Contacts of the helix formed by residues 2 - 29 (chain S) in PDB entry 1VF5
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 THR 2 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1S MET* 1.3 74.2 - - - +
3S GLU* 1.3 70.5 + - + +
4S GLU 2.7 17.4 + - - -
5S MET* 2.8 39.2 + - - +
6S LEU* 3.0 38.3 + - + +
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Residues in contact with GLU 3 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P GLU* 4.9 9.5 - - - +
35P GLU* 5.7 0.5 - - - +
1S MET* 3.4 2.1 - - - -
2S THR* 1.3 84.6 - - + +
4S GLU* 1.3 58.2 + - + +
5S MET 3.3 0.7 - - - -
6S LEU* 3.6 25.5 - - + +
7S TYR* 3.3 27.7 + - - +
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Residues in contact with GLU 4 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P GLU* 5.4 4.2 - - - +
245P THR* 4.9 4.8 + - - -
246P GLU* 5.1 7.8 - - - +
1R MET 6.1 0.9 - - - +
2R ILE* 4.2 11.2 - - + +
1S MET* 2.8 56.2 - - - +
2S THR 2.7 3.8 + - - -
3S GLU* 1.3 76.7 - - + +
5S MET* 1.3 59.6 + - - +
7S TYR* 3.8 20.3 - - + -
8S ALA* 3.1 19.2 + - - +
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Residues in contact with MET 5 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79O TRP* 4.1 15.3 - - + -
1R MET 3.6 30.5 - - - +
2R ILE 3.9 1.8 - - - +
5R ALA* 2.8 32.1 - - + +
8R TYR* 4.0 20.0 - - + -
1S MET 5.2 2.2 - - - +
2S THR* 2.8 31.6 + - - +
4S GLU* 1.3 74.3 - - - +
6S LEU* 1.3 68.6 + - + +
7S TYR 3.0 2.2 - - - -
8S ALA* 2.7 9.1 + - - -
9S ALA 2.5 33.4 + - - -
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Residues in contact with LEU 6 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R ALA* 4.9 0.7 - - - -
2S THR* 3.0 39.8 + - + +
3S GLU* 3.6 30.3 - - + -
4S GLU 3.6 0.2 - - - -
5S MET* 1.3 89.3 - - + +
7S TYR* 1.3 58.0 + - - +
9S ALA* 4.1 2.9 - - - +
10S LEU* 2.7 34.6 + - - +
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Residues in contact with TYR 7 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P GLN* 5.5 8.7 - - - +
3S GLU 3.3 22.0 + - - +
4S GLU* 3.8 19.1 - - + -
5S MET 3.0 0.2 - - - -
6S LEU* 1.3 78.0 - - - +
8S ALA* 1.3 71.5 + - + +
9S ALA 3.2 1.4 + - - -
10S LEU* 3.4 10.4 + - + +
11S LEU* 2.9 50.0 + - + +
15T PHE* 5.8 5.5 - - - -
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Residues in contact with ALA 8 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2R ILE* 3.3 32.5 - - + +
5R ALA* 4.2 2.2 - - + -
6R VAL* 4.4 7.4 - - + +
4S GLU 3.1 20.0 - - - +
5S MET* 2.7 12.9 + - - +
7S TYR* 1.3 91.4 - - + +
9S ALA* 1.3 54.4 + - - -
11S LEU* 4.0 8.8 - - - +
12S SER* 3.2 20.3 + - - -
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Residues in contact with ALA 9 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R ALA* 3.0 40.3 - - + +
8R TYR* 5.1 2.2 - - + -
9R ILE* 2.6 37.4 - - + +
5S MET 2.5 11.2 + - - +
6S LEU* 4.3 4.9 - - - +
8S ALA* 1.3 71.0 - - - +
10S LEU* 1.3 71.1 + - + +
11S LEU 3.0 2.7 + - - -
12S SER 3.1 5.9 + - - -
13S PHE 3.4 1.0 + - - -
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Residues in contact with LEU 10 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R ILE* 5.0 7.4 - - + -
6S LEU* 2.7 27.4 - - + +
7S TYR* 3.4 9.6 + - + +
9S ALA* 1.3 81.1 - - + +
11S LEU* 1.3 57.2 + - + +
13S PHE* 3.5 6.4 + - - +
14S GLY* 3.1 26.2 + - - -
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Residues in contact with LEU 11 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7S TYR* 2.9 48.0 + - + +
8S ALA* 4.0 9.4 - - - +
9S ALA 3.0 0.6 + - - -
10S LEU* 1.3 75.6 - - + +
12S SER* 1.3 60.4 + - - +
14S GLY* 5.4 0.2 - - - -
15S LEU* 2.9 51.5 + - + +
19T GLY* 6.4 2.0 - - - -
22T PHE* 5.3 0.2 - - - -
5U VAL* 4.1 30.3 - - + -
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Residues in contact with SER 12 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6R VAL* 3.4 26.4 + - - +
9R ILE* 3.3 17.5 - - - +
10R VAL* 4.1 15.2 - - - +
8S ALA 3.2 16.6 + - - -
9S ALA 3.1 1.6 + - - -
11S LEU* 1.3 75.0 - - - +
13S PHE* 1.3 65.2 + - - +
16S ILE* 3.0 27.0 + - - +
22T PHE* 4.1 12.8 - - - -
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Residues in contact with PHE 13 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R ILE* 3.4 29.9 - - + +
12R ILE* 3.6 17.7 - - + -
13R ALA* 3.4 42.4 - - + -
16R PHE* 4.3 23.6 - + - -
1101R BCR 4.5 0.4 - - + -
9S ALA 3.4 1.2 + - - -
10S LEU* 3.7 8.5 - - - +
11S LEU 3.4 0.4 - - - -
12S SER* 1.3 79.1 - - - +
14S GLY* 1.3 68.0 + - - +
16S ILE* 3.0 23.7 + - - +
17S PHE* 3.0 36.0 - + - -
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Residues in contact with GLY 14 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S LEU 3.1 11.8 + - - -
11S LEU* 4.9 0.4 - - - -
13S PHE* 1.3 79.3 - - - +
15S LEU* 1.3 57.7 + - - +
17S PHE* 2.6 38.6 + - - +
18S VAL* 3.1 14.4 + - - +
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Residues in contact with LEU 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11S LEU* 2.9 50.9 + - + +
12S SER 4.2 0.7 - - - +
14S GLY* 1.3 73.3 - - - +
16S ILE* 1.3 56.9 + - - +
18S VAL* 3.3 21.0 - - + +
19S GLY* 2.8 29.1 + - - -
19T GLY* 3.4 23.3 - - - +
22T PHE* 3.9 22.2 - - + -
26T TYR* 3.0 29.4 + - + +
5U VAL* 6.1 2.2 - - + -
9U VAL* 5.2 9.6 - - + -
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Residues in contact with ILE 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R VAL* 5.5 2.7 - - + -
13R ALA* 4.1 13.7 - - + -
1101R BCR 3.4 66.4 - - + -
12S SER 3.0 24.9 - - - +
13S PHE 3.0 13.3 + - - +
14S GLY 2.7 4.9 + - - -
15S LEU* 1.3 74.3 - - - +
17S PHE* 1.3 54.6 + - + +
19S GLY* 3.3 0.7 + - - -
20S TRP* 2.8 35.9 + - + +
22T PHE* 3.9 23.6 - - + -
26T TYR* 6.1 0.2 - - - -
29T TYR* 4.0 15.6 - - + +
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Residues in contact with PHE 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R ALA* 4.9 0.9 - - + -
1101R BCR 3.3 53.8 - - + -
13S PHE* 3.0 57.9 - + - -
14S GLY* 2.6 17.2 + - - +
16S ILE* 1.3 79.2 - - + +
18S VAL* 1.3 56.3 + - + +
20S TRP* 3.6 21.7 - + + +
21S GLY* 2.8 28.4 + - - -
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Residues in contact with VAL 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14S GLY 3.1 14.6 + - - +
15S LEU* 3.0 30.0 + - + +
17S PHE* 1.3 75.6 - - + +
19S GLY* 1.3 64.4 + - - +
21S GLY* 3.6 1.4 + - - -
22S LEU* 3.1 36.7 + - + +
26T TYR* 4.9 4.5 - - + -
13U VAL* 5.9 3.8 - - + -
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Residues in contact with GLY 19 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15S LEU 2.8 10.3 + - - -
18S VAL* 1.3 75.6 - - - +
20S TRP* 1.3 65.8 + - - +
22S LEU* 3.1 5.0 + - - +
23S GLY 2.9 18.7 + - - -
26T TYR* 3.5 24.1 - - - -
29T TYR* 3.0 30.1 - - - -
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Residues in contact with TRP 20 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101R BCR 3.4 63.3 - - + -
16S ILE* 2.8 19.8 + - + +
17S PHE* 3.6 26.0 - + + +
19S GLY* 1.3 74.0 - - - +
21S GLY* 1.3 65.3 + - - +
23S GLY* 3.0 3.3 + - - -
24S VAL* 2.9 43.9 + - + +
29T TYR* 3.2 21.9 - + + -
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Residues in contact with GLY 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17S PHE 2.8 19.1 + - - -
18S VAL* 3.9 2.0 - - - -
19S GLY 3.1 0.2 - - - -
20S TRP* 1.3 75.3 - - - +
22S LEU* 1.3 52.3 + - - +
24S VAL* 2.9 12.0 + - - +
25S LEU* 2.7 38.3 + - - +
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Residues in contact with LEU 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S VAL* 3.1 23.1 + - + +
19S GLY* 3.1 6.1 + - - +
21S GLY* 1.3 73.2 - - - +
23S GLY* 1.3 54.6 + - - +
25S LEU* 3.9 21.5 - - + -
26S LEU* 2.7 48.8 + - + +
23T TYR* 5.6 2.5 - - + -
26T TYR* 3.9 30.5 - - + +
13U VAL* 3.9 23.3 - - + -
17U TRP* 5.1 16.6 - - + +
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Residues in contact with GLY 23 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19S GLY 2.9 13.0 + - - -
20S TRP 3.5 3.8 - - - -
21S GLY 2.9 0.2 + - - -
22S LEU* 1.3 74.0 - - - +
24S VAL* 1.3 66.3 + - - +
26S LEU* 2.9 13.7 + - - +
27S LEU* 2.9 17.0 + - - +
26T TYR 3.9 10.0 + - - -
29T TYR 3.7 27.8 - - - -
30T LYS* 4.0 5.5 - - - +
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Residues in contact with VAL 24 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20S TRP* 2.9 41.7 + - + +
21S GLY* 3.3 7.6 - - - +
23S GLY* 1.3 75.8 - - - +
25S LEU* 1.3 64.3 + - - +
27S LEU* 3.0 11.4 + - + +
28S LYS* 2.8 42.4 + - + +
32S ALA* 5.5 0.2 - - - +
29T TYR 4.3 2.3 + - - +
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Residues in contact with LEU 25 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21S GLY 2.7 20.3 + - - +
22S LEU* 3.7 20.9 - - + +
24S VAL* 1.3 73.6 - - - +
26S LEU* 1.3 60.6 + - + +
28S LYS* 3.4 21.4 + - + +
29S ILE* 3.2 33.3 + - + +
17U TRP* 3.8 36.1 - - + -
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Residues in contact with LEU 26 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22S LEU* 2.7 36.1 + - + +
23S GLY* 2.9 6.9 + - - +
25S LEU* 1.3 72.0 - - + +
27S LEU* 1.3 65.9 + - - +
29S ILE* 3.0 32.7 - - + +
30S GLN* 3.2 12.4 - - + +
26T TYR 6.0 0.9 - - - +
27T GLN* 5.7 5.8 - - - +
30T LYS* 3.3 41.7 - - + +
17U TRP* 2.9 38.8 - - + +
20U ALA* 5.0 11.2 - - + -
21U MET* 5.1 5.6 - - - +
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Residues in contact with LEU 27 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278P GLN* 6.0 0.4 - - - +
23S GLY 2.9 13.9 + - - +
24S VAL* 3.4 11.4 - - + +
26S LEU* 1.3 75.5 - - - +
28S LYS* 1.3 56.1 + - - +
30S GLN* 2.9 33.0 + - - +
31S GLY 2.7 37.6 + - - +
32S ALA* 3.9 23.1 - - + -
29T TYR 4.8 3.1 - - - +
30T LYS* 3.1 35.0 - - + +
32T PRO* 3.3 33.0 - - + +
33T ASN* 5.2 2.7 - - + -
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Residues in contact with LYS 28 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24S VAL* 2.8 27.2 + - + +
25S LEU* 3.6 28.8 - - + +
26S LEU 3.2 0.2 - - - -
27S LEU* 1.3 77.0 - - - +
29S ILE* 1.3 58.4 + - + +
30S GLN 3.1 4.9 + - - -
31S GLY* 3.7 6.2 + - - +
32S ALA* 4.4 13.9 - - + +
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Residues in contact with ILE 29 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25S LEU* 3.2 32.3 - - + +
26S LEU* 3.0 36.1 - - + +
28S LYS* 1.3 77.5 - - + +
30S GLN* 1.3 61.1 + - - +
17U TRP* 4.0 14.8 - - + -
21U MET* 4.3 15.0 - - + -
24U TRP* 4.8 17.2 - - - -
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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