PCNA - HALSA - GREMLIN Contacts

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PCNA - DNA polymerase sliding clamp

UniProt:	Q9HN45	Sequences: MFKAIVSADTLQETLDSVSVLVDECKIHLDDDTLSIRAVDPASVGMVDLDLAATAFESYEADGGLIGVNLSRLEDIAGMADAGQLIQLELDEETRKLHIQIDGLEYTLALIDPDSIRQEPDIPDLDLPAHVAIEGRDIDRAVTAADMVSDHIALGVDTGDDLFYVNAEGDTDDVHLELAPDQLIDLDAGDAHSLFSLDYLKDMNKAIPTTAEVELELGDEFPIKLHFDIADAQGHVTYMLAPRIQSN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	247 (239)
Sequences:	637 (440)
Seq/√Len:	28.5

HALSA - PCNA
SULSO - PCNA1 PCNA2 PCNA3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
129_A	156_V	4.896	1.00
215_L	223_I	4.320	1.00
128_P	190_D	3.546	1.00
154_L	165_V	3.322	1.00
8_A	86_I	3.100	1.00
154_L	163_F	3.047	1.00
11_L	86_I	2.810	1.00
131_V	163_F	2.786	1.00
29_L	59_Y	2.647	1.00
229_I	234_G	2.545	0.99
153_A	192_H	2.527	0.99
226_H	237_T	2.488	0.99
30_D	53_A	2.468	0.99
68_V	97_L	2.457	0.99
51_L	234_G	2.387	0.99
27_I	36_I	2.358	0.99
195_F	217_L	2.356	0.99
49_L	236_V	2.354	0.99
207_I	227_F	2.313	0.99
149_S	167_A	2.224	0.98
42_A	199_Y	2.207	0.98
32_D	142_V	2.199	0.98
40_D	199_Y	2.174	0.98
43_S	46_M	2.116	0.98
30_D	59_Y	2.015	0.97
42_A	239_M	1.985	0.96
88_L	99_I	1.977	0.96
14_T	124_D	1.959	0.96
79_M	104_L	1.907	0.95
3_K	89_E	1.880	0.95
50_D	235_H	1.817	0.94
222_P	242_P	1.816	0.94
15_L	27_I	1.815	0.94
131_V	156_V	1.807	0.94
51_L	142_V	1.805	0.94
43_S	123_P	1.751	0.93
39_V	43_S	1.735	0.92
40_D	44_V	1.700	0.92
73_L	99_I	1.699	0.92
224_K	227_F	1.697	0.92
214_E	226_H	1.686	0.91
215_L	225_L	1.653	0.90
128_P	218_G	1.647	0.90
131_V	186_L	1.597	0.89
28_H	119_E	1.594	0.89
106_Y	167_A	1.587	0.89
72_R	174_V	1.585	0.89
67_G	169_G	1.553	0.87
26_K	113_P	1.543	0.87
126_D	189_G	1.541	0.87
110_L	205_K	1.540	0.87
11_L	36_I	1.539	0.87
195_F	200_L	1.537	0.87
204_N	207_I	1.536	0.87
40_D	67_G	1.531	0.87
44_V	199_Y	1.512	0.86
114_D	138_I	1.506	0.86
79_M	144_A	1.500	0.86
68_V	231_D	1.442	0.83
39_V	44_V	1.434	0.83
2_F	29_L	1.426	0.82
29_L	61_A	1.424	0.82
131_V	184_I	1.388	0.81
135_G	209_T	1.370	0.80
70_L	84_Q	1.346	0.79
30_D	35_S	1.344	0.79
77_A	154_L	1.342	0.78
32_D	54_T	1.336	0.78
46_M	123_P	1.327	0.78
27_I	66_I	1.301	0.76
105_E	175_H	1.298	0.76
45_G	199_Y	1.296	0.76
14_T	210_T	1.281	0.75
45_G	240_L	1.264	0.74
133_I	138_I	1.263	0.74
43_S	196_S	1.252	0.73
24_E	69_N	1.247	0.73
61_A	64_G	1.241	0.73
106_Y	132_A	1.239	0.73
142_V	201_K	1.233	0.72
25_C	36_I	1.224	0.72
34_L	97_L	1.221	0.71
18_V	29_L	1.220	0.71
75_D	120_P	1.213	0.71
149_S	204_N	1.192	0.70
55_A	234_G	1.187	0.69
220_E	244_I	1.185	0.69
121_D	221_F	1.185	0.69
126_D	231_D	1.173	0.68
14_T	96_K	1.171	0.68
167_A	195_F	1.164	0.68
162_L	177_E	1.160	0.67
62_D	92_E	1.159	0.67
135_G	229_I	1.148	0.67
123_P	244_I	1.124	0.65
203_M	240_L	1.121	0.65
235_H	239_M	1.118	0.64
78_G	84_Q	1.076	0.61
18_V	36_I	1.062	0.60
25_C	70_L	1.060	0.60
123_P	203_M	1.053	0.60
37_R	243_R	1.031	0.58
155_G	168_E	1.031	0.58
15_L	238_Y	1.027	0.58
31_D	41_P	1.025	0.58
11_L	168_E	1.023	0.57
136_R	152_I	1.019	0.57
148_V	174_V	1.017	0.57
156_V	188_A	1.009	0.56
21_L	48_D	0.992	0.55
14_T	230_A	0.988	0.55
139_D	197_L	0.987	0.55
44_V	241_A	0.982	0.54
22_V	25_C	0.974	0.54
224_K	237_T	0.972	0.54
167_A	198_D	0.970	0.53
2_F	45_G	0.970	0.53
57_E	86_I	0.969	0.53
148_V	183_L	0.967	0.53
93_E	131_V	0.966	0.53
47_V	147_M	0.958	0.53
161_D	188_A	0.957	0.52
14_T	27_I	0.952	0.52
156_V	180_P	0.949	0.52
228_D	235_H	0.939	0.51
88_L	192_H	0.929	0.50
8_A	111_I	0.927	0.50
139_D	143_T	0.927	0.50
127_L	218_G	0.925	0.50
5_I	105_E	0.913	0.49
40_D	43_S	0.913	0.49
155_G	215_L	0.911	0.49
44_V	222_P	0.910	0.49
77_A	132_A	0.908	0.49
133_I	141_A	0.907	0.49
20_V	202_D	0.900	0.48
190_D	229_I	0.895	0.48
131_V	233_Q	0.894	0.48
2_F	206_A	0.892	0.47
72_R	144_A	0.891	0.47
153_A	187_D	0.888	0.47
39_V	42_A	0.887	0.47
12_Q	240_L	0.887	0.47
80_A	184_I	0.886	0.47
47_V	68_V	0.886	0.47
5_I	141_A	0.884	0.47
24_E	150_D	0.883	0.47
42_A	172_D	0.872	0.46
82_A	101_I	0.872	0.46
73_L	114_D	0.869	0.46
17_S	105_E	0.869	0.46
164_Y	175_H	0.859	0.45
130_H	214_E	0.858	0.45
43_S	243_R	0.857	0.45
11_L	80_A	0.856	0.45
47_V	195_F	0.855	0.45
68_V	93_E	0.848	0.44
53_A	59_Y	0.847	0.44
58_S	106_Y	0.845	0.44
93_E	136_R	0.837	0.43
5_I	148_V	0.832	0.43
109_A	154_L	0.831	0.43
70_L	88_L	0.828	0.43
68_V	181_D	0.825	0.42
162_L	192_H	0.820	0.42
170_D	223_I	0.819	0.42
55_A	77_A	0.815	0.42
43_S	109_A	0.807	0.41
55_A	230_A	0.799	0.40
34_L	181_D	0.795	0.40
26_K	65_L	0.792	0.40
15_L	25_C	0.792	0.40
121_D	124_D	0.792	0.40
132_A	212_E	0.792	0.40
122_I	205_K	0.788	0.40
29_L	66_I	0.783	0.39
105_E	227_F	0.782	0.39
150_D	238_Y	0.782	0.39
200_L	206_A	0.782	0.39
14_T	189_G	0.779	0.39
121_D	234_G	0.777	0.39
16_D	32_D	0.777	0.39
88_L	191_A	0.776	0.39
88_L	181_D	0.774	0.38
219_D	238_Y	0.772	0.38
15_L	180_P	0.772	0.38
39_V	118_Q	0.771	0.38
47_V	200_L	0.771	0.38
22_V	113_P	0.770	0.38
75_D	144_A	0.766	0.38
168_E	216_E	0.764	0.38
186_L	189_G	0.763	0.38
141_A	178_L	0.762	0.38
238_Y	244_I	0.758	0.37
131_V	187_D	0.756	0.37
23_D	71_S	0.752	0.37
154_L	160_D	0.750	0.37
43_S	199_Y	0.741	0.36
106_Y	238_Y	0.735	0.36
145_A	165_V	0.734	0.36
142_V	217_L	0.734	0.36
29_L	34_L	0.731	0.35
126_D	187_D	0.730	0.35
37_R	46_M	0.729	0.35
40_D	169_G	0.726	0.35
229_I	233_Q	0.725	0.35
206_A	238_Y	0.724	0.35
199_Y	239_M	0.723	0.35
76_I	197_L	0.718	0.34
108_L	204_N	0.714	0.34
26_K	106_Y	0.713	0.34
77_A	187_D	0.713	0.34
139_D	207_I	0.712	0.34
42_A	131_V	0.711	0.34
16_D	229_I	0.706	0.34
10_T	157_D	0.706	0.34
16_D	154_L	0.705	0.34
7_S	148_V	0.704	0.34
5_I	139_D	0.702	0.33
65_L	99_I	0.700	0.33
152_I	165_V	0.697	0.33
52_A	182_Q	0.696	0.33
222_P	241_A	0.694	0.33
85_L	124_D	0.691	0.33
24_E	238_Y	0.690	0.33
14_T	167_A	0.684	0.32
55_A	193_S	0.684	0.32
55_A	233_Q	0.683	0.32
20_V	82_A	0.683	0.32
24_E	197_L	0.678	0.32
9_D	74_E	0.675	0.32
49_L	164_Y	0.674	0.31
192_H	211_A	0.673	0.31
145_A	167_A	0.672	0.31
134_E	217_L	0.672	0.31
26_K	129_A	0.671	0.31
193_S	197_L	0.667	0.31
21_L	194_L	0.667	0.31
43_S	240_L	0.666	0.31
127_L	131_V	0.663	0.31
15_L	36_I	0.659	0.30
17_S	27_I	0.653	0.30
110_L	122_I	0.650	0.30
124_D	170_D	0.649	0.30
34_L	60_E	0.647	0.30
88_L	93_E	0.647	0.30
223_I	244_I	0.646	0.30
178_L	181_D	0.644	0.30
88_L	220_E	0.642	0.29
128_P	209_T	0.641	0.29
88_L	173_D	0.638	0.29
4_A	29_L	0.637	0.29
48_D	237_T	0.635	0.29
163_F	245_Q	0.635	0.29
86_I	130_H	0.633	0.29
12_Q	56_F	0.630	0.29
34_L	76_I	0.629	0.29
153_A	225_L	0.628	0.28
30_D	64_G	0.627	0.28
147_M	173_D	0.627	0.28
61_A	165_V	0.624	0.28
34_L	236_V	0.624	0.28
80_A	226_H	0.621	0.28
41_P	218_G	0.621	0.28
102_D	144_A	0.620	0.28
163_F	186_L	0.617	0.28
2_F	224_K	0.616	0.28
98_H	148_V	0.615	0.28
166_N	204_N	0.615	0.28
146_D	167_A	0.613	0.28
63_G	143_T	0.613	0.28
80_A	84_Q	0.611	0.27
24_E	179_A	0.610	0.27
97_L	208_P	0.610	0.27
67_G	113_P	0.606	0.27
186_L	245_Q	0.606	0.27
155_G	166_N	0.606	0.27
106_Y	150_D	0.605	0.27
10_T	148_V	0.601	0.27
34_L	110_L	0.593	0.26
43_S	150_D	0.591	0.26
27_I	151_H	0.590	0.26
80_A	90_L	0.588	0.26
19_S	137_D	0.587	0.26
129_A	150_D	0.587	0.26
129_A	188_A	0.586	0.26
151_H	196_S	0.586	0.26
189_G	194_L	0.583	0.26
56_F	199_Y	0.580	0.26
79_M	87_Q	0.578	0.25
77_A	114_D	0.576	0.25
200_L	223_I	0.575	0.25
2_F	177_E	0.574	0.25
108_L	182_Q	0.572	0.25
21_L	50_D	0.572	0.25
36_I	47_V	0.572	0.25
31_D	35_S	0.571	0.25
75_D	110_L	0.571	0.25
200_L	207_I	0.571	0.25
52_A	65_L	0.570	0.25
125_L	128_P	0.569	0.25
5_I	87_Q	0.569	0.25
181_D	211_A	0.567	0.25
81_D	208_P	0.563	0.25
10_T	103_G	0.562	0.25
71_S	215_L	0.562	0.25
7_S	12_Q	0.561	0.24
130_H	223_I	0.559	0.24
59_Y	213_V	0.559	0.24
45_G	63_G	0.559	0.24
66_I	241_A	0.558	0.24
115_S	197_L	0.557	0.24
17_S	124_D	0.556	0.24
98_H	154_L	0.556	0.24
60_E	138_I	0.556	0.24
143_T	178_L	0.556	0.24
28_H	39_V	0.556	0.24
88_L	118_Q	0.554	0.24
43_S	239_M	0.554	0.24
24_E	41_P	0.549	0.24
67_G	112_D	0.549	0.24
130_H	211_A	0.545	0.24
64_G	190_D	0.545	0.24
23_D	125_L	0.543	0.23
140_R	149_S	0.543	0.23
80_A	114_D	0.542	0.23
58_S	112_D	0.541	0.23
76_I	156_V	0.537	0.23
143_T	156_V	0.532	0.23
17_S	236_V	0.532	0.23
37_R	160_D	0.531	0.23
44_V	137_D	0.529	0.23
150_D	217_L	0.528	0.23
138_I	216_E	0.528	0.23
5_I	62_D	0.528	0.23
41_P	101_I	0.527	0.23
212_E	238_Y	0.527	0.23
154_L	217_L	0.525	0.22
22_V	197_L	0.524	0.22
88_L	133_I	0.522	0.22
22_V	26_K	0.522	0.22
86_I	167_A	0.518	0.22
88_L	160_D	0.517	0.22
153_A	166_N	0.517	0.22
68_V	167_A	0.516	0.22
11_L	75_D	0.515	0.22
40_D	222_P	0.515	0.22
211_A	231_D	0.511	0.22
18_V	71_S	0.508	0.22
114_D	121_D	0.507	0.22
62_D	223_I	0.507	0.22
150_D	199_Y	0.502	0.21
32_D	133_I	0.502	0.21
176_L	227_F	0.501	0.21
145_A	149_S	0.501	0.21
80_A	86_I	0.501	0.21
170_D	199_Y	0.500	0.21
199_Y	241_A	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	0.9676	100	0.296	Contact Map
3k4xA	1	0.9555	100	0.309	Contact Map
3a1jB	1	0.9352	100	0.329	Contact Map
3g65A	1	0.9474	100	0.331	Contact Map
3a1jA	1	0.9636	100	0.357	Contact Map
3fdsC	1	0.9595	100	0.394	Contact Map
1plqA	3	0.9757	100	0.415	Contact Map
2zvvA	3	0.9676	100	0.417	Contact Map
1u7bA	3	0.9676	100	0.42	Contact Map
3ifvA	3	0.9717	100	0.424	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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