3IZU

structural insights into cognate vs. near-cognate discrimination during decoding. this entry contains the large subunit of a ribosome programmed with a cognate codon

• Total interactions analyzed: 528
• Total true interactions: 28
• Strongest Interaction:
  • Chains: L-Q
  • Int. Res.: 80
  • Norm. En. per Res.: -4.8547
• 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
D-I	-12.6368	8.3066	-124.419	-128.7491	44	7	0	4050	3	21	14
E-K	-6.0343	5.26	-29.7488	-30.5231	18	1	1	1177	0	1	6
E-L	0.0	-7.0261	-39.9726	-46.9987	20	2	0	1297	0	2	7
E-O	0.0	2.517	-13.9294	-11.4124	12	1	0	893	0	0	7
E-Q	0.0	2.2976	-115.308	-113.0104	54	1	3	5129	0	12	14
F-M	-6.9466	-27.0318	-160.613	-194.5914	47	4	5	5628	0	8	8
F-R	0.0	0.0	-1.0688	-1.0688	12	0	0	259	0	0	5
F-e	0.0	0.0	-0.5537	-0.5537	4	0	0	98	0	0	0
G-b	-10.409	-27.8824	-337.375	-375.6664	89	8	7	12021	3	37	44
H-g	0.0	0.0	-0.5094	-0.5094	6	0	0	150	0	3	6
I-Y	0.0	3.4469	-66.5069	-63.06	46	0	0	3030	0	8	13
K-R	-2.8638	-0.0308	-99.9209	-102.8155	47	1	4	4004	0	7	20
K-S	0.0	0.0	-15.4415	-15.4415	14	2	0	1053	0	0	4
L-Q	-47.7403	-89.5982	-251.034	-388.3725	80	11	2	8402	12	32	30
M-R	0.0	0.0	-0.0534	-0.0534	9	0	0	44	0	0	3
M-S	0.0	0.0	-36.5713	-36.5713	17	1	0	1122	0	0	7
M-f	-7.0959	18.9001	-175.846	-164.0418	58	4	4	7529	0	4	31
N-W	-7.7759	-9.7421	-75.6124	-93.1303	48	1	3	3217	0	5	10
N-X	-15.3431	16.6297	-69.2845	-67.9979	30	3	0	2512	0	2	15
N-g	0.0	0.0	-0.0303	-0.0303	2	0	0	17	0	0	1
O-T	0.0	0.0	-23.517	-23.517	17	1	0	646	0	2	2
O-c	-17.0878	30.3883	-275.784	-262.4835	61	5	9	8816	2	27	35
P-X	0.0	1.0676	-0.8398	0.2278	14	0	0	200	0	7	11
R-S	-22.5939	-34.8821	-227.311	-284.787	96	8	7	9545	4	22	42
R-c	0.0	8.6537	-6.9045	1.7492	13	0	0	360	0	0	5
T-c	-3.7425	5.864	-77.9844	-75.8629	47	0	6	3949	0	13	9
U-Z	-18.3788	27.2745	-128.163	-119.2673	56	3	5	5693	0	12	18
d-f	0.0	1.2154	-20.819	-19.6036	22	1	0	1014	0	1	7

Interface residues

• D-I: ALA121D, ALA122D, ALA169D, ALA185D, ARG123I, ARG132D, ARG166D, ARG188D, ASN119I, ASN127D, ASN133D, ASP120D, ASP167D, ASP186D, ASP71D, ASP86I, CYS187D, GLN116D, GLU184D, GLU87I, GLY118D, GLY120I, GLY168D, GLY72D, GLY85I, GLY88I, HIS128I, ILE123D, ILE134D, LEU129D, LEU90I, LYS89I, MET131D, PHE91I, PRO130D, PRO147D, SER117D, THR124I, THR125I, THR128D, TYR170D, VAL119D, VAL121I, VAL171D
• E-K: ASN42E, ASP43E, GLN148E, GLU129K, GLY158E, GLY79K, GLY82K, HIS77K, HIS80K, ILE146E, ILE81K, LYS154E, LYS157E, LYS159E, PHE156E, PRO152E, THR78K, VAL155E
• E-L: ARG128E, ARG13E, ARG31L, ARG70L, ARG71L, ASP18E, ASP73L, GLY19E, GLY74L, HIS29L, ILE14E, ILE22E, LYS190E, PHE15E, PRO23E, PRO72L, SER21E, SER75L, THR16E, VAL20E
• E-O: ALA196E, ARG4O, ASN167E, GLY115E, GLY117E, GLY198E, HIS3O, LYS114E, LYS116E, LYS123E, MET1O, THR197E
• E-Q: ALA57Q, ARG13E, ARG179E, ARG184E, ASP181E, ASP18E, GLN11Q, GLN6Q, GLN74Q, GLN9Q, GLU10Q, GLU17E, GLU28E, GLU8Q, GLY10E, GLY198E, GLY19E, GLY53Q, HIS55Q, HIS76Q, ILE14E, ILE22E, ILE27E, ILE3Q, ILE4Q, LEU186E, LEU188E, LEU54Q, LEU7Q, LYS13Q, LYS37Q, LYS5Q, LYS7E, LYS8E, MET11E, MET12Q, PHE15E, PRO23E, PRO78Q, SER21E, SER56Q, SER77Q, THR12E, THR16E, THR197E, THR75Q, TRP30Q, VAL20E, VAL24E, VAL26E, VAL32Q, VAL79Q, VAL80Q, VAL9E
• F-M: ALA182F, ALA26F, ALA9M, ARG114F, ARG117F, ARG2M, ARG33M, ARG41M, ARG69F, ASN24F, ASN4M, ASP145F, ASP184F, GLN115F, GLN30F, GLN94F, GLU10M, GLU111F, GLU25F, HIS29F, ILE108F, ILE181F, LEU112F, LEU180F, LEU27F, LEU3M, LEU6M, LYS13M, LYS185F, MET1M, PHE183F, PHE23F, PHE85F, PRO177F, PRO8M, SER107F, SER12M, SER179F, SER42M, SER7M, THR5M, VAL178F, VAL186F, VAL28F, VAL31F, VAL32F, VAL33F
• F-R: ALA1R, ALA45F, ARG2R, ARG44F, ARG5R, ARG79F, GLN46F, GLY81F, GLY82F, LYS47F, LYS4R, VAL83F
• F-e: GLY54F, LYS37e, SER55F, THR53F
• G-b: ALA106G, ALA14b, ALA1G, ALA57G, ALA58G, ARG101G, ARG109G, ARG111G, ARG114G, ARG25b, ARG91G, ARG94G, ASN20b, ASN33b, ASP112G, ASP141G, ASP31b, ASP35b, ASP4b, ASP55G, CYS16b, CYS37b, GLN62G, GLU100G, GLU10b, GLU11b, GLU139G, GLU93G, GLU97G, GLY115G, GLY19b, GLY29b, GLY61G, GLY92G, HIS30b, HIS41b, HIS6b, ILE103G, ILE105G, ILE110G, ILE12b, ILE136G, ILE140G, ILE24b, ILE59G, ILE5b, LEU102G, LEU116G, LEU169G, LEU32b, LEU34b, LEU35G, LEU56G, LEU90G, LYS144G, LYS23b, LYS2G, LYS2b, LYS39b, LYS3b, LYS63G, LYS8b, MET1b, MET22b, MET95G, PHE113G, PHE137G, PHE172G, PHE43b, PHE98G, PRO108G, PRO138G, PRO42b, PRO7b, SER15b, SER17b, SER26b, SER38b, SER60G, THR104G, THR13b, THR27b, THR89G, TRP96G, TYR9b, VAL107G, VAL28b, VAL36b, VAL88G
• H-g: ARG169H, GLU30g, LYS171H, LYS174H, LYS32g, PRO31g
• I-Y: ALA23I, ALA26I, ALA36I, ALA39I, ALA52Y, ARG27I, ARG36Y, ARG44Y, ARG56Y, ASN28I, ASN43I, ASP59Y, GLN2I, GLN33I, GLU40Y, GLY24I, GLY34I, GLY54Y, GLY62Y, HIS33Y, HIS35Y, ILE58Y, ILE63Y, LEU30I, LYS22I, LYS35I, LYS43Y, LYS53Y, LYS60Y, LYS61Y, MET1I, MET55Y, PHE29I, PHE37Y, PHE45Y, PRO32I, PRO38I, SER51Y, THR40I, THR65Y, TRP38Y, VAL31I, VAL39Y, VAL3I, VAL50Y, VAL57Y
• K-R: ALA42K, ALA62R, ALA66R, ALA67R, ALA68R, ALA6K, ALA95R, ALA98R, ARG34K, ARG35K, ARG54R, ARG57R, ARG63R, ARG69R, ARG91R, ASN65R, ASP101R, ASP96R, GLN55R, GLN58R, GLN70R, GLU31K, GLU43K, GLY38K, HIS40K, HIS47K, ILE142K, ILE61R, ILE64R, ILE93R, ILE97R, LEU59R, LYS2K, LYS39K, LYS41K, LYS92R, MET1K, PHE100R, PHE4K, PHE56R, PRO46K, THR3K, THR45K, THR5K, TRP60R, TYR44K, VAL99R
• K-S: ARG13S, ARG21S, GLN11S, HIS12S, LEU22S, LYS10S, LYS2K, MET1K, PHE4K, THR3K, TYR2S, VAL14S, VAL20S, VAL4S
• L-Q: ALA119L, ALA11L, ALA41Q, ALA57Q, ALA83L, ARG100Q, ARG105L, ARG108L, ARG18L, ARG38Q, ARG61Q, ARG64L, ARG70L, ARG71L, ARG71Q, ARG78L, ASN65Q, ASN82L, ASN9L, ASP73L, ASP80L, CYS84L, GLN40Q, GLN74Q, GLU101Q, GLU106L, GLU121L, GLU33Q, GLU67Q, GLU70Q, GLY101L, GLY34Q, GLY66Q, GLY68L, GLY68Q, GLY74L, GLY81L, HIS55Q, HIS76Q, ILE47Q, ILE63Q, ILE77L, ILE99L, LEU123L, LYS36Q, LYS62Q, LYS66L, MET113L, PHE100L, PHE42Q, PHE58Q, PHE73Q, PHE79L, PRO102L, PRO120L, PRO72L, PRO78Q, SER35Q, SER56Q, SER64Q, SER75L, SER77Q, THR104L, THR59Q, THR65L, THR75Q, VAL103L, VAL10L, VAL122L, VAL29Q, VAL31Q, VAL32Q, VAL60Q, VAL63L, VAL69L, VAL69Q, VAL72Q, VAL76L, VAL79Q, VAL80Q
• M-R: ARG12R, ARG18M, ARG21M, ARG5R, GLY22M, GLY24M, ILE23M, PHE35R, VAL3R
• M-S: ARG21M, ARG78S, ARG84S, GLY22M, GLY24M, GLY26M, GLY28M, GLY31M, HIS82S, ILE23M, LEU27M, LYS29M, LYS81S, LYS85S, PHE77S, SER25M, TYR83S
• M-f: ALA10f, ALA26f, ALA47f, ALA59f, ALA9f, ARG12f, ARG29f, ARG47M, ARG48M, ARG59M, ARG60M, ARG7f, ASN27f, ASP53f, CYS60f, GLN54M, GLU51M, GLY49M, GLY52f, GLY55f, GLY65M, GLY8f, HIS23f, HIS25f, ILE3f, ILE58f, LEU28f, LEU54f, LEU56f, LEU57M, LEU61M, LEU61f, LYS11f, LYS14f, LYS15f, LYS22f, LYS24f, LYS46f, LYS4f, LYS63M, MET48f, MET55M, PHE13f, PHE21f, PHE50M, PHE64M, PHE66M, PRO56M, PRO62M, PRO62f, SER50f, THR5f, THR67M, TYR58M, TYR63f, VAL49f, VAL57f, VAL6f
• N-W: ALA21N, ALA35N, ALA54W, ALA74W, ARG79W, ASP25N, ASP76W, ASP90W, GLN51W, GLN75W, GLN78W, GLN87W, GLN97N, GLU55W, GLU59W, GLY19N, GLY37N, GLY99N, HIS80W, ILE89W, LEU20N, LEU61W, LYS100N, LYS133N, LYS34N, LYS53W, LYS73W, LYS83W, MET136N, PHE130N, PHE56W, PHE91W, PRO81W, PRO84W, PRO98N, SER58W, THR128N, THR129N, THR134N, THR24N, TYR57W, TYR82W, VAL131N, VAL135N, VAL26N, VAL36N, VAL77W, VAL92W
• N-X: ALA1X, ALA5X, ARG10N, ARG6N, ASN88N, GLU75N, GLU90N, GLY6X, GLY7X, GLY85N, GLY87N, HIS2X, ILE73N, LYS11N, LYS3X, LYS4X, LYS84N, LYS86N, LYS8N, MET12N, PHE9N, PRO72N, PRO77N, SER8X, THR74N, THR7N, THR9X, TRP92N, TYR91N, VAL89N
• N-g: LYS118N, LYS8g
• O-T: ALA104O, ALA44T, ARG103O, ASN107O, ASN40T, ASP106O, CYS100O, GLY101O, ILE35T, LEU36T, LYS41T, LYS42T, PHE102O, THR37T, THR39T, TYR38T, VAL45T
• O-c: ALA111O, ALA122O, ALA124O, ALA125O, ALA126O, ALA44c, ALA55c, ARG118O, ARG39c, ARG49c, ARG51c, ARG86O, ARG96O, ASN107O, ASP30c, ASP45c, CYS100O, GLU114O, GLU120O, GLU123O, GLU127O, GLU32O, GLU35c, GLY101O, GLY34c, GLY46c, GLY50c, HIS31O, HIS37c, HIS40c, HIS41c, ILE113O, ILE33O, ILE34O, ILE42c, ILE54c, ILE97O, LEU115O, LEU38O, LEU38c, LEU98O, LYS121O, LYS31c, LYS35O, LYS52c, LYS56c, LYS99O, MET110O, PHE102O, PRO109O, SER119O, SER33c, THR22c, THR32c, THR43c, THR95O, TYR112O, TYR47c, TYR48c, VAL116O, VAL53c
• P-X: ALA46X, ARG13P, ARG16P, ARG76X, GLN19P, GLU20P, GLY47X, HIS45X, LEU21P, LYS71X, PHE44X, PHE78X, PRO73X, THR12P
• R-S: ALA104R, ALA107R, ALA115R, ALA3S, ALA41R, ALA42S, ALA45R, ALA85R, ALA95R, ARG12R, ARG13S, ARG47R, ARG49R, ARG50R, ARG52R, ARG63R, ARG78S, ARG79S, ARG84S, ARG91R, ASN43S, ASP90R, ASP96R, GLN11S, GLN19R, GLN36R, GLN43R, GLN6S, GLN86S, GLN87S, GLU110R, GLU37S, GLU45S, GLU46S, GLU88R, GLY42R, GLY44S, GLY50S, GLY88S, GLY8S, GLY9S, HIS12S, HIS89S, ILE39R, ILE41S, ILE49S, ILE74S, ILE89R, ILE93R, ILE97R, LEU108R, LEU39S, LEU82R, LEU94R, LYS102R, LYS10S, LYS111R, LYS15R, LYS18R, LYS40R, LYS48S, LYS53R, LYS71S, LYS73S, LYS76S, LYS84R, LYS85S, LYS92R, MET40S, PHE100R, PHE105R, PHE35R, PHE53S, PHE5S, PHE77S, PRO52S, SER7S, SER86R, THR106R, TRP60R, TYR2S, TYR44R, TYR46R, VAL103R, VAL109R, VAL14S, VAL38R, VAL38S, VAL47S, VAL4S, VAL51S, VAL54S, VAL72S, VAL75S, VAL87R, VAL99R
• R-c: ALA26R, ARG12c, ARG27R, ARG29R, ARG9c, GLY25R, LYS11c, LYS6c, MET14c, SER10c, THR8c, TYR24R, VAL30R
• T-c: ALA20c, ALA21T, ALA23c, ALA43T, ALA44T, ALA44c, ARG12c, ARG16c, ARG18T, ARG39c, ARG99T, ASN40T, ASP19c, ASP22T, ASP34T, GLN15T, GLN31T, GLU35c, GLY13c, HIS37c, HIS41c, ILE24T, ILE35T, ILE42c, LEU19T, LEU21c, LEU23T, LEU27c, LEU36T, LEU38c, LYS16T, LYS27T, LYS36c, LYS41T, SER13T, SER26c, SER28c, SER30T, THR22c, THR25c, THR37T, THR39T, THR43c, TYR38T, VAL17T, VAL20T, VAL24c
• U-Z: ALA13U, ALA32Z, ALA33Z, ALA35U, ALA45U, ALA46U, ALA99U, ARG12U, ARG23Z, ARG29Z, ARG69U, ARG6U, ARG77U, ASN20Z, ASN27Z, ASP94U, GLN25Z, GLN31Z, GLN36Z, GLN48U, GLU100U, GLU17Z, GLU24Z, GLU4U, GLU5U, GLY35Z, GLY97U, GLY98U, LEU11U, LEU18Z, LEU19Z, LEU21Z, LEU22Z, LEU28Z, LEU32U, LEU50U, LEU7U, LEU8U, LEU93U, LYS33U, LYS49U, LYS54Z, LYS68U, LYS9U, MET1U, MET30Z, PHE26Z, PHE51U, PRO14U, SER34Z, VAL10U, VAL16U, VAL46Z, VAL47U, VAL50Z, VAL96U
• d-f: ARG41f, ARG44f, GLU6d, HIS30f, ILE31f, ILE8d, LEU32f, LYS24d, LYS34f, LYS35f, LYS37d, LYS40f, LYS7d, LYS9d, PHE19d, PRO40d, THR21d, THR22d, THR23d, THR33f, THR37f, TYR20d