1YL3

crystal structure of 70s ribosome with thrs operator and trnas. large subunit. the coordinates for the small subunit are in the pdb entry 1yl4.

• Total interactions analyzed: 561
• Total true interactions: 30
• Strongest Interaction:
  • Chains: J-L
  • Int. Res.: 48
  • Norm. En. per Res.: -2.9159
• 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
E-M	0.0	-3.0794	-1.7386	-4.818	8	0	0	143	0	3	0
E-N	0.0	2.7499	-18.8087	-16.0588	15	1	0	605	0	4	3
E-R	0.0	0.0	-1.2157	-1.2157	6	0	0	182	0	1	0
E-5	0.0	0.0	-0.0003	-0.0003	2	0	0	1	0	0	0
F-S	0.0	0.0	-1.0657	-1.0657	5	0	0	137	0	0	1
F-1	0.0	0.0	-1.1549	-1.1549	6	0	0	206	0	0	3
G-Q	-4.5099	-3.6292	-6.9607	-15.0998	13	11	0	1069	1	9	15
H-9	0.0	0.0	-0.052	-0.052	6	0	0	31	0	0	2
I-J	-21.8325	79.8586	-260.701	-202.6749	158	76	29	16455	2	66	66
I-L	-5.1449	3.8335	-27.0188	-28.3302	29	35	3	3212	2	8	3
J-L	-19.1785	-2.308	-118.477	-139.9635	48	71	6	7732	0	11	9
K-4	0.0	-0.2155	-9.657	-9.8726	23	2	0	680	0	10	7
L-P	0.0	0.0	-0.0429	-0.0429	3	0	0	12	0	0	0
L-V	0.0	-0.9473	-29.1324	-30.0797	18	12	0	1363	0	4	3
M-1	0.0	-10.2996	-2.6991	-12.9987	10	0	0	296	0	5	1
M-9	0.0	0.0	-0.023	-0.023	2	0	0	5	0	5	1
N-R	-41.6139	21.448	-98.8136	-118.9795	56	32	1	5717	0	22	21
O-8	0.0	1.7045	-9.8865	-8.182	13	1	0	1078	0	0	11
P-V	-31.6268	13.305	-97.2327	-115.5545	90	81	1	8039	0	18	20
P-3	0.0	0.0	-6.8455	-6.8455	15	2	0	351	0	1	1
P-9	0.0	0.0	-0.0121	-0.0121	2	0	0	10	0	0	2
Q-3	0.0	0.9057	-10.1349	-9.2292	27	0	0	966	0	2	10
S-0	0.0	0.0	-7.1169	-7.1169	16	0	0	467	0	4	7
S-5	-17.4174	7.8025	-63.6123	-73.2272	54	56	6	5563	2	15	21
S-7	0.0	0.0	-0.0003	-0.0003	2	0	0	1	0	0	1
T-W	-9.5794	-33.0363	-51.3098	-93.9255	40	15	1	3346	3	12	17
0-5	0.0	4.9918	-26.6681	-21.6763	36	21	2	2338	0	7	13
1-2	-39.159	59.7797	66.001	86.6217	94	103	2	9057	0	23	54
1-5	0.0	0.0	-0.4811	-0.4811	10	0	0	163	0	0	5
6-8	0.0	1.0481	-19.8634	-18.8153	20	21	0	1470	0	3	7

Interface residues

• E-M: ALA4M, ARG247E, ARG94E, ASN67M, ASP66M, SER248E, THR249E, VAL246E
• E-N: ARG31N, ARG62E, ARG71N, ASP73N, GLN220E, GLU63E, GLU66E, GLY74N, MET65E, PRO61E, PRO72N, SER75N, THR67E, TYR76N, VAL68E
• E-R: ARG62E, GLU14R, GLY16R, PRO15R, THR17R, THR67E
• E-5: ARG245E, LYS95
• F-S: ARG65F, ARG92S, GLN67F, GLY66F, PHE61F
• F-1: LYS96F, PRO21, PRO91F, PRO92F, SER48F, TYR46F
• G-Q: ALA147G, ALA16Q, ARG11Q, ARG12Q, ARG13Q, ARG144G, ARG14Q, ARG17Q, ASP145G, GLU15Q, LYS146G, SER148G, THR18Q
• H-9: ARG169H, ASN299, LEU167H, PRO155H, SER289, VAL309
• I-J: ALA111I, ALA111J, ALA19I, ALA19J, ALA34I, ALA34J, ALA35I, ALA35J, ALA38I, ALA38J, ALA40I, ALA40J, ALA41I, ALA41J, ALA42I, ALA42J, ALA45I, ALA45J, ALA47I, ALA47J, ALA48I, ALA48J, ALA49I, ALA49J, ALA51I, ALA51J, ALA52I, ALA52J, ALA88I, ALA88J, ALA9I, ALA9J, ARG78I, ARG78J, ASP27I, ASP27J, ASP60I, ASP60J, ASP90J, ASP99I, ASP99J, GLN53I, GLN53J, GLU109I, GLU109J, GLU110I, GLU110J, GLU113I, GLU113J, GLU11I, GLU17I, GLU17J, GLU20I, GLU20J, GLU26I, GLU26J, GLU54J, GLU55I, GLU55J, GLU58I, GLU58J, GLU5I, GLU5J, GLU79I, GLU79J, GLU87I, GLU87J, GLU8I, GLU8J, GLY105I, GLY105J, GLY30I, GLY46I, GLY46J, GLY50I, GLY50J, GLY82I, GLY82J, GLY84I, GLY84J, ILE102I, ILE102J, ILE10I, ILE10J, ILE114I, ILE114J, ILE6I, ILE6J, ILE7I, ILE80I, ILE80J, LEU13I, LEU13J, LEU18I, LEU18J, LEU21I, LEU21J, LEU83I, LEU83J, LEU85I, LEU85J, LEU91I, LEU91J, LYS103I, LYS103J, LYS108I, LYS108J, LYS128J, LYS12I, LYS12J, LYS23I, LYS23J, LYS24I, LYS24J, LYS56I, LYS56J, LYS86I, LYS86J, LYS89J, MET1I, MET1J, PHE59I, PHE59J, PRO36I, PRO36J, PRO43I, PRO43J, SER104I, SER104J, SER107I, SER107J, SER16I, SER16J, THR14I, THR14J, THR2I, THR2J, THR32I, THR57I, THR57J, THR81I, THR81J, VAL101I, VAL101J, VAL106I, VAL106J, VAL15I, VAL15J, VAL22I, VAL22J, VAL31I, VAL31J, VAL39I, VAL39J, VAL44I, VAL44J, VAL61J, VAL77J
• I-L: ALA118L, ALA123L, ALA124L, ASN117L, ASN119L, ASP115L, ASP4I, GLU11I, GLU5I, GLU8I, ILE127L, ILE3I, ILE69L, ILE6I, ILE70L, ILE7I, LEU116L, LYS10L, LYS112L, LYS71L, MET113L, MET1I, PRO114L, PRO55L, SER120L, THR2I, THR59L, THR72L, VAL57L
• J-L: ALA88J, ARG78J, ASN69J, ASP63L, ASP90J, GLN68J, GLN72J, GLN8L, GLU62L, GLU79J, GLU87J, GLU93J, GLY32L, GLY67J, GLY84J, HIS31L, ILE58L, ILE69L, ILE70L, ILE71J, ILE74J, ILE9L, LEU11L, LEU83J, LEU85J, LYS10L, LYS64L, LYS70J, LYS71L, LYS75J, LYS86J, LYS89J, PHE38L, PHE66J, PHE66L, PHE68L, SER65L, THR59L, THR67L, TYR61L, VAL33L, VAL56L, VAL57L, VAL60L, VAL73J, VAL76J, VAL77J, VAL92J
• K-4: ALA39K, ALA42K, ARG624, ARG684, ASN27K, ASN28K, ASP23K, ASP654, GLU38K, GLU464, GLY24K, GLY454, ILE37K, LYS32K, LYS614, LYS734, MET1K, PHE634, PRO41K, SER664, THR40K, THR444, TYR674
• L-P: ARG94L, ASN74P, GLN73P
• L-V: ARG175V, ARG94L, GLN105V, GLN109V, GLU107V, GLU138L, GLY110V, GLY111V, ILE96L, LYS133L, LYS93L, LYS95L, LYS99L, PRO92L, SER104V, VAL108V, VAL140L, VAL97L
• M-1: ALA671, ARG701, ARG93M, ASN661, ASP32M, GLN25M, GLN29M, GLN631, GLU28M, LEU31M
• M-9: GLU51M, HIS209
• N-R: ALA103N, ALA118N, ALA11N, ALA27R, ALA83N, ARG17N, ARG64N, ARG67N, ARG70N, ARG71N, ARG78N, ASN82N, ASP12N, ASP25R, ASP41R, ASP73N, ASP80N, CYS84N, GLU120N, GLU14R, GLU18N, GLU81N, GLY100N, GLY16R, GLY18R, GLY26R, GLY68N, GLY74N, HIS23R, HIS30R, ILE122N, ILE77N, ILE98N, LYS24R, LYS66N, LYS9N, MET20R, PHE21R, PHE31R, PHE79N, PHE99N, PRO101N, PRO119N, PRO15R, SER75N, THR17R, THR19R, THR28R, THR29R, THR65N, TYR76N, VAL102N, VAL10N, VAL121N, VAL22R, VAL69N
• O-8: ALA108, ARG128, ARG138, ARG53O, ARG648, HIS78, ILE148, LYS118, LYS158, LYS52O, PHE258, PHE51O, PRO638
• P-V: ALA118P, ALA154P, ALA44P, ARG103V, ARG175V, ARG44V, ARG70P, ARG74V, ARG76V, ARG84P, ARG86P, ASN119P, ASN119V, ASN127P, ASN148P, ASN35P, ASN36P, ASN69P, ASN74P, ASP114V, ASP121P, ASP137V, ASP150P, ASP72V, GLN121V, GLN45P, GLN45V, GLN46V, GLN70V, GLN73P, GLU107V, GLU47P, GLU51P, GLY102V, GLY106V, GLY111V, GLY117P, GLY155P, GLY34P, GLY76P, HIS116P, HIS118V, HIS120P, HIS99V, ILE115V, ILE123P, ILE147V, LEU112V, LEU120V, LEU172V, LEU176V, LYS32P, LYS73V, LYS75V, LYS82P, MET141V, MET33P, MET71V, PHE43V, PHE83P, PRO128P, PRO153P, PRO173V, PRO174V, PRO43P, PRO97V, SER151P, SER152P, SER170V, SER47V, SER75P, THR100V, THR101V, THR41P, TRP125P, TYR42P, VAL113V, VAL116V, VAL117V, VAL126P, VAL135V, VAL136V, VAL138V, VAL168V, VAL169V, VAL171V, VAL49P, VAL50P, VAL72P, VAL98V
• P-3: ALA103P, ARG94P, ASP97P, ASP99P, GLY106P, GLY63, GLY83, ILE20P, LYS53, PHE105P, SER103, SER93, THR15P, TYR19P, VAL73
• P-9: LYS89, MET141P
• Q-3: ALA763, ARG11Q, ARG12Q, ARG13Q, ARG553, ARG773, ASN53Q, ASP55Q, GLN493, GLY30Q, GLY503, GLY523, GLY54Q, HIS21Q, LEU24Q, LEU27Q, LYS28Q, LYS443, LYS743, MET10Q, MET533, PHE453, PHE783, PRO52Q, SER29Q, THR433, VAL513
• S-0: ALA1010, ALA1090, ARG1030, ARG1050, ARG37S, ARG42S, ASN40S, ASP1070, GLU1020, GLY1060, GLY1080, LYS41S, PRO1100, THR39S, TYR38S, TYR45S
• S-5: ALA245, ALA275, ALA32S, ALA89S, ARG15S, ARG18S, ARG195, ARG205, ARG25S, ARG33S, ARG37S, ASN34S, ASN40S, ASN485, ASP175, ASP22S, CYS335, CYS365, CYS465, CYS495, GLU30S, GLU31S, GLU325, GLY385, HIS235, HIS375, HIS445, ILE24S, ILE35S, ILE455, LEU19S, LEU23S, LEU255, LEU305, LEU36S, LEU415, LYS16S, LYS27S, LYS35, LYS395, LYS405, LYS41S, PRO285, PRO475, SER215, SER28S, SER425, THR265, THR315, THR39S, TYR38S, VAL17S, VAL20S, VAL21S
• S-7: ARG88S, TYR57
• T-W: ALA27T, ALA30W, ALA35W, ALA36W, ALA39W, ALA40T, ALA54W, ALA78T, ARG31W, ARG50W, ASN29W, ASP21W, ASP29T, ASP3T, GLN34W, GLN44T, GLU43T, GLY37W, HIS7T, HIS9T, ILE53W, ILE5T, LEU20W, LEU23W, LEU27W, LEU28W, LYS24W, LYS57W, LYS6T, PHE26T, PRO8T, SER1T, THR25W, TRP2T, TYR45T, VAL10T, VAL33W, VAL41T, VAL4T, VAL77T
• 0-5: ALA1010, ALA1120, ARG1030, ARG330, ARG555, ARG960, ASN485, ASP535, CYS465, CYS495, GLN565, GLU1020, GLU1150, GLU1180, GLY505, GLY545, HIS435, HIS445, ILE455, LEU1000, LEU1110, LEU1130, LEU415, LEU585, LEU980, LYS405, LYS990, PRO1100, PRO285, PRO475, SER425, TYR525, VAL1170, VAL380, VAL575, VAL970
• 1-2: ALA1001, ALA1051, ALA1081, ALA1121, ALA351, ALA421, ALA431, ALA512, ALA861, ALA961, ALA991, ARG1011, ARG132, ARG201, ARG331, ARG481, ARG501, ARG722, ARG812, ARG822, ARG832, ARG872, ARG921, ASN411, ASN871, ASN892, ASN911, ASP502, ASP891, ASP971, GLN112, GLN371, GLN442, GLN62, GLN792, GLN882, GLU1021, GLU1041, GLU432, GLU461, GLU492, GLY412, GLY422, GLY482, GLY522, GLY772, GLY852, GLY92, HIS862, ILE42, ILE52, ILE881, ILE981, LEU1091, LEU391, LEU401, LEU901, LEU951, LYS102, LYS161, LYS191, LYS531, LYS532, LYS732, LYS752, LYS931, PHE1061, PHE22, PHE361, PHE392, PHE472, PHE902, PRO1031, SER762, THR381, THR441, THR452, THR552, THR72, THR842, TRP611, TYR122, TYR451, TYR471, TYR542, TYR742, TYR802, VAL142, VAL171, VAL402, VAL462, VAL562, VAL782, VAL941
• 1-5: GLN311, GLY261, LYS105, LYS135, LYS301, SER125, SER145, SER271, SER291, TRP251
• 6-8: ALA26, ARG308, ARG428, ASN338, GLN328, GLU136, GLY358, GLY388, ILE418, LYS116, LYS266, LYS36, LYS368, MET126, SER378, THR236, THR246, THR256, THR348, TYR406