Contacts of the helix formed by residues 3 - 32 (chain G) in PDB entry 2HY6
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 3 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 5.2 14.8 - - + -
1F MET* 3.7 43.0 - - + +
2F LYS 3.4 36.4 - - - +
3F VAL* 4.7 1.1 - - - -
5F GLN* 4.2 4.7 + - - +
6F LEU* 4.5 25.6 - - + +
201F HEZ 5.1 4.7 - - - +
4G LYS* 1.3 62.1 + - - +
5G GLN 3.3 2.7 - - - -
6G LEU* 3.3 13.5 + - + +
7G ALA* 2.9 28.1 + - - +
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Residues in contact with LYS 4 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F GLN* 3.4 37.4 + - - +
3G VAL* 1.3 77.3 - - - +
5G GLN* 1.3 58.0 + - - +
7G ALA* 3.3 3.0 + - - +
8G ASP* 2.8 31.2 + - + +
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Residues in contact with GLN 5 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 3.5 31.2 + - - +
14A ALA* 3.8 18.1 - - + +
15A SER* 5.7 2.4 + - - -
18A TYR* 3.5 26.3 + - + +
3G VAL 3.3 0.4 - - - -
4G LYS* 1.3 79.2 - - - +
6G LEU* 1.3 64.3 + - - +
8G ASP* 3.2 2.3 + - - -
9G ALA* 3.0 21.7 + - - +
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Residues in contact with LEU 6 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 4.2 29.1 - - + +
13A LEU* 3.9 28.3 - - + -
14A ALA* 3.8 20.5 - - + +
17A ASN* 3.9 24.5 - - - +
202A HEZ 5.0 1.6 - - - +
6F LEU* 4.1 29.2 - - + -
201F HEZ 4.8 15.0 - - + +
3G VAL* 3.3 13.7 + - + +
5G GLN* 1.3 79.3 - - - +
7G ALA* 1.3 61.9 + - - +
9G ALA* 3.2 1.9 + - - +
10G VAL* 3.0 25.9 + - + +
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Residues in contact with ALA 7 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F GLN* 3.6 41.7 - - + +
6F LEU* 3.9 15.2 - - - +
9F ALA* 3.4 4.5 - - + +
3G VAL 2.9 17.4 + - - +
4G LYS 3.7 3.8 - - - +
6G LEU* 1.3 76.6 - - - +
8G ASP* 1.3 56.9 - - - +
10G VAL 3.3 1.0 + - - -
11G GLU* 2.9 35.1 + - + +
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Residues in contact with ASP 8 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 2.6 33.5 + - - +
4G LYS* 2.8 21.1 + - + +
5G GLN* 3.5 2.0 - - - +
7G ALA* 1.3 76.6 - - - +
9G ALA* 1.3 57.5 + - - +
11G GLU* 3.3 11.6 + - - +
12G GLU* 3.0 38.9 + - - +
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Residues in contact with ALA 9 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA* 3.4 29.2 - - - +
17A ASN* 3.9 19.0 - - + +
18A TYR* 3.5 24.8 - - + +
5G GLN 3.0 13.7 + - - +
6G LEU* 3.6 7.9 - - + +
8G ASP* 1.3 76.6 - - - +
10G VAL* 1.3 57.2 + - - +
12G GLU* 3.2 3.5 + - - +
13G LEU* 3.0 27.0 + - - +
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Residues in contact with VAL 10 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASN* 4.1 11.0 - - - +
202A HEZ 4.0 29.8 - - + -
6F LEU* 4.2 11.0 - - + -
9F ALA* 3.5 32.3 - - + +
10F VAL* 3.9 10.1 - - + +
13F LEU* 4.2 18.0 - - + +
6G LEU* 3.0 16.6 + - + +
7G ALA 3.7 6.7 - - - +
9G ALA* 1.3 75.9 - - - +
11G GLU* 1.3 57.5 + - - +
13G LEU* 3.2 8.0 + - - +
14G ALA* 2.9 27.0 + - - +
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Residues in contact with GLU 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F GLN 4.6 1.6 - - - +
8F ASP* 4.0 7.3 - - - +
9F ALA* 3.4 29.7 + - + +
12F GLU* 3.5 23.3 - - - +
7G ALA* 2.9 22.3 + - + +
8G ASP* 3.4 14.6 - - - +
10G VAL* 1.3 77.0 - - - +
12G GLU* 1.3 58.1 + - + +
14G ALA* 3.2 6.3 + - - +
15G SER* 3.0 30.8 + - - -
----------------------------------------------------------
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Residues in contact with GLU 12 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 3.3 31.1 - - + +
21A ALA* 3.6 15.0 - - + +
8G ASP* 3.0 27.4 + - - +
9G ALA* 3.2 8.9 + - - +
11G GLU* 1.3 73.0 - - + +
13G LEU* 1.3 62.1 + - - +
15G SER* 3.3 8.5 + - - -
16G ALA* 3.0 28.2 + - - +
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Residues in contact with LEU 13 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASN* 4.7 5.4 - - + +
20A LEU* 3.9 27.4 - - + -
21A ALA* 3.5 20.1 - - + +
24A VAL* 4.0 7.9 - - + -
202A HEZ 3.4 44.9 - - + +
203D HEZ 4.6 6.7 - - - -
13F LEU* 3.9 15.7 - - + -
9G ALA 3.0 13.5 + - - +
10G VAL* 3.5 9.9 - - - +
12G GLU* 1.3 74.3 - - - +
14G ALA* 1.3 63.9 + - - +
16G ALA* 3.3 1.3 + - - +
17G ASN* 3.0 40.0 + - - +
204G HEZ 5.9 0.2 - - - +
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Residues in contact with ALA 14 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F GLU* 3.7 18.4 - - + +
13F LEU* 3.6 38.9 - - - +
16F ALA* 3.3 10.9 - - + +
10G VAL 2.9 13.0 + - - +
11G GLU* 3.4 10.1 - - - +
13G LEU* 1.3 76.2 - - - +
15G SER* 1.3 61.6 + - - +
17G ASN 3.3 1.2 + - - -
18G TYR* 3.0 21.6 + - - +
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Residues in contact with SER 15 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G GLU 3.0 15.0 + - - -
12G GLU* 3.6 11.5 - - - -
14G ALA* 1.3 78.1 - - - +
16G ALA* 1.3 63.1 + - - +
18G TYR* 3.2 9.8 + - - +
19G HIS* 3.0 38.7 + - - -
----------------------------------------------------------
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Residues in contact with ALA 16 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 3.4 28.3 - - - +
24A VAL* 3.6 17.7 - - + +
25A ALA* 3.8 13.7 - - + +
28A ALA* 4.5 2.1 - - - +
12G GLU 3.0 16.9 + - - +
13G LEU 3.7 4.0 - - - +
15G SER* 1.3 76.0 - - - +
17G ASN* 1.3 57.6 + - - +
19G HIS* 3.2 11.0 + - - +
20G LEU* 2.8 27.4 + - - +
----------------------------------------------------------
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Residues in contact with ASN 17 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 3.1 19.6 - - - +
203D HEZ 4.5 4.9 - - - -
20E LEU* 6.1 0.2 - - - +
13F LEU* 3.7 11.3 - - + +
16F ALA* 4.0 9.4 - - + +
17F ASN* 2.6 34.6 + - - +
20F LEU* 4.4 9.6 - - + +
13G LEU* 3.0 29.9 + - - +
14G ALA 3.8 3.4 - - - +
16G ALA* 1.3 72.6 - - - +
18G TYR* 1.3 60.5 + - - +
20G LEU* 3.6 6.3 - - - +
21G ALA* 2.9 29.6 + - - +
204G HEZ 3.6 20.5 + - - -
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Residues in contact with TYR 18 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F ALA* 3.9 11.3 - - + +
19F HIS* 4.0 18.2 - + - -
14G ALA 3.0 13.3 + - - +
15G SER* 3.4 13.0 - - - +
17G ASN* 1.3 75.5 - - - +
19G HIS* 1.3 88.8 - + - +
21G ALA* 3.2 7.3 + - - +
22G ASN* 3.0 54.7 + - - +
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Residues in contact with HIS 19 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 5.9 3.7 - - + +
28A ALA* 3.7 13.5 - - + +
15G SER* 3.0 30.8 + - - -
16G ALA* 3.2 9.3 + - - +
18G TYR* 1.3 98.9 - + - +
20G LEU* 1.3 66.8 + - - +
22G ASN* 3.3 8.5 + - - +
23G ALA* 3.0 23.7 + - - +
26G ARG* 4.9 1.9 + - - -
----------------------------------------------------------
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Residues in contact with LEU 20 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 4.2 9.4 - - + -
27A LEU* 4.0 28.9 - - + -
28A ALA* 3.5 28.1 - - + +
31A VAL* 4.2 9.9 - - + -
20F LEU* 3.9 28.5 - - + -
16G ALA 2.8 16.7 + - - +
17G ASN* 3.6 6.7 - - - +
18G TYR 3.3 0.2 - - - -
19G HIS* 1.3 77.3 - - - +
21G ALA* 1.3 61.8 + - - +
23G ALA* 3.2 1.9 + - - +
24G VAL* 2.9 40.5 + - + +
204G HEZ 4.1 29.2 - - + +
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Residues in contact with ALA 21 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F HIS* 3.5 27.1 - - + +
20F LEU* 3.5 35.1 - - - +
23F ALA* 3.3 11.4 - - - +
17G ASN 2.9 17.0 + - - +
18G TYR* 3.2 6.0 + - - +
20G LEU* 1.3 75.2 - - - +
22G ASN* 1.3 58.6 + - - +
24G VAL 3.3 0.3 + - - -
25G ALA* 2.9 26.4 + - - +
----------------------------------------------------------
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Residues in contact with ASN 22 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F HIS* 2.8 28.2 + - - -
18G TYR* 3.0 51.7 + - - +
19G HIS* 3.8 9.3 - - + +
21G ALA* 1.3 76.8 - - - +
23G ALA* 1.3 57.0 + - - +
25G ALA* 3.3 7.5 + - - +
26G ARG* 3.0 50.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA 23 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA* 3.5 26.0 - - - +
31A VAL* 3.9 13.0 - - + +
32A GLY* 3.8 13.3 - - - +
19G HIS 3.0 16.3 + - - +
20G LEU 3.2 5.1 + - - +
22G ASN* 1.3 75.5 - - - +
24G VAL* 1.3 57.5 + - - +
26G ARG* 3.4 22.7 + - - +
27G LEU* 3.0 27.5 + - - +
----------------------------------------------------------
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Residues in contact with VAL 24 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 4.3 10.5 - - + -
20F LEU* 4.3 7.2 - - + -
23F ALA* 3.5 31.2 - - + +
24F VAL* 3.9 14.4 - - + +
27F LEU* 4.1 18.9 - - + +
20G LEU* 2.9 39.0 + - + +
21G ALA* 3.7 4.3 - - - +
23G ALA* 1.3 71.7 - - - +
25G ALA* 1.3 61.0 + - - +
27G LEU* 3.2 8.7 + - + +
28G ALA* 2.9 25.8 + - - +
204G HEZ 5.3 7.0 - - - +
----------------------------------------------------------
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Residues in contact with ALA 25 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F HIS* 5.7 4.9 - - + -
23F ALA* 3.9 14.3 - - + +
26F ARG* 5.6 8.7 - - - +
21G ALA 2.9 16.8 + - - +
22G ASN* 3.3 8.7 + - - +
24G VAL* 1.3 78.5 - - - +
26G ARG* 1.3 61.5 + - + +
28G ALA* 3.3 8.6 + - - +
29G LYS* 3.1 30.7 + - + +
----------------------------------------------------------
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Residues in contact with ARG 26 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA 5.3 0.6 + - - -
32A GLY* 4.4 15.5 + - - -
19G HIS 4.9 1.8 + - - -
22G ASN* 3.0 44.5 + - - +
23G ALA* 3.6 25.8 - - - +
25G ALA* 1.3 75.9 - - + +
27G LEU* 1.3 63.1 + - - +
29G LYS* 3.3 14.5 + - + +
30G ALA* 3.0 22.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 27 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 4.3 25.1 - - + +
27F LEU* 4.1 27.8 - - + -
205F HEZ 4.9 16.6 - - + +
23G ALA 3.0 14.5 + - - +
24G VAL* 3.2 10.1 + - + +
26G ARG* 1.3 77.0 - - - +
28G ALA* 1.3 57.4 + - - +
30G ALA* 3.1 11.0 + - + +
31G VAL* 2.9 43.9 + - + +
----------------------------------------------------------
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Residues in contact with ALA 28 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F ALA 4.6 0.2 - - - +
26F ARG* 3.8 16.2 - - + +
27F LEU* 3.5 42.8 - - - +
30F ALA* 3.5 10.3 - - + +
24G VAL 2.9 12.0 + - - +
25G ALA* 3.3 10.3 + - - +
27G LEU* 1.3 76.6 - - - +
29G LYS* 1.3 62.4 + - + +
31G VAL 3.5 0.3 + - - -
32G GLY* 3.0 19.8 + - - -
----------------------------------------------------------
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Residues in contact with LYS 29 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G ALA* 3.1 19.3 + - + +
26G ARG* 3.5 15.5 - - + +
27G LEU 3.2 0.2 - - - -
28G ALA* 1.3 75.4 - - + +
30G ALA* 1.3 58.7 + - - +
32G GLY* 3.0 25.3 + - - +
----------------------------------------------------------
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Residues in contact with ALA 30 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G ARG 3.0 13.6 + - - +
27G LEU* 3.1 16.8 + - + +
29G LYS* 1.3 77.2 - - - +
31G VAL* 1.3 62.7 + - - +
32G GLY 3.5 6.9 - - - +
----------------------------------------------------------
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Residues in contact with VAL 31 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F LEU* 4.2 14.4 - - + -
30F ALA* 3.7 31.5 - - + +
31F VAL* 4.0 11.7 - - + +
205F HEZ 5.0 5.8 - - - +
27G LEU* 2.9 32.4 + - + +
28G ALA* 3.8 4.7 - - - +
30G ALA* 1.3 75.9 - - - +
32G GLY* 1.3 61.3 + - - +
----------------------------------------------------------
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Residues in contact with GLY 32 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F ALA* 4.1 11.6 - - - +
28G ALA 3.0 15.3 + - - -
29G LYS 3.0 17.4 + - - +
30G ALA 3.5 5.5 - - - +
31G VAL* 1.3 82.7 - - - +
----------------------------------------------------------
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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