3IZV

structural insights into cognate vs. near-cognate discrimination during decoding. this entry contains the small subunit of a ribosome programmed with a near-cognate codon, a/t-site trna, p-site trna, mrna and ef-tu

• Total interactions analyzed: 300
• Total true interactions: 28
• Strongest Interaction:
  • Chains: N-R
  • Int. Res.: 52
  • Norm. En. per Res.: -4.7062
• Hub Node: F(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-P	0.0	0.0	-0.1715	-0.1715	4	0	0	36	0	5	5
F-G	0.0	0.0	-0.0003	-0.0003	2	0	0	1	0	1	0
F-I	0.0	-1.9342	-102.439	-104.3732	42	0	2	3864	0	6	9
F-L	0.0	0.0	-0.4727	-0.4727	4	0	0	93	0	0	1
F-Y	-6.2505	0.0	-17.8844	-24.1349	13	1	0	828	0	1	7
G-I	-8.6956	-1.6323	-14.8147	-25.1427	22	0	0	849	1	11	10
G-N	-19.391	-14.2877	-348.659	-382.3377	120	5	7	13400	2	36	43
G-R	-11.8357	-20.6847	-299.783	-332.3034	78	10	4	10364	3	30	30
H-I	0.0	-16.5907	-62.7759	-79.3666	32	0	1	2280	1	11	9
I-L	-7.0248	0.0	-136.202	-143.2268	46	3	3	5285	1	9	7
J-O	0.0	0.0	-0.0003	-0.0003	2	0	0	1	0	0	1
J-V	-25.5664	-26.0161	-322.714	-374.2965	92	7	3	11619	5	44	58
J-Y	0.0	0.0	-0.0008	-0.0008	2	0	0	2	0	0	1
K-M	-10.329	8.7756	-96.2163	-97.7697	49	7	0	3835	0	16	19
K-O	0.0	0.0	-24.0576	-24.0576	15	0	0	934	2	3	4
K-Y	-10.6613	2.081	-34.6306	-43.2109	23	1	0	1148	0	1	9
L-P	0.0	0.0	-1.7218	-1.7218	7	0	1	188	0	0	0
L-U	0.0	0.0	-45.2794	-45.2794	19	1	0	1879	0	4	11
M-N	-7.8146	0.0	-32.7383	-40.5529	20	3	0	1492	0	12	13
M-R	0.0	0.0	-14.6459	-14.6459	13	0	0	534	0	0	2
N-R	-23.5571	-12.2477	-208.92	-244.7248	52	5	7	8100	1	16	25
O-V	-12.0346	-1.7603	-46.9022	-60.6971	27	2	0	1830	0	4	10
O-Y	-22.5664	-48.7926	-301.945	-373.304	81	7	5	11523	4	31	34
P-U	0.0	15.5742	-80.7899	-65.2157	24	1	4	3231	0	0	10
Q-W	-18.3967	-2.1422	-127.565	-148.1039	62	3	0	5496	0	13	46
R-W	-6.5337	-6.5462	-176.062	-189.1419	53	4	1	6975	1	19	23
S-U	0.0	0.0	-0.652	-0.652	6	0	0	123	0	0	0
V-Y	0.0	-11.9787	-5.2306	-17.2094	13	0	0	402	0	5	2

Interface residues

• C-P: ARG30P, GLU249C, GLU284C, LYS119P
• F-G: GLU214G, LYS127F
• F-I: ALA184F, ALA52F, ALA54F, ARG68I, ASN177F, ASN50F, ASN57F, ASP196F, GLU162I, GLU51F, GLU55F, GLY165I, ILE163I, ILE185F, ILE199F, LEU164I, LEU178F, LEU53F, LEU56F, LYS104F, LYS166I, LYS58F, LYS65I, MET48F, PHE161F, PHE183F, PHE197F, PHE29F, PHE31F, PHE49F, PRO200F, PRO28F, PRO47F, SER159I, THR101F, THR45F, TYR212F, VAL160I, VAL182F, VAL186F, VAL198F, VAL46F
• F-L: ALA19L, ASN20L, LYS21L, LYS27F
• F-Y: ALA64Y, ARG138F, ARG66Y, ARG68Y, ARG73F, ARG94F, ASN145F, GLU141F, HIS93F, LEU69Y, LYS142F, THR67Y, TYR70Y
• G-I: ALA57I, ARG130G, ARG163G, ARG168G, ARG28I, ARG53I, GLN60I, GLU165G, GLU169G, GLU54I, ILE161G, LYS134G, LYS149G, MET128G, MET133G, PHE129G, PHE30I, PHE32I, PRO56I, TRP166G, TYR167G, VAL55I
• G-N: ALA12N, ALA21N, ALA23G, ALA23N, ALA34N, ALA60G, ALA61N, ALA86N, ALA93N, ALA94N, ALA98G, ARG10G, ARG16N, ARG228G, ARG231G, ARG31N, ARG37N, ARG45N, ARG48N, ARG58G, ARG64G, ARG68N, ARG72N, ARG87G, ARG89N, ARG9N, ASN101G, ASN24G, ASN31G, ASN58N, ASP14N, ASP19N, ASP63N, ASP75N, ASP85N, ASP91N, ASP97N, GLN20N, GLN222G, GLN226G, GLN227G, GLN2G, GLN35N, GLN99G, GLN99N, GLU104G, GLU24N, GLU27G, GLU27N, GLU47N, GLU57G, GLY12G, GLY1G, GLY230G, GLY38N, GLY8G, GLY95N, HIS15N, HIS70N, ILE100G, ILE13G, ILE18N, ILE25N, ILE40N, ILE53N, ILE56G, ILE63G, ILE67N, ILE76N, ILE9G, LEU10N, LEU11G, LEU17N, LEU32G, LEU71N, LEU73N, LEU87N, LEU90N, LEU92N, LYS11N, LYS224G, LYS225G, LYS229G, LYS26G, LYS30N, LYS46N, LYS61G, MET1N, MET88N, PHE13N, PHE22G, PHE28G, PHE49N, PRO16G, PRO223G, PRO39N, PRO41N, PRO59G, PRO97G, SER19G, SER62G, THR20G, THR22N, THR25G, THR28N, THR44N, THR69N, TRP17G, TRP21G, TYR65N, VAL14G, VAL26N, VAL36N, VAL4G, VAL51N, VAL74N, VAL84N, VAL96G, VAL96N, VAL98N
• G-R: ALA23G, ALA29G, ALA86R, ALA87R, ALA98R, ARG10G, ARG39G, ARG53G, ARG58G, ARG64R, ARG74R, ARG84R, ARG89R, ASN184G, ASN18G, ASN24G, ASN31G, ASN7G, ASP30G, ASP33G, ASP35G, CYS63R, GLN2G, GLN40G, GLN65R, GLU187G, GLU27G, GLU57G, GLU85R, GLU91R, GLY12G, GLY1G, GLY77R, GLY8G, GLY90R, GLY94R, HIS5G, ILE13G, ILE54G, ILE56G, ILE92R, ILE9G, LEU11G, LEU177G, LEU32G, LEU73R, LEU78R, LEU95R, LYS198G, LYS26G, LYS37G, LYS3G, LYS75R, LYS82R, LYS96R, LYS97R, MET88R, PHE22G, PHE28G, PHE36G, PHE76R, PRO16G, PRO6G, PRO93R, SER19G, SER34G, SER99R, THR185G, THR20G, THR25G, THR66R, TRP17G, TRP200G, TRP21G, TYR183G, VAL4G, VAL55G, VAL83R
• H-I: ALA106I, ARG111I, ASN121I, ASN195H, ASN84H, ASP49H, GLN53H, GLU100I, GLU115I, GLU196H, GLU201H, GLU87H, GLY101I, GLY103I, GLY107I, GLY108I, GLY78I, GLY83H, GLY86H, HIS120I, HIS197H, ILE104I, ILE105I, ILE199H, LEU114I, LEU198H, SER204H, THR102I, THR85H, VAL119I, VAL200H, VAL52H
• I-L: ALA129L, ALA153I, ALA154I, ALA69L, ALA96L, ARG113L, ARG156I, ASN145I, ASN147I, GLN66L, GLN81I, GLU144I, GLU150I, GLU42L, GLU46L, GLU72L, GLY157I, GLY43L, GLY67L, GLY97L, GLY99L, HIS82I, ILE100L, LEU62L, LEU98L, LYS155I, LYS158I, LYS63L, LYS68L, LYS85I, LYS93L, MET146I, MET151I, MET95L, PHE44L, PHE65L, PRO149I, PRO83I, SER148I, SER73L, TYR64L, VAL128L, VAL152I, VAL70L, VAL71L, VAL94L
• J-O: ARG112J, HIS117O
• J-V: ALA105J, ALA117J, ALA26V, ALA48J, ALA57J, ALA57V, ALA61V, ALA95J, ARG109J, ARG110J, ARG112J, ARG113J, ARG38J, ARG44J, ARG45J, ARG60V, ARG62V, ARG72V, ARG86J, ARG91J, ASN30V, ASN63J, ASP107J, ASP114J, ASP115J, ASP21V, ASP24V, ASP41J, ASP71V, GLN18V, GLN46J, GLN74V, GLU108J, GLU111J, GLU135J, GLU19V, GLU34V, GLU40J, GLU5J, GLU98J, GLY36V, GLY43J, HIS55J, HIS73V, HIS94J, ILE25V, ILE32V, ILE6J, LEU28V, LEU39J, LEU47J, LEU61J, LEU64V, LEU66V, LEU67V, LYS104J, LYS106J, LYS23V, LYS29V, LYS37V, LYS56J, LYS93J, MET102J, MET62J, MET88J, MET90J, MET9J, PHE116J, PHE8J, PRO101J, PRO68V, SER35V, SER65V, SER87J, THR27V, THR33V, THR70V, THR92J, THR97J, TRP42J, TYR22V, TYR49J, TYR4J, TYR59J, TYR63V, TYR69V, VAL103J, VAL60J, VAL64J, VAL7J, VAL89J, VAL96J
• J-Y: ARG112J, LYS4Y
• K-M: ALA107M, ALA43M, ALA75M, ARG105M, ARG108M, ARG11M, ARG121M, ARG40M, ARG44M, ARG48M, ARG79M, ARG9K, ASN27K, ASP106M, ASP14K, GLN109M, GLN49M, GLU20K, GLU35M, GLU39K, GLU41M, GLU52M, GLY101M, GLY18K, GLY76M, ILE11K, ILE71M, LEU12K, LEU53M, LYS10K, LYS12M, LYS16K, LYS35K, MET45M, PHE102M, PHE17K, PRO13K, PRO15K, SER19K, SER36K, SER40K, SER72M, THR104M, THR37K, THR42M, TYR43K, VAL26K, VAL46M, VAL47M
• K-O: ALA144K, ALA146K, ALA61O, ALA98O, ARG55O, ARG97O, ASN147K, GLN63O, GLU145K, LYS148K, PHE60O, PRO59O, SER94O, THR58O, TRP155K
• K-Y: ALA14Y, ALA167K, ARG159K, ARG16Y, ARG17Y, ARG20Y, GLN171K, LEU156K, LEU158K, LEU15Y, LYS170K, LYS24Y, LYS58Y, PHE161K, PHE18Y, PRO172K, SER157K, SER160K, SER162K, SER168K, SER169K, TRP155K, VAL13Y
• L-P: ARG79L, ASN4P, GLY81L, LEU82L, PRO80L, VAL3P, VAL7P
• L-U: ARG79L, ARG83L, GLU123L, GLY34U, GLY81L, HIS30U, ILE124L, ILE37U, ILE84L, LEU82L, LYS29U, LYS35U, LYS86L, PHE27U, PHE36U, PRO80L, SER78L, TYR33U, TYR85L
• M-N: ALA61N, ARG112M, ARG118M, ARG48N, ARG62N, ASN58N, ASP60N, ASP63N, GLN64N, GLU66N, GLY116M, LEU117M, LYS113M, LYS114M, LYS59N, PHE49N, THR50N, TYR65N, VAL115M, VAL51N
• M-R: ALA98R, ARG112M, ARG80R, GLN109M, GLU111M, GLY116M, LYS113M, LYS114M, LYS97R, SER99R, TRP100R, VAL110M, VAL115M
• N-R: ALA12N, ALA87R, ALA98R, ARG45N, ARG48N, ARG62N, ARG68N, ARG68R, ARG80R, ARG84R, ASN58N, ASP14N, ASP63N, GLN64N, GLU47N, GLU66N, GLU85R, GLY71R, GLY94R, GLY95N, HIS15N, HIS56N, HIS70N, ILE53N, ILE67N, ILE81R, ILE92R, LEU17N, LEU52N, LEU73R, LEU95R, LYS46N, LYS59N, LYS75R, LYS82R, LYS96R, LYS97R, MET88R, PHE13N, PHE49N, PHE76R, PRO55N, PRO93R, SER54N, SER79R, SER99R, THR50N, THR69N, TRP100R, TYR65N, VAL51N, VAL83R
• O-V: ARG62V, ARG72V, ASN118O, ASP111O, ASP71V, GLN74V, GLU34V, GLY119O, GLY36V, HIS117O, HIS73V, ILE115O, LEU67V, LYS37V, LYS86O, PRO114O, PRO116O, PRO68V, SER35V, THR110O, THR113O, THR33V, THR70V, TYR63V, TYR69V, VAL112O, VAL85O
• O-Y: ALA101O, ALA14Y, ALA24O, ALA25Y, ALA98O, ARG105O, ARG121O, ARG126O, ARG127O, ARG16Y, ARG20Y, ARG32Y, ARG33Y, ARG34Y, ARG6Y, ARG92O, ARG97O, ASN100O, ASN108O, ASN118O, ASN8Y, ASP111O, ASP12Y, CYS120O, CYS22Y, GLU23Y, GLU30Y, GLU7Y, GLU82O, GLU93O, GLU9Y, GLY87O, GLY89O, GLY91O, HIS117O, HIS23O, ILE106O, ILE109O, ILE115O, ILE22O, ILE3Y, ILE96O, LEU15Y, LEU28Y, LEU81O, LEU99O, LYS124O, LYS125O, LYS19Y, LYS24Y, LYS4Y, LYS86O, MET84O, PHE104O, PHE11Y, PHE18Y, PHE26O, PHE36Y, PRO10Y, PRO114O, PRO116O, PRO122O, PRO123O, PRO1Y, PRO88O, PRO90O, SER21Y, SER94O, THR107O, THR110O, THR113O, THR95O, VAL112O, VAL128O, VAL13Y, VAL27Y, VAL2Y, VAL31Y, VAL5Y, VAL83O, VAL85O
• P-U: ARG11P, ARG13P, ARG39U, ARG8P, ASN4P, GLN5P, GLY34U, HIS30U, ILE32U, ILE37U, LEU6P, LYS29U, LYS35U, LYS38U, LYS9P, PHE27U, PHE36U, PRO10P, PRO31U, THR40U, TYR33U, VAL28U, VAL3P, VAL7P
• Q-W: ALA74W, ALA83W, ALA84W, ARG2W, ARG35W, ARG77W, ARG78Q, ARG80W, ARG86Q, ARG89Q, ARG91Q, ARG92Q, ARG97Q, ASN52W, ASP63W, ASP81Q, ASP85W, CYS84Q, GLN99Q, GLU64W, GLU72W, GLY71W, GLY81W, GLY83Q, GLY87Q, GLY93Q, GLY98Q, HIS68W, HIS82W, ILE115Q, LEU4W, LEU79Q, LEU82Q, LEU88Q, LEU94Q, LYS109Q, LYS113Q, LYS116Q, LYS117Q, LYS69W, LYS86W, LYS87W, LYS91W, MET65W, MET74Q, PHE60W, PHE73W, PRO1W, PRO75W, SER3W, SER75Q, THR101Q, THR62W, THR76W, THR78W, TYR79W, TYR85Q, VAL57W, VAL59W, VAL61W, VAL66W, VAL96Q
• R-W: ALA35R, ALA43R, ARG36W, ARG40R, ARG52R, ARG58R, ASN34R, ASN42R, ASN42W, ASP11W, ASP32R, ASP37R, ASP39R, ASP53R, GLN48R, GLU19W, GLU38R, GLY67W, GLY7W, HIS13W, ILE10W, ILE30R, ILE39W, LEU12W, LEU14W, LEU15W, LEU45R, LEU46W, LEU47R, LEU4W, LEU50R, LYS16W, LYS20W, LYS27R, LYS46R, LYS5W, LYS69W, LYS6W, MET43W, PHE40W, PHE9W, PRO41W, PRO51R, PRO8W, SER31R, SER36R, SER37W, THR38W, THR49R, TRP41R, VAL18W, VAL33R, VAL44R
• S-U: ARG71S, ASP73S, LEU83U, LYS70S, VAL74S, VAL82U
• V-Y: ARG72V, ASP71V, GLU30Y, GLU34V, GLY26Y, LYS37V, LYS4Y, PHE18Y, PRO1Y, SER21Y, SER35V, THR70V, VAL27Y