SVWC - PFAM28P - GREMLIN Contacts

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SVWC - Single domain von Willebrand factor type C

PFAM:	PF15430	Sequences: CYYEGGLTLKPGETWKLPGPCERWTCNADGTLTIEGCGPVALPPGCKLVPYDPSKPYPDCCPKYVC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	66 (65)
Sequences:	569 (490)
Seq/√Len:	60.8
META:	0.077

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
52_D	55_K	3.754	1.00
46_C	66_C	3.051	1.00
10_K	13_E	2.661	1.00
36_G	57_Y	2.570	1.00
25_T	35_E	2.542	1.00
16_K	23_R	2.391	1.00
5_G	8_T	1.957	1.00
27_N	33_T	1.883	1.00
17_L	20_P	1.852	1.00
25_T	33_T	1.741	0.99
23_R	35_E	1.642	0.99
36_G	39_P	1.615	0.99
58_P	61_C	1.490	0.98
35_E	38_G	1.465	0.98
21_C	37_C	1.430	0.98
7_L	15_W	1.411	0.97
24_W	34_I	1.385	0.97
42_L	46_C	1.371	0.97
22_E	36_G	1.308	0.96
14_T	23_R	1.305	0.96
14_T	25_T	1.189	0.93
41_A	47_K	1.175	0.93
47_K	65_V	1.174	0.92
21_C	26_C	1.112	0.90
26_C	37_C	1.112	0.90
21_C	60_C	1.100	0.90
37_C	60_C	1.100	0.90
2_Y	5_G	1.058	0.88
18_P	34_I	1.031	0.87
28_A	59_D	0.993	0.84
37_C	58_P	0.983	0.84
21_C	58_P	0.983	0.84
44_P	64_Y	0.928	0.80
1_C	5_G	0.925	0.80
1_C	26_C	0.924	0.80
32_L	55_K	0.912	0.79
27_N	38_G	0.910	0.79
37_C	61_C	0.907	0.79
21_C	61_C	0.907	0.79
27_N	30_G	0.896	0.78
23_R	39_P	0.886	0.77
24_W	29_D	0.874	0.76
17_L	24_W	0.866	0.75
27_N	35_E	0.849	0.74
14_T	40_V	0.843	0.73
31_T	59_D	0.842	0.73
45_G	53_P	0.841	0.73
3_Y	24_W	0.835	0.73
7_L	17_L	0.830	0.72
19_G	54_S	0.825	0.72
48_L	62_P	0.810	0.70
2_Y	8_T	0.797	0.69
11_P	30_G	0.777	0.67
16_K	56_P	0.773	0.67
2_Y	7_L	0.767	0.66
26_C	60_C	0.762	0.66
29_D	43_P	0.755	0.65
1_C	21_C	0.753	0.65
1_C	37_C	0.753	0.65
46_C	51_Y	0.739	0.63
20_P	24_W	0.735	0.63
50_P	62_P	0.733	0.63
18_P	55_K	0.718	0.61
48_L	63_K	0.708	0.60
8_T	34_I	0.702	0.59
49_V	62_P	0.694	0.58
56_P	59_D	0.677	0.57
14_T	31_T	0.669	0.56
49_V	65_V	0.664	0.55
3_Y	32_L	0.663	0.55
5_G	36_G	0.658	0.54
1_C	4_E	0.644	0.53
47_K	59_D	0.643	0.53
18_P	56_P	0.642	0.53
3_Y	40_V	0.617	0.50
19_G	47_K	0.607	0.49
41_A	45_G	0.587	0.46
3_Y	34_I	0.573	0.45
60_C	66_C	0.572	0.45
10_K	62_P	0.571	0.45
4_E	9_L	0.565	0.44
43_P	50_P	0.560	0.43
44_P	56_P	0.554	0.43
5_G	20_P	0.552	0.42
39_P	57_Y	0.548	0.42
26_C	58_P	0.543	0.41
26_C	61_C	0.541	0.41
61_C	66_C	0.538	0.41
27_N	31_T	0.537	0.41
16_K	22_E	0.536	0.41
19_G	52_D	0.535	0.41
22_E	45_G	0.531	0.40
9_L	13_E	0.519	0.39
16_K	64_Y	0.514	0.38
32_L	44_P	0.512	0.38
4_E	24_W	0.511	0.38
3_Y	22_E	0.502	0.37
28_A	38_G	0.500	0.37

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
1u5mA	1	0.8182	62.1	0.731	Contact Map
2mhpA	1	0.5455	16.8	0.804	Contact Map
3bk3C	1	0.8182	5.1	0.845	Contact Map
2cg7A	1	0.5909	4.5	0.85	Contact Map
1r02A	1	0.1818	2.7	0.865	Contact Map
2lzyA	1	0.3485	2.5	0.867	Contact Map
1xhhA	1	0.8485	2.2	0.872	Contact Map
1c4eA	1	0.3485	2.1	0.873	Contact Map
3ix0A	2	0.8485	2	0.874	Contact Map
2rl0A	1	0.5758	1.5	0.883	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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