RL3 - HALSA - GREMLIN Contacts

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RL3 - 50S ribosomal protein L3

UniProt:	Q9HPD4	Sequences: MPQPNRPRKGSMGFSPRKRAESEVPRFNSWPADDGEVGLQGFAGYKAGMTHVVLVDDKANAPTEGMETTVPVTVVETPPMRAAAVRLYEDTPYGKKPLTEVWADDTHESLDRTLSVPDEGGDTDELIEALDTEEIADIRVITHTVPGDTAGVPKKNPDVMETRVGGGTLADRLEFAADLIEDGGVHAFGDVFRAGEFTDAAGITKGKGTQGPVKRWGVQKRKGKHARQGWRRRIGNLGPWNPSRVRSTVPQQGQTGYHQRTELNKRLIDINDGDEPTPDGGFPNYGEVDGPYTLVKGSVPGPEQRLVRFRPAVRPNESPRLDPEVRYVSTASNQG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	335 (328)
Sequences:	394 (233)
Seq/√Len:	12.9

HALSA - RL3
SULSO - RL3

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
168_T	171_D	6.271	1.00
262_E	265_K	5.337	1.00
44_G	75_V	4.749	1.00
75_V	299_V	4.305	1.00
210_Q	214_K	4.194	1.00
74_V	294_L	3.850	0.99
210_Q	255_T	3.804	0.99
277_T	287_E	3.783	0.99
213_V	218_V	3.615	0.99
295_V	299_V	3.604	0.99
202_G	300_P	3.454	0.99
56_D	63_T	3.336	0.98
214_K	255_T	3.165	0.97
140_V	176_A	3.026	0.97
175_F	179_L	2.990	0.96
80_M	142_T	2.912	0.96
115_S	118_D	2.893	0.96
141_I	159_V	2.854	0.95
12_M	248_T	2.762	0.94
115_S	121_G	2.753	0.94
23_E	257_Y	2.645	0.93
189_G	272_D	2.525	0.91
126_L	131_D	2.501	0.91
115_S	119_E	2.470	0.90
125_E	131_D	2.432	0.89
118_D	121_G	2.410	0.89
209_T	252_Q	2.389	0.88
142_T	162_T	2.386	0.88
202_G	307_V	2.303	0.87
115_S	122_D	2.298	0.86
44_G	77_T	2.233	0.85
115_S	123_T	2.200	0.84
126_L	129_A	2.160	0.83
15_S	216_W	2.141	0.82
117_P	121_G	2.088	0.80
277_T	283_P	2.086	0.80
12_M	15_S	1.997	0.77
119_E	122_D	1.978	0.77
118_D	122_D	1.977	0.77
127_I	131_D	1.971	0.76
22_S	28_N	1.882	0.73
163_R	172_R	1.852	0.72
110_L	141_I	1.834	0.71
117_P	122_D	1.805	0.69
37_V	179_L	1.758	0.67
299_V	307_V	1.733	0.66
332_S	335_G	1.708	0.65
85_V	180_I	1.668	0.63
124_D	130_L	1.666	0.63
109_S	147_G	1.664	0.63
214_K	220_K	1.642	0.62
81_R	183_G	1.605	0.60
47_A	277_T	1.600	0.60
209_T	228_Q	1.564	0.58
124_D	127_I	1.548	0.57
20_A	203_I	1.546	0.57
37_V	175_F	1.542	0.57
223_G	228_Q	1.535	0.57
7_P	11_S	1.535	0.57
40_Q	163_R	1.494	0.54
200_A	299_V	1.483	0.54
72_V	76_E	1.479	0.54
89_E	98_L	1.456	0.52
39_L	140_V	1.445	0.52
81_R	145_V	1.442	0.52
271_N	274_D	1.438	0.51
230_W	233_R	1.424	0.51
117_P	123_T	1.423	0.51
227_R	230_W	1.419	0.51
28_N	201_A	1.415	0.50
140_V	186_H	1.398	0.49
85_V	176_A	1.377	0.48
216_W	252_Q	1.373	0.48
127_I	130_L	1.371	0.48
219_Q	228_Q	1.366	0.48
43_A	306_L	1.364	0.48
76_E	290_G	1.363	0.48
137_D	172_R	1.354	0.47
7_P	10_G	1.345	0.47
220_K	230_W	1.342	0.47
121_G	126_L	1.320	0.45
126_L	130_L	1.318	0.45
22_S	26_R	1.313	0.45
118_D	123_T	1.308	0.45
190_D	207_K	1.301	0.44
37_V	164_V	1.284	0.44
33_D	38_G	1.283	0.43
237_L	251_Q	1.278	0.43
183_G	187_A	1.276	0.43
226_A	229_G	1.274	0.43
196_E	244_R	1.267	0.43
220_K	228_Q	1.259	0.42
295_V	322_D	1.247	0.42
91_T	330_T	1.242	0.41
300_P	307_V	1.240	0.41
262_E	284_N	1.232	0.41
85_V	140_V	1.232	0.41
277_T	282_F	1.225	0.41
215_R	260_R	1.224	0.40
226_A	230_W	1.219	0.40
229_G	296_K	1.218	0.40
112_R	293_T	1.204	0.39
292_Y	302_P	1.175	0.38
52_V	66_M	1.170	0.38
200_A	307_V	1.165	0.38
104_D	178_D	1.161	0.37
152_V	307_V	1.156	0.37
214_K	217_G	1.153	0.37
209_T	213_V	1.147	0.37
15_S	247_S	1.146	0.37
82_A	188_F	1.146	0.37
12_M	247_S	1.143	0.36
86_R	100_E	1.121	0.35
98_L	136_A	1.119	0.35
111_D	141_I	1.105	0.35
119_E	123_T	1.095	0.34
6_R	9_K	1.095	0.34
8_R	11_S	1.090	0.34
104_D	198_T	1.085	0.34
27_F	201_A	1.085	0.34
141_I	295_V	1.080	0.34
130_L	159_V	1.080	0.34
212_P	218_V	1.078	0.33
120_G	248_T	1.052	0.32
109_S	277_T	1.050	0.32
125_E	129_A	1.049	0.32
210_Q	217_G	1.049	0.32
220_K	243_S	1.048	0.32
17_R	27_F	1.047	0.32
123_T	159_V	1.040	0.32
124_D	128_E	1.039	0.32
179_L	190_D	1.032	0.31
104_D	293_T	1.023	0.31
89_E	134_E	1.016	0.31
24_V	203_I	1.015	0.31
222_K	226_A	1.014	0.31
56_D	323_P	1.010	0.30
22_S	164_V	1.010	0.30
273_G	277_T	1.006	0.30
57_D	92_P	1.005	0.30
271_N	293_T	1.005	0.30
11_S	20_A	1.004	0.30
234_I	249_V	1.003	0.30
197_F	316_N	0.998	0.30
87_L	135_I	0.993	0.30
14_F	141_I	0.989	0.29
203_I	306_L	0.988	0.29
3_Q	8_R	0.983	0.29
202_G	247_S	0.980	0.29
213_V	228_Q	0.980	0.29
164_V	178_D	0.978	0.29
178_D	182_D	0.974	0.29
143_H	240_W	0.971	0.29
226_A	233_R	0.966	0.28
75_V	191_V	0.966	0.28
198_T	267_L	0.963	0.28
312_A	315_P	0.959	0.28
80_M	160_M	0.958	0.28
207_K	214_K	0.955	0.28
23_E	200_A	0.949	0.28
218_V	228_Q	0.945	0.28
217_G	255_T	0.941	0.27
75_V	295_V	0.940	0.27
222_K	227_R	0.937	0.27
237_L	245_V	0.934	0.27
138_I	180_I	0.933	0.27
125_E	130_L	0.931	0.27
29_S	186_H	0.924	0.27
148_D	183_G	0.922	0.27
50_T	72_V	0.920	0.27
45_Y	144_T	0.916	0.26
224_K	229_G	0.913	0.26
174_E	257_Y	0.913	0.26
60_N	112_R	0.913	0.26
160_M	308_R	0.913	0.26
61_A	102_W	0.910	0.26
84_A	158_D	0.905	0.26
43_A	160_M	0.900	0.26
228_Q	233_R	0.900	0.26
224_K	230_W	0.892	0.25
168_T	271_N	0.891	0.25
91_T	321_L	0.889	0.25
98_L	207_K	0.885	0.25
38_G	311_P	0.884	0.25
223_G	230_W	0.881	0.25
221_R	226_A	0.879	0.25
213_V	315_P	0.875	0.25
124_D	129_A	0.875	0.25
22_S	41_G	0.874	0.25
148_D	195_G	0.873	0.25
85_V	187_A	0.872	0.25
115_S	126_L	0.871	0.25
53_V	57_D	0.863	0.24
53_V	326_R	0.862	0.24
200_A	295_V	0.861	0.24
220_K	227_R	0.855	0.24
118_D	131_D	0.854	0.24
32_A	267_L	0.853	0.24
45_Y	48_G	0.853	0.24
11_S	17_R	0.852	0.24
90_D	257_Y	0.852	0.24
168_T	289_D	0.846	0.24
327_Y	331_A	0.846	0.24
85_V	170_A	0.844	0.24
119_E	272_D	0.843	0.24
229_G	233_R	0.841	0.23
170_A	174_E	0.838	0.23
237_L	242_P	0.827	0.23
260_R	305_R	0.826	0.23
234_I	237_L	0.825	0.23
93_Y	134_E	0.822	0.23
232_R	260_R	0.821	0.23
196_E	311_P	0.819	0.23
160_M	216_W	0.819	0.23
220_K	237_L	0.818	0.23
222_K	230_W	0.817	0.23
125_E	200_A	0.815	0.22
215_R	232_R	0.811	0.22
43_A	80_M	0.809	0.22
39_L	186_H	0.805	0.22
242_P	271_N	0.805	0.22
52_V	202_G	0.804	0.22
173_L	294_L	0.803	0.22
118_D	126_L	0.802	0.22
216_W	259_Q	0.796	0.22
221_R	233_R	0.791	0.22
114_L	159_V	0.791	0.22
85_V	291_P	0.789	0.22
17_R	306_L	0.788	0.22
23_E	41_G	0.788	0.22
172_R	229_G	0.786	0.21
29_S	313_V	0.786	0.21
171_D	320_R	0.785	0.21
175_F	218_V	0.784	0.21
122_D	125_E	0.781	0.21
163_R	167_G	0.779	0.21
59_A	269_D	0.773	0.21
47_A	59_A	0.772	0.21
87_L	138_I	0.771	0.21
229_G	244_R	0.771	0.21
11_S	247_S	0.770	0.21
164_V	175_F	0.769	0.21
23_E	203_I	0.769	0.21
174_E	177_A	0.767	0.21
110_L	210_Q	0.765	0.21
195_G	322_D	0.765	0.21
119_E	307_V	0.764	0.21
28_N	58_K	0.761	0.21
119_E	126_L	0.761	0.21
89_E	114_L	0.757	0.20
76_E	285_Y	0.754	0.20
213_V	227_R	0.754	0.20
98_L	134_E	0.753	0.20
232_R	305_R	0.751	0.20
97_P	186_H	0.750	0.20
221_R	227_R	0.748	0.20
291_P	328_V	0.746	0.20
71_P	251_Q	0.745	0.20
196_E	312_A	0.744	0.20
59_A	277_T	0.744	0.20
51_H	76_E	0.742	0.20
297_G	301_G	0.739	0.20
169_L	200_A	0.737	0.20
189_G	273_G	0.731	0.20
277_T	333_N	0.727	0.19
279_D	331_A	0.725	0.19
115_S	127_I	0.725	0.19
136_A	205_K	0.723	0.19
275_E	302_P	0.722	0.19
31_P	310_R	0.718	0.19
103_A	106_T	0.716	0.19
142_T	160_M	0.715	0.19
61_A	64_E	0.715	0.19
14_F	167_G	0.712	0.19
20_A	292_Y	0.711	0.19
241_N	291_P	0.711	0.19
44_G	48_G	0.709	0.19
146_P	149_T	0.709	0.19
3_Q	9_K	0.709	0.19
227_R	240_W	0.708	0.19
33_D	47_A	0.707	0.19
77_T	216_W	0.707	0.19
74_V	193_R	0.706	0.19
77_T	302_P	0.703	0.19
14_F	77_T	0.701	0.19
83_A	141_I	0.699	0.19
12_M	156_N	0.698	0.19
151_G	290_G	0.697	0.19
122_D	129_A	0.696	0.18
151_G	289_D	0.695	0.18
107_H	143_H	0.693	0.18
263_L	295_V	0.692	0.18
123_T	126_L	0.692	0.18
199_D	238_G	0.692	0.18
47_A	325_V	0.691	0.18
83_A	143_H	0.689	0.18
198_T	202_G	0.686	0.18
52_V	261_T	0.686	0.18
94_G	332_S	0.685	0.18
51_H	72_V	0.684	0.18
45_Y	49_M	0.683	0.18
20_A	298_S	0.682	0.18
115_S	124_D	0.681	0.18
257_Y	324_E	0.681	0.18
12_M	152_V	0.681	0.18
268_I	325_V	0.680	0.18
6_R	219_Q	0.680	0.18
6_R	273_G	0.680	0.18
7_P	18_K	0.678	0.18
288_V	307_V	0.677	0.18
41_G	308_R	0.672	0.18
43_A	146_P	0.670	0.18
77_T	138_I	0.667	0.18
53_V	69_T	0.665	0.18
83_A	159_V	0.663	0.17
224_K	240_W	0.662	0.17
21_E	177_A	0.661	0.17
52_V	177_A	0.660	0.17
56_D	68_T	0.659	0.17
57_D	290_G	0.659	0.17
110_L	300_P	0.657	0.17
282_F	287_E	0.656	0.17
80_M	159_V	0.656	0.17
87_L	133_E	0.655	0.17
37_V	312_A	0.654	0.17
124_D	131_D	0.654	0.17
250_P	266_R	0.651	0.17
171_D	273_G	0.651	0.17
124_D	190_D	0.650	0.17
113_T	156_N	0.650	0.17
235_G	251_Q	0.650	0.17
118_D	124_D	0.649	0.17
223_G	227_R	0.645	0.17
106_T	114_L	0.642	0.17
141_I	262_E	0.641	0.17
149_T	257_Y	0.640	0.17
192_F	267_L	0.637	0.17
30_W	40_Q	0.637	0.17
329_S	333_N	0.636	0.17
172_R	259_Q	0.635	0.17
22_S	25_P	0.635	0.17
243_S	318_S	0.631	0.17
167_G	221_R	0.631	0.17
178_D	219_Q	0.631	0.17
88_Y	215_R	0.630	0.16
98_L	135_I	0.630	0.16
224_K	228_Q	0.627	0.16
188_F	270_I	0.627	0.16
43_A	144_T	0.626	0.16
40_Q	245_V	0.625	0.16
238_G	245_V	0.625	0.16
265_K	284_N	0.625	0.16
55_V	65_G	0.624	0.16
107_H	213_V	0.623	0.16
202_G	304_Q	0.621	0.16
138_I	183_G	0.620	0.16
213_V	258_H	0.620	0.16
283_P	293_T	0.618	0.16
54_L	68_T	0.618	0.16
84_A	196_E	0.618	0.16
16_P	19_R	0.616	0.16
5_N	180_I	0.615	0.16
246_R	257_Y	0.611	0.16
11_S	22_S	0.611	0.16
13_G	42_F	0.610	0.16
37_V	171_D	0.610	0.16
281_G	310_R	0.609	0.16
173_L	313_V	0.607	0.16
147_G	189_G	0.607	0.16
277_T	288_V	0.607	0.16
13_G	202_G	0.606	0.16
13_G	221_R	0.604	0.16
224_K	245_V	0.604	0.16
326_R	329_S	0.603	0.16
9_K	171_D	0.602	0.16
211_G	261_T	0.600	0.16
196_E	229_G	0.599	0.16
76_E	327_Y	0.597	0.16
242_P	249_V	0.597	0.16
253_G	297_G	0.596	0.16
57_D	267_L	0.594	0.15
82_A	191_V	0.593	0.15
37_V	293_T	0.593	0.15
91_T	94_G	0.592	0.15
153_P	306_L	0.590	0.15
22_S	201_A	0.590	0.15
229_G	242_P	0.588	0.15
69_T	247_S	0.587	0.15
214_K	334_Q	0.586	0.15
131_D	138_I	0.585	0.15
91_T	112_R	0.585	0.15
238_G	242_P	0.585	0.15
250_P	290_G	0.584	0.15
218_V	315_P	0.583	0.15
276_P	289_D	0.583	0.15
45_Y	146_P	0.582	0.15
175_F	213_V	0.581	0.15
172_R	233_R	0.581	0.15
5_N	228_Q	0.580	0.15
31_P	218_V	0.577	0.15
177_A	219_Q	0.577	0.15
221_R	228_Q	0.574	0.15
234_I	242_P	0.574	0.15
108_E	288_V	0.572	0.15
292_Y	299_V	0.572	0.15
132_T	174_E	0.571	0.15
180_I	189_G	0.570	0.15
20_A	23_E	0.569	0.15
95_K	137_D	0.569	0.15
286_G	297_G	0.568	0.15
281_G	301_G	0.566	0.15
118_D	125_E	0.564	0.15
6_R	144_T	0.563	0.15
62_P	241_N	0.563	0.15
224_K	227_R	0.563	0.15
213_V	303_E	0.562	0.15
148_D	210_Q	0.560	0.15
280_G	332_S	0.559	0.15
6_R	213_V	0.558	0.15
49_M	67_E	0.557	0.15
224_K	242_P	0.557	0.15
234_I	251_Q	0.556	0.14
67_E	140_V	0.556	0.14
58_K	69_T	0.556	0.14
175_F	288_V	0.555	0.14
222_K	228_Q	0.553	0.14
156_N	328_V	0.553	0.14
82_A	198_T	0.552	0.14
236_N	330_T	0.552	0.14
113_T	145_V	0.551	0.14
21_E	155_K	0.550	0.14
146_P	314_R	0.549	0.14
51_H	283_P	0.548	0.14
220_K	226_A	0.547	0.14
6_R	58_K	0.547	0.14
274_D	328_V	0.546	0.14
159_V	257_Y	0.542	0.14
267_L	293_T	0.542	0.14
229_G	252_Q	0.541	0.14
10_G	19_R	0.541	0.14
97_P	257_Y	0.540	0.14
224_K	237_L	0.539	0.14
14_F	244_R	0.538	0.14
318_S	325_V	0.537	0.14
123_T	130_L	0.536	0.14
128_E	322_D	0.536	0.14
5_N	148_D	0.536	0.14
56_D	65_G	0.533	0.14
80_M	312_A	0.533	0.14
92_P	247_S	0.530	0.14
301_G	305_R	0.530	0.14
109_S	112_R	0.530	0.14
236_N	312_A	0.528	0.14
166_G	215_R	0.528	0.14
121_G	124_D	0.524	0.14
191_V	270_I	0.523	0.14
126_L	295_V	0.523	0.14
3_Q	309_F	0.522	0.14
54_L	74_V	0.521	0.14
136_A	248_T	0.521	0.14
170_A	188_F	0.519	0.14
69_T	292_Y	0.518	0.14
12_M	217_G	0.518	0.14
59_A	294_L	0.517	0.14
17_R	250_P	0.517	0.14
44_G	300_P	0.515	0.13
297_G	310_R	0.514	0.13
243_S	258_H	0.514	0.13
99_T	106_T	0.514	0.13
96_K	140_V	0.513	0.13
136_A	149_T	0.512	0.13
73_T	300_P	0.511	0.13
163_R	329_S	0.510	0.13
85_V	269_D	0.510	0.13
226_A	311_P	0.509	0.13
159_V	300_P	0.509	0.13
51_H	282_F	0.508	0.13
59_A	287_E	0.506	0.13
93_Y	309_F	0.506	0.13
157_P	235_G	0.506	0.13
208_G	281_G	0.505	0.13
74_V	325_V	0.505	0.13
118_D	130_L	0.505	0.13
249_V	328_V	0.504	0.13
26_R	43_A	0.503	0.13
107_H	190_D	0.503	0.13
82_A	243_S	0.502	0.13
28_N	186_H	0.502	0.13
224_K	249_V	0.501	0.13
71_P	214_K	0.500	0.13
33_D	229_G	0.500	0.13
79_P	299_V	0.500	0.13

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4ujqE	1	0.9851	100	0.184	Contact Map
3zf7f	1	0.9821	100	0.186	Contact Map
1vx7E	1	0.9791	100	0.187	Contact Map
4a17B	1	0.9791	100	0.195	Contact Map
3j61B	1	0.9881	100	0.197	Contact Map
4w20B	1	0.9851	100	0.202	Contact Map
3j21C	1	0.9731	100	0.227	Contact Map
1vq8B	1	0.991	100	0.246	Contact Map
1vw3C	1	0.7224	100	0.591	Contact Map
4tp9D	1	0.6119	100	0.62	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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