Contacts of the helix formed by residues 2 - 33 (chain A) in PDB entry 1W5J
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 ARG 2 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A TYZ 1.3 71.2 - - - +
3A MET* 1.3 65.2 + - - +
4A ARG* 3.1 16.0 - - + +
5A GLN* 3.1 60.3 + - + +
6A ILE* 3.2 13.3 + - - +
33B ARG* 3.8 0.4 - - - -
32C GLU* 3.8 23.3 - - - +
33C ARG* 3.6 14.1 - - - +
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Residues in contact with MET 3 (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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2A ARG* 1.3 72.6 - - - +
4A ARG* 1.3 62.3 + - - +
6A ILE* 3.2 15.0 + - + +
7A GLU* 3.0 43.2 + - - +
30B LEU* 3.9 21.3 - - + -
33B ARG* 3.3 35.7 - - - +
33C ARG* 3.0 21.0 + - - +
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Residues in contact with ARG 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ARG* 3.1 14.7 - - + +
3A MET* 1.3 77.2 - - - +
5A GLN* 1.3 56.7 + - + +
7A GLU* 3.3 24.4 + - - +
8A ASP* 3.0 49.1 + - - +
11A GLU* 5.2 6.3 + - - -
33C ARG 5.1 0.6 + - - -
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Residues in contact with GLN 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A TYZ 3.0 31.7 - - + +
2A ARG* 3.1 54.7 + - - +
4A ARG* 1.3 74.5 - - + +
6A ILE* 1.4 61.2 + - + +
8A ASP* 3.6 7.7 + - - +
9A ARG* 3.0 28.2 + - - +
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Residues in contact with ILE 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A TYZ 5.0 4.9 - - + +
2A ARG 3.2 13.2 + - - +
3A MET* 3.2 19.9 + - - +
5A GLN* 1.4 74.2 - - + +
7A GLU* 1.3 67.5 + - + +
9A ARG* 3.2 6.5 + - - +
10A LEU* 3.0 33.0 + - + +
26B ILE* 3.8 30.2 - - + +
29B LEU* 4.1 34.8 - - + -
30B LEU* 3.7 31.2 - - + +
33B ARG* 4.8 8.1 - - - +
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Residues in contact with GLU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A MET* 3.0 43.0 + - + +
4A ARG* 3.3 34.1 + - - +
6A ILE* 1.3 78.1 - - + +
8A ASP* 1.3 66.0 + - - +
10A LEU* 3.4 11.8 + - + +
11A GLU* 3.0 33.8 + - - +
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Residues in contact with ASP 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG* 3.0 40.6 + - - +
5A GLN* 3.8 6.4 - - - +
7A GLU* 1.3 76.1 - - - +
9A ARG* 1.3 52.1 + - - +
11A GLU* 3.1 17.0 + - - +
12A GLU* 2.8 51.8 + - - +
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Residues in contact with ARG 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN 3.0 18.1 + - - +
6A ILE* 3.2 6.5 + - - +
8A ASP* 1.3 72.7 - - - +
10A LEU* 1.3 59.6 + - - +
12A GLU* 3.1 27.1 + - - +
13A ILE* 2.7 44.2 + - + +
22B GLU* 3.9 26.6 - - + +
25B ARG* 5.6 7.5 - - - +
26B ILE* 3.8 21.8 - - + -
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.0 28.3 + - + +
7A GLU* 3.6 13.9 - - + +
9A ARG* 1.3 79.3 - - - +
11A GLU* 1.3 61.3 + - + +
13A ILE* 3.2 9.2 + - + +
14A LEU* 3.0 33.1 + - + +
23B LEU* 4.2 19.1 - - + -
26B ILE* 4.1 23.6 - - + -
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Residues in contact with GLU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG* 5.2 5.9 + - - -
7A GLU* 3.0 27.2 + - + +
8A ASP* 3.1 18.2 + - - +
10A LEU* 1.3 79.4 - - + +
12A GLU* 1.3 58.4 + - + +
14A LEU* 3.3 13.3 + - + +
15A SER* 2.9 32.2 + - - -
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Residues in contact with GLU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASP* 2.8 36.3 + - + +
9A ARG* 3.1 29.5 + - - +
11A GLU* 1.3 73.7 - - + +
13A ILE* 1.4 62.3 + - - +
15A SER* 3.3 9.1 + - - -
16A LYS* 3.2 22.2 + - - +
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Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 2.7 43.7 + - + +
10A LEU* 3.6 9.6 - - + +
12A GLU* 1.4 69.9 - - - +
14A LEU* 1.3 62.3 + - + +
16A LYS* 3.1 7.6 + - - +
17A LEU* 2.8 47.5 + - + +
19B ILE* 4.0 25.5 - - + +
22B GLU* 4.0 17.5 - - + -
23B LEU* 4.0 31.2 - - + -
26B ILE* 4.0 10.8 - - + -
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.0 21.7 + - + +
11A GLU* 3.4 16.8 - - + +
13A ILE* 1.3 79.2 - - + +
15A SER* 1.3 65.9 + - - +
17A LEU* 3.8 15.8 - - + +
18A TYR* 2.9 56.3 + - + +
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Residues in contact with SER 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU 2.9 18.7 + - - -
12A GLU* 3.6 11.0 - - - -
13A ILE 3.3 0.4 - - - -
14A LEU* 1.3 75.6 - - - +
16A LYS* 1.4 58.9 + - - +
18A TYR* 3.3 8.8 + - - +
19A HIS* 3.0 27.1 + - - +
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Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU 3.2 9.1 + - - +
13A ILE* 3.1 9.5 + - - +
15A SER* 1.4 80.1 - - - +
17A LEU* 1.3 50.8 + - - +
19A HIS* 3.2 31.7 + - - +
20A ILE* 2.7 41.5 + - + +
15B LYS* 3.7 50.2 - - + +
19B ILE* 4.0 11.2 - - + -
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 2.8 36.3 + - + +
14A LEU* 3.2 15.2 + - + +
16A LYS* 1.3 76.2 - - - +
18A TYR* 1.3 62.4 + - + +
20A ILE* 3.7 6.9 - - + +
21A CYS* 2.8 41.4 + - - -
16B LEU* 3.7 30.3 - - + -
19B ILE* 3.8 17.0 - - + -
23B LEU* 5.8 2.5 - - + -
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Residues in contact with TYR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 2.9 52.4 + - + +
15A SER* 3.7 7.6 - - - +
17A LEU* 1.3 77.2 - - + +
19A HIS* 1.3 58.8 + - - +
21A CYS* 3.3 11.4 + - + +
22A ASN* 3.0 36.2 + - - +
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Residues in contact with HIS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER 3.0 12.7 + - - +
16A LYS* 3.3 33.2 + - + +
18A TYR* 1.3 74.3 - - - +
20A ILE* 1.3 67.5 + - - +
22A ASN* 3.4 12.7 + - + +
23A GLU* 3.0 35.0 + - + +
8B ARG* 3.8 24.9 + - - -
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Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 2.7 32.8 + - + +
17A LEU* 3.7 8.5 - - + +
19A HIS* 1.3 75.7 - - - +
21A CYS* 1.3 60.1 + - - +
23A GLU* 3.2 8.4 + - - +
24A LEU* 2.8 39.9 + - + +
12B ILE* 3.8 28.5 - - + +
15B LYS* 3.8 27.1 - - + -
16B LEU* 3.6 38.4 - - + +
19B ILE* 4.3 7.9 - - + -
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Residues in contact with CYS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 2.8 31.3 + - - +
18A TYR* 3.6 12.6 - - + +
20A ILE* 1.3 80.0 - - - +
22A ASN* 1.3 58.2 + - - +
24A LEU* 3.1 12.2 + - - +
25A ALA* 2.8 30.5 + - - +
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Residues in contact with ASN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 3.0 23.3 + - - +
19A HIS* 3.5 16.4 - - + +
21A CYS* 1.3 77.8 - - - +
23A GLU* 1.3 60.5 + - - +
25A ALA* 3.3 8.4 + - - +
26A ARG* 3.0 28.1 + - - +
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A HIS* 3.0 28.3 + - + +
20A ILE* 3.4 10.5 - - - +
22A ASN* 1.3 78.5 - - - +
24A LEU* 1.3 66.8 + - - +
26A ARG* 3.0 39.2 + - - +
27A ILE* 3.1 28.2 + - + +
8B ARG* 2.9 42.6 + - - +
12B ILE* 4.2 16.2 - - + -
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 2.8 38.4 + - + +
21A CYS* 3.1 10.3 + - - +
23A GLU* 1.3 74.2 - - - +
25A ALA* 1.3 62.2 + - - +
27A ILE* 3.2 7.2 + - + +
28A ARG* 3.0 23.4 + - - +
9B LEU* 3.8 20.2 - - + -
12B ILE* 3.7 29.8 - - + -
16B LEU* 5.5 3.8 - - + -
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A CYS 2.8 19.4 + - - +
22A ASN* 3.7 8.1 - - - +
24A LEU* 1.3 72.9 - - - +
26A ARG* 1.3 63.0 + - - +
28A ARG* 3.4 10.2 + - - +
29A ARG* 3.1 22.7 + - - +
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Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASN 3.0 16.6 + - - +
23A GLU* 3.0 39.9 + - - +
24A LEU 3.2 0.2 - - - -
25A ALA* 1.3 76.4 - - - +
27A ILE* 1.3 58.2 + - - +
29A ARG* 3.2 9.2 + - + +
30A LEU* 2.8 69.7 + - + +
8B ARG* 4.8 9.1 - - - +
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU 3.1 19.0 + - - +
24A LEU* 3.2 9.6 + - + +
26A ARG* 1.3 74.6 - - - +
28A ARG* 1.3 68.7 + - - +
30A LEU* 3.0 15.9 + - + +
31A LEU* 2.8 36.2 + - + +
5B ILE* 3.8 29.6 - - + +
8B ARG* 4.0 22.4 - - + -
9B LEU* 4.0 22.4 - - + -
12B ILE* 3.7 27.4 - - + -
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Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU 3.0 11.8 + - - +
25A ALA* 3.5 13.2 + - - +
27A ILE* 1.3 78.9 - - - +
29A ARG* 1.3 57.8 - - - +
31A LEU* 3.2 11.5 + - - +
32A GLY* 3.0 22.7 + - - -
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Residues in contact with ARG 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA 3.1 13.8 + - - +
26A ARG* 3.5 9.6 - - + +
27A ILE 3.1 0.2 - - - -
28A ARG* 1.3 79.0 - - - +
30A LEU* 1.4 64.4 + - + +
32A GLY* 3.2 4.4 + - - +
33A GLU* 3.2 36.1 + - - +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG* 2.8 55.0 + - + +
27A ILE* 3.7 12.3 - - + +
29A ARG* 1.4 74.7 - - + +
31A LEU* 1.3 63.6 + - - +
33A GLU* 3.0 37.7 + - + +
34A ARG* 3.5 13.5 + - - +
1B ARG* 5.2 17.7 - - - -
5B ILE* 4.3 28.0 - - + -
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 2.8 32.3 + - + +
28A ARG* 3.5 11.7 - - - +
30A LEU* 1.3 73.4 - - - +
32A GLY* 1.3 62.2 + - - +
33A GLU 3.2 1.0 + - - -
34A ARG* 3.4 23.0 + - - +
2B MET* 3.8 25.1 - - + -
5B ILE* 3.8 27.8 - - + -
9B LEU* 6.2 1.6 - - + -
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Residues in contact with GLY 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG 3.0 12.9 + - - -
29A ARG* 3.2 6.2 + - - -
30A LEU 3.2 0.4 - - - -
31A LEU* 1.3 80.1 - - - +
33A GLU* 1.3 55.8 + - - +
34A ARG 3.4 3.2 + - - +
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 3.2 24.6 + - - +
30A LEU* 3.0 41.1 + - + +
32A GLY* 1.3 76.9 - - - +
34A ARG* 1.3 65.1 + - - +
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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