Contacts of the helix formed by residues 1 - 32 (chain D) 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 1 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D MET* 1.3 59.6 + - - +
3D ARG* 3.4 10.7 - - - +
4D GLN* 3.1 18.2 + - - +
5D ILE* 3.0 32.3 + - - +
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Residues in contact with MET 2 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 3.9 42.0 - - + +
33C ARG* 5.5 11.7 - - + +
1D ARG* 1.3 68.2 - - - +
3D ARG* 1.3 67.1 + - - +
5D ILE* 3.3 23.4 + - + +
6D GLU* 2.9 39.0 + - - +
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Residues in contact with ARG 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D ARG 3.4 6.6 - - - +
2D MET* 1.3 77.2 - - - +
4D GLN* 1.3 62.7 + - - +
6D GLU* 3.3 17.2 + - - +
7D ASP* 3.0 30.4 + - - +
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Residues in contact with GLN 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D ARG* 3.1 20.8 + - - +
3D ARG* 1.3 78.7 - - - +
5D ILE* 1.3 64.4 + - + +
7D ASP* 3.1 13.4 + - + +
8D ARG* 2.9 32.6 + - + +
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Residues in contact with ILE 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 3.9 25.4 - - + -
1D ARG 3.0 12.0 + - - +
2D MET* 3.4 32.1 - - + +
4D GLN* 1.3 76.0 - - + +
6D GLU* 1.3 56.7 + - - +
8D ARG* 3.1 9.2 + - - +
9D LEU* 2.9 35.5 + - + +
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Residues in contact with GLU 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ARG* 3.1 38.6 + - + +
30C LEU* 3.0 44.2 - - + +
31C GLY* 3.1 16.4 + - - +
2D MET* 2.9 30.1 + - - +
3D ARG* 3.5 14.6 + - - +
4D GLN 3.3 0.2 - - - -
5D ILE* 1.3 68.4 - - - +
7D ASP* 1.3 66.3 + - - +
9D LEU* 3.5 4.3 + - - -
10D GLU* 3.1 17.5 + - - +
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Residues in contact with ASP 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ARG* 5.3 4.6 + - - +
3D ARG* 3.0 18.5 + - - +
4D GLN* 3.3 12.8 - - + +
6D GLU* 1.3 76.5 - - - +
8D ARG* 1.4 60.5 + - + +
10D GLU* 3.3 8.2 + - - +
11D GLU* 3.0 39.5 + - - +
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Residues in contact with ARG 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D GLN* 2.9 31.2 + - + +
5D ILE* 3.1 9.8 + - - +
7D ASP* 1.4 72.9 - - + +
9D LEU* 1.3 62.3 + - + +
11D GLU* 3.3 19.5 + - - +
12D ILE* 2.9 37.6 + - + +
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Residues in contact with LEU 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 4.3 28.2 - - + +
26C ILE* 4.1 15.3 - - + -
27C ARG* 4.3 20.4 - - + -
30C LEU* 3.7 30.1 - - + -
5D ILE* 2.9 26.2 + - + +
6D GLU* 3.9 5.4 - - - +
7D ASP 3.3 0.2 - - - -
8D ARG* 1.3 76.6 - - + +
10D GLU* 1.4 51.6 + - - +
12D ILE* 3.1 21.8 + - + +
13D LEU* 2.7 41.3 + - + +
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Residues in contact with GLU 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ARG* 2.7 44.5 + - - +
6D GLU 3.1 14.8 + - - +
7D ASP* 3.5 11.0 - - - +
9D LEU* 1.4 76.4 - - - +
11D GLU* 1.4 61.8 + - - +
13D LEU* 3.1 17.0 + - - +
14D SER* 3.0 22.7 + - - -
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Residues in contact with GLU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ASP* 3.0 29.6 + - - +
8D ARG* 3.3 22.2 + - - +
10D GLU* 1.4 73.6 - - - +
12D ILE* 1.4 66.0 + - + +
14D SER* 3.2 9.5 + - - -
15D LYS* 3.0 40.7 + - - +
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Residues in contact with ILE 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 4.4 12.1 - - + -
8D ARG* 2.9 26.5 + - + +
9D LEU* 3.4 27.4 - - + +
11D GLU* 1.4 76.4 - - + +
13D LEU* 1.3 64.4 + - - +
15D LYS* 3.1 15.1 + - + +
16D LEU* 2.9 42.9 + - + +
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C CYS* 3.3 38.6 - - + +
23C LEU* 4.0 18.8 - - + +
24C ALA* 3.6 32.1 - - + +
27C ARG* 4.8 5.2 - - + +
9D LEU 2.7 22.7 + - - +
10D GLU* 3.1 25.5 + - - +
12D ILE* 1.3 73.3 - - - +
14D SER* 1.3 63.5 + - - +
16D LEU* 3.0 14.2 + - + +
17D TYR* 3.0 39.9 + - + -
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Residues in contact with SER 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D GLU* 3.0 13.0 + - - -
11D GLU* 3.4 12.8 - - - -
13D LEU* 1.3 76.6 - - - +
15D LYS* 1.3 63.5 + - - -
17D TYR* 4.1 6.7 - - - +
18D HIS* 3.0 46.0 + - - -
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Residues in contact with LYS 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D GLU* 3.0 31.0 + - - +
12D ILE* 3.1 13.0 + - - +
14D SER* 1.3 77.5 - - - +
16D LEU* 1.3 58.5 + - + +
18D HIS* 3.4 9.5 + - - +
19D ILE* 2.9 40.7 + - + +
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Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 4.5 19.1 - - + -
19C ILE* 4.4 9.6 - - + -
20C CYS* 3.5 21.3 - - - -
23C LEU* 3.7 29.8 - - + -
12D ILE* 2.9 25.2 + - + +
13D LEU* 3.0 7.6 + - - +
15D LYS* 1.3 75.2 - - + +
17D TYR* 1.3 52.1 + - - +
19D ILE* 3.1 21.6 + - + +
20D CYS* 2.8 38.9 + - - -
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Residues in contact with TYR 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR* 4.4 25.7 + + - -
20C CYS* 3.4 32.3 + - + +
21C ASN* 3.7 16.6 + - - -
24C ALA* 5.7 2.9 - - + +
13D LEU* 3.0 45.6 + - + +
14D SER* 4.1 6.1 - - - +
16D LEU* 1.3 73.8 - - - +
18D HIS* 1.3 60.0 + - + +
20D CYS* 3.2 4.5 + - - +
21D ASN* 2.8 42.6 + - - +
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Residues in contact with HIS 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D SER* 3.0 36.5 + - - +
15D LYS* 3.7 8.9 - - - +
17D TYR* 1.3 76.8 - - + +
19D ILE* 1.3 61.6 + - + +
21D ASN* 3.4 15.3 + - - +
22D GLU* 3.0 33.3 + - + +
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Residues in contact with ILE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 4.5 8.1 - - + -
15D LYS* 2.9 29.9 + - + +
16D LEU* 3.1 22.2 + - + +
18D HIS* 1.3 72.6 - - + +
20D CYS* 1.4 57.0 + - - +
22D GLU* 3.0 21.1 + - - +
23D LEU* 2.8 52.9 + - + +
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Residues in contact with CYS 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 3.3 14.7 - - + +
16C LEU* 3.6 35.7 - - - -
17C TYR* 3.6 36.8 - - + +
20C CYS* 4.5 6.1 - - - -
16D LEU 2.8 25.9 + - - -
17D TYR* 3.5 9.2 - - - +
19D ILE* 1.4 72.3 - - - +
21D ASN* 1.3 59.4 + - - +
23D LEU* 3.2 3.6 + - - -
24D ALA* 2.9 27.5 + - - +
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Residues in contact with ASN 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR* 4.7 7.0 + - - -
17D TYR* 2.8 35.2 + - - +
18D HIS* 3.7 18.4 - - - +
20D CYS* 1.3 78.0 - - - +
22D GLU* 1.4 61.7 + - + +
24D ALA* 3.5 7.0 + - - +
25D ARG* 3.1 23.2 + - - +
28D ARG* 4.7 2.3 + - - -
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Residues in contact with GLU 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D HIS* 3.0 27.0 + - + +
19D ILE* 3.0 22.9 + - - +
21D ASN* 1.4 75.0 - - + +
23D LEU* 1.3 58.9 + - + +
25D ARG* 3.3 10.0 + - - +
26D ILE* 2.9 38.2 + - + +
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 4.6 23.3 - - + +
12C ILE* 4.4 13.9 - - + -
13C LEU* 3.9 13.9 - - + +
16C LEU* 3.7 29.6 - - + -
19D ILE* 2.8 28.4 + - + +
20D CYS* 3.2 7.2 + - - +
22D GLU* 1.3 73.4 - - + +
24D ALA* 1.3 65.8 + - - +
26D ILE* 3.2 17.1 + - + +
27D ARG* 2.9 22.2 + - - +
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Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 3.6 21.2 - - + +
17C TYR* 4.7 7.2 - - - +
20D CYS 2.9 19.7 + - - +
21D ASN* 3.8 7.6 - - - +
23D LEU* 1.3 72.2 - - - +
25D ARG* 1.4 65.1 + - - +
27D ARG* 3.2 5.4 + - - +
28D ARG* 2.8 46.7 + - - +
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Residues in contact with ARG 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ASN 3.1 14.1 + - - +
22D GLU* 3.4 12.6 - - - +
24D ALA* 1.4 77.0 - - - +
26D ILE* 1.3 65.7 + - + +
28D ARG* 3.2 23.5 + - - +
29D LEU* 2.9 49.7 + - + +
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Residues in contact with ILE 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 4.2 18.2 - - + -
22D GLU* 2.9 26.3 + - + +
23D LEU* 3.7 18.6 - - + +
24D ALA 3.2 0.2 - - - -
25D ARG* 1.3 75.1 - - + +
27D ARG* 1.3 64.2 + - - +
29D LEU* 3.1 17.2 + - + +
30D LEU* 2.9 35.3 + - + +
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Residues in contact with ARG 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLU* 4.2 18.1 - - - +
9C LEU* 4.2 22.1 - - + +
10C GLU* 3.4 39.0 - - + +
13C LEU* 4.6 4.7 - - + -
23D LEU 2.9 17.4 + - - +
24D ALA* 3.3 13.5 - - - +
26D ILE* 1.3 72.6 - - - +
28D ARG* 1.4 65.5 + - - +
30D LEU* 3.4 5.2 + - - +
31D GLY* 2.9 24.9 + - - -
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Residues in contact with ARG 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ASN 4.7 2.0 + - - -
24D ALA* 2.8 40.5 + - - +
25D ARG* 3.5 33.3 - - - +
27D ARG* 1.4 79.6 - - - +
29D LEU* 1.4 62.3 + - + +
31D GLY* 3.0 12.7 + - - +
32D GLU* 3.1 21.2 + - + +
----------------------------------------------------------
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Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ARG* 2.9 53.5 + - + +
26D ILE* 3.4 19.1 - - + +
28D ARG* 1.4 70.9 - - + +
30D LEU* 1.3 65.7 + - + +
32D GLU* 3.1 18.7 + - + +
33D ARG* 3.5 16.7 + - - +
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C MET* 3.7 27.9 - - + +
5C ILE* 3.8 29.2 - - + -
6C GLU* 3.6 20.3 - - + +
9C LEU* 3.9 18.4 - - + -
26D ILE* 2.9 25.7 + - + +
27D ARG 3.5 4.9 - - - +
29D LEU* 1.3 78.4 - - + +
31D GLY* 1.3 56.5 + - - +
33D ARG* 3.1 42.9 + - - +
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Residues in contact with GLY 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLU* 3.7 16.7 + - - -
27D ARG* 2.9 15.3 + - - -
28D ARG* 3.0 7.0 + - - -
30D LEU* 1.3 73.9 - - - +
32D GLU* 1.3 60.2 + - - +
33D ARG 3.5 2.9 + - - +
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Residues in contact with GLU 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ARG* 3.1 17.1 + - + +
29D LEU* 3.1 13.1 + - + +
31D GLY* 1.3 76.7 - - - +
33D ARG* 1.3 65.6 + - - +
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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