Contacts of the helix formed by residues 1 - 30 (chain G) in PDB entry 1VZJ
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 ASP 1 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G THR* 1.3 71.7 + - - +
3G LEU* 2.6 39.8 + - - +
4G ASP* 2.8 44.8 + - - +
5G GLU* 3.1 15.8 + - - +
8G ARG* 4.8 3.1 + - - +
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Residues in contact with THR 2 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ASP* 1.3 75.2 + - - +
3G LEU* 1.3 62.4 + - - +
5G GLU* 3.3 14.2 + - + +
6G ALA* 3.1 20.4 + - - +
7H GLU* 3.8 22.9 - - - +
11H LYS* 4.1 11.2 + - - +
15J PHE* 4.5 4.4 - - - -
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Residues in contact with LEU 3 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F LEU* 3.3 39.7 - - + -
1G ASP* 2.6 25.3 + - - +
2G THR* 1.3 70.7 - - - +
4G ASP* 1.3 55.4 + - - +
6G ALA* 3.0 4.7 + - - +
7G GLU* 2.7 43.2 + - + +
13J PRO* 3.9 23.6 - - + +
14J PHE* 5.5 0.4 - - - -
15J PHE* 3.5 52.4 - - + +
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Residues in contact with ASP 4 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ASP* 2.8 39.9 + - - +
3G LEU* 1.3 80.5 - - - +
5G GLU* 1.3 56.7 + - - +
7G GLU* 2.8 11.8 + - - +
8G ARG* 2.8 49.2 + - + +
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Residues in contact with GLU 5 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ASP 3.1 13.6 + - - +
2G THR* 3.4 15.3 - - + +
3G LEU 3.2 0.2 - - - -
4G ASP* 1.3 74.9 - - - +
6G ALA* 1.3 61.6 + - - +
8G ARG* 3.2 35.3 + - - +
9G GLN* 3.1 38.3 + - - +
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Residues in contact with ALA 6 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G THR 3.1 4.7 + - - +
3G LEU 3.0 9.0 + - - +
5G GLU* 1.3 78.7 - - - +
7G GLU* 1.3 57.3 + - - +
9G GLN* 3.5 10.3 + - - +
10G TRP* 3.0 28.6 + - - +
10H TRP* 3.8 15.5 - - + -
11H LYS* 5.0 6.3 - - - -
13J PRO* 3.7 14.7 - - + +
15J PHE* 3.7 28.3 - - + -
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Residues in contact with GLU 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F THR* 4.6 11.9 - - + +
3F LEU* 3.4 26.1 - - + +
6F ALA* 4.1 17.2 - - - +
3G LEU* 2.7 27.1 + - + +
4G ASP* 2.8 15.4 + - - +
6G ALA* 1.3 76.0 - - - +
8G ARG* 1.3 57.6 + - + +
10G TRP* 3.3 14.3 + - - +
11G LYS* 2.9 36.4 + - - +
13J PRO* 3.7 28.5 - - + +
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Residues in contact with ARG 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ASP 4.8 3.6 + - - +
4G ASP* 2.8 24.9 + - + +
5G GLU* 3.2 51.7 - - - +
7G GLU* 1.3 74.3 - - + +
9G GLN* 1.3 62.1 + - + +
11G LYS* 3.4 5.9 + - - +
12G ALA* 3.0 29.5 + - - +
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Residues in contact with GLN 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G GLU* 3.1 30.9 + - - +
6G ALA* 3.9 8.3 - - - +
7G GLU 3.3 0.2 - - - -
8G ARG* 1.3 77.2 - - + +
10G TRP* 1.3 61.8 + - - +
12G ALA* 3.9 5.5 - - - +
13G GLU* 3.2 24.8 + - - +
10H TRP* 6.4 0.4 - - - -
14H PHE* 3.6 19.3 - - + -
15H HIS* 3.9 21.8 + - - -
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Residues in contact with TRP 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ALA* 3.8 23.1 - - + -
9F GLN* 5.0 0.9 - - + -
10F TRP* 4.0 10.5 - + + -
6G ALA 3.0 19.6 + - - +
7G GLU* 3.7 10.5 - - - +
9G GLN* 1.3 76.5 - - - +
11G LYS* 1.3 92.2 + - - +
13G GLU* 3.4 2.8 + - + +
14G PHE* 2.8 59.5 + + + +
10H TRP* 4.1 10.3 - + + -
14H PHE* 4.0 17.2 - + - -
17H TRP* 5.9 0.9 - + - -
9J LEU* 4.3 8.1 - - + +
10J PHE* 2.6 33.1 + - + +
11J PRO 3.8 10.5 - - - -
12J PRO* 3.5 30.3 - - + -
13J PRO* 3.6 11.4 - - + -
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Residues in contact with LYS 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ALA* 4.4 10.3 - - - +
9F GLN* 3.5 20.7 + - - +
7G GLU* 2.9 23.0 + - - +
8G ARG* 3.7 7.2 - - - +
10G TRP* 1.3 106.5 - - + +
12G ALA* 1.3 54.0 + - - +
14G PHE* 2.8 15.0 + - + +
15G HIS* 2.7 63.7 + - + +
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Residues in contact with ALA 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ARG 3.0 18.3 + - - +
9G GLN* 3.9 6.7 - - - +
11G LYS* 1.3 75.0 - - - +
13G GLU* 1.3 60.8 + - - +
15G HIS* 3.2 15.2 + - - +
16G ARG* 3.1 33.5 + - - +
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Residues in contact with GLU 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G GLN 3.2 16.0 + - - +
10G TRP* 3.7 3.6 - - + +
12G ALA* 1.3 77.3 - - - +
14G PHE* 1.3 59.4 + - - +
16G ARG* 3.4 36.6 + - - +
17G TRP* 3.0 27.0 + - - +
14H PHE* 4.1 11.4 - - + -
17H TRP* 3.2 35.0 - - + -
18H SER* 3.8 28.2 + - - +
21H MSE 4.3 11.0 - - + +
22H VAL* 6.0 1.0 - - - +
9J LEU* 5.2 0.2 - - - -
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Residues in contact with PHE 14 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F GLN* 4.3 23.1 - - + -
13F GLU* 3.7 30.5 - - + -
10G TRP* 2.8 49.1 + + + +
11G LYS* 2.8 22.4 + - + +
13G GLU* 1.3 76.8 - - - +
15G HIS* 1.3 66.9 + + + +
17G TRP* 3.1 5.3 + + - +
18G SER* 2.9 35.7 + - - -
9J LEU* 3.8 33.0 - - + -
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Residues in contact with HIS 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G LYS* 2.7 51.3 + - + +
12G ALA* 3.5 11.4 - - - +
14G PHE* 1.3 79.1 - + + +
16G ARG* 1.3 62.3 + - - +
18G SER* 3.3 7.2 + - - -
19G SER* 3.2 20.8 + - - -
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Residues in contact with ARG 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ARG* 6.1 1.2 - - - +
12G ALA* 3.1 19.9 + - - +
13G GLU* 3.4 37.3 + - - +
14G PHE 3.2 0.2 - - - -
15G HIS* 1.3 77.4 - - - +
17G TRP* 1.3 60.8 + - - +
19G SER* 3.2 8.9 + - - -
20G TYR* 3.1 59.3 + - + -
21H MSE 5.6 2.5 - - - -
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Residues in contact with TRP 17 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F GLU* 3.7 48.5 - - + -
16F ARG* 6.2 0.7 - - + -
17F TRP* 3.8 18.6 - + + -
13G GLU 3.0 18.5 + - - +
14G PHE* 3.1 16.1 + + - +
16G ARG* 1.3 75.4 - - - +
18G SER* 1.3 68.1 + - - +
20G TYR* 3.0 5.7 + - - +
21G MSE 2.8 61.1 + - + +
17H TRP* 4.1 8.1 - + + -
21H MSE 3.7 29.8 - - + -
6J PRO* 3.9 8.2 - - + +
7J PRO 2.8 24.9 + - - -
9J LEU* 3.7 33.5 - - + +
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Residues in contact with SER 18 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F GLU* 4.8 5.7 + - - -
14G PHE* 2.9 30.2 + - - -
15G HIS* 3.3 10.5 + - - -
17G TRP* 1.3 82.8 - - - +
19G SER* 1.3 57.3 + - - +
21G MSE 3.3 9.4 + - - +
22G VAL* 2.8 33.8 + - - +
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Residues in contact with SER 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G HIS 3.2 12.2 + - - -
16G ARG* 3.4 12.8 - - - -
17G TRP 3.0 0.6 - - - -
18G SER* 1.3 75.6 - - - +
20G TYR* 1.3 71.1 + - - +
22G VAL* 3.2 6.9 + - - +
23G HIS* 3.1 43.0 + - - -
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Residues in contact with TYR 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ARG* 3.1 49.2 + - + -
17G TRP 3.0 7.6 + - - +
19G SER* 1.3 80.7 - - - +
21G MSE 1.3 63.1 + - - +
23G HIS* 4.0 7.0 - + - +
24G TRP* 2.9 28.6 + - - +
21H MSE 3.9 37.7 + - + +
22H VAL* 5.4 2.3 - - - +
24H TRP* 3.4 32.1 - + + -
25H LYS* 3.2 53.4 + - + +
28H PHE* 6.1 0.2 - - - -
6J PRO* 4.0 8.7 - - + -
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Residues in contact with MSE 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F GLU* 5.9 0.4 - - - +
16F ARG* 5.0 9.9 - - + -
17F TRP* 4.0 11.0 - - - -
20F TYR* 3.1 43.0 + - + +
17G TRP* 2.8 48.0 + - + +
18G SER* 3.3 14.8 - - - +
20G TYR* 1.3 77.6 - - - +
22G VAL* 1.3 61.7 + - + +
24G TRP* 3.7 8.5 - - + -
25G LYS* 3.2 21.8 + - - +
5J PRO* 3.4 11.2 - - + -
6J PRO* 3.3 34.3 - - + +
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Residues in contact with VAL 22 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F TYR* 6.1 0.2 - - - -
18G SER* 2.8 21.0 + - - +
19G SER* 3.2 10.7 + - - +
21G MSE 1.3 74.8 - - - +
23G HIS* 1.3 72.4 + - + +
25G LYS* 3.1 15.1 + - - +
26G ASN* 3.2 14.2 + - + +
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Residues in contact with HIS 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G SER* 3.1 38.8 + - - +
20G TYR* 4.0 7.4 - + + +
22G VAL* 1.3 86.5 - - + +
24G TRP* 1.3 62.7 + - - +
26G ASN* 3.5 5.5 + - - +
27G GLN* 3.1 28.9 + - - +
25H LYS* 6.0 5.6 - - - -
28H PHE* 3.9 20.0 - + + -
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Residues in contact with TRP 24 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F TYR* 3.3 48.2 - + + -
24F TRP* 4.1 9.2 - + + -
20G TYR 2.9 20.2 + - - +
21G MSE 3.7 13.9 - - + +
23G HIS* 1.3 75.8 - - - +
25G LYS* 1.3 74.7 + - + +
27G GLN* 3.5 0.7 + - - +
28G PHE* 2.9 54.9 + + + +
24H TRP* 4.0 9.6 - + + -
28H PHE* 3.7 29.6 - + + -
2J LEU* 3.4 8.3 - - + +
3J THR* 2.9 23.4 + - - -
4J PRO 3.3 15.6 + - - -
5J PRO* 3.6 24.7 - - + -
6J PRO* 4.3 3.4 - - + -
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Residues in contact with LYS 25 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F ARG* 4.6 11.0 - - - +
20F TYR* 3.0 49.6 + - + +
21G MSE 3.2 8.2 + - - +
22G VAL* 3.1 6.6 + - - +
24G TRP* 1.3 88.3 - - + +
26G ASN* 1.3 68.0 - - - +
28G PHE* 3.1 3.7 + - + +
29G ASP* 2.8 47.3 + - - +
----------------------------------------------------------
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Residues in contact with ASN 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G VAL* 3.2 12.2 + - + +
23G HIS* 3.7 10.8 - - - +
25G LYS* 1.3 81.7 - - - +
27G GLN* 1.3 63.0 + - - +
29G ASP* 2.9 17.3 + - - +
30G HIS* 3.0 53.1 + - - -
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Residues in contact with GLN 27 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G HIS* 3.1 15.4 + - - +
24G TRP 3.8 1.8 - - - +
26G ASN* 1.3 79.3 - - - +
28G PHE* 1.3 63.1 + - - +
30G HIS* 3.6 7.1 + - - +
31G TYR* 3.0 43.2 + - + -
28H PHE* 3.4 33.6 + - + -
31H TYR 2.7 30.2 + - - -
32H SER* 3.8 16.7 + - - -
2J LEU* 3.7 19.0 - - + +
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Residues in contact with PHE 28 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F TYR* 6.1 0.9 - + - -
23F HIS* 3.9 45.3 - + + -
24F TRP* 4.2 14.4 - + - -
27F GLN* 4.3 3.6 - - + -
24G TRP* 2.9 51.4 + + + +
25G LYS* 3.1 6.7 + - + +
27G GLN* 1.3 76.5 - - - +
29G ASP* 1.3 70.5 + - - +
31G TYR* 2.9 6.9 + - - +
32G SER* 2.9 43.8 + - - -
1J LEU* 3.5 31.4 - - + -
2J LEU* 4.1 10.9 - - + +
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Residues in contact with ASP 29 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G LYS* 2.8 52.4 + - - +
26G ASN* 2.9 11.7 + - - +
28G PHE* 1.3 83.1 - - - +
30G HIS* 1.3 66.1 + - + +
31G TYR 3.0 5.0 + - - -
32G SER* 3.2 8.3 + - - +
33G LYS* 3.2 20.4 + - - +
----------------------------------------------------------
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Residues in contact with HIS 30 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G ASN* 3.0 53.5 + - - +
27G GLN* 4.0 6.5 + - - +
28G PHE 3.4 0.2 - - - -
29G ASP* 1.3 76.9 - - + +
31G TYR* 1.3 63.9 + - + +
33G LYS* 3.4 34.6 - - + +
34G GLN* 4.0 13.5 + - - +
----------------------------------------------------------
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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