3IZW

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

• Total interactions analyzed: 300
• Total true interactions: 26
• Strongest Interaction:
  • Chains: N-R
  • Int. Res.: 52
  • Norm. En. per Res.: -5.0692
• Hub Node: G(3)

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	-1.4636	-1.4636	6	0	0	75	1	6	7
F-I	0.0	0.0	-0.1785	-0.1785	5	0	0	70	0	1	3
F-L	0.0	0.0	-1.1246	-1.1246	5	0	0	136	0	1	3
F-Y	0.0	-4.3274	-0.0293	-4.3567	2	0	0	6	0	7	3
G-I	0.0	-10.3939	-6.6068	-17.0006	18	0	0	460	0	9	6
G-N	-10.8985	-9.7488	-238.252	-258.8993	107	5	4	9538	2	30	38
G-R	-19.6173	-23.2338	-247.433	-290.2841	72	10	5	8079	4	27	29
H-I	0.0	-0.6072	-65.0492	-65.6564	37	0	0	2488	0	12	9
H-T	0.0	0.0	-0.0324	-0.0324	3	0	0	7	0	1	0
I-L	-8.716	4.4931	-105.418	-109.641	57	5	4	4744	1	17	15
J-V	-27.4116	-39.8109	-317.387	-384.6095	84	11	5	12183	4	45	56
K-M	0.0	18.7808	-48.3841	-29.6033	38	0	0	2190	0	13	12
K-O	-8.1635	0.0	-36.6323	-44.7958	21	0	1	1521	0	4	3
K-Y	-18.9759	18.7701	-68.1848	-68.3906	29	8	0	2814	0	1	18
L-P	0.0	0.0	-3.4981	-3.4981	9	0	1	249	0	0	0
L-U	0.0	0.8979	-18.6735	-17.7756	15	0	0	1209	0	3	8
M-N	0.0	0.0	-23.3514	-23.3514	19	0	0	1203	0	10	14
M-R	0.0	0.0	-25.5808	-25.5808	10	0	0	726	0	0	2
N-R	-37.514	-8.1363	-217.947	-263.5973	52	8	8	8098	2	18	24
O-V	-11.4499	9.7743	-39.2272	-40.9029	22	1	0	1797	0	5	10
O-Y	-8.8194	-10.8993	-237.919	-257.6377	74	8	4	9584	0	30	35
P-U	0.0	0.0	-51.8346	-51.8346	20	0	4	2196	0	0	7
Q-W	-10.1367	19.2177	-160.041	-150.96	71	8	1	6549	0	17	59
R-W	0.0	-1.3249	-99.2609	-100.5858	46	5	1	4533	0	15	20
S-U	0.0	0.0	-0.2348	-0.2348	3	0	0	61	0	0	0
V-Y	0.0	0.0	-2.6633	-2.6633	11	0	0	333	0	7	6

Interface residues

• C-P: ALA123P, GLU249C, LYS119P, LYS122P, SER393C, THR250C
• F-I: ARG68I, GLU64I, LYS104F, LYS61I, LYS65I
• F-L: ALA18L, ALA19L, ASN20L, LYS25F, PRO24F
• F-Y: ARG68Y, ASP204F
• G-I: ALA57I, ARG130G, ARG131G, ARG163G, ARG19I, ARG28I, ARG53I, GLU160G, GLU54I, ILE161G, ILE29I, LYS134G, MET128G, MET133G, PHE30I, PHE32I, PRO56I, TYR167G
• G-N: ALA12N, ALA23G, ALA23N, ALA29N, ALA34N, ALA60G, ALA61N, ALA86N, ALA93N, ALA94N, ALA98G, ARG16N, ARG228G, ARG231G, ARG31N, ARG37N, ARG45N, ARG58G, ARG64G, ARG68N, ARG72N, ARG89N, ASN24G, ASP14N, ASP19N, ASP60N, ASP63N, ASP75N, ASP91N, ASP97N, GLN20N, GLN226G, GLN227G, GLN2G, GLN35N, GLN64N, GLN99G, GLN99N, GLU27N, GLU47N, GLU57G, GLU66N, GLU81N, GLY12G, GLY1G, GLY230G, GLY33N, GLY38N, GLY8G, GLY95N, HIS15N, HIS70N, ILE18N, ILE25N, ILE40N, ILE53N, ILE56G, ILE63G, ILE67N, ILE76N, ILE9G, LEU10N, LEU17N, LEU71N, LEU87N, LEU90N, LEU92N, LYS11N, LYS224G, LYS225G, LYS229G, LYS232G, LYS26G, LYS30N, LYS3G, LYS46N, LYS61G, MET1N, MET210G, MET88N, PHE13N, PHE22G, PHE28G, PHE49N, PRO16G, PRO39N, PRO41N, PRO59G, PRO97G, SER19G, SER62G, THR20G, THR25G, THR28N, THR32N, THR69N, THR80N, TRP17G, TRP21G, TYR65N, VAL26N, VAL36N, VAL4G, VAL74N, VAL96G, VAL96N, VAL98N
• G-R: ALA23G, ALA29G, ALA86R, ALA87R, ARG10G, ARG39G, ARG58G, ARG64R, ARG74R, ARG84R, ARG89R, ASN184G, ASN18G, ASN31G, ASN7G, ASP30G, ASP33G, ASP35G, GLN2G, GLN40G, GLN65R, GLU27G, GLU57G, GLU85R, GLU91R, GLY12G, GLY1G, GLY77R, GLY8G, GLY90R, GLY94R, HIS5G, ILE13G, ILE54G, ILE56G, ILE92R, ILE9G, LEU11G, LEU177G, LEU32G, LEU73R, LEU78R, LEU95R, LYS26G, LYS37G, LYS3G, LYS75R, LYS82R, LYS96R, LYS97R, MET88R, PHE22G, PHE28G, PHE36G, PHE76R, PRO16G, PRO6G, PRO93R, SER19G, SER34G, SER99R, THR185G, THR20G, THR25G, THR43G, THR66R, TRP17G, TRP21G, TYR183G, VAL4G, VAL55G, VAL83R
• H-I: ALA106I, ALA112I, ARG111I, ASN121I, ASN195H, ASN84H, ASN88H, ASP49H, GLN53H, GLU100I, GLU115I, GLU196H, GLU201H, GLU87H, GLY101I, GLY103I, GLY107I, GLY108I, GLY83H, GLY86H, HIS120I, HIS197H, ILE104I, ILE105I, ILE199H, LEU198H, LEU202H, LYS205H, LYS82H, MET110I, SER204H, SER99I, THR102I, THR85H, TYR75H, VAL119I, VAL200H
• H-T: ARG127H, ASN125H, GLU45T
• I-L: ALA129L, ALA153I, ALA154I, ALA69L, ALA96L, ARG113L, ARG156I, ASN147I, ASP47L, GLN66L, GLN81I, GLN96I, GLU150I, GLU161I, GLU162I, GLU41L, GLU42L, GLU46L, GLU72L, GLY165I, GLY43L, GLY86I, GLY97L, GLY99L, HIS82I, ILE100L, ILE163I, ILE45L, LEU164I, LEU39L, LEU80I, LEU98L, LYS155I, LYS166I, LYS40L, LYS63L, LYS68L, LYS85I, LYS93L, MET146I, MET151I, MET95L, PHE44L, PHE65L, PHE94I, PRO149I, PRO83I, PRO97I, SER73L, TYR64L, VAL128L, VAL152I, VAL160I, VAL38L, VAL70L, VAL71L, VAL94L
• J-V: ALA105J, ALA117J, ALA26V, ALA48J, ALA57J, ALA57V, ALA61V, ALA95J, ARG109J, ARG110J, ARG112J, ARG113J, ARG38J, ARG45J, ARG56V, ARG60V, ARG62V, ARG72V, ARG86J, ASN118J, ASN30V, ASN63J, ASP107J, ASP114J, ASP115J, ASP21V, ASP24V, ASP71V, GLN18V, GLN46J, GLN74V, GLU108J, GLU19V, GLU40J, GLU5J, GLU98J, GLY36V, HIS55J, HIS73V, HIS94J, ILE25V, ILE32V, ILE51J, ILE58V, ILE6J, LEU28V, LEU47J, LEU61J, LEU64V, LEU66V, LEU67V, LYS104J, LYS106J, LYS23V, LYS29V, LYS53J, LYS56J, LYS59V, LYS93J, MET102J, MET62J, MET88J, MET90J, MET9J, PHE116J, PHE8J, PRO101J, PRO50J, PRO68V, SER65V, SER87J, THR27V, THR70V, TRP42J, TYR22V, TYR31V, TYR49J, TYR59J, TYR63V, TYR69V, VAL103J, VAL7J, VAL89J, VAL96J
• K-M: ALA100M, ALA43M, ARG108M, ARG121M, ARG40M, ARG44M, ARG48M, ARG79M, ARG9K, ASP106M, ASP14K, GLN49M, GLU39K, GLU41M, GLU52M, GLY101M, GLY18K, ILE11K, ILE71M, LEU12K, LYS10K, LYS16K, LYS35K, MET45M, PHE102M, PHE17K, PRO13K, PRO15K, SER36K, SER40K, SER72M, THR104M, THR37K, THR42M, TYR43K, VAL26K, VAL46M, VAL47M
• K-O: ALA144K, ALA146K, ALA149K, ALA61O, ARG154K, ARG55O, ASN147K, GLN63O, GLN85K, GLU145K, LYS148K, PHE150K, PHE51O, PHE60O, PRO59O, PRO87K, SER54O, SER82K, THR58O, VAL64O, VAL86K
• K-Y: ALA14Y, ALA165K, ALA167K, ARG159K, ARG16Y, ARG17Y, ARG20Y, ARG54Y, ARG61Y, GLN164K, GLN171K, HIS163K, LEU156K, LEU158K, LEU15Y, LYS170K, LYS53Y, LYS57Y, LYS58Y, PHE161K, PHE18Y, PRO172K, SER157K, SER160K, SER162K, SER168K, SER169K, TRP155K, VAL13Y
• L-P: ARG79L, ARG83L, ASN4P, GLY81L, ILE84L, LEU82L, PRO80L, THR2P, VAL3P
• L-U: ARG79L, ARG83L, GLY34U, GLY81L, ILE124L, ILE84L, LEU82L, LYS29U, LYS35U, LYS86L, PHE27U, PHE36U, PRO80L, TYR33U, TYR85L
• M-N: ALA61N, ARG112M, ARG118M, ARG48N, ARG62N, ASN58N, ASP60N, ASP63N, GLN64N, GLY116M, LEU117M, LYS113M, LYS114M, LYS59N, PHE49N, THR50N, TYR65N, VAL115M, VAL51N
• M-R: ALA98R, ARG112M, GLU111M, LYS113M, LYS114M, LYS97R, SER99R, TRP100R, VAL110M, VAL115M
• N-R: ALA61N, ALA87R, ALA98R, 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, PHE72R, PHE76R, PRO55N, PRO93R, SER54N, SER79R, SER99R, THR50N, THR69N, TRP100R, TYR65N, VAL51N, VAL83R
• O-V: ARG62V, ARG72V, ASP111O, ASP71V, GLY36V, HIS117O, HIS73V, ILE115O, LYS37V, LYS86O, MET84O, PRO114O, PRO116O, PRO68V, SER35V, THR110O, THR113O, THR70V, TYR63V, TYR69V, VAL112O, VAL85O
• O-Y: ALA101O, ALA24O, ALA29Y, ALA98O, ARG105O, ARG121O, ARG126O, ARG127O, ARG20Y, ARG32Y, ARG33Y, ARG34Y, ARG92O, ARG97O, ASN100O, ASN108O, ASN118O, ASN8Y, ASP111O, ASP12Y, CYS120O, CYS22Y, GLU23Y, GLU30Y, GLU35Y, GLU7Y, GLU82O, GLU93O, GLU9Y, GLY119O, GLY87O, GLY89O, ILE106O, ILE109O, ILE115O, ILE22O, ILE3Y, ILE96O, LEU28Y, LEU81O, LEU99O, LYS124O, LYS125O, LYS19Y, LYS24Y, LYS4Y, LYS86O, MET84O, PHE11Y, 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: ALA1P, ARG11P, ARG13P, ARG8P, ASN4P, GLN5P, GLY34U, HIS30U, ILE32U, ILE37U, LEU6P, LYS35U, LYS9P, PHE36U, PRO10P, PRO31U, THR2P, TYR33U, VAL3P, VAL7P
• Q-W: ALA105Q, ALA74W, ALA83W, ALA84W, ALA88W, ARG108Q, ARG112Q, ARG2W, ARG35W, ARG77W, ARG78Q, ARG80W, ARG86Q, ARG89Q, ARG91Q, ARG92Q, ARG97Q, ASN52W, ASP63W, ASP81Q, ASP85W, CYS84Q, GLN99Q, GLU64W, GLU72W, GLY110Q, GLY67W, GLY71W, GLY81W, GLY83Q, GLY87Q, GLY93Q, GLY98Q, HIS68W, HIS82W, ILE115Q, ILE39W, LEU70W, LEU79Q, LEU82Q, LEU88Q, LEU94Q, LYS109Q, LYS113Q, LYS116Q, LYS117Q, LYS69W, LYS86W, LYS87W, LYS89W, LYS90W, LYS91W, MET65W, PHE60W, PHE73W, PRO111Q, PRO114Q, PRO1W, PRO75W, SER3W, SER75Q, THR101Q, THR62W, THR76W, THR78W, TYR79W, TYR85Q, VAL59W, VAL61W, VAL66W, VAL96Q
• R-W: ALA35R, ALA43R, ARG36W, ARG40R, ARG52R, ARG58R, ASN34R, ASN42R, ASN42W, ASP11W, ASP32R, ASP37R, ASP39R, GLN48R, GLU19W, GLU38R, GLY7W, HIS13W, ILE10W, ILE30R, ILE39W, LEU12W, LEU14W, LEU15W, LEU45R, LEU47R, LEU4W, LEU50R, LYS16W, LYS20W, LYS27R, LYS46R, LYS5W, LYS6W, MET43W, PHE40W, PHE9W, PRO41W, PRO8W, SER31R, SER36R, THR38W, THR49R, TRP41R, VAL33R, VAL44R
• S-U: LEU83U, VAL74S, VAL82U
• V-Y: ARG72V, ASP71V, GLU34V, ILE3Y, LYS37V, LYS4Y, PHE18Y, SER21Y, SER35V, VAL27Y, VAL5Y