2VQF

modified uridines with c5-methylene substituents at the first position of the trna anticodon stabilize u-g wobble pairing during decoding

• Total interactions analyzed: 276
• Total true interactions: 27
• Strongest Interaction:
  • Chains: J-N
  • Int. Res.: 53
  • Norm. En. per Res.: -5.5131
• 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
B-C	0.0	0.0	-5.3881	-5.3881	6	0	0	234	0	2	3
B-E	0.0	0.0	-0.0042	-0.0042	5	0	0	7	0	1	2
B-H	-13.8771	-43.9231	-72.3709	-130.1711	33	14	0	3019	2	17	18
C-D	0.0	0.0	-0.2112	-0.2112	2	0	0	53	0	0	6
C-E	-4.8796	-28.5883	-12.1584	-45.6264	14	0	0	658	2	4	4
C-J	0.0	8.3994	-80.2207	-71.8213	57	7	2	3480	0	15	25
C-N	-16.3362	4.2028	-213.939	-226.0725	76	12	3	8960	0	19	37
D-E	0.0	-40.1295	-49.7935	-89.923	47	4	0	2582	3	6	11
E-H	-53.0045	-35.6133	-143.83	-232.4478	64	21	2	6439	2	42	43
F-O	0.0	0.0	-2.0902	-2.0902	4	0	0	169	0	4	3
F-R	-74.031	-44.5243	-287.47	-406.0253	85	35	7	10698	3	14	23
G-I	0.0	2.0013	-33.8605	-31.8592	35	3	4	2055	0	5	9
G-K	0.0	0.0	-46.1663	-46.1663	26	1	3	2072	0	3	7
G-U	0.0	0.0	-0.0332	-0.0332	2	0	0	16	0	1	0
H-L	0.0	0.0	-8.0696	-8.0696	10	1	0	415	0	0	1
H-Q	0.0	2.4638	-26.8805	-24.4167	14	1	0	1240	0	2	8
I-J	0.0	-0.906	-25.6225	-26.5285	19	6	0	1391	0	12	16
I-M	0.0	2.3623	-9.0304	-6.6681	6	4	0	429	0	0	4
I-N	0.0	0.0	-12.0881	-12.0881	8	1	0	505	0	0	0
J-N	-38.2288	-39.1416	-214.822	-292.1924	53	15	7	8459	2	13	35
K-R	-35.3052	-24.5286	-83.3107	-143.1445	37	18	2	3964	4	15	20
L-Q	0.0	0.0	-50.6329	-50.6329	23	3	4	2305	0	0	8
M-S	0.0	-2.7407	-74.3865	-77.1272	46	4	0	3552	0	9	22
M-U	0.0	0.947	-1.5071	-0.5601	13	0	0	276	0	3	9
N-S	0.0	0.0	-0.2003	-0.2003	5	0	0	46	0	0	0
O-Q	0.0	-1.0799	-0.0984	-1.1783	12	0	0	66	0	8	6
S-U	0.0	0.0	-0.0231	-0.0231	2	0	0	18	0	0	0

Interface residues

• B-C: ARG130B, ARG179C, GLU134B, GLU206C, PRO131B, VAL207C
• B-E: ARG64E, LEU180B, LYS106B, PHE181B, TYR60E
• B-H: ALA177B, ARG175B, ARG178B, ARG30B, ARG53B, ARG68H, ARG69H, ARG75H, ASP193B, ASP195B, ASP198B, ASP73H, GLN70H, GLU176B, GLY71H, ILE182B, ILE200B, LEU180B, LEU196B, LYS179B, LYS27B, PHE181B, PRO183B, PRO194B, PRO72H, PRO74H, PRO76H, TYR199B, TYR20H, VAL174B, VAL184B, VAL197B, VAL19H
• C-D: ARG132C, ARG47D
• C-E: ALA54E, ARG131C, ARG132C, ARG15E, ARG164C, GLU166C, GLU50E, LEU53E, LYS135C, PHE26E, PHE28E, PRO49E, PRO52E, VAL51E
• C-J: ALA24C, ALA60C, ALA61C, ALA65C, ARG21C, ARG43J, ARG45J, ARG51J, ARG59C, ARG66J, ARG9J, ASN3C, ASN63C, ASN69J, ASP12J, ASP17C, ASP89J, GLN28C, GLU58C, GLU61J, GLU64J, GLU95J, GLY10J, GLY25C, GLY93J, GLY9C, HIS13J, HIS68J, HIS6C, ILE14C, ILE57C, ILE5C, ILE96J, LEU12C, LEU16J, LEU32C, LEU65J, LEU8J, LEU90J, LYS26C, LYS27C, LYS4C, PHE10C, PHE11J, PHE47J, PHE63J, PRO91J, SER20C, THR15J, THR67J, THR92J, TRP18C, TRP22C, TYR23C, TYR29C, VAL64C, VAL94J
• C-N: ALA24C, ALA48N, ARG11C, ARG12N, ARG16C, ARG21C, ARG26N, ARG30C, ARG35N, ARG38C, ARG40C, ARG45N, ARG54C, ARG57N, ARG59C, ASN3C, ASP17C, ASP36C, ASP56C, CYS43N, GLN28C, GLN37C, GLN52N, GLU19C, GLU35C, GLU44C, GLU46N, GLU58C, GLY13C, GLY185C, GLY25C, GLY38N, GLY41C, GLY51N, GLY55N, GLY9C, HIS31C, HIS49N, HIS6C, ILE14C, ILE39C, ILE57C, ILE5C, ILE8C, LEU12C, LEU178C, LEU32C, LEU33C, LEU34C, LEU39N, LEU44N, LEU47N, LEU53N, LYS26C, LYS27C, LYS4C, LYS50N, LYS58N, PHE10C, PHE186C, PHE36N, PHE37N, PRO54N, PRO7C, SER20C, SER60N, THR22N, TRP18C, TRP22C, TYR184C, TYR23C, TYR29C, TYR34N, VAL25N, VAL55C, VAL56N
• D-E: ALA102E, ALA104E, ALA108E, ALA95E, ARG107E, ARG209D, ARG37E, ARG50D, ARG57D, ASN199D, ASP117E, ASP53D, GLN201D, GLU111E, GLU200D, GLU205D, GLY103E, GLY87D, GLY90D, GLY97E, GLY99E, ILE101E, ILE118E, ILE11E, ILE13E, ILE204D, LEU12E, LEU202D, LYS9E, MET10E, PHE206D, PHE79D, PRO51D, PRO96E, SER208D, SER52D, SER83D, SER91D, THR116E, THR89D, THR98E, TYR54D, VAL100E, VAL105E, VAL115E, VAL56D, VAL88D
• E-H: ALA138E, ALA146E, ALA40H, ALA94E, ALA95E, ARG102H, ARG104H, ARG105H, ARG122H, ARG140E, ARG143E, ARG150E, ARG152E, ARG41H, ARG69H, ARG84H, ASP147E, GLN141E, GLN72E, GLN78H, GLU149E, GLU42H, GLU77H, GLU79E, GLU81E, GLY106H, GLY108H, GLY154E, GLY43H, GLY66H, HIS78E, HIS81H, HIS82H, ILE109H, ILE118E, ILE45H, ILE76E, ILE80E, ILE80H, LEU107H, LEU119E, LEU142E, LEU151E, LEU39H, LEU91E, LYS145E, LYS153E, LYS46H, LYS64H, LYS92E, PHE44H, PRO67H, PRO76H, PRO77E, PRO93E, THR144E, THR75E, TRP138H, TYR65H, VAL103H, VAL137H, VAL148E, VAL79H, VAL82E
• F-O: ARG2F, GLU69F, ILE3O, PRO2O
• F-R: ALA101F, ALA24R, ALA49F, ALA73R, ALA99F, ARG32R, ARG35R, ARG46F, ARG47F, ARG72R, ARG74R, ARG80F, ARG87F, ASN100F, ASN36R, ASN7F, ASP30R, ASP33R, GLN63R, GLN64F, GLN94F, GLU28R, GLU38R, GLU41F, GLU42F, GLU5F, GLU62R, GLU83R, GLU95F, GLY27R, GLY48R, GLY58F, GLY77R, ILE52F, ILE65R, ILE75R, ILE8F, LEU26R, LEU31R, LEU43F, LEU44R, LEU48F, LEU58R, LEU61F, LEU66R, LEU76R, LEU78R, LEU79R, LEU98F, LYS21R, LYS23R, LYS39F, LYS41R, LYS61R, LYS68R, LYS71R, LYS92F, MET89F, PHE29R, PHE43R, PHE60F, PHE81R, PHE97F, PRO51F, PRO80R, PRO96F, SER59R, SER93F, THR25R, THR69R, THR82R, TRP62F, TYR34R, TYR4F, TYR50F, TYR63F, VAL22R, VAL37R, VAL39R, VAL40F, VAL6F, VAL88F, VAL90F, VAL91F, VAL9F
• G-I: ALA39G, ALA40G, ALA43I, ALA45I, ALA46I, ARG107I, ARG10G, ARG41G, ARG42I, ARG51I, ASN37G, ASP15G, ASP75I, GLN13G, GLN38I, GLU48I, GLY39I, ILE27G, ILE42G, ILE74I, LEU16G, LEU38G, LEU40I, LEU47I, LEU99I, LYS36G, LYS78I, PHE101I, PHE43G, PRO14G, SER71I, TYR44G, VAL17G, VAL41I, VAL44I
• G-K: ALA147G, ALA150G, ALA152G, ALA60K, ALA61K, ALA89K, ARG149G, ARG155G, ARG54K, ASN148G, GLN62K, GLN93K, GLU146G, GLY56K, GLY90K, HIS153G, LEU63K, LYS55K, PRO58K, SER53K, THR57K, TYR151G, TYR154G, TYR50K, TYR59K, TYR85G
• G-U: ARG10U, LYS35G
• H-L: ARG91H, ARG92H, ASN8L, GLY90H, ILE7L, LEU10L, LYS88H, PRO89H, THR6L, VAL11L
• H-Q: ARG91H, ARG92H, GLY33Q, GLY90H, HIS29Q, LEU31Q, LYS34Q, LYS88H, PRO28Q, PRO89H, TYR32Q, TYR94H, VAL35Q, VAL93H
• I-J: ARG111I, ARG46J, ARG51J, ARG60J, ASP58J, GLU61J, GLY115I, HIS117I, HIS62J, ILE50J, LYS112I, LYS113I, LYS116I, LYS57J, PRO123I, SER59J, THR48J, TYR114I, VAL49J
• I-M: ARG125M, ARG128I, LYS126M, LYS127I, PRO124M, SER126I
• I-N: ALA59N, ARG111I, LYS112I, LYS113I, LYS58N, SER60N, TRP61N, TYR114I
• J-N: ALA48N, ALA59N, ARG29N, ARG35N, ARG41N, ARG45J, ARG45N, ARG46J, ARG51J, ARG57N, ARG60J, ARG66J, ASP12J, CYS40N, CYS43N, GLU46N, GLU61J, GLU64J, GLY52J, GLY55N, GLY93J, HIS13J, HIS49N, HIS56J, HIS62J, HIS68J, ILE42N, ILE50J, LEU44N, LEU47N, LEU53N, LEU65J, LYS55J, LYS57J, LYS58N, PHE11J, PHE36N, PHE37N, PHE47J, PHE54J, PHE63J, PRO53J, PRO54N, SER32N, SER59J, SER60N, THR48J, THR67J, TRP61N, TYR34N, VAL44J, VAL49J, VAL56N
• K-R: ALA23K, ARG18K, ARG74R, ARG85K, ARG87R, ARG91K, ARG96K, ASP110K, ASP111K, GLN99K, GLU83R, GLU92K, GLY86K, GLY88K, HIS116K, ILE108K, ILE21K, ILE83K, ILE95K, LEU85R, LYS49R, LYS84R, LYS88R, PHE81R, PRO113K, PRO80R, SER107K, THR112K, THR47R, THR82R, THR87K, TYR20K, VAL109K, VAL114K, VAL82K, VAL84K, VAL86R
• L-Q: ARG12L, ARG15L, ARG38Q, ASN8L, GLN9L, GLU16L, GLY14L, GLY33Q, HIS29Q, ILE36Q, ILE7L, LEU10L, LEU31Q, LYS13L, LYS17L, LYS34Q, LYS37Q, PHE27Q, PRO30Q, THR6L, TYR32Q, VAL11L, VAL35Q
• M-S: ALA75S, ARG102M, ARG36S, ARG3S, ARG78S, ARG80M, ARG81S, ARG88M, ARG91M, ARG94M, ARG99M, ASN65S, ASP83M, CYS86M, GLU64S, GLU73S, GLY100M, GLY68S, GLY72S, GLY85M, GLY89M, HIS69S, ILE40S, ILE62S, ILE84M, LEU71S, LEU81M, LEU90M, LEU96M, LYS111M, LYS70S, MET66S, PHE74S, PRO2S, PRO76S, THR103M, THR63S, THR77S, THR79S, TYR61S, TYR80S, TYR87M, VAL117M, VAL60S, VAL67S, VAL98M
• M-U: ALA28M, ARG29M, ARG6U, ARG7U, ARG99M, ASP5U, GLU32M, GLY26M, LYS20U, LYS27M, LYS31M, THR8U, TYR21U
• N-S: ARG19N, ARG37S, HIS14S, LYS15N, PHE16N
• O-Q: ALA105Q, ARG64O, ARG68O, ARG72O, ARG88O, ASP83Q, GLN71O, GLU86Q, ILE90Q, LYS104Q, LYS87Q, MET82Q
• S-U: ARG6U, PRO2S