3MS1

recognition of the amber stop codon by release factor rf1. this entry 3ms1 contains 50s ribosomal subunit. the 30s ribosomal subunit can be found in pdb entry 3mr8. molecule b in the same asymmetric unit is deposited as 3mrz (50s) and 3ms0 (30s).

• Total interactions analyzed: 496
• Total true interactions: 28
• Strongest Interaction:
  • Chains: K-P
  • Int. Res.: 77
  • Norm. En. per Res.: -4.1289
• Hub Node: D(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-J	0.0	0.0	-37.7165	-37.7165	14	1	0	1361	0	0	2
D-K	-4.4586	-0.047	-29.1884	-33.694	16	1	0	1067	0	7	8
D-N	0.0	0.935	-28.8646	-27.9296	15	6	0	1601	0	0	10
D-P	0.0	-7.6234	-121.065	-128.6884	75	6	6	6407	1	19	17
E-L	-7.8705	20.9855	-99.9148	-86.7998	37	4	1	4230	0	17	21
E-Q	0.0	0.0	-1.478	-1.478	8	0	0	324	0	0	2
E-4	0.0	0.0	-0.0108	-0.0108	2	0	0	7	0	0	0
F-1	-10.1496	-23.4216	-132.845	-166.4162	63	11	4	6528	1	13	10
G-J	0.0	0.0	-0.0005	-0.0005	2	0	0	1	0	0	0
H-X	0.0	0.0	-47.004	-47.004	39	2	1	2531	0	10	11
J-Q	-5.7224	-1.7156	-103.648	-111.086	49	3	1	5007	0	8	25
J-R	0.0	0.0	-0.0743	-0.0743	3	0	0	27	0	1	4
K-P	-48.6141	-46.1508	-223.158	-317.9229	77	20	6	9229	6	37	38
L-Q	0.0	0.0	-0.0047	-0.0047	4	0	0	4	0	0	1
L-R	0.0	0.0	-2.6926	-2.6926	11	4	0	426	0	0	6
L-5	-19.7388	51.2763	-159.786	-128.2485	61	22	0	8129	0	16	56
M-V	-20.8659	-38.6735	-343.52	-403.0594	132	28	8	15060	5	66	61
M-W	0.0	0.0	-4.831	-4.831	10	0	0	424	0	0	5
N-S	0.0	6.2778	-12.4168	-6.139	19	0	1	670	0	4	8
N-2	0.0	1.2267	-38.9993	-37.7726	27	0	3	2043	0	2	7
O-W	0.0	-6.8237	-12.5673	-19.391	21	4	0	752	0	8	14
Q-R	-28.8501	-3.8025	-210.565	-243.2176	88	30	10	9872	0	17	36
Q-2	0.0	2.2872	-6.2917	-4.0045	10	0	0	637	0	0	9
S-2	0.0	47.4815	-87.6831	-40.2016	54	7	3	4525	0	11	21
T-Y	-7.013	-17.2019	-93.672	-117.887	48	3	3	4342	2	8	10
T-4	0.0	12.7312	-7.2164	5.5148	13	0	0	572	0	2	7
W-5	0.0	0.0	-0.0017	-0.0017	3	0	0	5	0	2	1
3-5	0.0	0.0	-40.4624	-40.4624	18	8	0	1499	0	2	1

Interface residues

• D-J: ARG149D, GLY100J, GLY103J, GLY104J, GLY153D, LYS152D, LYS154D, PRO102J, PRO147D, SER99J, TYR101J, TYR151D, TYR98J, VAL150D
• D-K: ALA20D, ALA76K, ARG13D, ARG16D, ARG19D, ARG71K, ASP18D, ASP73K, GLY74K, ILE14D, LYS70K, PHE15D, PRO22D, PRO72K, SER75K, VAL21D
• D-N: ALA114D, ARG111D, ARG119D, ARG136D, ARG2N, GLY110D, GLY112D, GLY115D, HIS3N, LYS109D, LYS118D, LYS5N, PHE113D, PRO191D, TYR160D
• D-P: ALA20D, ALA28D, ALA5P, ARG13D, ARG13P, ARG16D, ARG19D, ARG3P, ARG53P, ARG76D, ASN180D, ASN192D, ASN55P, ASN58P, ASP174D, ASP17D, ASP18D, GLU11P, GLU178D, GLU179D, GLY10D, GLY193D, GLY29D, GLY4P, GLY56P, GLY6D, HIS79P, ILE14D, ILE176D, ILE26D, ILE75P, ILE7P, ILE83P, LEU181D, LEU182D, LEU183D, LEU27D, LEU52D, LEU6P, LEU78P, LEU82P, LEU9P, LYS33P, LYS35P, LYS8D, LYS8P, MET11D, MET1P, PHE15D, PHE51D, PHE57P, PHE61P, PHE76P, PRO177D, PRO53D, PRO77P, PRO81P, SER12P, SER80P, THR12D, THR24D, THR40P, THR59P, THR60P, TYR14P, TYR32P, VAL10P, VAL15P, VAL173D, VAL175D, VAL184D, VAL23D, VAL25D, VAL7D, VAL9D
• E-L: ALA113E, ALA12L, ARG117E, ARG119E, ARG15L, ARG16L, ARG188E, ARG18L, ARG38E, ARG7L, ASN13L, ASN29E, ASN9L, ASP116E, ASP5L, GLU120E, GLU190E, GLU35E, GLY11L, HIS31E, ILE186E, ILE28E, LEU32E, LEU33E, LEU41E, LEU6L, LYS14L, LYS17L, MET112E, PRO10L, PRO30E, PRO8L, THR189E, TRP34E, TYR184E, VAL187E, VAL37E
• E-Q: ALA49E, ARG3Q, ARG45E, PRO2Q, PRO92E, THR51E, TYR97E, VAL88E
• E-4: ALA58E, LYS374
• F-1: ALA110F, ALA381, ALA61F, ALA6F, ARG113F, ARG98F, ASN108F, ASN461, ASP4F, ASP97F, CYS421, CYS441, CYS621, CYS651, GLN66F, GLU104F, GLU143F, GLU491, GLU561, GLU601, GLY65F, ILE101F, ILE114F, ILE140F, ILE144F, ILE401, ILE411, ILE481, ILE571, ILE63F, LEU103F, LEU106F, LEU107F, LEU111F, LEU139F, LEU3F, LEU5F, LEU62F, LEU7F, LYS105F, LYS10F, LYS541, LYS641, PHE102F, PHE141F, PRO112F, PRO142F, PRO179F, PRO2F, PRO371, SER521, SER631, THR145F, THR501, THR531, THR64F, TRP100F, TYR511, TYR581, VAL109F, VAL361, VAL591, VAL611
• G-J: ARG60G, LYS88J
• H-X: ALA26H, ALA39H, ALA64X, ARG27H, ARG33H, ARG50X, ARG52X, ARG76X, ASN28H, ASN43H, GLU41H, GLU72X, GLU75X, GLY24H, GLY34H, HIS66X, ILE4H, ILE67X, LEU31H, LEU38H, LEU73X, LYS48X, LYS69X, LYS78X, MET1H, PRO23H, PRO32H, PRO68X, SER42H, THR40H, TYR29H, TYR71X, VAL37H, VAL49X, VAL51X, VAL53X, VAL62X, VAL70X, VAL74X
• J-Q: ALA67Q, ALA68Q, ALA96Q, ALA99Q, ARG101Q, ARG35J, ARG58J, ARG59Q, ARG62J, ARG64Q, ARG70Q, ASN66Q, ASN68J, ASN94Q, ASP56Q, ASP64J, ASP97Q, CYS69Q, GLN71Q, GLY59J, HIS61J, HIS72Q, ILE62Q, ILE65Q, LEU56J, LEU60Q, LEU95Q, LEU98Q, LYS25J, LYS52J, LYS60J, LYS93Q, MET71J, PHE106Q, PHE57Q, PRO103Q, PRO29J, PRO63J, PRO67J, THR26J, THR55J, THR66J, TRP61Q, TRP65J, TYR27J, VAL100Q, VAL28J, VAL63Q, VAL69J
• J-R: ARG13R, LYS25J, TYR12R
• K-P: ALA103K, ALA118K, ALA11K, ALA76K, ALA83K, ARG103P, ARG104K, ARG107K, ARG39P, ARG41P, ARG51P, ARG64K, ARG64P, ARG71K, ARG74P, ARG78K, ARG97K, ASN38P, ASP44P, ASP73K, ASP80K, ASP81K, GLN43P, GLU105K, GLU108K, GLU120K, GLU36P, GLU46P, GLU68K, GLU73P, GLU9K, GLY100K, GLY37P, GLY69P, GLY71P, GLY74K, ILE50P, ILE75P, ILE77K, ILE83P, LEU122K, LEU82P, LYS33P, LYS35P, LYS65P, LYS66K, LYS70K, PHE45P, PHE61P, PHE76P, PHE79K, PHE99K, PRO101K, PRO119K, PRO72K, PRO77P, PRO81P, SER106P, SER67P, SER75K, SER80P, THR60P, THR62P, THR65K, TYR100P, TYR32P, TYR68P, VAL102K, VAL121K, VAL34P, VAL63K, VAL63P, VAL66P, VAL69K, VAL70P, VAL72P, VAL98K
• L-Q: ARG36Q, GLY26L, LYS13Q, SER25L
• L-R: ALA31L, ARG82R, ARG83R, GLN80R, GLY26L, GLY28L, HIS27L, LYS29L, THR30L, THR32L, TYR81R
• L-5: ALA105, ALA245, ALA555, ARG135, ARG305, ARG465, ARG49L, ARG50L, ARG55L, ARG575, ARG61L, ARG65L, ASP47L, GLN68L, GLN70L, GLU52L, GLU545, GLU565, GLY285, GLY455, GLY66L, GLY69L, GLY95, HIS75, ILE165, ILE585, LEU505, LEU59L, LEU605, LEU615, LEU625, LEU62L, LYS115, LYS125, LYS155, LYS265, LYS295, LYS445, LYS475, LYS55, LYS595, LYS64L, LYS85, MET255, MET45, MET60L, MET67L, PHE485, PHE51L, PRO48L, PRO535, PRO635, PRO63L, THR175, THR275, THR57L, THR58L, THR65, VAL145, VAL225, VAL235
• M-V: ALA107M, ALA136M, ALA140M, ALA184V, ALA187V, ALA20M, ALA28M, ALA36M, ALA51V, ALA53M, ARG101M, ARG122V, ARG133M, ARG134M, ARG49V, ARG51M, ARG56M, ARG59M, ARG60M, ARG67M, ARG6M, ARG72V, ARG79V, ARG80V, ARG81V, ARG82V, ASN75V, ASP123V, ASP135M, ASP138M, ASP179V, ASP25M, ASP31M, ASP45V, ASP77V, ASP87V, GLN118V, GLN141M, GLN50V, GLN73V, GLU105M, GLU119V, GLU139M, GLU178V, GLU181V, GLU186V, GLU190V, GLU38M, GLU48M, GLU84V, GLU97V, GLY100M, GLY108M, GLY114V, GLY115V, GLY19M, GLY23M, GLY24M, GLY30M, GLY33M, GLY61M, GLY62M, HIS54V, HIS55V, HIS57M, HIS85V, ILE120V, ILE131M, ILE53V, ILE57V, ILE64M, ILE66M, LEU117V, LEU125V, LEU183V, LEU24V, LEU37M, LEU70V, LEU76V, LEU91V, LYS130M, LYS182V, LYS18M, LYS22M, LYS46V, LYS63M, LYS78V, LYS98M, MET54M, MET98V, PHE29M, PHE32M, PHE44V, PHE48V, PHE58M, PHE65M, PHE88V, PHE89V, PRO101V, PRO176V, PRO177V, PRO39M, PRO83V, PRO99M, SER52V, THR129M, THR21M, THR69V, TYR137M, TYR26M, TYR29V, TYR99V, VAL100V, VAL102M, VAL106M, VAL109M, VAL111V, VAL116V, VAL126V, VAL132M, VAL174V, VAL175V, VAL180V, VAL27M, VAL35M, VAL52M, VAL55M, VAL56V, VAL71V, VAL74V, VAL86V, VAL96V
• M-W: ASN12W, GLY84M, GLY86M, LYS11M, LYS11W, LYS77M, LYS85M, LYS87M, MET83M, THR10W
• N-S: ALA101N, ALA109N, ARG103N, ARG104N, ARG105N, ARG37S, ARG42S, ASN40S, ASP107N, GLU102N, GLY106N, GLY108N, LEU100N, LYS41S, PHE46S, PRO110N, THR39S, TYR38S, TYR45S
• N-2: ALA101N, ALA112N, ALA532, ARG103N, ARG96N, CYS462, GLU102N, GLU115N, GLU118N, HIS432, LEU100N, LEU111N, LEU113N, LEU302, LEU98N, LYS402, LYS99N, MET392, PRO282, PRO412, PRO422, PRO472, THR442, TYR512, TYR522, VAL117N, VAL452
• O-W: ARG20O, ARG72W, ARG82W, ASN16O, ASN50W, GLU43O, GLY48W, GLY52W, HIS80W, LEU75W, LYS19O, LYS46W, LYS49W, MET53W, PHE12O, PRO47W, PRO83W, THR43W, TYR78W, VAL51W, VAL79W
• Q-R: ALA107Q, ALA3R, ALA41Q, ALA42Q, ALA46Q, ALA48Q, ALA77R, ALA86Q, ALA96Q, ARG101Q, ARG112Q, ARG13R, ARG36Q, ARG50Q, ARG53Q, ARG82R, ARG83R, ARG92Q, ASN44Q, ASN94Q, ASP91Q, ASP97Q, GLN104Q, GLN11R, GLU102Q, GLU108Q, GLU111Q, GLU15R, GLU37Q, GLU43R, GLU89Q, GLY41R, GLY42R, GLY43Q, GLY48R, GLY86R, GLY87Q, GLY8R, GLY9R, HIS87R, ILE17Q, ILE4R, ILE70R, ILE88Q, LEU109Q, LEU20Q, LEU38R, LEU39Q, LEU39R, LEU40R, LEU71R, LEU83Q, LEU95Q, LEU98Q, LYS10R, LYS16Q, LYS44R, LYS54Q, LYS6R, LYS74R, LYS76R, LYS84R, LYS85R, LYS93Q, MET1R, PHE106Q, PHE2R, PHE40Q, PHE75R, PRO103Q, PRO50R, SER73R, THR45R, THR49R, THR7R, TYR12R, TYR45Q, TYR47Q, TYR81R, VAL105Q, VAL14R, VAL46R, VAL47R, VAL51R, VAL52R, VAL5R, VAL72R, VAL90Q
• Q-2: ALA142, ARG152, GLY26Q, LEU27Q, LYS102, LYS132, LYS30Q, SER122, THR112, TRP25Q
• S-2: ALA22, ALA242, ALA382, ALA44S, ARG15S, ARG162, ARG18S, ARG192, ARG202, ARG33S, ARG37S, ARG88S, ARG90S, ARG92S, ASN34S, ASN40S, ASP172, ASP22S, CYS332, CYS462, CYS492, GLU30S, GLU31S, GLU482, GLY43S, HIS232, ILE24S, ILE292, ILE35S, LEU19S, LEU23S, LEU252, LEU302, LEU36S, LYS16S, LYS27S, LYS32, LYS372, LYS402, LYS41S, MET392, PRO272, PRO282, PRO412, PRO472, THR262, THR39S, THR442, TYR38S, VAL17S, VAL20S, VAL21S, VAL312, VAL452
• T-Y: ALA10T, ALA39Y, ALA42T, ALA46T, ALA4T, ALA91T, ARG26Y, ARG30Y, ARG36Y, ASP6T, GLN38Y, GLU27Y, GLU31Y, GLU34Y, GLY42Y, GLY94T, HIS31T, ILE41Y, ILE57Y, ILE89T, ILE8T, LEU13T, LEU32Y, LEU44Y, LEU61Y, LEU92T, LEU9T, LYS23Y, LYS28Y, LYS29Y, LYS48T, MET33Y, PHE28T, PHE37Y, PHE47T, PRO11T, SER40Y, THR27T, THR3T, THR45T, TRP29T, TYR18T, TYR26T, TYR5T, VAL12T, VAL25Y, VAL43T, VAL7T
• T-4: ARG414, ARG474, ARG60T, ARG68T, ARG94, ASP75T, GLY61T, LEU70T, LYS484, LYS63T, LYS72T, TRP404, VAL464
• W-5: ARG55W, LYS395, SER375
• 3-5: ALA223, ASN263, ASN335, GLN355, GLU123, GLU243, GLY385, ILE415, LEU103, LEU113, LEU93, LYS253, LYS273, LYS365, SER375, THR233, TRP345, TYR393