1VS8

crystal structure of the bacterial ribosome from escherichia coli in complex with the antibiotic kasugamyin at 3.5a resolution. this file contains the 30s subunit of one 70s ribosome. the entire crystal structure contains two 70s ribosomes and is described in remark 400.

• Total interactions analyzed: 465
• Total true interactions: 28
• Strongest Interaction:
  • Chains: L-3
  • Int. Res.: 61
  • Norm. En. per Res.: -2.9111
• Hub Node: E(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
V-M	-7.9385	-4.7714	-81.8409	-94.5508	44	4	1	3776	0	8	13
D-J	0.0	3.4095	-30.8653	-27.4558	15	5	1	1146	0	0	8
D-K	0.0	24.2604	-33.1418	-8.8814	16	2	0	1143	0	6	2
D-N	-2.5604	16.2632	-42.998	-29.2953	20	3	0	2039	0	0	11
D-P	0.0	39.3158	-108.859	-69.5432	60	21	2	5554	0	18	16
E-L	-6.2238	-18.3006	-60.6602	-85.1846	45	8	1	2834	2	14	14
E-Q	0.0	0.0	-0.5569	-0.5569	4	0	0	85	0	0	2
E-S	0.0	0.0	-0.0057	-0.0057	2	0	0	4	0	0	0
E-2	0.0	0.0	-0.0003	-0.0003	2	0	0	1	0	0	0
G-4	0.0	-11.8573	-27.3933	-39.2506	20	3	0	1490	2	10	15
H-Z	0.0	1.6534	-51.0435	-49.3901	42	2	0	2662	0	6	14
J-Q	-12.1203	10.1585	-111.682	-113.6437	51	27	2	5715	0	11	27
J-R	0.0	3.0758	-30.5538	-27.478	18	2	0	1669	0	1	6
K-P	-14.7901	82.7061	-147.462	-79.5459	75	22	4	6684	2	29	35
L-Q	0.0	0.0	-0.0101	-0.0101	3	0	0	9	0	0	2
L-R	-5.5599	16.0444	-26.2086	-15.7241	10	14	0	1126	0	0	10
L-3	-15.2642	15.1669	-177.479	-177.5763	61	41	5	8046	0	5	32
M-W	0.0	0.0	-1.0439	-1.0439	5	0	0	106	0	0	3
M-4	0.0	0.0	-0.1224	-0.1224	3	0	0	43	0	1	2
N-S	0.0	0.0	-7.9915	-7.9915	14	7	0	474	0	2	2
N-0	0.0	2.8428	-56.4355	-53.5927	37	5	1	2804	0	10	21
O-W	0.0	27.0012	-51.6298	-24.6286	22	14	0	2102	0	3	13
Q-R	0.0	11.5751	-250.366	-238.7909	94	37	6	10809	0	27	57
Q-0	0.0	15.7498	-19.178	-3.4282	13	3	0	805	0	0	7
S-0	0.0	16.2912	-50.8899	-34.5987	44	8	4	2914	0	12	9
T-X	0.0	32.2543	-61.3413	-29.087	46	8	2	3813	0	8	17
T-2	0.0	0.0	-0.0022	-0.0022	4	0	0	6	0	0	2
1-3	0.0	3.1611	-23.1374	-19.9763	17	5	0	1524	0	4	12

Interface residues

• V-M: ALA35M, ALA52V, ALA54V, ALA74V, ARG79V, ASN49V, ASP25M, GLN22M, GLN51V, GLN75V, GLN97M, GLU55V, GLY23M, GLY37M, HIS80V, ILE126M, ILE96M, LEU124M, LEU86V, LYS127M, LYS133M, LYS34M, LYS53V, LYS83V, MET136M, MET48V, MET50V, PHE130M, PHE56V, PRO125M, PRO81V, PRO84V, PRO98M, THR128M, THR129M, THR132M, THR134M, THR24M, TYR57V, TYR82V, VAL131M, VAL135M, VAL36M, VAL77V
• D-J: GLN148D, GLY158D, GLY79J, GLY82J, GLY83J, HIS77J, HIS80J, ILE146D, ILE81J, ILE84J, LYS154D, LYS157D, PHE156D, THR78J, VAL155D
• D-K: ARG70K, ARG71K, ASP18D, ASP73K, GLU17D, GLY19D, GLY74K, ILE14D, LYS190D, PHE15D, PRO72K, SER21D, SER75K, THR12D, THR16D, VAL20D
• D-N: ALA119D, ALA196D, ARG124D, ARG141D, ARG2N, ARG4N, ASN167D, GLN164D, GLY115D, GLY117D, GLY120D, GLY163D, GLY166D, HIS3N, LYS114D, LYS116D, LYS123D, MET165D, MET1N, PHE118D
• D-P: ALA57P, ARG13D, ARG179D, ARG184D, ASN185D, ASN2P, ASP15P, ASP181D, ASP18D, ASP81P, GLN11P, GLN14P, GLN6P, GLN9P, GLU10P, GLU17D, GLU28D, GLU33P, GLU8P, GLY10D, GLY19D, GLY34P, GLY6D, HIS55P, HIS76P, ILE14D, ILE27D, ILE3P, ILE4P, LEU186D, LEU187D, LEU188D, LEU7P, LYS13P, LYS5P, LYS7D, LYS8D, MET11D, MET12P, PHE15D, PHE58P, PRO23D, PRO78P, SER1P, SER21D, SER56P, SER77P, SER82P, THR12D, THR16D, THR25D, THR59P, VAL20D, VAL24D, VAL26D, VAL31P, VAL32P, VAL79P, VAL80P, VAL9D
• E-L: ALA142E, ALA15L, ALA182E, ALA26E, ALA86E, ARG114E, ARG117E, ARG18L, ASN24E, ASP116E, ASP184E, GLN115E, GLN30E, GLN94E, GLU10L, GLU111E, GLU25E, GLY11L, GLY16L, GLY20L, GLY22L, HIS29E, ILE181E, ILE23L, LEU112E, LEU147E, LEU180E, LEU19L, LEU27E, LYS13L, LYS14L, LYS17L, LYS185E, LYS29L, MET141E, PHE183E, PHE23E, PHE85E, SER12L, VAL146E, VAL178E, VAL28E, VAL32E, VAL33E, VAL46L
• E-Q: ALA1Q, ARG2Q, ARG40E, ARG44E
• E-S: ARG67E, ARG95S
• E-2: GLY54E, LYS372
• G-4: ALA173G, ALA294, ARG152G, ARG169G, ARG364, GLU172G, GLU304, HIS334, LYS171G, LYS174G, LYS175G, LYS324, LYS344, PRO153G, PRO155G, PRO314, THR170G, TYR156G, VAL167G, VAL168G
• H-Z: ALA23H, ALA26H, ALA36H, ALA39H, ALA52Z, ARG27H, ARG49Z, ARG56Z, ARG59Z, ASN28H, ASN43H, ASN61Z, ASP35Z, ASP50Z, ASP58Z, CYS37Z, GLN33H, GLN48Z, GLY24H, GLY34H, GLY54Z, GLY55Z, LEU34Z, LYS41H, LYS42H, LYS47Z, LYS62Z, MET1H, PHE29H, PHE60Z, PRO32H, PRO38H, PRO42Z, SER38Z, THR40H, THR53Z, TYR25H, VAL31H, VAL36Z, VAL37H, VAL51Z, VAL57Z
• J-Q: ALA42J, ALA62Q, ALA66Q, ALA67Q, ALA68Q, ALA6J, ALA95Q, ARG34J, ARG35J, ARG37J, ARG49Q, ARG50Q, ARG52Q, ARG63Q, ARG69Q, ASN65Q, ASN71Q, ASP96Q, GLN55Q, GLN58Q, GLN70Q, GLU31J, GLU43J, GLY38J, HIS40J, HIS47J, ILE64Q, ILE93Q, ILE97Q, LEU59Q, LEU94Q, LYS102Q, LYS2J, LYS39J, LYS41J, LYS53Q, LYS7J, PHE100Q, PHE4J, PHE56Q, PRO46J, PRO8J, THR106Q, THR10J, THR3J, THR45J, THR5J, TRP60Q, TYR44J, VAL48J, VAL99Q
• J-R: ALA6J, ARG13R, ARG21R, GLN11R, GLN18R, GLY17R, GLY9R, HIS12R, LYS10R, LYS2J, LYS97R, MET1J, PHE4J, THR19R, THR3J, THR5J, VAL14R, VAL20R
• K-P: ALA119K, ALA11K, ALA57P, ALA83K, ARG100P, ARG102P, ARG105K, ARG108K, ARG38P, ARG50P, ARG64K, ARG70K, ARG71K, ARG71P, ARG78K, ASN65P, ASN82K, ASN9K, ASP73K, ASP80K, ASP81P, GLN74P, GLU106K, GLU110K, GLU121K, GLU33P, GLU43P, GLU67P, GLU70P, GLY101K, GLY104P, GLY34P, GLY44P, GLY68K, GLY68P, GLY74K, GLY81K, HIS76P, ILE63P, ILE77K, LEU39P, LYS28P, LYS36P, LYS37P, LYS62P, LYS66K, LYS67K, MET113K, PHE100K, PHE73P, PHE79K, PRO102K, PRO120K, PRO72K, PRO78P, SER109K, SER35P, SER64P, SER75K, SER77P, THR103P, THR104K, THR59P, THR75P, VAL103K, VAL122K, VAL31P, VAL45P, VAL60P, VAL69K, VAL69P, VAL72P, VAL76K, VAL79P, VAL80P
• L-Q: ARG12Q, GLY34L, PHE35Q
• L-R: ARG33L, ARG80R, ARG84R, GLN86R, GLY32L, GLY34L, HIS35L, LYS36L, LYS85R, TYR83R
• L-3: ALA103, ALA263, ALA593, ALA643, ALA72L, ALA93, ARG123, ARG293, ARG59L, ARG60L, ARG69L, ARG73, ASN273, ASP533, GLN54L, GLU51L, GLY523, GLY52L, GLY53L, GLY553, GLY65L, GLY83, HIS233, HIS253, HIS303, ILE33, ILE583, ILE73L, LEU283, LEU433, LEU543, LEU563, LEU57L, LEU61L, LYS113, LYS143, LYS223, LYS23, LYS243, LYS43, LYS513, LYS63L, MET483, MET55L, PHE133, PHE213, PHE50L, PHE64L, PHE66L, PRO56L, PRO62L, SER503, SER68L, THR53, THR67L, THR74L, TYR58L, TYR633, VAL493, VAL573, VAL63
• M-W: GLY6W, GLY7W, GLY83M, LYS84M, THR9W
• M-4: ARG114M, LYS84, LYS94
• N-S: ALA104N, ALA108N, ARG103N, ASN107N, ASN40S, ASP106N, CYS100N, GLY101N, LYS41S, LYS42S, PHE102N, THR37S, THR39S, TYR38S
• N-0: ALA111N, ALA440, ARG118N, ARG390, ARG490, ARG510, ARG96N, ASP450, CYS100N, GLU114N, GLU32N, GLY101N, GLY460, GLY500, HIS370, HIS400, HIS410, ILE113N, ILE33N, ILE34N, ILE420, ILE540, ILE97N, LEU380, LEU38N, LEU98N, LYS35N, LYS360, LYS520, LYS99N, MET110N, PHE102N, THR430, TYR112N, TYR470, TYR480, VAL530
• O-W: ALA46W, ALA48W, ARG15O, ARG16O, ARG54W, ARG76W, ASN43O, ASN75W, GLN19O, GLU20O, GLU84W, GLY44O, ILE79W, LEU18O, LEU21O, LYS17O, LYS43W, LYS74W, LYS77W, PHE78W, PRO73W, THR12O
• Q-R: ALA104Q, ALA107Q, ALA112Q, ALA3R, ALA41Q, ALA42R, ALA45Q, ALA85Q, ALA95Q, ALA98Q, ARG12Q, ARG13R, ARG21R, ARG47Q, ARG49Q, ARG50Q, ARG52Q, ARG78R, ARG79R, ARG80R, ARG90R, ARG91Q, ASN43R, ASP101Q, ASP48Q, ASP55R, ASP90Q, ASP96Q, GLN11R, GLN19Q, GLN43Q, GLN51Q, GLN6R, GLN87R, GLN91R, GLU110Q, GLU45R, GLU46R, GLU88Q, GLY42Q, GLY44R, GLY50R, GLY88R, GLY9R, HIS12R, HIS13Q, HIS82R, HIS89R, ILE16Q, ILE39Q, ILE41R, ILE49R, ILE79Q, ILE89Q, ILE93Q, ILE97Q, LEU108Q, LEU82Q, LEU94Q, LYS10R, LYS111Q, LYS15Q, LYS48R, LYS76R, LYS81R, LYS85R, LYS92Q, MET40R, PHE100Q, PHE105Q, PHE35Q, PHE53R, PHE5R, PHE77R, PHE78Q, PRO52R, SER7R, SER86Q, THR106Q, TRP60Q, TRP92R, TYR2R, TYR44Q, TYR46Q, TYR83R, VAL103Q, VAL109Q, VAL38Q, VAL47R, VAL4R, VAL51R, VAL54R, VAL75R, VAL87Q
• Q-0: ALA26Q, ARG120, ARG27Q, ARG29Q, ARG90, GLY25Q, LYS110, LYS60, SER100, SER28Q, THR80, TYR24Q, VAL30Q
• S-0: ALA200, ALA21S, ALA230, ALA32S, ARG120, ARG150, ARG160, ARG18S, ARG25S, ARG99S, ASN40S, ASP190, ASP22S, ASP34S, GLN15S, GLN31S, GLU350, GLY130, GLY340, HIS180, HIS370, HIS400, HIS410, ILE24S, ILE35S, ILE420, LEU19S, LEU210, LEU23S, LEU36S, LEU380, LYS16S, LYS28S, LYS360, LYS41S, SER280, SER330, THR220, THR250, THR37S, THR39S, TYR38S, VAL20S, VAL240
• T-X: ALA13T, ALA32X, ALA46T, ARG12T, ARG23X, ARG29X, ARG47X, ARG6T, ASN20X, ASN27X, GLN25X, GLN31X, GLU12X, GLU17X, GLU24X, GLU4T, GLU52T, HIS15T, ILE2T, LEU11T, LEU18X, LEU19X, LEU21X, LEU22X, LEU28X, LEU32T, LEU50T, LEU7T, LEU8T, LYS33T, LYS44X, LYS49T, LYS54X, LYS9T, MET30X, PHE26X, PHE51T, PRO14T, THR16X, TRP80T, VAL10T, VAL16T, VAL47T, VAL50X, VAL53T, VAL96T
• T-2: ARG412, ARG73T, GLY75T, ILE74T
• 1-3: ALA363, HIS303, ILE313, LEU101, LEU323, LYS241, LYS343, LYS353, LYS403, LYS91, PHE191, PHE381, THR211, THR221, THR231, THR333, THR373