1VSP

interactions and dynamics of the shine-dalgarno helix in the 70s ribosome. this file, 1vsp, contains the 50s ribosome subunit. 30s ribosome subunit is in the file 2qnh

• Total interactions analyzed: 435
• Total true interactions: 31
• Strongest Interaction:
  • Chains: H-b
  • Int. Res.: 3
  • Norm. En. per Res.: -2.9888
• 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
C-H	0.0	0.0	-20.5533	-20.5533	13	0	0	963	0	0	0
C-I	0.0	-8.5793	-21.133	-29.7123	15	1	0	953	0	5	7
C-L	-2.6482	13.3588	-46.4998	-35.7892	18	8	0	1608	0	2	12
C-N	-3.2256	-52.388	-84.36	-139.9736	73	8	4	5222	3	22	17
D-J	-17.6394	2.7984	-102.277	-117.118	41	20	1	4185	0	16	15
D-O	0.0	0.0	-3.8458	-3.8458	16	0	0	325	0	1	3
D-Q	0.0	0.0	-0.0502	-0.0502	4	0	0	21	0	0	2
D-Y	0.0	0.0	-0.0109	-0.0109	2	0	0	8	0	0	1
F-H	0.0	0.0	-0.0024	-0.0024	2	0	0	3	0	0	0
F-b	0.0	-1.1864	-0.2533	-1.4397	8	0	0	63	0	2	5
G-V	0.0	3.8414	-15.8766	-12.0352	27	0	1	1111	0	5	8
H-O	-13.7585	14.5638	-100.24	-99.4347	50	33	1	5772	0	9	25
H-P	-5.2817	8.5771	-21.3034	-18.008	12	4	0	892	0	2	4
H-b	0.0	-8.1385	-0.8278	-8.9663	3	0	0	63	0	4	1
I-N	-24.579	-3.162	-189.353	-217.094	78	29	7	8551	2	40	38
J-O	0.0	0.0	-0.0949	-0.0949	4	0	0	34	0	0	1
J-P	0.0	2.7779	-9.6858	-6.9079	11	1	0	487	0	0	9
J-a	0.0	40.5081	-73.9682	-33.4601	53	9	0	4926	0	13	48
K-T	-13.3922	-16.7141	-129.631	-159.7374	97	18	2	8321	3	51	49
K-U	0.0	0.0	-0.0052	-0.0052	2	0	0	6	0	0	0
K-b	0.0	-4.7347	-6.9175	-11.6522	9	4	0	280	0	2	3
L-Q	-9.1373	5.9567	-36.5015	-39.6822	20	1	0	1187	0	6	8
L-Y	0.0	22.7614	-31.163	-8.4016	29	5	2	1759	0	6	16
M-U	0.0	-7.5029	-11.7787	-19.2816	22	2	0	919	0	14	17
O-P	-6.7159	11.1663	-198.645	-194.1946	89	30	6	9849	0	23	58
O-Y	0.0	0.0	-0.2233	-0.2233	11	0	0	78	0	0	6
Q-Y	0.0	26.0191	-66.962	-40.9429	53	16	4	4277	0	16	25
Q-Z	0.0	0.0	-0.2921	-0.2921	6	0	0	61	0	0	1
R-W	-12.7423	0.9729	-68.6106	-80.38	45	18	1	3802	0	13	17
R-Z	0.0	0.0	-0.346	-0.346	6	0	0	73	0	0	7
U-a	0.0	0.0	-0.0484	-0.0484	3	0	0	25	0	2	2

Interface residues

• C-H: ARG149C, GLY100H, GLY103H, GLY153C, LYS152C, LYS154C, LYS155C, PRO102H, SER99H, TYR101H, TYR151C, TYR98H, VAL150C
• C-I: ALA20C, ARG13C, ARG16C, ARG19C, ARG71I, ASP18C, ASP73I, GLY74I, ILE14C, LYS70I, PHE15C, PRO22C, PRO72I, SER75I, VAL21C
• C-L: ALA114C, ALA162C, ARG111C, ARG2L, GLY110C, GLY112C, GLY161C, GLY190C, HIS3L, LEU4L, LYS109C, LYS5L, MET1L, PHE113C, PRO189C, PRO191C, SER108C, TYR160C
• C-N: ALA20C, ALA28C, ALA5N, ARG13C, ARG13N, ARG16C, ARG16N, ARG19C, ARG39N, ARG3N, ARG53N, ARG76C, ASN180C, ASN192C, ASN2N, ASN55N, ASN58N, ASP174C, ASP17C, ASP18C, GLU11N, GLU178C, GLU179C, GLY10C, GLY193C, GLY194C, GLY29C, GLY4N, GLY56N, HIS79N, ILE14C, ILE176C, ILE26C, ILE7N, LEU181C, LEU182C, LEU183C, LEU27C, LEU52C, LEU6N, LEU78N, LEU82N, LEU9N, LYS8C, LYS8N, MET11C, MET1N, PHE15C, PHE51C, PHE57N, PRO177C, PRO191C, PRO22C, PRO53C, PRO77N, PRO81N, PRO98C, SER12N, SER80N, THR12C, THR59N, THR60N, TYR14N, TYR32N, VAL10N, VAL15N, VAL173C, VAL175C, VAL23C, VAL25C, VAL34N, VAL7C, VAL9C
• D-J: ALA108D, ALA12J, ARG112D, ARG15J, ARG16J, ARG183D, ARG18J, ARG33D, ARG7J, ASN13J, ASN24D, ASN9J, ASP111D, ASP180D, ASP5J, GLU115D, GLU185D, GLU30D, GLY11J, HIS26D, ILE181D, LEU27D, LEU28D, LEU36D, LEU6J, LYS14J, MET107D, PRO10J, PRO25D, PRO8J, THR184D, TRP29D, TRP34D, TYR179D, TYR92D, TYR94D, VAL109D, VAL178D, VAL182D, VAL31D, VAL32D
• D-O: ALA44D, ALA4O, ARG3O, ARG40D, ASP91D, GLY42D, GLY86D, LYS5O, LYS88D, PRO2O, PRO87D, SER45D, THR43D, TYR92D, VAL79D, VAL83D
• D-Q: ARG90Q, ARG92Q, GLY66D, HIS64D
• D-Y: ARG67D, LYS8Y
• F-H: ARG23F, LYS82H
• F-b: ARG170F, ASN29b, GLU28b, LYS172F, LYS31b, PRO168F, PRO30b, VAL169F
• G-V: ALA26G, ALA39G, ALA54V, ARG27G, ARG52V, ASN28G, ASN43G, GLU41G, GLU72V, GLU75V, GLY24G, ILE67V, LEU31G, LEU38G, MET1G, PRO23G, PRO32G, PRO68V, SER42G, THR40G, TYR25G, TYR29G, TYR71V, VAL51V, VAL53V, VAL70V, VAL74V
• H-O: ALA67O, ALA68O, ALA96O, ALA99O, ARG101O, ARG35H, ARG58H, ARG59O, ARG62H, ARG64O, ARG70O, ARG92O, ASN66O, ASN68H, ASN94O, ASP56O, ASP64H, ASP97O, CYS69O, GLN71O, GLY59H, HIS61H, HIS72O, ILE62O, ILE65O, LEU56H, LEU60O, LEU95O, LEU98O, LYS25H, LYS30H, LYS60H, MET71H, PHE106O, PHE57O, PRO103O, PRO29H, PRO63H, PRO67H, THR26H, THR55H, THR66H, TRP61O, TRP65H, TYR27H, VAL100O, VAL24H, VAL28H, VAL63O, VAL69H
• H-P: ARG13P, ARG21P, GLN11P, ILE4P, LEU18P, LEU20P, LYS10P, LYS25H, THR26H, TYR12P, TYR27H, VAL24H
• H-b: GLU91H, HIS20b, LYS88H
• I-N: ALA103I, ALA76I, ALA83I, ARG103N, ARG104I, ARG107I, ARG41N, ARG51N, ARG64I, ARG64N, ARG71I, ARG74N, ARG78I, ASN104N, ASN38N, ASN82I, ASP44N, ASP73I, ASP80I, ASP81I, GLN43N, GLU105I, GLU108I, GLU120I, GLU36N, GLU46N, GLU68I, GLU73N, GLU9I, GLY100I, GLY37N, GLY69N, GLY71N, GLY74I, ILE102N, ILE42N, ILE50N, ILE75N, ILE77I, LEU105N, LEU122I, LEU78N, LEU82N, LYS33N, LYS35N, LYS65N, LYS66I, LYS67I, LYS70I, MET112I, PHE45N, PHE61N, PHE76N, PHE79I, PHE99I, PRO101I, PRO72I, PRO77N, PRO81N, SER31N, SER67N, SER75I, THR59N, THR60N, THR62N, THR65I, TYR100N, TYR32N, TYR68N, VAL102I, VAL121I, VAL34N, VAL63I, VAL63N, VAL66N, VAL69I, VAL70N, VAL72N
• J-O: ARG36O, GLY26J, LYS13O, SER25J
• J-P: ALA31J, ARG82P, ARG83P, GLY26J, GLY28J, HIS27J, LYS29J, LYS84P, LYS85P, SER25J, TYR81P
• J-a: ALA10a, ALA24a, ALA51a, ALA55a, ARG13a, ARG30a, ARG46a, ARG49J, ARG50J, ARG55J, ARG61J, ARG65J, ASP47J, GLN68J, GLU52J, GLU56a, GLU74J, GLY28a, GLY53J, GLY66J, GLY69J, GLY9a, HIS31a, HIS7a, ILE16a, LEU50a, LEU59J, LEU62J, LYS11a, LYS12a, LYS15a, LYS26a, LYS52a, LYS59a, LYS5a, LYS64J, LYS8a, MET25a, MET4a, MET60J, MET67J, PHE48a, PHE51J, PRO53a, PRO63J, THR27a, THR57J, THR58J, THR6a, TYR64a, VAL14a, VAL22a, VAL49a
• K-T: ALA107K, ALA113T, ALA136K, ALA184T, ALA28K, ALA36K, ALA51T, ARG101K, ARG122T, ARG133K, ARG134K, ARG49T, ARG51K, ARG56K, ARG59K, ARG60K, ARG79T, ARG80T, ARG81T, ARG82T, ASN75T, ASP123T, ASP135K, ASP25K, ASP31K, ASP45T, ASP77T, GLN118T, GLN50T, GLN73T, GLU105K, GLU119T, GLU181T, GLU185T, GLU48K, GLY100K, GLY108K, GLY114T, GLY115T, GLY23K, GLY24K, GLY30K, GLY33K, GLY61K, GLY62K, HIS121T, HIS54T, ILE120T, ILE124T, ILE131K, ILE171T, ILE53T, ILE64K, LEU102T, LEU117T, LEU125T, LEU183T, LEU2K, LEU76T, LYS130K, LYS182T, LYS22K, LYS63K, LYS78T, LYS98K, MET1K, MET54K, MET98T, PHE104T, PHE29K, PHE32K, PHE44T, PHE48T, PHE58K, PHE65K, PRO101T, PRO176T, PRO177T, PRO83T, PRO99K, SER52T, TYR137K, TYR26K, TYR99T, VAL100T, VAL102K, VAL111T, VAL116T, VAL132K, VAL175T, VAL180T, VAL27K, VAL35K, VAL52K, VAL55K, VAL71T, VAL74T
• K-U: LYS85K, THR10U
• K-b: ALA5b, ARG119K, GLU116K, HIS123K, ILE120K, LYS128K, LYS8b, SER6b, VAL7b
• L-Q: ALA101L, ALA109L, ALA44Q, ARG103L, ARG104L, ARG105L, ARG37Q, ARG42Q, ASN40Q, ASP107L, GLU102L, GLY106L, GLY108L, ILE35Q, LEU100L, LEU36Q, LYS41Q, LYS99L, THR39Q, TYR38Q
• L-Y: ALA101L, ALA53Y, ARG103L, ARG33L, ARG55Y, ARG86L, ARG96L, CYS46Y, GLU102L, GLU115L, GLU118L, GLY32L, GLY54Y, HIS31L, HIS43Y, ILE29Y, LEU100L, LEU113L, LEU116L, LEU98L, LYS56Y, LYS99L, PRO110L, PRO28Y, PRO41Y, PRO42Y, THR44Y, TYR51Y, VAL45Y
• M-U: ARG20M, ARG23M, ARG72U, ASP41M, ASP42M, GLU43M, GLY22M, GLY45M, GLY48U, GLY76U, HIS80U, ILE18M, LEU24M, LEU75U, LYS19M, LYS44M, LYS46U, LYS49U, PRO47U, THR21M, TYR78U, VAL79U
• O-P: ALA35O, ALA3P, ALA41O, ALA42O, ALA46O, ALA48O, ALA55P, ALA77P, ALA86O, ALA96O, ARG101O, ARG112O, ARG13P, ARG28O, ARG36O, ARG50O, ARG82P, ARG83P, ARG88P, ARG92O, ASN44O, ASN94O, ASP91O, ASP97O, GLN104O, GLN11P, GLN89P, GLU102O, GLU108O, GLU37O, GLU43P, GLU53P, GLU89O, GLY41P, GLY42P, GLY43O, GLY48P, GLY54P, GLY86P, GLY87O, GLY8P, GLY9P, ILE17O, ILE4P, ILE88O, LEU109O, LEU20O, LEU38P, LEU39O, LEU39P, LEU40P, LEU83O, LEU95O, LEU98O, LYS10P, LYS13O, LYS16O, LYS44P, LYS54O, LYS6P, LYS74P, LYS76P, LYS78P, LYS85P, LYS93O, PHE106O, PHE2P, PHE40O, PHE75P, PRO103O, PRO50P, SER73P, THR38O, THR45P, THR49P, THR7P, TYR12P, TYR45O, TYR47O, TYR81P, VAL100O, VAL105O, VAL47P, VAL51P, VAL52P, VAL5P, VAL72P, VAL79P, VAL90O
• O-Y: ALA14Y, ARG15Y, LEU27O, LYS10Y, LYS13Y, LYS30O, LYS34O, LYS9Y, SER12Y, THR11Y, TRP25O
• Q-Y: ALA24Y, ALA32Q, ALA38Y, ALA44Q, ARG15Q, ARG16Y, ARG18Q, ARG19Y, ARG20Y, ARG33Q, ARG37Q, ASN34Q, ASN40Q, ASP17Y, ASP22Q, ASP67Q, CYS46Y, GLU30Q, GLU31Q, GLU48Y, GLU66Q, GLY43Q, HIS22Y, HIS23Y, ILE24Q, ILE29Y, ILE35Q, LEU19Q, LEU23Q, LEU25Y, LEU30Y, LEU36Q, LYS16Q, LYS27Q, LYS37Y, LYS40Y, LYS41Q, MET39Y, PRO14Q, PRO27Y, PRO28Y, PRO41Y, PRO42Y, SER21Y, THR26Y, THR39Q, THR44Y, TYR38Q, VAL17Q, VAL20Q, VAL21Q, VAL45Y, VAL47Q
• Q-Z: ALA89Q, ARG3Z, ARG88Q, ARG90Q, ARG92Q, GLY91Q
• R-W: ALA10R, ALA42R, ALA46R, ALA4R, ARG26W, ARG30W, ARG36W, ARG51W, ASN41R, ASP6R, GLU22W, GLU27W, GLU31W, GLU34W, GLU44R, GLU93R, GLY94R, HIS31R, ILE89R, ILE8R, LEU13R, LEU24W, LEU32W, LEU92R, LEU9R, LYS23W, LYS28W, LYS29W, LYS48R, LYS88R, MET33W, PHE47R, PRO11R, PRO18W, THR3R, THR45R, TRP29R, TYR18R, TYR5R, VAL12R, VAL19W, VAL25W, VAL30R, VAL43R, VAL7R
• R-Z: ARG41Z, ARG68R, GLY67R, LEU66R, TRP40Z, TYR69R
• U-a: ARG55U, GLN43a, LYS39a