PCNA3 - SULSO - GREMLIN Contacts

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PCNA3 - DNA polymerase sliding clamp 3

UniProt:	P57765	Sequences: MKVVYDDVRVLKDIIQALARLVDEAVLKFKQDSVELVALDRAHISLISVNLPREMFKEYDVNDEFKFGFNTQYLMKILKVAKRKEAIEIASESPDSVIINIIGSTNREFNVRNLEVSEQEIPEINLQFDISATISSDGFKSAISEVSTVTDNVVVEGHEDRILIKAEGESEVEVEFSKDTGGLQDLEFSKESKNSYSAEYLDDVLSLTKLSDYVKISFGNQKPLQLFFNMEGGGKVTYLLAPKV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	244 (239)
Sequences:	643 (449)
Seq/√Len:	29.0

HALSA - PCNA
SULSO - PCNA3 PCNA2 PCNA1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
130_I	157_G	4.823	1.00
216_I	224_L	3.791	1.00
129_D	190_K	3.737	1.00
11_L	87_I	3.046	1.00
69_F	97_V	2.925	1.00
74_L	99_I	2.671	1.00
132_A	162_I	2.546	0.99
227_F	237_T	2.496	0.99
196_Y	218_F	2.415	0.99
29_F	59_Y	2.408	0.99
155_V	162_I	2.408	0.99
230_M	234_G	2.375	0.99
51_L	234_G	2.352	0.99
154_V	193_K	2.318	0.99
30_K	53_R	2.312	0.99
27_L	36_L	2.262	0.99
208_T	228_F	2.241	0.98
8_V	87_I	2.233	0.98
155_V	164_I	2.174	0.98
42_A	239_L	2.155	0.98
50_N	235_K	2.114	0.98
49_V	236_V	2.114	0.98
89_I	99_I	2.082	0.97
32_D	143_I	2.057	0.97
40_D	200_Y	2.055	0.97
223_P	242_P	2.026	0.97
42_A	200_Y	2.017	0.97
150_T	166_A	1.976	0.96
43_H	124_I	1.951	0.96
43_H	46_L	1.920	0.96
132_A	184_Q	1.913	0.96
129_D	219_G	1.843	0.95
196_Y	201_L	1.841	0.95
15_I	27_L	1.830	0.95
132_A	157_G	1.804	0.94
39_L	43_H	1.755	0.93
30_K	59_Y	1.747	0.93
157_G	188_F	1.737	0.93
51_L	143_I	1.731	0.93
40_D	68_G	1.719	0.92
215_K	227_F	1.692	0.92
89_I	97_V	1.680	0.92
40_D	44_I	1.667	0.91
108_E	173_E	1.610	0.90
181_G	212_D	1.601	0.89
14_I	125_N	1.598	0.89
28_K	120_E	1.563	0.88
216_I	226_L	1.550	0.88
127_Q	189_S	1.548	0.88
225_Q	228_F	1.537	0.87
80_V	145_E	1.519	0.87
29_F	61_V	1.487	0.86
34_V	97_V	1.480	0.85
111_V	205_L	1.474	0.85
44_I	200_Y	1.465	0.85
26_V	116_V	1.460	0.85
73_Y	172_V	1.455	0.84
24_E	70_N	1.454	0.84
205_L	208_T	1.453	0.84
105_T	138_G	1.453	0.84
156_E	167_E	1.453	0.84
109_F	166_A	1.414	0.83
27_L	67_F	1.394	0.82
39_L	44_I	1.386	0.81
78_L	155_V	1.378	0.81
150_T	205_L	1.372	0.81
181_G	228_F	1.356	0.80
45_S	200_Y	1.352	0.80
30_K	35_E	1.346	0.79
46_L	124_I	1.335	0.79
134_I	139_F	1.333	0.79
32_D	54_E	1.328	0.78
113_N	206_S	1.315	0.78
108_E	228_F	1.312	0.78
43_H	197_S	1.293	0.76
69_F	111_V	1.281	0.76
77_I	198_A	1.280	0.76
122_P	222_K	1.273	0.75
11_L	36_L	1.263	0.75
189_S	192_S	1.259	0.75
79_K	85_E	1.240	0.73
166_A	196_Y	1.237	0.73
140_K	198_A	1.234	0.73
136_S	210_L	1.219	0.72
45_S	240_L	1.218	0.72
229_N	235_K	1.206	0.71
204_V	240_L	1.206	0.71
18_L	29_F	1.190	0.70
109_F	133_T	1.184	0.70
62_N	93_S	1.158	0.68
25_A	36_L	1.148	0.67
125_N	169_E	1.140	0.67
14_I	96_S	1.137	0.67
78_L	133_T	1.137	0.67
235_K	239_L	1.126	0.66
137_D	153_V	1.116	0.65
225_Q	237_T	1.115	0.65
80_V	107_R	1.113	0.65
24_E	151_D	1.112	0.65
71_T	85_E	1.111	0.65
160_D	178_K	1.107	0.65
12_K	240_L	1.106	0.64
89_I	193_K	1.100	0.64
134_I	142_A	1.097	0.64
124_I	204_V	1.092	0.63
153_V	164_I	1.072	0.62
18_L	36_L	1.054	0.61
155_V	168_G	1.049	0.60
21_L	48_S	1.046	0.60
143_I	202_D	1.044	0.60
212_D	233_G	1.032	0.59
98_I	149_V	1.022	0.58
61_V	64_E	1.007	0.57
131_S	215_K	1.004	0.57
68_G	168_G	0.997	0.56
11_L	81_A	0.993	0.56
92_E	98_I	0.982	0.55
37_V	243_K	0.979	0.55
43_H	240_L	0.977	0.55
14_I	211_S	0.975	0.55
231_E	238_Y	0.974	0.55
183_L	190_K	0.973	0.54
146_V	164_I	0.972	0.54
55_M	194_N	0.971	0.54
128_F	219_G	0.971	0.54
83_R	207_L	0.969	0.54
100_N	108_E	0.964	0.54
22_V	25_A	0.960	0.53
15_I	25_A	0.959	0.53
58_E	109_F	0.958	0.53
122_P	125_N	0.958	0.53
87_I	179_D	0.958	0.53
156_E	216_I	0.947	0.52
140_K	144_S	0.941	0.52
47_I	201_L	0.939	0.52
40_D	43_H	0.937	0.52
101_I	196_Y	0.933	0.51
148_T	171_E	0.929	0.51
55_M	234_G	0.926	0.51
230_M	233_G	0.925	0.51
49_V	163_L	0.923	0.51
31_Q	41_R	0.921	0.50
12_K	56_F	0.919	0.50
41_R	219_G	0.911	0.50
53_R	59_Y	0.904	0.49
23_D	72_Q	0.904	0.49
25_A	71_T	0.902	0.49
106_N	160_D	0.900	0.49
24_E	238_Y	0.892	0.48
155_V	159_E	0.889	0.48
143_I	233_G	0.887	0.48
45_S	63_D	0.886	0.48
14_I	27_L	0.884	0.48
39_L	119_Q	0.882	0.47
149_V	198_A	0.870	0.46
39_L	42_A	0.870	0.46
132_A	186_L	0.866	0.46
46_L	109_F	0.866	0.46
9_R	75_M	0.863	0.46
20_R	203_D	0.860	0.46
76_K	121_I	0.859	0.46
74_L	185_D	0.854	0.45
191_E	208_T	0.853	0.45
201_L	224_L	0.851	0.45
161_R	175_E	0.851	0.45
86_A	125_N	0.850	0.45
168_G	172_V	0.847	0.45
89_I	105_T	0.847	0.45
140_K	208_T	0.845	0.44
154_V	226_L	0.840	0.44
57_K	87_I	0.839	0.44
42_A	170_S	0.837	0.44
77_I	176_F	0.837	0.44
26_V	66_K	0.832	0.43
215_K	234_G	0.832	0.43
16_Q	230_M	0.827	0.43
47_I	148_T	0.823	0.43
55_M	78_L	0.822	0.43
64_E	209_K	0.821	0.43
66_K	141_S	0.821	0.43
207_L	238_Y	0.816	0.42
131_S	212_D	0.813	0.42
133_T	213_Y	0.807	0.42
107_R	112_R	0.807	0.42
44_I	241_A	0.806	0.42
112_R	155_V	0.805	0.41
111_V	151_D	0.803	0.41
156_E	191_E	0.802	0.41
130_I	186_L	0.799	0.41
59_Y	202_D	0.797	0.41
87_I	183_L	0.797	0.41
163_L	173_E	0.795	0.41
17_A	27_L	0.790	0.40
158_H	191_E	0.788	0.40
24_E	198_A	0.784	0.40
15_I	238_Y	0.774	0.39
59_Y	99_I	0.769	0.39
22_V	198_A	0.753	0.38
47_I	69_F	0.750	0.37
123_E	206_S	0.748	0.37
43_H	243_K	0.745	0.37
127_Q	187_E	0.744	0.37
136_S	230_M	0.739	0.37
117_S	139_F	0.723	0.35
81_A	227_F	0.723	0.35
22_V	26_V	0.722	0.35
76_K	114_L	0.722	0.35
7_D	149_V	0.719	0.35
46_L	126_L	0.719	0.35
10_V	149_V	0.716	0.35
63_D	151_D	0.709	0.34
76_K	113_N	0.702	0.34
94_P	151_D	0.702	0.34
38_A	160_D	0.699	0.34
89_I	192_S	0.698	0.34
166_A	199_E	0.697	0.34
21_L	195_S	0.696	0.33
127_Q	173_E	0.693	0.33
201_L	207_L	0.692	0.33
36_L	186_L	0.692	0.33
77_I	93_S	0.686	0.33
150_T	203_D	0.683	0.33
59_Y	214_V	0.681	0.32
135_S	179_D	0.678	0.32
208_T	211_S	0.677	0.32
44_I	71_T	0.677	0.32
85_E	198_A	0.675	0.32
46_L	121_I	0.674	0.32
224_L	231_E	0.674	0.32
51_L	233_G	0.670	0.32
149_V	172_V	0.667	0.31
127_Q	213_Y	0.666	0.31
16_Q	32_D	0.665	0.31
47_I	196_Y	0.664	0.31
53_R	161_R	0.663	0.31
11_L	76_K	0.662	0.31
19_A	138_G	0.659	0.31
129_D	220_N	0.658	0.31
217_S	227_F	0.657	0.31
89_I	131_S	0.657	0.31
14_I	231_E	0.657	0.31
71_T	89_I	0.655	0.31
26_V	130_I	0.649	0.30
6_D	57_K	0.648	0.30
60_D	93_S	0.648	0.30
73_Y	145_E	0.646	0.30
151_D	238_Y	0.646	0.30
130_I	188_F	0.645	0.30
16_Q	155_V	0.642	0.30
11_L	167_E	0.640	0.30
14_I	189_S	0.637	0.29
154_V	165_K	0.636	0.29
40_D	168_G	0.636	0.29
122_P	234_G	0.634	0.29
143_I	218_F	0.633	0.29
163_L	191_E	0.632	0.29
90_A	99_I	0.630	0.29
194_N	198_A	0.630	0.29
18_L	72_Q	0.629	0.29
21_L	198_A	0.628	0.29
42_A	132_A	0.627	0.29
153_V	162_I	0.623	0.29
139_F	217_S	0.621	0.28
43_H	200_Y	0.620	0.28
87_I	233_G	0.619	0.28
129_D	210_L	0.616	0.28
23_D	204_V	0.615	0.28
89_I	134_I	0.615	0.28
24_E	149_V	0.613	0.28
127_Q	232_G	0.610	0.28
200_Y	239_L	0.609	0.28
36_L	47_I	0.606	0.28
37_V	46_L	0.604	0.27
73_Y	95_D	0.603	0.27
76_K	145_E	0.603	0.27
160_D	188_F	0.602	0.27
141_S	150_T	0.600	0.27
94_P	235_K	0.599	0.27
92_E	99_I	0.595	0.27
52_P	57_K	0.595	0.27
95_D	114_L	0.593	0.27
69_F	94_P	0.592	0.27
78_L	107_R	0.592	0.27
72_Q	148_T	0.591	0.27
10_V	151_D	0.591	0.27
66_K	99_I	0.585	0.26
231_E	236_V	0.582	0.26
174_V	228_F	0.581	0.26
59_Y	201_L	0.580	0.26
72_Q	216_I	0.577	0.26
29_F	67_F	0.576	0.26
176_F	184_Q	0.575	0.26
126_L	129_D	0.574	0.26
81_A	101_I	0.573	0.26
87_I	175_E	0.573	0.26
128_F	132_A	0.573	0.26
18_L	185_D	0.570	0.25
156_E	215_K	0.569	0.25
165_K	205_L	0.568	0.25
44_I	223_P	0.568	0.25
15_I	36_L	0.567	0.25
220_N	238_Y	0.565	0.25
13_D	37_V	0.565	0.25
97_V	171_E	0.564	0.25
78_L	187_E	0.562	0.25
43_H	239_L	0.561	0.25
22_V	44_I	0.559	0.25
57_K	221_Q	0.558	0.25
27_L	152_N	0.556	0.25
106_N	218_F	0.556	0.25
177_S	180_T	0.555	0.24
130_I	151_D	0.553	0.24
124_I	151_D	0.553	0.24
114_L	121_I	0.552	0.24
90_A	100_N	0.550	0.24
128_F	136_S	0.549	0.24
135_S	218_F	0.549	0.24
144_S	176_F	0.547	0.24
74_L	111_V	0.547	0.24
201_L	208_T	0.546	0.24
167_E	171_E	0.542	0.24
228_F	240_L	0.541	0.24
234_G	238_Y	0.538	0.23
17_A	236_V	0.537	0.23
89_I	125_N	0.537	0.23
194_N	197_S	0.536	0.23
131_S	224_L	0.534	0.23
177_S	190_K	0.533	0.23
182_G	239_L	0.533	0.23
32_D	134_I	0.531	0.23
193_K	212_D	0.530	0.23
115_E	225_Q	0.527	0.23
57_K	153_V	0.526	0.23
34_V	77_I	0.523	0.23
162_I	168_G	0.523	0.23
18_L	229_N	0.520	0.22
43_H	113_N	0.517	0.22
42_A	240_L	0.517	0.22
141_S	145_E	0.516	0.22
151_D	242_P	0.515	0.22
146_V	150_T	0.513	0.22
149_V	233_G	0.513	0.22
62_N	216_I	0.513	0.22
110_N	168_G	0.513	0.22
23_D	126_L	0.513	0.22
95_D	243_K	0.512	0.22
126_L	226_L	0.512	0.22
14_I	89_I	0.511	0.22
202_D	232_G	0.510	0.22
88_E	135_S	0.510	0.22
138_G	141_S	0.508	0.22
81_A	117_S	0.508	0.22
83_R	155_V	0.508	0.22
109_F	238_Y	0.507	0.22
49_V	150_T	0.505	0.22
81_A	91_S	0.501	0.21
161_R	193_K	0.501	0.21
215_K	229_N	0.500	0.21

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
3a1jC	1	0.9877	100	0.276	Contact Map
3g65A	1	0.9631	100	0.292	Contact Map
3k4xA	1	0.9918	100	0.31	Contact Map
3a1jA	1	0.9918	100	0.324	Contact Map
3a1jB	1	0.959	100	0.327	Contact Map
3fdsC	1	0.9918	100	0.379	Contact Map
2ijxA	3	1	100	0.407	Contact Map
1ud9A	2	0.9877	100	0.407	Contact Map
3aizA	1	0.9918	100	0.413	Contact Map
3aizC	1	0.9959	100	0.418	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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