RL4 - SULSO - GREMLIN Contacts

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RL4 - 50S ribosomal protein L4

UniProt:	Q9UXA6	Sequences: MYLELVKKKSDILDKDGNRIKEVELPIIFSFPVRKDLIRRVFIAEFTHSLQPKGRDPNAGKRTSAESFGINLGMARVPRVKNSGEAALAPNTVGGRLAFPPSVNKKLAEEANVKEKRLAVISALSATADIAFVRARGHVFKDSVRFPIVVTDDIVNLKTTSEVEEFLKKIGVYDDVERVKERIRIRAGKGKMRGRKYKEPIGPLIIVHDSNSPIIKAARNLAGVDVVNAKDVSVIHLAPGAHPGRLTIYTESSIKILDERLSKRVVS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	267 (252)
Sequences:	443 (269)
Seq/√Len:	17.0

HALSA - RL4
SULSO - RL4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
152_D	252_S	5.099	1.00
206_I	247_T	4.230	1.00
45_E	111_A	3.706	1.00
127_T	247_T	3.361	0.99
124_L	249_Y	3.328	0.99
166_F	170_I	3.203	0.99
21_K	251_E	3.061	0.99
173_Y	176_V	3.032	0.99
251_E	255_K	2.908	0.98
14_D	18_N	2.873	0.98
77_V	89_A	2.614	0.97
86_A	92_T	2.605	0.96
50_L	53_K	2.549	0.96
179_V	221_L	2.529	0.96
150_V	170_I	2.527	0.96
183_I	199_E	2.518	0.96
40_R	44_A	2.451	0.95
68_F	72_L	2.437	0.95
172_V	246_L	2.378	0.94
56_D	62_R	2.221	0.92
38_I	243_P	2.209	0.91
182_R	200_P	2.190	0.91
185_I	197_Y	2.151	0.90
50_L	107_L	2.134	0.90
163_V	218_A	2.111	0.89
170_I	248_I	2.068	0.88
106_K	109_E	1.908	0.84
39_R	43_I	1.905	0.84
70_I	76_R	1.890	0.83
172_V	175_D	1.791	0.80
41_V	111_A	1.789	0.80
189_K	192_M	1.767	0.79
39_R	241_A	1.761	0.79
143_S	171_G	1.750	0.78
33_V	243_P	1.713	0.77
42_F	46_F	1.696	0.76
230_K	256_I	1.691	0.76
86_A	94_G	1.687	0.75
154_I	166_F	1.685	0.75
211_N	214_I	1.682	0.75
54_G	101_P	1.682	0.75
53_K	101_P	1.665	0.74
209_D	212_S	1.661	0.74
164_E	173_Y	1.648	0.74
133_V	146_F	1.643	0.73
155_V	208_H	1.642	0.73
40_R	115_E	1.616	0.72
65_A	87_A	1.604	0.72
25_L	29_F	1.592	0.71
226_V	261_L	1.544	0.69
188_G	195_R	1.538	0.68
92_T	253_S	1.509	0.67
64_S	87_A	1.502	0.66
64_S	107_L	1.500	0.66
221_L	224_V	1.458	0.64
154_I	250_T	1.453	0.64
172_V	248_I	1.451	0.64
151_T	251_E	1.443	0.63
31_F	121_I	1.430	0.62
53_K	107_L	1.423	0.62
143_S	146_F	1.417	0.62
208_H	252_S	1.412	0.61
87_A	94_G	1.390	0.60
117_R	229_A	1.364	0.59
42_F	241_A	1.364	0.59
142_D	174_D	1.359	0.58
134_R	141_K	1.350	0.58
124_L	146_F	1.344	0.57
80_V	83_S	1.342	0.57
123_A	238_A	1.335	0.57
185_I	216_K	1.330	0.57
198_K	225_D	1.318	0.56
182_R	199_E	1.311	0.56
157_L	166_F	1.293	0.54
9_K	22_E	1.286	0.54
89_A	92_T	1.283	0.54
70_I	84_G	1.259	0.52
140_F	205_I	1.259	0.52
190_G	196_K	1.256	0.52
124_L	128_A	1.248	0.52
168_K	173_Y	1.225	0.50
176_V	221_L	1.223	0.50
79_R	111_A	1.220	0.50
152_D	162_E	1.215	0.50
47_T	50_L	1.212	0.50
203_P	248_I	1.194	0.49
44_A	48_H	1.193	0.49
127_T	249_Y	1.184	0.48
90_P	97_L	1.166	0.47
63_T	86_A	1.163	0.47
101_P	178_R	1.157	0.46
14_D	151_T	1.135	0.45
13_L	150_V	1.135	0.45
161_S	250_T	1.130	0.45
190_G	193_R	1.129	0.45
188_G	193_R	1.123	0.44
131_A	134_R	1.118	0.44
23_V	208_H	1.112	0.44
209_D	213_P	1.110	0.44
94_G	145_R	1.105	0.43
63_T	94_G	1.101	0.43
155_V	209_D	1.098	0.43
93_V	105_K	1.093	0.43
42_F	235_I	1.090	0.42
61_K	96_R	1.088	0.42
204_L	225_D	1.088	0.42
18_N	189_K	1.085	0.42
181_E	221_L	1.079	0.42
54_G	146_F	1.076	0.42
63_T	67_S	1.072	0.41
165_E	169_K	1.063	0.41
158_K	213_P	1.051	0.40
173_Y	180_K	1.041	0.40
65_A	70_I	1.037	0.39
154_I	169_K	1.028	0.39
29_F	124_L	1.025	0.39
67_S	87_A	1.019	0.38
153_D	156_N	1.015	0.38
40_R	109_E	1.010	0.38
120_V	260_R	1.001	0.37
63_T	88_L	1.000	0.37
176_V	224_V	0.997	0.37
233_S	236_H	0.994	0.37
136_R	243_P	0.982	0.36
17_G	155_V	0.981	0.36
152_D	251_E	0.980	0.36
252_S	259_E	0.976	0.36
249_Y	254_I	0.971	0.36
46_F	236_H	0.968	0.36
229_A	249_Y	0.965	0.35
165_E	187_A	0.965	0.35
31_F	196_K	0.960	0.35
67_S	149_V	0.959	0.35
140_F	202_G	0.956	0.35
166_F	205_I	0.956	0.35
150_V	154_I	0.945	0.34
48_H	53_K	0.942	0.34
169_K	252_S	0.941	0.34
183_I	187_A	0.941	0.34
93_V	157_L	0.939	0.34
160_T	221_L	0.939	0.34
238_A	245_R	0.932	0.34
70_I	85_E	0.922	0.33
47_T	53_K	0.916	0.33
117_R	203_P	0.916	0.33
33_V	129_D	0.897	0.32
57_P	255_K	0.896	0.32
235_I	241_A	0.894	0.32
159_T	162_E	0.894	0.32
68_F	220_N	0.893	0.32
179_V	199_E	0.887	0.31
57_P	61_K	0.885	0.31
66_E	88_L	0.882	0.31
27_I	118_L	0.879	0.31
67_S	137_G	0.871	0.30
17_G	166_F	0.869	0.30
45_E	116_K	0.869	0.30
38_I	122_S	0.869	0.30
123_A	206_I	0.868	0.30
202_G	221_L	0.867	0.30
37_L	198_K	0.866	0.30
87_A	116_K	0.865	0.30
197_Y	201_I	0.863	0.30
80_V	87_A	0.860	0.30
175_D	202_G	0.858	0.30
75_A	81_K	0.853	0.29
64_S	68_F	0.848	0.29
110_E	225_D	0.847	0.29
144_V	148_I	0.843	0.29
149_V	167_L	0.835	0.29
67_S	70_I	0.834	0.29
61_K	88_L	0.830	0.28
85_E	148_I	0.830	0.28
37_L	115_E	0.828	0.28
174_D	177_E	0.826	0.28
15_K	154_I	0.826	0.28
65_A	72_L	0.825	0.28
33_V	241_A	0.824	0.28
90_P	96_R	0.823	0.28
41_V	114_K	0.821	0.28
31_F	99_F	0.816	0.28
188_G	240_G	0.814	0.28
48_H	107_L	0.812	0.28
155_V	217_A	0.812	0.28
124_L	224_V	0.811	0.27
55_R	107_L	0.809	0.27
25_L	33_V	0.807	0.27
122_S	175_D	0.805	0.27
18_N	152_D	0.797	0.27
33_V	127_T	0.790	0.26
65_A	100_P	0.785	0.26
56_D	61_K	0.784	0.26
136_R	225_D	0.783	0.26
76_R	93_V	0.775	0.26
11_D	19_R	0.772	0.26
61_K	203_P	0.769	0.26
86_A	114_K	0.767	0.25
89_A	175_D	0.766	0.25
17_G	22_E	0.765	0.25
86_A	142_D	0.764	0.25
9_K	183_I	0.764	0.25
186_R	193_R	0.759	0.25
68_F	74_M	0.758	0.25
179_V	202_G	0.758	0.25
192_M	241_A	0.754	0.25
55_R	103_V	0.747	0.25
141_K	156_N	0.747	0.25
37_L	205_I	0.745	0.24
134_R	150_V	0.745	0.24
22_E	155_V	0.742	0.24
26_P	34_R	0.737	0.24
12_I	145_R	0.735	0.24
150_V	252_S	0.733	0.24
158_K	162_E	0.728	0.24
151_T	217_A	0.725	0.24
70_I	97_L	0.724	0.24
77_V	91_N	0.722	0.23
65_A	84_G	0.722	0.23
21_K	227_V	0.721	0.23
76_R	82_N	0.715	0.23
103_V	192_M	0.715	0.23
50_L	56_D	0.713	0.23
218_A	235_I	0.712	0.23
90_P	93_V	0.711	0.23
11_D	166_F	0.711	0.23
188_G	206_I	0.709	0.23
102_S	229_A	0.708	0.23
53_K	110_E	0.708	0.23
20_I	151_T	0.707	0.23
172_V	176_V	0.705	0.23
120_V	124_L	0.703	0.23
162_E	165_E	0.696	0.22
238_A	250_T	0.696	0.22
17_G	169_K	0.693	0.22
65_A	89_A	0.691	0.22
71_N	88_L	0.688	0.22
78_P	89_A	0.686	0.22
158_K	214_I	0.682	0.22
25_L	51_Q	0.682	0.22
120_V	234_V	0.682	0.22
205_I	218_A	0.681	0.22
226_V	231_D	0.680	0.22
141_K	162_E	0.680	0.22
23_V	230_K	0.677	0.22
48_H	116_K	0.671	0.21
82_N	93_V	0.671	0.21
190_G	195_R	0.670	0.21
171_G	178_R	0.669	0.21
184_R	198_K	0.667	0.21
198_K	201_I	0.666	0.21
69_G	220_N	0.663	0.21
76_R	79_R	0.662	0.21
130_I	156_N	0.659	0.21
102_S	112_N	0.657	0.21
205_I	224_V	0.656	0.21
175_D	222_A	0.656	0.21
9_K	81_K	0.652	0.21
80_V	85_E	0.652	0.21
224_V	257_L	0.651	0.21
50_L	117_R	0.649	0.20
73_G	101_P	0.646	0.20
75_A	156_N	0.644	0.20
83_S	257_L	0.643	0.20
170_I	209_D	0.640	0.20
68_F	232_V	0.638	0.20
45_E	121_I	0.637	0.20
52_P	189_K	0.637	0.20
106_K	129_D	0.636	0.20
181_E	185_I	0.631	0.20
149_V	207_V	0.631	0.20
74_M	91_N	0.628	0.20
37_L	209_D	0.627	0.20
17_G	59_A	0.626	0.20
141_K	174_D	0.625	0.20
239_P	253_S	0.625	0.20
190_G	244_G	0.625	0.20
177_E	252_S	0.625	0.20
206_I	231_D	0.622	0.19
69_G	137_G	0.621	0.19
35_K	252_S	0.619	0.19
234_V	241_A	0.618	0.19
44_A	47_T	0.618	0.19
166_F	169_K	0.617	0.19
50_L	63_T	0.617	0.19
46_F	225_D	0.616	0.19
157_L	208_H	0.613	0.19
52_P	196_K	0.612	0.19
153_D	183_I	0.612	0.19
46_F	235_I	0.609	0.19
64_S	257_L	0.608	0.19
127_T	194_G	0.608	0.19
25_L	155_V	0.604	0.19
50_L	64_S	0.601	0.19
179_V	252_S	0.599	0.19
189_K	260_R	0.598	0.19
103_V	146_F	0.598	0.19
49_S	71_N	0.598	0.19
124_L	241_A	0.596	0.18
22_E	25_L	0.595	0.18
156_N	161_S	0.594	0.18
144_V	171_G	0.593	0.18
161_S	253_S	0.591	0.18
39_R	115_E	0.591	0.18
70_I	90_P	0.591	0.18
81_K	251_E	0.588	0.18
156_N	169_K	0.580	0.18
15_K	250_T	0.579	0.18
75_A	224_V	0.578	0.18
161_S	209_D	0.577	0.18
22_E	142_D	0.576	0.18
39_R	44_A	0.576	0.18
70_I	88_L	0.575	0.18
187_A	201_I	0.573	0.18
49_S	58_N	0.573	0.18
127_T	206_I	0.570	0.18
77_V	175_D	0.570	0.18
171_G	227_V	0.569	0.18
208_H	256_I	0.568	0.17
62_R	77_V	0.567	0.17
76_R	84_G	0.567	0.17
29_F	34_R	0.565	0.17
114_K	194_G	0.564	0.17
55_R	86_A	0.563	0.17
23_V	114_K	0.562	0.17
23_V	254_I	0.562	0.17
132_F	135_A	0.561	0.17
49_S	235_I	0.559	0.17
30_S	103_V	0.555	0.17
68_F	93_V	0.554	0.17
201_I	204_L	0.553	0.17
39_R	184_R	0.549	0.17
38_I	234_V	0.549	0.17
152_D	248_I	0.547	0.17
18_N	178_R	0.547	0.17
161_S	174_D	0.545	0.17
50_L	80_V	0.545	0.17
52_P	191_K	0.541	0.17
68_F	71_N	0.540	0.17
39_R	196_K	0.539	0.17
81_K	171_G	0.539	0.17
195_R	240_G	0.538	0.16
120_V	227_V	0.536	0.16
70_I	82_N	0.535	0.16
50_L	76_R	0.534	0.16
40_R	153_D	0.530	0.16
178_R	246_L	0.529	0.16
124_L	151_T	0.528	0.16
68_F	110_E	0.527	0.16
11_D	38_I	0.526	0.16
200_P	246_L	0.526	0.16
29_F	161_S	0.526	0.16
35_K	243_P	0.524	0.16
168_K	175_D	0.523	0.16
181_E	212_S	0.522	0.16
17_G	158_K	0.522	0.16
186_R	191_K	0.522	0.16
230_K	249_Y	0.521	0.16
52_P	224_V	0.521	0.16
211_N	215_I	0.520	0.16
87_A	97_L	0.519	0.16
28_I	126_A	0.518	0.16
133_V	178_R	0.517	0.16
35_K	125_S	0.517	0.16
150_V	166_F	0.516	0.16
146_F	249_Y	0.514	0.16
159_T	228_N	0.514	0.16
44_A	109_E	0.513	0.16
156_N	165_E	0.507	0.15
250_T	261_L	0.507	0.15
52_P	255_K	0.506	0.15
179_V	228_N	0.506	0.15
205_I	258_D	0.504	0.15
81_K	227_V	0.503	0.15
57_P	134_R	0.503	0.15
36_D	193_R	0.503	0.15
88_L	91_N	0.503	0.15
234_V	243_P	0.502	0.15
208_H	212_S	0.500	0.15

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
3j21D	1	0.9513	100	0.308	Contact Map
1vx7F	1	0.97	100	0.31	Contact Map
4ujqF	1	0.9775	100	0.311	Contact Map
3j39C	1	0.9925	100	0.312	Contact Map
4a17C	1	0.985	100	0.315	Contact Map
3j61C	1	0.9738	100	0.317	Contact Map
3j3bC	1	0.9775	100	0.32	Contact Map
3zf7r	1	0.9738	100	0.321	Contact Map
4w20C	1	0.985	100	0.322	Contact Map
1vq8C	1	0.9213	100	0.339	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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