 45
• Total true interactions: 23
• Strongest Interaction:
  • Chains: E-F
  • Int. Res.: 157
  • Norm. En. per Res.: -5.7332
• Hub Node: A(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
A-B	-117.9107	-41.0736	-708.503	-867.4873	156	39	43	30549	2	57	64
A-C	0.0	0.0	-2.6116	-2.6116	11	0	0	178	0	2	5
A-E	-21.8071	-77.7058	-158.566	-258.0789	59	6	7	6875	4	23	35
A-G	-48.5009	0.9978	-131.088	-178.5911	72	7	4	5950	0	7	9
A-H	0.0	0.0	-0.0124	-0.0124	4	0	0	12	0	2	0
B-C	0.0	0.0	-0.3533	-0.3533	7	0	0	72	0	2	3
B-D	-19.8456	-30.2496	-137.024	-187.1192	53	7	1	4898	2	19	25
B-G	-42.9094	2.6333	-96.2869	-136.563	47	5	5	3955	0	0	6
B-H	-18.0534	-20.0755	-70.5087	-108.6376	29	1	2	2398	1	5	2
C-D	-109.9417	-68.6448	-737.659	-916.2455	172	34	48	30364	7	44	44
C-E	-32.0416	0.9782	-140.837	-171.9004	71	6	5	6226	0	8	8
C-F	-38.3786	2.8519	-92.8712	-128.3979	49	3	5	3908	0	0	6
C-G	-7.6535	-2.0644	-25.8338	-35.5517	19	1	0	925	0	7	4
C-H	0.0	1.4907	-8.4345	-6.9437	11	0	0	316	0	0	8
D-E	0.0	0.0	-0.0733	-0.0733	5	0	0	34	0	2	0
D-F	0.0	-18.7929	-69.8763	-88.6692	27	1	2	2303	2	5	1
D-G	0.0	0.0	-10.1384	-10.1384	13	0	0	326	0	0	8
D-H	0.0	-2.3482	-0.9737	-3.3219	16	0	0	180	0	11	9
E-F	-108.1323	-53.6814	-738.303	-900.1167	157	29	45	31423	1	66	73
E-G	0.0	0.0	-4.1242	-4.1242	11	0	0	221	0	2	5
F-G	0.0	0.0	-0.1029	-0.1029	8	0	0	47	0	2	3
F-H	-29.7403	-14.5985	-135.318	-179.6568	49	5	2	4921	1	18	25
G-H	-91.5447	-68.6745	-722.723	-882.9422	174	30	47	29597	7	47	42

Interface residues

• A-B: ALA102A, ALA111A, ALA127A, ALA33B, ALA38B, ALA47A, ALA69B, ALA75A, ALA76B, ALA83B, ALA88A, ALA89B, ALA91A, ALA95A, ALA98A, ARG116A, ARG128A, ARG131A, ARG23B, ARG35B, ARG36B, ARG39B, ARG40B, ARG45B, ARG49A, ARG52A, ARG53A, ARG55B, ARG63A, ARG67B, ARG69A, ARG72A, ARG78B, ARG83A, ARG95B, ASN108A, ASN25B, ASN64B, ASP106A, ASP123A, ASP24B, ASP68B, ASP77A, ASP81A, ASP85B, GLN125A, GLN27B, GLN55A, GLN68A, GLN76A, GLN85A, GLN93A, GLN93B, GLU105A, GLU133A, GLU50A, GLU52B, GLU53B, GLU59A, GLU63B, GLU73A, GLU74B, GLU94A, GLU97A, GLY101B, GLY28B, GLY41B, GLY42B, GLY44A, GLY48B, GLY56B, GLY99B, HIS75B, ILE112A, ILE119A, ILE124A, ILE26B, ILE29B, ILE34B, ILE46B, ILE50B, ILE51A, ILE62A, ILE66B, ILE74A, LEU100A, LEU103A, LEU109A, LEU37B, LEU48A, LEU49B, LEU58B, LEU60A, LEU61A, LEU62B, LEU65A, LEU70A, LEU82A, LEU90B, LEU92A, LEU97B, LYS122A, LYS44B, LYS56A, LYS59B, LYS64A, LYS77B, LYS79A, LYS79B, MET120A, MET84B, MET90A, PHE100B, PHE104A, PHE61B, PHE67A, PHE78A, PHE84A, PRO121A, PRO32B, PRO43A, PRO66A, SER47B, SER57A, SER86A, SER87A, SER96A, THR107A, THR118A, THR30B, THR45A, THR54B, THR58A, THR71B, THR73B, THR80A, THR80B, THR82B, THR96B, TYR51B, TYR54A, TYR98B, TYR99A, VAL101A, VAL117A, VAL43B, VAL46A, VAL57B, VAL60B, VAL65B, VAL70B, VAL71A, VAL81B, VAL86B, VAL87B, VAL89A
• A-C: ARG128A, ARG129A, ARG131A, ARG99C, ASN110C, GLN112C, GLU133A, GLY132A, GLY98C, ILE130A, LYS95C
• A-E: ALA102A, ALA102E, ALA111A, ALA111E, ALA114A, ALA114E, ALA127A, ALA127E, ARG116A, ARG116E, ARG128A, ARG128E, ARG129A, ARG129E, ARG131A, ARG131E, ASN108A, ASN108E, ASP106A, ASP106E, ASP123A, ASP123E, CYS110A, CYS110E, GLN125A, GLN125E, GLU105A, GLU105E, GLU133A, GLY132A, GLY132E, HIS113A, HIS113E, ILE112A, ILE112E, ILE119A, ILE119E, ILE124A, ILE124E, ILE130A, ILE130E, LEU103A, LEU103E, LEU109A, LEU109E, LEU126A, LEU126E, LYS115A, LYS115E, LYS122A, LYS122E, MET120A, MET120E, PHE104E, PRO121A, PRO121E, THR107A, THR107E, THR118E
• A-G: ALA102A, ALA103G, ALA111A, ALA47A, ALA91A, ALA95A, ALA98A, ARG116A, ARG131A, ARG42A, ARG49A, ARG52A, ARG53A, ARG81G, ARG88G, ARG99G, ASN108A, ASN110G, ASP106A, GLN104G, GLN112G, GLN55A, GLN84G, GLN93A, GLU105A, GLU50A, GLU59A, GLU94A, GLU97A, GLY105G, GLY106G, GLY44A, HIS113A, HIS82G, ILE102G, ILE111G, ILE112A, ILE119A, ILE51A, ILE79G, LEU108G, LEU109A, LEU115G, LEU116G, LEU48A, LEU60A, LEU61A, LEU85G, LYS115A, LYS118G, LYS119G, LYS56A, LYS64A, MET90A, PRO109G, PRO117G, PRO43A, PRO80G, SER113G, SER57A, SER96A, THR101G, THR118A, THR45A, THR58A, TYR54A, TYR99A, VAL100G, VAL101A, VAL107G, VAL114G, VAL117A
• A-H: GLU94A, LYS54H, LYS64A, MET90A
• B-C: ARG67B, ARG99C, ASN64B, GLN93B, GLY94B, LYS95C, VAL60B
• B-D: ALA104D, ALA69B, ALA74D, ALA76B, ALA78D, ALA89B, ALA94D, ARG67B, ARG69D, ARG76D, ARG78B, ARG83D, ARG89D, ARG92B, ARG96D, ASN64B, ASN81D, ASP68B, ASP85B, GLN92D, GLN93B, GLU73D, GLU74B, GLU90D, GLY101D, GLY102B, HIS75B, HIS79D, ILE66B, ILE70D, ILE86D, ILE91D, LEU77D, LEU97D, LEU98D, LEU99D, LYS77B, LYS82D, LYS91B, MET84B, PRO100D, SER88D, THR71B, THR73B, THR85D, THR87D, THR93D, TYR72B, TYR80D, TYR88B, VAL70B, VAL87B, VAL95D
• B-G: ALA103G, ARG39B, ARG40B, ARG45B, ARG81G, ARG88G, ARG95B, ARG99G, ASN110G, GLN104G, GLN112G, GLN93B, GLY105G, GLY106G, GLY41B, GLY42B, GLY94B, GLY98G, GLY99B, ILE102G, ILE111G, ILE62G, LEU108G, LEU115G, LEU116G, LEU37B, LEU83G, LEU90B, LEU96G, LEU97B, LEU97G, LYS118G, LYS44B, LYS91B, PHE100B, PRO109G, PRO117G, PRO80G, SER113G, THR101G, THR96B, TYR98B, VAL100G, VAL107G, VAL114G, VAL43B, VAL87G
• B-H: ALA55H, ARG69H, ASN60H, ASN64H, ASP65H, GLU68H, GLY101B, GLY102B, GLY99B, ILE58H, LEU97B, LYS31H, LYS54H, LYS91B, MET56H, MET59H, MET84B, PHE100B, PHE62H, SER53H, SER57H, SER61H, THR96B, TYR34H, TYR88B, TYR98B, VAL63H, VAL66H, VAL87B
• C-D: ALA103C, ALA104D, ALA107D, ALA114D, ALA121D, ALA21C, ALA35D, ALA40C, ALA45C, ALA47C, ALA52C, ALA53C, ALA55D, ALA60C, ALA66C, ALA69C, ALA70C, ALA71D, ALA74D, ALA78D, ALA94D, ARG17C, ARG20C, ARG29C, ARG30D, ARG32C, ARG35C, ARG42C, ARG69D, ARG71C, ARG76D, ARG77C, ARG81C, ARG83D, ARG89D, ARG96D, ARG99C, ASN38C, ASN60D, ASN64D, ASN68C, ASN94C, ASP48D, ASP65D, ASP90C, GLN104C, GLN24C, GLN44D, GLN84C, GLN92D, GLU102D, GLU110D, GLU32D, GLU41C, GLU56C, GLU61C, GLU64C, GLU68D, GLU73D, GLU90D, GLU91C, GLU92C, GLY101D, GLY105C, GLY111D, GLY22C, GLY28C, GLY37C, GLY44C, GLY46C, GLY50D, GLY67C, GLY72D, GLY98C, HIS106D, HIS31C, HIS46D, HIS79D, HIS82C, ILE102C, ILE36D, ILE51D, ILE58D, ILE62C, ILE70D, ILE78C, ILE79C, ILE86D, ILE91D, LEU103D, LEU23C, LEU33C, LEU34C, LEU42D, LEU51C, LEU55C, LEU58C, LEU63C, LEU65C, LEU83C, LEU93C, LEU96C, LEU97C, LEU98D, LEU99D, LYS105D, LYS113D, LYS117D, LYS122D, LYS15C, LYS31D, LYS36C, LYS40D, LYS43D, LYS54D, LYS75C, LYS95C, MET56D, MET59D, PHE25C, PHE62D, PHE67D, PRO100D, PRO26C, PRO47D, PRO48C, PRO80C, SER109D, SER120D, SER18C, SER19C, SER33D, SER52D, SER53D, SER57D, SER61D, SER75D, SER84D, SER88D, THR101C, THR112D, THR116D, THR119D, THR16C, THR49D, THR59C, THR76C, THR85D, THR87D, THR93D, TYR118D, TYR34D, TYR37D, TYR39C, TYR39D, TYR50C, TYR57C, VAL100C, VAL108D, VAL115D, VAL27C, VAL30C, VAL38D, VAL41D, VAL43C, VAL45D, VAL49C, VAL54C, VAL63D, VAL66D, VAL87C, VAL95D
• C-E: ALA102E, ALA103C, ALA111E, ALA47E, ALA91E, ALA95E, ALA98E, ARG116E, ARG131E, ARG42E, ARG49E, ARG52E, ARG53E, ARG81C, ARG99C, ASN108E, ASN110C, ASN73C, GLN104C, GLN112C, GLN55E, GLN84C, GLN93E, GLU105E, GLU50E, GLU59E, GLU94E, GLU97E, GLY105C, GLY106C, GLY44E, HIS113E, HIS82C, ILE102C, ILE111C, ILE112E, ILE119E, ILE51E, ILE79C, LEU108C, LEU109E, LEU115C, LEU116C, LEU48E, LEU60E, LEU61E, LEU85C, LYS115E, LYS118C, LYS119C, LYS56E, LYS64E, MET90E, PRO109C, PRO117C, PRO43E, PRO80C, SER113C, SER57E, SER96E, THR101C, THR118E, THR45E, THR58E, TYR54E, TYR99E, VAL100C, VAL101E, VAL107C, VAL114C, VAL117E
• C-F: ALA103C, ARG39F, ARG40F, ARG45F, ARG81C, ARG88C, ARG95F, ARG99C, ASN110C, GLN104C, GLN112C, GLN84C, GLN93F, GLY102F, GLY105C, GLY106C, GLY41F, GLY42F, GLY94F, GLY98C, GLY99F, ILE102C, ILE111C, ILE62C, LEU108C, LEU115C, LEU116C, LEU37F, LEU83C, LEU90F, LEU96C, LEU97C, LEU97F, LYS118C, LYS44F, LYS91F, PHE100F, PRO109C, PRO117C, PRO80C, SER113C, THR101C, THR96F, TYR98F, VAL100C, VAL107C, VAL114C, VAL43F, VAL87C
• C-G: ALA40C, ALA40G, ARG35C, ARG35G, ARG42C, ARG42G, ARG99C, ARG99G, ASN38C, ASN38G, GLU41C, GLU41G, GLY37C, GLY37G, LYS36C, LYS36G, TYR39C, TYR39G, VAL43C
• C-H: ARG35C, ARG76H, ARG83H, ASN38C, GLY37C, HIS79H, LYS36C, LYS82H, SER75H, SER84H, TYR39C
• D-E: GLU94E, LEU60E, LYS54D, LYS64E, MET90E
• D-F: ALA55D, ARG69D, ASN60D, ASN64D, ASP65D, GLU68D, GLY101F, GLY102F, GLY99F, ILE58D, LEU97F, LYS54D, LYS91F, MET56D, MET59D, MET84F, PHE100F, PHE62D, SER53D, SER57D, SER61D, THR96F, TYR88F, TYR98F, VAL63D, VAL66D, VAL87F
• D-G: ALA78D, ARG35G, ARG76D, ARG83D, ASN38G, GLY37G, HIS79D, ILE86D, LYS36G, SER75D, SER84D, TYR39G, TYR80D
• D-H: ARG30D, ARG30H, ARG76D, ARG76H, GLU32H, GLU68D, GLU68H, HIS79D, LYS31D, LYS31H, LYS82D, LYS82H, THR29D, THR29H, TYR80D, TYR80H
• E-F: ALA102E, ALA111E, ALA127E, ALA33F, ALA38F, ALA47E, ALA69F, ALA75E, ALA83F, ALA88E, ALA89F, ALA91E, ALA95E, ALA98E, ARG116E, ARG128E, ARG131E, ARG19F, ARG23F, ARG35F, ARG36F, ARG39F, ARG40F, ARG42E, ARG45F, ARG49E, ARG52E, ARG53E, ARG55F, ARG63E, ARG67F, ARG69E, ARG72E, ARG78F, ARG83E, ARG95F, ASN108E, ASN25F, ASN64F, ASP106E, ASP123E, ASP24F, ASP68F, ASP77E, ASP81E, ASP85F, GLN125E, GLN27F, GLN55E, GLN68E, GLN76E, GLN85E, GLN93E, GLU105E, GLU133E, GLU50E, GLU52F, GLU53F, GLU59E, GLU63F, GLU73E, GLU74F, GLU94E, GLU97E, GLY101F, GLY28F, GLY41F, GLY42F, GLY44E, GLY48F, GLY56F, GLY99F, ILE112E, ILE119E, ILE124E, ILE26F, ILE29F, ILE34F, ILE46F, ILE50F, ILE51E, ILE62E, ILE66F, ILE74E, LEU100E, LEU103E, LEU109E, LEU22F, LEU37F, LEU48E, LEU49F, LEU58F, LEU60E, LEU61E, LEU62F, LEU65E, LEU70E, LEU82E, LEU90F, LEU92E, LEU97F, LYS122E, LYS16F, LYS20F, LYS44F, LYS56E, LYS59F, LYS79E, LYS79F, MET120E, MET84F, MET90E, PHE100F, PHE104E, PHE61F, PHE67E, PHE78E, PHE84E, PRO121E, PRO32F, PRO43E, PRO66E, SER47F, SER57E, SER86E, SER87E, SER96E, THR107E, THR118E, THR30F, THR45E, THR54F, THR58E, THR71F, THR73F, THR80E, THR80F, THR82F, THR96F, TYR51F, TYR54E, TYR98F, TYR99E, VAL101E, VAL117E, VAL21F, VAL43F, VAL46E, VAL57F, VAL60F, VAL65F, VAL70F, VAL71E, VAL81F, VAL86F, VAL87F, VAL89E
• E-G: ARG128E, ARG129E, ARG131E, ARG99G, ASN110G, GLN112G, GLU133E, GLY132E, GLY98G, ILE130E, LYS95G
• F-G: ARG67F, ARG92F, ARG99G, ASN64F, GLN93F, GLY94F, LEU96G, LYS95G
• F-H: ALA69F, ALA74H, ALA76F, ALA78H, ALA89F, ALA94H, ARG67F, ARG69H, ARG76H, ARG78F, ARG83H, ARG89H, ARG92F, ARG96H, ASN64F, ASN81H, ASP68F, ASP85F, GLN92H, GLN93F, GLU73H, GLU74F, GLU90H, GLY101H, HIS75F, HIS79H, ILE86H, ILE91H, LEU77H, LEU97H, LEU98H, LEU99H, LYS77F, LYS82H, LYS91F, MET84F, PRO100H, SER88H, THR71F, THR73F, THR85H, THR87H, THR93H, TYR72F, TYR80H, TYR88F, VAL70F, VAL87F, VAL95H
• G-H: ALA103G, ALA104H, ALA107H, ALA114H, ALA121H, ALA14G, ALA21G, ALA35H, ALA40G, ALA45G, ALA47G, ALA52G, ALA53G, ALA55H, ALA60G, ALA66G, ALA69G, ALA70G, ALA71H, ALA74H, ALA78H, ALA94H, ARG17G, ARG20G, ARG29G, ARG30H, ARG32G, ARG35G, ARG42G, ARG69H, ARG71G, ARG76H, ARG77G, ARG81G, ARG83H, ARG88G, ARG89H, ARG96H, ARG99G, ASN38G, ASN60H, ASN64H, ASN68G, ASN94G, ASP48H, ASP65H, ASP90G, GLN104G, GLN24G, GLN44H, GLN84G, GLN92H, GLU102H, GLU110H, GLU32H, GLU41G, GLU56G, GLU61G, GLU64G, GLU68H, GLU73H, GLU90H, GLU91G, GLU92G, GLY101H, GLY105G, GLY111H, GLY22G, GLY28G, GLY37G, GLY44G, GLY46G, GLY50H, GLY67G, GLY72H, GLY98G, HIS106H, HIS31G, HIS46H, HIS79H, HIS82G, ILE102G, ILE36H, ILE51H, ILE58H, ILE62G, ILE70H, ILE78G, ILE79G, ILE86H, ILE91H, LEU103H, LEU23G, LEU33G, LEU34G, LEU42H, LEU51G, LEU55G, LEU58G, LEU63G, LEU65G, LEU83G, LEU93G, LEU96G, LEU97G, LEU97H, LEU98H, LEU99H, LYS105H, LYS113H, LYS117H, LYS122H, LYS15G, LYS31H, LYS36G, LYS40H, LYS43H, LYS54H, LYS75G, LYS95G, MET56H, MET59H, PHE25G, PHE62H, PHE67H, PRO100H, PRO26G, PRO48G, PRO80G, SER109H, SER120H, SER18G, SER19G, SER33H, SER52H, SER53H, SER57H, SER61H, SER75H, SER84H, SER88H, THR101G, THR112H, THR116H, THR119H, THR16G, THR49H, THR59G, THR76G, THR85H, THR87H, THR93H, TYR118H, TYR34H, TYR37H, TYR39G, TYR39H, TYR50G, TYR57G, VAL100G, VAL108H, VAL115H, VAL27G, VAL30G, VAL38H, VAL41H, VAL43G, VAL45H, VAL49G, VAL54G, VAL63H, VAL66H, VAL87G, VAL95H