3OFX

crystal structure of the e. coli ribosome bound to clindamycin. this file contains the 30s subunit of the first 70s ribosome.

• Total interactions analyzed: 210
• Total true interactions: 23
• Strongest Interaction:
  • Chains: J-N
  • Int. Res.: 56
  • Norm. En. per Res.: -4.6682
• 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
B-E	0.0	0.0	-0.1281	-0.1281	6	0	0	46	0	2	4
B-H	0.0	0.0	-0.0003	-0.0003	2	0	0	1	0	1	2
C-D	0.0	0.0	-0.6264	-0.6264	7	0	0	122	0	0	1
C-E	0.0	-7.9312	-6.8196	-14.7508	10	1	0	336	0	7	6
C-J	0.0	-0.616	-67.9836	-68.5996	58	0	3	3034	0	11	9
C-N	-6.6676	-53.5997	-222.591	-282.8582	76	18	5	9578	5	36	36
D-E	0.0	-39.1221	-28.3671	-67.4892	39	5	0	1626	2	11	11
E-H	-4.363	-7.3332	-92.7949	-104.4911	53	17	2	4488	0	17	13
F-R	-18.9189	21.8879	-136.041	-133.072	62	35	3	7682	2	13	24
G-I	0.0	3.1128	-17.6518	-14.539	29	0	0	1154	1	10	8
G-K	0.0	0.0	-18.3692	-18.3692	30	0	2	1218	0	3	2
H-L	0.0	0.0	-9.564	-9.564	12	0	1	511	0	0	0
H-Q	0.0	0.0	-24.4751	-24.4751	19	1	0	1319	0	4	9
I-J	0.0	0.0	-25.9196	-25.9196	19	1	0	1137	0	9	12
I-N	0.0	0.0	-23.0715	-23.0715	9	0	0	568	0	0	1
J-N	-40.9757	-64.1062	-156.336	-261.4179	56	43	6	8649	5	18	30
K-R	0.0	5.7226	-8.3086	-2.5859	18	0	0	556	0	5	8
K-U	-50.2421	39.6613	-226.401	-236.9818	81	79	4	12104	2	34	42
L-Q	0.0	0.0	-45.95	-45.95	21	3	4	2041	0	0	7
M-S	-15.5743	8.3478	-57.2768	-64.5033	40	7	0	2869	0	13	21
N-S	0.0	-1.4557	-25.051	-26.5067	29	2	1	1956	0	5	10
O-Q	0.0	0.0	-0.0147	-0.0147	3	0	0	4	0	0	0
R-U	0.0	-11.2046	-29.8017	-41.0063	22	3	0	1576	0	14	9

Interface residues

• B-E: ARG68E, ASN177B, ASN69E, GLU64E, LEU178B, LYS104B
• B-H: LYS21H, LYS27B
• C-D: ARG130C, ARG131C, ARG135C, ARG43D, ARG46D, LYS44D, MET128C
• C-E: ALA57E, ARG168C, ARG53E, GLU165C, GLU54E, ILE29E, LYS134C, PRO56E, TRP166C, TYR167C
• C-J: ALA12J, ALA23C, ALA60C, ALA93J, ALA94J, ARG10C, ARG16J, ARG45J, ARG58C, ARG64C, ARG68J, ASN24C, ASP14J, ASP63J, ASP91J, ASP97J, GLN2C, GLN99C, GLN99J, GLU47J, GLU57C, GLU66J, GLY12C, GLY1C, GLY95J, HIS15J, HIS5C, HIS70J, ILE13C, ILE18J, ILE53J, ILE67J, LEU11C, LEU17J, LEU32C, LEU71J, LEU92J, LYS11J, LYS15C, LYS3C, PHE13J, PHE22C, PHE28C, PHE49J, PRO16C, PRO59C, SER19C, SER54J, THR20C, THR25C, THR69J, TRP17C, TRP21C, TYR65J, VAL14C, VAL4C, VAL96J, VAL98J
• C-N: ALA23C, ALA29C, ALA86N, ALA87N, ARG10C, ARG39C, ARG53C, ARG58C, ARG64N, ARG74N, ARG84N, ARG89N, ASN184C, ASN18C, ASN24C, ASN31C, ASN7C, ASP30C, ASP33C, ASP35C, GLN2C, GLN40C, GLN65N, GLU187C, GLU27C, GLU57C, GLU85N, GLU91N, GLY12C, GLY1C, GLY77N, GLY8C, GLY90N, GLY94N, HIS5C, ILE13C, ILE54C, ILE56C, ILE92N, ILE9C, LEU11C, LEU32C, LEU73N, LEU78N, LEU95N, LYS113C, LYS15C, LYS26C, LYS37C, LYS3C, LYS75N, LYS82N, LYS96N, LYS97N, MET88N, PHE22C, PHE28C, PHE36C, PHE72N, PHE76N, PRO16C, PRO6C, PRO93N, SER19C, SER34C, THR185C, THR20C, THR25C, THR43C, TRP17C, TRP21C, TYR183C, VAL38C, VAL4C, VAL55C, VAL83N
• D-E: ALA106E, ALA109E, ALA78D, ALA79D, ARG111E, ARG46D, ASN84D, ASN88D, ASP49D, GLN53D, GLU100E, GLU115E, GLU196D, GLU201D, GLU87D, GLY101E, GLY103E, GLY107E, GLY108E, GLY83D, GLY86D, HIS120E, HIS197D, ILE104E, ILE105E, ILE199D, LEU198D, LEU202D, LYS13E, LYS205D, LYS82D, SER204D, THR102E, THR85D, TYR203D, TYR50D, TYR75D, VAL200D, VAL55E
• E-H: ALA129H, ALA153E, ALA154E, ALA69H, ALA96H, ALA98E, ARG113H, ARG156E, ASN145E, ASN147E, ASN76E, GLN66H, GLN75H, GLN81E, GLN96E, GLU144E, GLU150E, GLU41H, GLU42H, GLU46H, GLU72H, GLY157E, GLY43H, GLY97H, GLY99H, HIS82E, ILE100H, ILE45H, LEU39H, LEU98H, LYS155E, LYS158E, LYS40H, LYS63H, LYS68H, LYS85E, LYS93H, MET146E, MET151E, MET95H, PHE44H, PHE65H, PRO149E, PRO83E, PRO97E, SER148E, SER73H, TYR64H, VAL152E, VAL70H, VAL71H, VAL84E, VAL94H
• F-R: ALA26R, ALA48F, ALA57F, ALA57R, ALA61R, ALA99F, ARG38F, ARG45F, ARG56R, ARG60R, ARG62R, ARG72R, ARG86F, ARG91F, ASN63F, ASP21R, ASP24R, ASP71R, GLN46F, GLN53R, GLU40F, GLU5F, GLU98F, HIS55F, HIS73R, ILE20R, ILE25R, ILE51F, ILE6F, ILE85F, LEU47F, LEU61F, LEU64R, LEU66R, LEU67R, LYS23R, LYS56F, LYS59R, LYS93F, MET62F, MET88F, MET90F, MET9F, PHE8F, PRO50F, PRO68R, SER100F, SER65R, SER87F, THR70R, THR92F, TRP42F, TYR22R, TYR49F, TYR4F, TYR59F, TYR63R, TYR69R, VAL60F, VAL7F, VAL89F, VAL96F
• G-I: ALA100I, ALA38G, ALA43I, ARG108I, ARG40I, ARG44I, ARG79I, ARG9G, ASP14G, GLN49I, GLU39G, GLU41I, GLY33G, ILE71I, LEU12G, LYS16G, LYS34G, LYS35G, MET45I, PHE102I, PRO13G, PRO15G, SER36G, SER40G, SER72I, THR37G, THR42I, TYR43G, VAL46I
• G-K: ALA144G, ALA146G, ALA149G, ALA151G, ALA61K, ALA62K, ARG142G, ARG55K, ARG97K, ASN147G, GLN63K, GLN85G, GLU145G, GLU67K, GLU93K, GLY91K, LYS148G, MET143G, PHE150G, PHE51K, PHE60K, PRO59K, PRO90K, SER54K, SER57K, SER82G, SER94K, THR58K, TYR84G, VAL64K
• H-L: ALA1L, ARG79H, ARG83H, ASN4L, GLN5L, GLY81H, ILE84H, LEU82H, PRO80H, THR2L, VAL3L, VAL7L
• H-Q: ARG79H, ARG83H, ARG87H, GLU90H, GLY34Q, GLY81H, HIS30Q, ILE32Q, ILE84H, LEU82H, LYS29Q, LYS35Q, LYS86H, PHE27Q, PHE36Q, PRO80H, SER78H, TYR33Q, TYR85H
• I-J: ALA61J, ARG112I, ARG123I, ARG48J, ARG62J, ASP60J, ASP63J, GLN64J, GLY116I, ILE53J, LEU117I, LEU52J, LYS113I, LYS114I, LYS59J, PRO124I, THR50J, VAL115I, VAL51J
• I-N: ALA98N, ARG112I, GLU111I, LYS113I, LYS114I, SER99N, TRP100N, VAL110I, VAL115I
• J-N: ALA12J, ALA61J, ALA86N, ALA87N, ALA98N, ARG45J, ARG48J, ARG62J, ARG68J, ARG68N, ARG74N, ARG80N, ARG84N, ASN58J, ASP14J, ASP63J, GLN64J, GLU47J, GLU66J, GLU85N, GLY71N, GLY94N, GLY95J, HIS56J, HIS70J, HIS70N, ILE53J, ILE67J, ILE81N, ILE92N, LEU52J, LEU73N, LEU95N, LYS46J, LYS59J, LYS75N, LYS82N, LYS96N, LYS97N, MET88N, PHE13J, PHE49J, PHE72N, PHE76N, PRO55J, PRO93N, SER54J, SER79N, SER99N, THR50J, THR69J, TRP100N, TYR65J, VAL51J, VAL57J, VAL83N
• K-R: ARG62R, ARG72R, ASP111K, ASP71R, HIS117K, HIS21K, ILE115K, LYS37R, LYS86K, MET84K, PRO114K, THR110K, THR113K, THR70R, TYR63R, TYR69R, VAL112K, VAL85K
• K-U: ALA101K, ALA14U, ALA24K, ALA25U, ALA29U, ARG105K, ARG121K, ARG126K, ARG127K, ARG16U, ARG20U, ARG32U, ARG33U, ARG34U, ARG6U, ARG92K, ARG97K, ASN100K, ASN108K, ASN118K, ASN27K, ASN8U, ASP111K, ASP12U, CYS120K, CYS22U, GLU23U, GLU30U, GLU35U, GLU7U, GLU82K, GLU93K, GLU9U, GLY119K, GLY26U, GLY87K, GLY89K, HIS117K, ILE106K, ILE109K, ILE115K, ILE22K, ILE3U, ILE96K, LEU15U, LEU28U, LYS124K, LYS125K, LYS19U, LYS24U, LYS39U, LYS4U, LYS86K, MET84K, PHE104K, PHE11U, PHE18U, PHE26K, PHE36U, PRO114K, PRO116K, PRO122K, PRO123K, PRO88K, PRO90K, SER21U, SER25K, SER94K, THR107K, THR110K, THR113K, THR95K, TYR37U, VAL112K, VAL128K, VAL13U, VAL27U, VAL31U, VAL5U, VAL83K, VAL85K
• L-Q: ALA12L, ALA1L, ARG11L, ARG39Q, ARG8L, ASN4L, GLN5L, GLY34Q, HIS30Q, ILE32Q, ILE37Q, LEU6L, LYS35Q, LYS9L, PHE36Q, PRO10L, PRO31Q, THR2L, TYR33Q, VAL3L, VAL7L
• M-S: ALA74S, ARG100M, ARG2S, ARG35S, ARG77S, ARG78M, ARG80S, ARG86M, ARG89M, ARG91M, ARG92M, ASP63S, ASP81M, CYS84M, GLN99M, GLU64S, GLU72S, GLY67S, GLY71S, GLY83M, GLY87M, GLY98M, HIS68S, ILE39S, LEU70S, LEU79M, LEU82M, LEU88M, LEU94M, LYS69S, MET65S, PHE73S, PRO75S, THR101M, THR62S, THR76S, TYR79S, TYR85M, VAL59S, VAL66S
• N-S: ALA35N, ALA43N, ARG36S, ARG40N, ARG52N, ASN34N, ASN42N, ASP11S, ASP32N, GLN48N, GLY7S, HIS13S, ILE10S, LEU12S, LEU15S, LEU45N, LEU47N, LEU4S, LYS46N, LYS5S, LYS6S, PHE40S, PHE9S, PRO8S, SER31N, SER34S, THR49N, VAL33N, VAL44N
• O-Q: ALA81Q, VAL74O, VAL82Q
• R-U: ALA47U, ALA51U, ARG42R, ARG72R, ASP71R, CYS22U, GLU23U, GLU34R, GLY26U, GLY36R, ILE3U, LYS19U, LYS37R, LYS48U, LYS4U, PHE18U, SER21U, SER35R, THR33R, THR70R, VAL27U, VAL5U