Contacts of the helix formed by residues 37 - 64 (chain A) in PDB entry 2GS4
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 ASN 37 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A THR* 3.1 8.0 + - - +
36A SER* 1.3 76.2 + - - +
38A GLU* 1.3 57.8 + - - +
39A LYS* 2.9 14.0 + - - +
40A LEU* 2.6 39.2 + - + +
41A SER* 2.8 25.7 + - - -
99A ASP* 3.4 27.3 + - - +
103A ILE* 5.8 2.8 - - - +
153A LEU* 5.8 3.6 + - - +
157A ASN* 5.3 5.9 + - - +
160A LYS* 4.2 22.7 - - - +
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Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER 3.2 9.0 + - - +
37A ASN* 1.3 71.2 + - - +
39A LYS* 1.3 63.1 + - + +
41A SER* 3.4 9.7 + - - -
42A GLN* 3.0 61.5 + - - +
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 2.9 9.0 + - - +
38A GLU* 1.3 82.3 - - + +
40A LEU* 1.3 62.0 + - - +
42A GLN* 3.6 21.0 + - - +
43A ALA* 3.2 20.6 + - - +
153A LEU* 4.4 19.4 - - + +
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR* 3.9 19.5 - - + +
37A ASN* 2.6 28.8 + - + +
39A LYS* 1.3 71.1 - - - +
41A SER* 1.3 65.9 + - - +
43A ALA* 3.0 13.4 + - + +
44A PHE* 3.0 46.9 + - + -
99A ASP* 4.0 19.5 - - + +
102A LEU* 4.3 5.4 - - + -
103A ILE* 3.8 32.8 - - + -
150A LEU* 4.6 5.8 - - + -
153A LEU* 4.2 19.5 - - + +
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA* 2.7 38.4 + - - +
35A THR* 3.9 13.1 + - - +
37A ASN 2.8 15.5 + - - -
38A GLU* 3.5 13.2 + - - -
40A LEU* 1.3 76.8 - - - +
42A GLN* 1.3 58.5 + - - +
44A PHE* 3.3 2.3 + - - -
45A HIS* 3.0 27.4 + - - +
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Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 3.0 46.3 + - + +
39A LYS* 3.8 24.1 - - - +
40A LEU 3.1 0.2 - - - -
41A SER* 1.3 76.2 - - - +
43A ALA* 1.3 54.6 + - - +
45A HIS* 3.2 7.7 + - - +
46A ALA* 2.7 35.9 + - - +
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS 3.2 13.5 + - - +
40A LEU* 3.0 12.2 + - + +
42A GLN* 1.3 76.7 - - - +
44A PHE* 1.3 59.2 + - - +
46A ALA* 3.7 6.9 - - - +
47A HIS* 2.9 29.1 + - - +
146A THR* 5.7 1.0 - - - +
149A LYS* 4.7 12.3 - - + -
150A LEU* 5.3 6.7 - - + -
153A LEU* 3.8 23.1 - - + -
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Residues in contact with PHE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 4.0 19.7 - - + +
31A LEU* 3.6 53.2 - - + -
32A ALA* 3.8 17.7 - - + +
35A THR* 4.6 1.6 - - + -
40A LEU* 3.0 54.5 + - + -
41A SER* 3.6 5.8 - - - +
43A ALA* 1.3 75.0 - - - +
45A HIS* 1.3 62.0 + - - +
47A HIS* 3.3 5.6 + - + +
48A LEU* 2.9 28.6 + - - +
102A LEU* 4.0 23.8 - - + -
106A ALA* 3.6 24.5 - - + -
150A LEU* 4.7 6.5 - - + -
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Residues in contact with HIS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA* 4.1 11.2 - - + +
41A SER 3.0 17.4 + - - +
42A GLN* 3.6 8.3 - - - +
44A PHE* 1.3 75.2 - - - +
46A ALA* 1.3 66.0 + - - +
48A LEU* 3.2 19.5 + - + +
49A GLU* 3.2 48.8 + - + +
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN 2.7 21.7 + - - +
43A ALA* 3.7 8.1 - - - +
45A HIS* 1.3 76.0 - - - +
47A HIS* 1.3 61.9 + - - +
49A GLU* 3.2 9.1 + - - +
50A GLU* 3.0 22.4 + - - +
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Residues in contact with HIS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 4.2 12.8 - - + -
28A LEU* 3.8 20.4 - - + +
43A ALA 2.9 18.0 + - - +
44A PHE* 3.8 6.0 - - + +
45A HIS 3.3 0.2 - - - -
46A ALA* 1.3 74.0 - - - +
48A LEU* 1.3 60.5 + - - +
50A GLU* 3.6 25.1 - - + -
51A THR* 2.8 49.0 + - - -
54A GLN* 4.4 0.2 + - - -
109A VAL* 5.4 0.2 - - + -
110A GLU* 2.9 31.2 + - - -
143A GLU* 3.0 25.6 + - - -
146A THR* 3.8 20.4 - - + +
150A LEU* 6.3 0.2 - - - +
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 3.4 30.3 - - - +
28A LEU* 3.7 14.3 - - + +
29A ALA* 4.0 28.9 - - + -
44A PHE 2.9 14.3 + - - +
45A HIS* 3.3 27.4 - - + +
46A ALA 3.2 0.2 - - - -
47A HIS* 1.3 76.3 - - - +
49A GLU* 1.3 73.0 + - - +
51A THR* 3.5 1.6 + - - -
52A HIS* 3.3 41.3 + - + +
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A HIS* 3.2 39.8 + - + +
46A ALA* 3.6 8.3 - - - +
47A HIS 3.2 0.2 - - - -
48A LEU* 1.3 85.1 - - - +
50A GLU* 1.3 66.0 + - - +
52A HIS* 3.1 17.1 + - - +
53A GLY* 3.1 17.7 + - - -
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Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA 3.0 15.6 + - - +
47A HIS* 3.6 10.6 - - + +
49A GLU* 1.3 75.7 - - - +
51A THR* 1.3 56.3 + - - +
53A GLY* 3.1 3.8 + - - +
54A GLN* 2.9 48.6 + - - +
142A GLU* 3.4 29.5 - - - +
143A GLU* 2.9 18.7 - - - +
146A THR* 2.9 27.7 + - - -
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Residues in contact with THR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU* 3.3 45.8 + - + +
24A LEU* 4.3 7.8 - - + +
25A THR* 4.0 10.5 - - + +
28A LEU* 3.4 15.7 - - - +
47A HIS* 2.8 39.1 + - - -
48A LEU 3.7 5.8 - - - -
49A GLU 3.1 0.4 - - - -
50A GLU* 1.3 71.1 - - - +
52A HIS* 1.3 65.3 + - - +
54A GLN* 3.1 11.4 + - - +
55A ILE* 3.0 22.0 + - - +
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Residues in contact with HIS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A THR* 3.8 22.7 - - + +
48A LEU* 3.3 39.0 + - + +
49A GLU* 3.1 18.7 + - - +
51A THR* 1.3 78.4 - - - +
53A GLY* 1.3 62.6 + - - +
55A ILE* 3.3 14.6 + - + +
56A GLU* 3.2 25.5 + - - +
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Residues in contact with GLY 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLU 3.1 12.6 + - - -
50A GLU* 3.1 6.0 + - - -
51A THR 3.1 0.2 - - - -
52A HIS* 1.3 79.3 - - - +
54A GLN* 1.3 56.6 + - - +
56A GLU* 3.2 11.5 + - - +
57A ARG* 3.1 30.8 + - - +
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Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 3.4 26.5 - - - +
50A GLU* 2.9 31.1 + - - +
51A THR* 3.1 17.8 + - - +
53A GLY* 1.3 74.5 - - - +
55A ILE* 1.3 67.0 + - - +
57A ARG* 3.2 11.5 + - - +
58A ILE* 3.0 26.8 + - - +
117A TYR* 4.5 1.2 + - - +
139A THR* 3.7 24.4 + - + +
142A GLU* 3.0 30.5 + - - +
143A GLU* 2.7 31.7 + - - +
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Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TYR* 3.6 31.6 - - + +
21A GLU* 3.5 38.1 - - + -
22A LYS* 3.9 24.0 - - + +
25A THR* 4.0 19.1 - - + -
51A THR 3.0 11.2 + - - +
52A HIS* 3.6 14.4 - - + +
53A GLY 3.2 0.4 - - - -
54A GLN* 1.3 75.7 - - - +
56A GLU* 1.3 66.9 + - - +
58A ILE* 3.0 20.0 + - + +
59A ASP* 3.1 16.0 + - - +
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A HIS 3.2 13.8 + - - +
53A GLY* 3.2 12.9 + - - +
55A ILE* 1.3 82.8 - - - +
57A ARG* 1.3 61.5 + - - +
59A ASP* 3.1 30.3 + - - +
60A GLN* 3.1 18.9 + - + +
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Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLY 3.1 18.6 + - - +
54A GLN* 3.4 14.3 - - - +
55A ILE 3.1 0.2 - - - -
56A GLU* 1.3 78.1 - - - +
58A ILE* 1.3 56.9 + - + +
60A GLN* 3.1 25.6 + - - +
61A VAL* 2.9 28.5 + - + +
135A LEU* 3.3 39.6 - - + +
138A GLU* 3.6 23.5 + - - +
139A THR* 3.0 31.6 + - - +
142A GLU* 3.2 36.6 + - - -
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 4.4 20.2 - - + +
17A THR* 4.1 9.0 - - + -
18A TYR* 3.5 48.0 - - + +
21A GLU* 4.2 8.3 - - + -
54A GLN 3.0 15.7 + - - +
55A ILE* 3.0 12.5 + - - +
57A ARG* 1.3 73.8 - - + +
59A ASP* 1.3 66.4 + - - +
61A VAL* 3.1 9.0 + - + +
62A VAL* 3.0 22.5 + - + +
70A ILE* 4.0 17.9 - - + -
117A TYR* 3.7 26.7 - - + +
136A LEU* 5.7 1.3 - - + -
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Residues in contact with ASP 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 3.7 25.6 + - - -
55A ILE* 3.1 14.2 + - - +
56A GLU* 3.1 30.1 + - - +
58A ILE* 1.3 75.3 - - - +
60A GLN* 1.3 58.2 + - + +
62A VAL* 3.3 7.5 + - - +
63A GLU* 3.0 45.4 + - - +
70A ILE* 5.8 1.2 - - - +
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLU* 3.1 10.8 + - + +
57A ARG* 3.1 36.7 + - - +
58A ILE 3.1 0.2 - - - -
59A ASP* 1.3 78.3 - - + +
61A VAL* 1.3 64.7 + - - +
63A GLU* 3.3 13.2 + - - +
64A SER* 3.0 23.9 + - - -
131A LYS* 4.7 14.9 + - - -
135A LEU* 3.8 23.5 - - + +
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Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 4.4 8.1 - - + -
14A LEU* 3.9 24.2 - - + -
57A ARG* 2.9 18.6 + - + +
58A ILE* 3.1 12.1 + - - +
60A GLN* 1.3 75.9 - - - +
62A VAL* 1.3 62.9 + - - +
64A SER* 2.6 24.7 + - - -
68A LEU* 3.4 14.1 - - + +
132A ALA* 3.9 19.1 - - + -
135A LEU* 3.9 26.5 - - + -
136A LEU* 4.1 22.4 - - + -
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Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.9 12.6 - - + -
58A ILE* 3.0 13.9 + - + +
59A ASP* 3.6 11.0 - - - +
60A GLN 3.3 0.2 - - - -
61A VAL* 1.3 78.3 - - - +
63A GLU* 1.3 60.4 + - + +
64A SER 3.4 0.3 + - - -
65A GLU 3.0 24.4 + - - +
68A LEU* 3.5 31.1 - - + +
69A LYS* 4.1 10.8 - - - +
70A ILE* 3.6 35.0 - - + +
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 3.0 31.5 + - - +
60A GLN* 3.8 14.5 - - - +
62A VAL* 1.3 74.6 - - + +
64A SER* 1.3 59.8 + - - +
65A GLU* 3.1 9.9 + - - -
66A SER* 4.9 0.9 + - - -
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Residues in contact with SER 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLN 3.0 13.9 + - - -
61A VAL* 2.6 22.9 + - - -
63A GLU* 1.3 77.2 - - - +
65A GLU* 1.3 79.0 + - - +
131A LYS* 4.1 34.9 - - - +
132A ALA* 4.0 11.6 + - - +
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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