3D5A

structural basis for translation termination on the 70s ribosome. this file contains the 30s subunit, release factor 1 (rf1), two trna, and mrna molecules of one 70s ribosome. the entire crystal structure contains two 70s ribosomes as described in remark 400.

• Total interactions analyzed: 300
• Total true interactions: 26
• Strongest Interaction:
  • Chains: J-N
  • Int. Res.: 56
  • Norm. En. per Res.: -4.223
• 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-C	0.0	0.0	-0.0784	-0.0784	5	0	0	35	0	1	2
B-E	0.0	0.0	-0.5791	-0.5791	5	0	0	80	0	0	2
B-H	-3.9735	-45.4131	-66.3906	-115.7772	36	9	0	2728	2	16	17
C-D	0.0	0.0	-0.2191	-0.2191	4	0	0	50	0	0	5
C-E	-10.3351	-21.5068	-1.6396	-33.4815	14	4	0	678	1	4	4
C-J	0.0	1.8702	-87.8104	-85.9402	56	3	2	3851	0	17	27
C-N	-3.5759	12.4073	-222.345	-213.5136	82	15	2	9272	0	19	39
D-E	0.0	-6.6425	-67.5652	-74.2078	52	2	0	3186	2	10	13
E-H	-2.156	-25.0435	-118.11	-145.3095	65	10	2	5971	2	44	42
F-O	0.0	0.0	-2.5272	-2.5272	5	1	0	137	0	5	3
F-R	-38.6435	-32.5374	-238.737	-309.9178	83	24	8	9649	1	13	21
G-I	-8.7107	8.1712	-42.3884	-42.9279	40	4	5	2415	0	4	7
G-K	0.0	0.0	-65.3848	-65.3848	29	7	3	2470	0	3	6
G-U	0.0	0.0	-0.0025	-0.0025	2	0	0	1	0	2	0
H-L	0.0	0.0	-12.2232	-12.2232	12	1	0	598	0	0	1
H-Q	-2.9331	5.8679	-27.5508	-24.616	14	0	0	1286	0	2	8
I-J	-4.2628	-2.3843	-25.8484	-32.4955	19	8	0	1361	0	9	17
I-N	0.0	0.0	-11.2831	-11.2831	9	0	0	445	0	0	0
J-N	-40.1855	-18.9547	-177.348	-236.4882	56	15	5	8066	1	15	34
K-R	-9.2256	-14.4329	-65.2449	-88.9035	34	5	2	3375	1	13	17
L-Q	0.0	0.0	-42.2265	-42.2265	21	2	4	2159	0	0	8
L-X	0.0	0.0	-18.8082	-18.8082	20	1	0	1115	0	4	4
M-S	-6.7866	41.6259	-101.263	-66.4236	47	13	1	4256	0	9	20
M-U	0.0	1.0517	-2.0437	-0.992	12	0	0	343	0	3	9
N-S	0.0	0.0	-0.0123	-0.0123	2	0	0	7	0	1	1
O-Q	0.0	-1.3535	-0.6628	-2.0162	13	0	0	200	0	9	6

Interface residues

• B-C: ARG130B, ARG179C, GLU129B, GLU206C, VAL207C
• B-E: ARG64E, ASN65E, LEU180B, LYS179B, PHE181B
• B-H: ALA177B, ARG175B, ARG178B, ARG30B, ARG53B, ARG68H, ARG69H, ARG75H, ASP195B, ASP198B, ASP73H, GLN70H, GLU176B, GLU22H, GLY71H, ILE182B, ILE200B, LEU180B, LEU196B, LYS179B, LYS21H, LYS27B, PHE181B, PHE57B, PRO183B, PRO194B, PRO26B, PRO72H, PRO74H, PRO76H, TYR199B, TYR20H, VAL174B, VAL184B, VAL197B, VAL19H
• C-D: ALA129C, ARG132C, ARG47D, PHE128C
• C-E: ALA54E, ARG131C, ARG132C, ARG15E, ARG164C, GLN56E, GLU166C, GLU50E, LEU53E, LYS135C, PHE26E, PHE28E, PRO52E, VAL51E
• C-J: ALA24C, ALA60C, ALA61C, ALA65C, ARG16C, ARG21C, ARG43J, ARG45J, ARG51J, ARG59C, ARG66J, ARG9J, ASN3C, ASN63C, ASN69J, ASP12J, ASP17C, GLU58C, GLU61J, GLU64J, GLU95J, GLU97J, GLY10J, GLY13C, GLY25C, GLY93J, GLY9C, HIS13J, HIS68J, HIS6C, ILE14C, ILE5C, ILE96J, LEU12C, LEU16J, LEU32C, LEU65J, LYS14J, LYS26C, LYS27C, LYS4C, PHE10C, PHE11J, PHE47J, PHE63J, PRO91J, SER59J, THR15C, THR15J, THR67J, THR92J, TRP18C, TRP22C, TYR23C, TYR29C, VAL94J
• C-N: ALA187C, ALA24C, ALA48N, ARG11C, ARG16C, ARG21C, ARG23N, ARG26N, ARG30C, ARG35N, ARG38C, ARG40C, ARG45N, ARG54C, ARG57N, ARG59C, ASN3C, ASP17C, ASP36C, ASP56C, CYS24N, CYS43N, GLN118C, GLN28C, GLN37C, GLN52N, GLU19C, GLU35C, GLU44C, GLU46N, GLU58C, GLY13C, GLY185C, GLY25C, GLY38N, GLY51N, GLY55N, GLY9C, HIS31C, HIS49N, HIS6C, ILE14C, ILE57C, ILE5C, ILE8C, LEU12C, LEU178C, LEU188C, LEU32C, LEU33C, LEU34C, LEU39N, LEU44N, LEU47N, LEU53N, LYS11N, LYS26C, LYS27C, LYS4C, LYS50N, LYS58N, PHE10C, PHE186C, PHE36N, PHE37N, PRO114C, PRO54N, PRO7C, SER20C, SER60N, THR15C, THR22N, TRP18C, TRP22C, TYR184C, TYR23C, TYR29C, TYR34N, VAL25N, VAL33N, VAL55C, VAL56N
• D-E: ALA102E, ALA104E, ALA108E, ALA95E, ARG107E, ARG209D, ARG37E, ARG49D, ARG50D, ARG57D, ASN199D, ASP117E, ASP53D, GLN201D, GLU111E, GLU200D, GLU205D, GLU7E, GLU8E, GLY103E, GLY74E, GLY87D, GLY90D, GLY97E, GLY99E, ILE101E, ILE118E, ILE11E, ILE13E, ILE204D, LEU202D, LYS9E, MET10E, PHE206D, PHE79D, PRO51D, PRO96E, SER208D, SER52D, SER83D, SER91D, THR116E, THR89D, THR98E, TYR207D, TYR54D, VAL100E, VAL105E, VAL115E, VAL56D, VAL88D, VAL92D
• E-H: ALA138E, ALA146E, ALA40H, ALA94E, ALA95E, ARG102H, ARG104H, ARG105H, ARG122H, ARG140E, ARG143E, ARG150E, ARG152E, ARG41H, ARG64E, ARG69H, ARG84H, ASP147E, GLN141E, GLN78H, GLU149E, GLU155E, GLU42H, GLU77H, GLU79E, GLU81E, GLY106H, GLY108H, GLY154E, GLY43H, GLY66H, HIS78E, HIS81H, HIS82H, ILE109H, ILE45H, ILE76E, ILE80E, ILE80H, LEU107H, LEU119E, LEU142E, LEU151E, LEU39H, LYS145E, LYS153E, LYS46H, LYS64H, LYS88E, LYS92E, PHE44H, PRO67H, PRO70E, PRO72H, PRO76H, PRO77E, PRO93E, THR144E, TRP138H, TYR65H, VAL103H, VAL137H, VAL148E, VAL79H, VAL82E
• F-O: ARG2F, ARG38O, GLU69F, ILE3O, PRO2O
• F-R: ALA101F, ALA24R, ALA49F, ALA73R, ALA99F, ARG32R, ARG35R, ARG46F, ARG47F, ARG72R, ARG74R, ARG80F, ARG87F, ASN100F, ASN36R, ASN7F, ASP30R, ASP33R, GLN57F, GLN64F, GLN94F, GLU28R, GLU38R, GLU41F, GLU42F, GLU5F, GLU62R, GLU83R, GLU95F, GLY27R, GLY57R, GLY58F, GLY77R, ILE52F, ILE65R, ILE75R, ILE8F, LEU26R, LEU31R, LEU43F, LEU48F, LEU58R, LEU61F, LEU66R, LEU76R, LEU78R, LEU79R, LEU98F, LYS23R, LYS41R, LYS61R, LYS68R, LYS71R, LYS92F, MET89F, PHE29R, PHE43R, PHE60F, PHE81R, PHE97F, PRO51F, PRO80R, PRO96F, SER59R, SER93F, THR25R, THR69R, THR82R, TRP62F, TYR34R, TYR4F, TYR50F, TYR59F, TYR63F, VAL22R, VAL37R, VAL39R, VAL40F, VAL6F, VAL88F, VAL90F, VAL91F, VAL9F
• G-I: ALA39G, ALA40G, ALA43I, ALA45I, ALA46I, ARG107I, ARG10G, ARG120I, ARG41G, ARG42I, ARG51I, ASN37G, ASP15G, ASP75I, GLN11G, GLN13G, GLN38I, GLU48I, GLY39I, ILE27G, ILE74I, LEU12G, LEU16G, LEU38G, LEU40I, LEU99I, LYS36G, LYS70I, LYS78I, PHE37I, PHE43G, PRO14G, SER71I, THR24G, TYR18G, TYR44G, VAL17G, VAL23G, VAL41I, VAL44I
• G-K: ALA147G, ALA150G, ALA152G, ALA60K, ALA61K, ALA89K, ARG149G, ARG155G, ARG54K, ASN148G, ASN84G, GLN62K, GLN86G, GLN93K, GLU146G, GLY56K, HIS153G, LEU63K, LEU66K, LYS51K, LYS55K, PRO58K, SER53K, THR57K, TYR151G, TYR154G, TYR50K, TYR59K, TYR85G
• G-U: ASP33G, LYS3U
• H-L: ARG91H, ARG92H, ASN7L, GLY90H, ILE6L, ILE86H, LEU9L, LYS88H, PRO89H, THR5L, VAL10L, VAL93H
• H-Q: ARG91H, ARG92H, GLY33Q, GLY90H, HIS29Q, LEU31Q, LYS34Q, LYS88H, PRO28Q, PRO89H, TYR32Q, TYR94H, VAL35Q, VAL93H
• I-J: ARG111I, ARG46J, ARG51J, ARG60J, ASP58J, GLU61J, GLY115I, HIS56J, HIS62J, ILE50J, LYS112I, LYS113I, LYS116I, LYS57J, PRO123I, SER59J, THR48J, TYR114I, VAL49J
• I-N: ALA59N, ARG111I, GLU110I, LYS112I, LYS113I, LYS58N, SER60N, TRP61N, TYR114I
• J-N: ALA48N, ALA59N, ARG29N, ARG35N, ARG41N, ARG45J, ARG45N, ARG46J, ARG51J, ARG57N, ARG60J, ARG66J, ASP12J, ASP58J, CYS40N, GLU46N, GLU61J, GLU64J, GLY10J, GLY38N, GLY52J, GLY55N, GLY93J, HIS13J, HIS49N, HIS56J, HIS62J, HIS68J, ILE42N, ILE50J, LEU44N, LEU47N, LEU53N, LEU65J, LYS14J, LYS55J, LYS57J, LYS58N, PHE11J, PHE36N, PHE37N, PHE47J, PHE54J, PHE63J, PRO53J, PRO54N, SER32N, SER59J, SER60N, THR48J, THR67J, TRP61N, TYR34N, VAL44J, VAL49J, VAL56N
• K-R: ARG74R, ARG85K, ARG87R, ARG91K, ARG96K, ASP110K, ASP111K, GLN99K, GLU83R, GLU92K, GLY48R, HIS116K, ILE108K, ILE21K, ILE83K, ILE95K, LEU85R, LYS106K, LYS49R, LYS84R, LYS88R, PHE81R, PRO113K, PRO115K, SER107K, THR112K, THR82R, TYR20K, VAL105K, VAL109K, VAL114K, VAL82K, VAL84K, VAL86R
• L-Q: ARG11L, ARG14L, ARG38Q, ASN7L, GLN8L, GLY13L, GLY33Q, HIS29Q, ILE36Q, ILE6L, LEU31Q, LEU9L, LYS12L, LYS34Q, LYS37Q, PRO30Q, PRO4L, THR5L, TYR32Q, VAL10L, VAL35Q
• L-X: ALA50L, ARG179X, ARG298X, ARG40L, ASN48L, GLU297X, GLU300X, GLY296X, LEU51L, LYS301X, LYS45L, LYS46L, PRO44L, SER299X, SER49L, THR194X, THR295X, THR41L, THR43L, VAL42L
• M-S: ALA75S, ARG102M, ARG36S, ARG78S, ARG80M, ARG81S, ARG88M, ARG91M, ARG93M, ARG94M, ASN53S, ASN65S, ASN77M, ASP83M, CYS86M, GLU64S, GLU73S, GLY100M, GLY68S, GLY72S, GLY85M, GLY89M, HIS69S, HIS92M, ILE40S, ILE62S, ILE84M, LEU81M, LEU90M, LEU96M, LYS70S, LYS79M, MET66S, MET82M, PHE74S, PRO76S, PRO97M, THR103M, THR63S, THR77S, THR79S, TYR61S, TYR80S, TYR87M, VAL58S, VAL60S, VAL67S
• M-U: ALA28M, ARG29M, ARG6U, ARG7U, ARG99M, GLY26M, LYS20U, LYS27M, LYS31M, THR20M, THR8U, TYR21U
• N-S: ARG37S, PHE16N
• O-Q: ARG64O, ARG68O, ARG72O, ARG81Q, ARG88O, ASP83Q, GLN71O, GLU86Q, GLY80Q, ILE90Q, LYS87Q, MET82Q, PRO75O