Contacts of the helix formed by residues 36 - 67 (chain F) in PDB entry 3GHG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 36 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D PHE* 3.4 28.5 - - + -
93E ILE* 5.2 6.1 - - + -
94E ARG* 6.6 0.4 - - + -
97E VAL* 3.6 36.8 - - + -
32F TYR* 3.4 23.3 - - + +
35F LYS* 1.3 84.9 - - + +
37F ASP* 1.3 62.4 + - - +
38F LYS 3.3 2.0 - - - -
39F ASP* 2.9 28.9 + - + +
40F LEU* 3.1 18.6 + - + +
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Residues in contact with ASP 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D PHE* 3.9 14.4 - - + -
65D ARG* 3.0 32.6 + - - -
33F GLN* 3.1 30.8 - - - +
34F THR* 3.1 5.2 + - - -
36F VAL* 1.3 80.3 - - - +
38F LYS* 1.3 52.3 + - - +
40F LEU* 3.1 8.9 + - - +
41F GLN* 2.6 55.8 + - - +
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Residues in contact with LYS 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F THR* 3.3 15.8 + - + +
35F LYS 5.9 0.4 - - - -
36F VAL 3.3 0.8 - - - -
37F ASP* 1.3 77.5 - - - +
39F ASP* 1.3 56.4 + - - +
41F GLN* 3.5 19.1 + - - +
42F SER* 3.0 26.6 + - - -
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Residues in contact with ASP 39 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E VAL* 4.9 9.9 - - + +
101E ASN* 3.8 26.6 + - - +
35F LYS 5.5 1.5 + - - +
36F VAL* 2.9 18.4 + - + +
38F LYS* 1.3 77.1 - - - +
40F LEU* 1.3 54.6 + - + +
42F SER* 3.1 9.5 + - - -
43F LEU* 2.8 51.7 + - + +
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Residues in contact with LEU 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D PHE* 3.3 43.1 - - + -
65D ARG* 3.8 23.6 - - + +
66D ILE* 3.5 32.1 - - + -
69D LEU* 6.3 2.2 - - + -
93E ILE* 6.2 0.9 - - + -
97E VAL* 4.6 13.7 - - + -
100E LEU* 4.9 1.8 - - + -
36F VAL* 3.1 19.5 + - + +
37F ASP* 3.4 12.1 - - - +
39F ASP* 1.3 77.0 - - + +
41F GLN* 1.3 52.1 + - - +
43F LEU* 2.9 16.1 + - + +
44F GLU* 2.5 40.0 + - + +
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Residues in contact with GLN 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ARG* 4.0 6.7 - - - +
37F ASP* 2.6 54.5 + - - +
38F LYS* 3.5 20.5 - - + +
40F LEU* 1.3 71.5 - - - +
42F SER* 1.3 59.1 + - - +
43F LEU 3.3 0.5 + - - -
44F GLU* 3.5 10.1 + - - +
45F ASP* 2.9 36.3 + - - +
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Residues in contact with SER 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F LYS* 3.0 19.8 + - - -
39F ASP* 3.1 12.8 + - - -
41F GLN* 1.3 75.0 - - - +
43F LEU* 1.3 59.3 + - - +
45F ASP* 4.0 10.5 - - - +
46F ILE* 3.5 26.0 + - - +
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Residues in contact with LEU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LEU* 4.4 10.8 - - + +
97E VAL* 5.4 3.6 - - + +
100E LEU* 4.4 33.9 - - + +
101E ASN* 4.2 16.6 - - - +
104E VAL* 4.8 12.3 - - + -
105E GLU* 5.9 4.3 - - + +
39F ASP* 2.8 41.8 + - - +
40F LEU* 2.9 17.7 + - + +
42F SER* 1.3 81.4 - - - +
44F GLU* 1.3 66.1 + - - +
45F ASP 3.1 1.3 - - - -
46F ILE* 3.2 28.2 + - + +
47F LEU* 3.5 14.6 + - - +
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Residues in contact with GLU 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ARG* 3.2 45.4 + - - +
69D LEU* 4.5 22.7 - - + +
40F LEU* 2.5 21.5 + - + +
41F GLN* 3.8 10.6 - - - +
43F LEU* 1.3 71.4 - - - +
45F ASP* 1.3 68.2 + - - +
47F LEU* 3.7 3.1 + - - +
48F HIS* 3.6 26.6 + - + +
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Residues in contact with ASP 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F GLN* 2.9 25.3 - - - +
42F SER* 4.0 10.1 - - - +
44F GLU* 1.3 76.9 - - - +
46F ILE* 1.3 57.3 + - + +
47F LEU 2.9 1.4 + - - -
48F HIS* 3.0 4.7 + - - -
49F GLN* 2.5 56.0 + - + +
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Residues in contact with ILE 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E VAL* 3.8 29.2 - - + -
105E GLU* 6.4 2.0 - - + -
108E SER* 4.3 16.6 - - - +
42F SER* 3.5 17.5 - - - +
43F LEU* 3.2 21.5 + - + +
45F ASP* 1.3 78.6 - - + +
47F LEU* 1.3 53.8 + - + +
49F GLN* 4.1 6.1 - - - -
50F VAL* 2.7 60.3 + - + +
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Residues in contact with LEU 47 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D LYS* 4.8 0.9 - - + +
69D LEU* 3.3 40.2 - - + +
72D SER* 3.7 40.4 - - - +
73D LEU* 5.5 2.9 - - - +
76D TYR* 6.2 2.7 - - + -
104E VAL* 5.5 11.9 - - + -
43F LEU 3.5 5.5 + - - +
44F GLU 4.0 6.1 - - - +
45F ASP 2.9 2.0 + - - -
46F ILE* 1.3 82.1 - - + +
48F HIS* 1.3 64.1 + - + +
50F VAL* 3.5 7.7 - - + +
51F GLU* 2.7 35.8 + - - +
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Residues in contact with HIS 48 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D LYS* 5.9 7.4 - - + -
44F GLU* 3.6 15.8 + - + +
45F ASP* 3.0 5.6 + - - +
47F LEU* 1.3 87.6 - - + +
49F GLN* 1.3 62.1 + - + +
51F GLU* 3.5 13.2 - - + +
52F ASN* 3.4 24.9 + - - +
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Residues in contact with GLN 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F ASP* 2.5 54.9 + - + +
46F ILE* 4.1 4.3 - - - +
48F HIS* 1.3 73.4 - - + +
50F VAL* 1.3 58.4 + - + +
51F GLU 3.2 1.1 - - - -
52F ASN* 3.5 7.1 + - - +
53F LYS* 3.3 47.0 + - - +
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Residues in contact with VAL 50 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D TYR* 5.0 16.2 - - + -
108E SER* 5.7 2.5 - - - +
111E SER* 4.5 17.7 - - - +
115E PHE* 5.3 3.1 - - + -
46F ILE* 2.7 50.5 + - + +
47F LEU* 3.7 11.2 - - + +
49F GLN* 1.3 72.6 - - + +
51F GLU* 1.3 55.1 + - - +
53F LYS* 3.8 24.0 - - + +
54F THR* 2.6 36.0 + - - +
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Residues in contact with GLU 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F LEU 2.7 23.2 + - - +
48F HIS* 3.5 17.9 - - + +
49F GLN 3.2 0.6 - - - -
50F VAL* 1.3 73.7 - - - +
52F ASN* 1.3 65.1 + - - +
53F LYS 3.2 1.3 - - - -
54F THR* 3.3 15.6 - - - +
55F SER* 3.1 30.1 + - - -
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Residues in contact with ASN 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F HIS 3.4 13.2 + - - +
49F GLN* 3.5 8.0 + - - +
51F GLU* 1.3 83.3 - - - +
53F LYS* 1.3 60.9 + - + +
55F SER* 4.2 9.2 - - - -
56F GLU* 4.2 10.4 + - - +
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Residues in contact with LYS 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E PHE* 3.7 22.6 - - + -
49F GLN* 3.3 38.9 + - - +
50F VAL* 3.8 21.6 - - + +
51F GLU 3.2 0.6 - - - -
52F ASN* 1.3 79.9 - - + +
54F THR* 1.3 61.6 + - - +
55F SER 3.2 1.1 - - - -
56F GLU* 3.5 20.8 + - - +
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Residues in contact with THR 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D TYR* 3.7 19.7 - - + -
79D ASN* 4.4 17.1 + - - +
115E PHE* 3.6 24.2 - - - -
50F VAL 2.6 21.9 + - - +
51F GLU* 3.2 35.9 - - - +
53F LYS* 1.3 70.7 - - - +
55F SER* 1.3 66.8 + - - +
56F GLU 3.2 0.9 - - - -
57F VAL* 3.6 5.0 + - - +
58F LYS* 3.2 21.2 + - + +
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Residues in contact with SER 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F GLU* 3.1 24.3 + - - -
52F ASN* 4.2 10.5 - - - -
53F LYS 3.2 0.2 - - - -
54F THR* 1.3 78.6 - - - +
56F GLU* 1.3 54.2 + - - +
58F LYS* 4.0 9.2 - - - +
59F GLN* 2.5 70.2 + - - +
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Residues in contact with GLU 56 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E PHE* 6.4 0.2 - - + -
119E TYR* 4.8 17.6 + - + -
52F ASN 4.2 5.4 + - - +
53F LYS* 3.5 20.9 + - + +
54F THR 3.2 0.8 - - - -
55F SER* 1.3 78.9 - - - +
57F VAL* 1.3 60.1 + - + +
59F GLN* 4.6 7.5 - - - +
60F LEU* 3.2 40.5 + - + +
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Residues in contact with VAL 57 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D SER* 4.9 17.5 - - - -
114E SER 5.0 3.1 - - - +
115E PHE* 3.3 45.8 - - + +
118E MET* 4.2 26.2 - - + -
53F LYS 4.1 0.8 + - - -
54F THR 3.6 5.6 + - - +
56F GLU* 1.3 80.6 - - + +
58F LYS* 1.3 58.8 + - - +
60F LEU* 3.4 4.8 + - - +
61F ILE* 3.1 41.6 + - + +
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Residues in contact with LYS 58 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ASN* 5.5 12.3 + - - +
54F THR* 3.2 18.5 + - + +
55F SER* 3.1 10.9 + - - +
57F VAL* 1.3 75.6 - - - +
59F GLN* 1.3 65.5 + - + +
61F ILE* 3.5 22.5 + - + +
62F LYS* 4.0 5.9 + - - +
65F GLN* 6.1 0.8 - - - +
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Residues in contact with GLN 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F SER* 2.5 44.7 + - - +
56F GLU* 4.6 7.9 - - - +
58F LYS* 1.3 73.4 - - + +
60F LEU* 1.3 59.3 + - - +
61F ILE 3.5 0.5 + - - -
62F LYS* 3.7 16.1 + - - +
63F ALA* 4.3 3.6 + - - +
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Residues in contact with LEU 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E MET* 3.4 41.5 - - + -
119E TYR* 6.2 2.2 - - + -
122E LYS* 4.0 31.4 - - + +
56F GLU* 3.2 31.0 + - + +
57F VAL 3.8 4.0 - - - +
58F LYS 3.3 0.4 - - - -
59F GLN* 1.3 78.9 - - - +
61F ILE* 1.3 61.7 + - + +
62F LYS 3.4 0.2 - - - -
63F ALA* 3.4 19.3 + - + +
64F ILE* 3.4 13.4 + - + +
----------------------------------------------------------
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Residues in contact with ILE 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D SER* 6.2 1.1 - - - -
86D LEU* 3.0 48.0 - - + -
90D ILE* 4.5 7.2 - - + -
118E MET* 6.0 6.3 - - + -
57F VAL* 3.1 38.1 + - + +
58F LYS* 3.8 16.2 - - + +
59F GLN 3.3 0.8 - - - -
60F LEU* 1.3 74.5 - - + +
62F LYS* 1.3 59.7 + - - +
63F ALA 3.1 2.2 - - - -
64F ILE* 3.1 18.5 + - + +
65F GLN* 3.0 48.7 + - + +
----------------------------------------------------------
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Residues in contact with LYS 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F LYS 4.0 5.5 + - - +
59F GLN* 3.7 12.2 + - - +
60F LEU 3.4 0.6 - - - -
61F ILE* 1.3 77.8 - - - +
63F ALA* 1.3 57.8 + - - +
64F ILE 3.5 0.2 - - - -
65F GLN* 4.1 10.0 - - + +
66F LEU* 3.4 44.0 + - + +
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Residues in contact with ALA 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F GLN 4.3 3.2 + - - +
60F LEU* 3.4 20.9 + - + +
61F ILE 3.1 0.8 - - - -
62F LYS* 1.3 78.6 - - - +
64F ILE* 1.3 58.9 + - - +
65F GLN 3.4 0.4 - - - -
66F LEU* 4.4 5.6 - - - +
67F THR* 3.4 23.6 + - - -
68F TYR* 4.8 2.9 - - - -
----------------------------------------------------------
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Residues in contact with ILE 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D LEU* 5.7 1.1 - - + -
90D ILE* 3.7 30.6 - - + +
93D ILE* 6.3 1.1 - - + -
122E LYS* 5.2 13.7 - - + +
125E TRP* 5.1 7.6 - - + -
126E GLN* 5.2 1.1 - - - +
60F LEU* 3.4 8.1 + - + +
61F ILE* 3.1 46.3 + - + +
63F ALA* 1.3 77.6 - - - +
65F GLN* 1.3 65.3 + - + +
66F LEU 3.7 0.2 - - - -
67F THR 4.7 1.3 - - - -
68F TYR* 3.9 44.6 + - + +
----------------------------------------------------------
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Residues in contact with GLN 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D LEU* 3.7 19.1 - - + +
58F LYS* 6.1 0.4 - - - +
61F ILE* 3.0 39.6 + - + +
62F LYS* 4.4 10.5 - - + +
63F ALA 3.4 0.2 - - - -
64F ILE* 1.3 83.5 - - + +
66F LEU* 1.3 65.7 + - + +
68F TYR 4.9 0.2 - - - -
69F ASN* 3.8 20.3 - - - +
----------------------------------------------------------
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Residues in contact with LEU 66 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F LYS* 3.4 38.2 + - + +
63F ALA* 4.4 3.8 + - - +
65F GLN* 1.3 81.9 - - + +
67F THR* 1.3 67.7 + - - +
69F ASN* 4.4 8.0 - - - +
----------------------------------------------------------
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Residues in contact with THR 67 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F ALA 3.4 15.2 + - - -
65F GLN 3.6 0.4 - - - -
66F LEU* 1.3 82.9 - - - +
68F TYR* 1.3 98.5 + - + +
69F ASN* 3.2 12.0 + - - +
72F GLU* 4.5 7.6 - - - +
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il