Contacts of the helix formed by residues 1 - 30 (chain H) in PDB entry 4DZL
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 GLY 1 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0H ACE 1.3 70.5 - - - +
2H GLU* 1.3 64.0 + - - +
4H ALA* 3.5 6.2 + - - +
5H ALA* 3.1 25.1 + - - +
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Residues in contact with GLU 2 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G ILE* 4.2 11.9 - - + +
7G LYS* 2.6 45.0 + - + +
0H ACE 3.4 0.4 - - - -
1H GLY* 1.3 77.2 - - - +
3H ILE* 1.3 63.2 + - + +
5H ALA* 3.3 6.6 + - - +
6H ILE* 3.0 36.6 + - + +
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Residues in contact with ILE 3 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G ILE* 5.3 17.3 - - + -
0H ACE 3.5 12.2 + - + +
1H GLY 3.4 0.4 - - - -
2H GLU* 1.3 78.3 - - + +
4H ALA* 1.3 60.0 + - - +
6H ILE* 3.3 12.5 + - + +
7H LYS* 3.1 55.3 + - + +
6I ILE* 6.2 1.1 - - + -
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Residues in contact with ALA 4 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0H ACE 3.4 14.0 + - - +
1H GLY* 3.9 7.0 - - - +
2H GLU 3.3 0.4 - - - -
3H ILE* 1.3 79.9 - - - +
5H ALA* 1.3 60.5 + - - +
7H LYS* 3.5 11.4 + - - +
8H GLN* 3.2 23.0 + - - +
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Residues in contact with ALA 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H GLY 3.1 18.8 + - - +
2H GLU* 3.7 7.2 - - - +
3H ILE 3.3 0.2 - - - -
4H ALA* 1.3 76.0 - - - +
6H ILE* 1.3 63.5 + - + +
8H GLN* 3.5 12.5 + - - +
9H GLU* 3.2 29.3 + - - +
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Residues in contact with ILE 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G ILE* 3.7 29.6 - - + -
6G ILE* 4.0 14.1 - - + -
7G LYS* 4.0 23.3 - - + -
10G ILE* 3.4 23.8 - - + -
2H GLU* 3.0 25.1 + - + +
3H ILE* 3.3 11.2 + - + +
5H ALA* 1.3 76.0 - - + +
7H LYS* 1.3 64.5 + - - +
9H GLU* 3.2 15.5 + - - +
10H ILE* 3.0 30.6 + - + +
6I ILE* 5.2 5.8 - - + -
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Residues in contact with LYS 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ILE* 3.1 42.3 + - + +
4H ALA* 3.8 9.4 - - - +
5H ALA 3.4 0.2 - - - -
6H ILE* 1.3 76.4 - - - +
8H GLN* 1.3 57.8 + - - +
10H ILE* 3.4 10.1 + - - +
11H ALA* 3.0 27.4 + - - +
2I GLU* 5.6 6.0 + - - -
6I ILE* 4.0 27.1 - - + -
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Residues in contact with GLN 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ALA 3.2 15.7 + - - +
5H ALA* 3.8 10.4 + - - +
6H ILE 3.2 0.2 - - - -
7H LYS* 1.3 75.8 - - - +
9H GLU* 1.3 60.8 + - + +
11H ALA* 3.4 9.7 + - + +
12H ALA* 3.0 27.7 + - - +
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Residues in contact with GLU 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G LYS* 5.7 2.3 - - - +
10G ILE* 4.0 24.3 - - + +
14G LYS* 2.8 33.8 + - - +
5H ALA* 3.2 19.1 + - - +
6H ILE* 3.2 22.2 + - - +
8H GLN* 1.3 74.5 - - + +
10H ILE* 1.3 59.4 + - - +
12H ALA* 3.2 5.9 + - - +
13H ILE* 2.9 35.2 + - + +
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Residues in contact with ILE 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ILE* 4.3 13.5 - - + -
6H ILE* 3.0 28.0 + - + +
7H LYS* 3.7 7.2 - - - +
8H GLN 3.3 0.2 - - - -
9H GLU* 1.3 76.5 - - - +
11H ALA* 1.3 62.8 + - - +
13H ILE* 3.2 9.4 + - + +
14H LYS* 3.0 28.9 + - + +
6I ILE* 3.8 30.1 - - + +
9I GLU* 4.1 26.9 - - + +
10I ILE* 4.2 26.5 - - + -
13I ILE* 4.2 17.7 - - + +
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Residues in contact with ALA 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H LYS 3.0 14.2 + - - +
8H GLN* 3.6 13.2 - - + +
9H GLU 3.3 0.2 - - - -
10H ILE* 1.3 79.2 - - - +
12H ALA* 1.3 59.8 + - - +
14H LYS* 3.4 11.8 + - - +
15H LYS* 3.2 27.9 + - + +
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Residues in contact with ALA 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H GLN 3.0 16.9 + - - +
9H GLU* 3.7 7.0 - - - +
10H ILE 3.2 0.2 - - - -
11H ALA* 1.3 72.3 - - - +
13H ILE* 1.3 61.5 + - + +
15H LYS* 3.1 14.3 + - + +
16H GLU* 2.9 35.5 + - + +
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Residues in contact with ILE 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ILE* 4.1 31.2 - - + +
13G ILE* 3.9 19.1 - - + -
14G LYS* 4.6 12.1 - - + -
17G ILE* 3.8 25.6 - - + -
9H GLU* 2.9 23.7 + - + +
10H ILE* 3.6 9.0 - - + +
12H ALA* 1.3 75.8 - - - +
14H LYS* 1.3 57.4 + - - +
16H GLU* 3.2 13.6 + - - +
17H ILE* 2.9 32.5 + - + +
13I ILE* 3.9 32.5 - - + -
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Residues in contact with LYS 14 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H ILE* 3.0 23.4 + - + +
11H ALA* 3.5 13.2 - - - +
13H ILE* 1.3 76.8 - - - +
15H LYS* 1.3 61.5 + - - +
17H ILE* 3.4 9.3 + - - +
18H ALA* 3.1 22.2 + - - +
9I GLU* 2.7 37.9 + - - +
13I ILE* 4.2 19.7 - - + -
16I GLU* 5.9 1.3 - - - +
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Residues in contact with LYS 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ALA* 3.2 15.2 + - + +
12H ALA* 3.1 14.4 + - + +
14H LYS* 1.3 75.2 - - - +
16H GLU* 1.3 66.2 + - + +
18H ALA* 3.2 8.7 + - - +
19H ALA* 3.1 22.2 + - - +
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Residues in contact with GLU 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LYS* 5.4 4.9 - - - +
17G ILE* 3.9 30.3 - - + +
21G LYS* 2.7 35.5 + - - +
12H ALA* 2.9 21.7 + - + +
13H ILE* 3.5 18.5 + - - +
15H LYS* 1.3 72.4 - - + +
17H ILE* 1.3 63.1 + - - +
19H ALA* 3.3 7.2 + - - +
20H ILE* 3.0 29.7 + - - +
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Residues in contact with ILE 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G ILE* 4.9 4.0 - - + -
13H ILE* 2.9 24.3 + - + +
14H LYS* 3.6 7.9 - - - +
15H LYS 3.2 0.2 - - - -
16H GLU* 1.3 76.4 - - - +
18H ALA* 1.3 56.2 + - - +
20H ILE* 3.2 11.1 + - + +
21H LYS* 2.9 55.0 + - - +
13I ILE* 3.9 28.5 - - + -
16I GLU* 3.9 28.9 - - + +
17I ILE* 4.1 22.7 - - + -
20I ILE* 4.2 10.8 - - + -
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Residues in contact with ALA 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LYS 3.1 13.8 + - - +
15H LYS* 3.2 10.7 + - - +
17H ILE* 1.3 78.0 - - - +
19H ALA* 1.3 60.6 + - - +
21H LYS* 3.6 10.8 + - - +
22H PHI 3.2 21.7 + - - +
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Residues in contact with ALA 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H LYS 3.1 12.3 + - - +
16H GLU* 3.3 9.4 + - - +
18H ALA* 1.3 73.3 - - - +
20H ILE* 1.3 60.8 + - + +
22H PHI 3.3 9.1 + - - +
23H GLU* 3.0 35.8 + - + +
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Residues in contact with ILE 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G ILE* 4.0 30.1 - - + -
20G ILE* 3.9 34.3 - - + -
21G LYS* 4.3 16.4 - - + -
24G ILE* 4.0 8.7 - - + -
16H GLU 3.0 19.8 + - - +
17H ILE* 3.2 11.2 + - + +
19H ALA* 1.3 75.6 - - + +
21H LYS* 1.3 65.8 + - - +
23H GLU* 3.1 12.5 + - - +
24H ILE* 2.9 42.5 + - + +
17I ILE* 6.1 0.4 - - + -
20I ILE* 3.9 15.7 - - + -
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Residues in contact with LYS 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ILE* 2.9 33.3 + - + +
18H ALA* 3.7 11.4 - - - +
20H ILE* 1.3 78.0 - - - +
22H PHI 1.3 61.4 + - - +
24H ILE* 3.6 8.4 + - - +
25H ALA* 3.2 23.0 + - - +
16I GLU* 2.8 33.6 + - - -
20I ILE* 4.5 14.6 - - + -
23I GLU* 6.1 0.4 - - - +
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Residues in contact with PHI 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H ALA 3.2 14.3 + - - +
19H ALA* 3.4 12.6 - - - +
20H ILE 3.1 0.6 - - - -
21H LYS* 1.3 74.1 + - - +
23H GLU* 1.3 71.0 + - + +
25H ALA* 3.3 8.1 + - + +
26H ALA* 3.1 27.1 + - + +
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Residues in contact with GLU 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G LYS* 5.7 4.0 - - - +
24G ILE* 4.0 31.4 - - + +
28G LYS* 3.1 28.5 + - + +
19H ALA* 3.0 20.8 + - + +
20H ILE* 3.1 12.9 + - - +
22H PHI 1.3 80.8 + - + +
24H ILE* 1.3 57.8 + - - +
26H ALA* 3.3 8.3 + - - +
27H ILE* 2.9 33.4 + - + +
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Residues in contact with ILE 24 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G ILE* 4.1 14.1 - - + -
20H ILE* 2.9 38.1 + - + +
21H LYS* 3.9 6.3 - - - +
23H GLU* 1.3 74.5 - - - +
25H ALA* 1.3 66.2 + - - +
27H ILE* 3.1 11.8 + - + +
28H LYS* 3.0 35.2 + - - +
20I ILE* 3.9 26.0 - - + +
23I GLU* 3.5 27.8 - - + +
24I ILE* 4.0 17.5 - - + -
27I ILE* 4.4 9.6 - - + -
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Residues in contact with ALA 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H LYS 3.2 12.7 + - - +
22H PHI 3.3 11.2 + - + +
24H ILE* 1.3 79.6 - - - +
26H ALA* 1.3 63.0 + - - +
28H LYS* 3.4 10.6 + - - +
29H GLN* 3.2 32.5 + - - +
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Residues in contact with ALA 26 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H PHI 3.1 21.2 + - + +
23H GLU* 3.6 10.8 - - - +
25H ALA* 1.3 72.5 - - - +
27H ILE* 1.3 66.2 + - + +
29H GLN* 3.3 17.2 + - - +
30H GLY* 3.2 17.0 + - - -
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Residues in contact with ILE 27 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G ILE* 3.8 33.2 - - + +
27G ILE* 3.9 32.5 - - + -
28G LYS* 4.1 22.4 - - + -
23H GLU 2.9 22.0 + - - +
24H ILE* 3.1 13.7 + - + +
26H ALA* 1.3 75.1 - - + +
28H LYS* 1.3 64.6 + - - +
30H GLY* 3.1 23.3 + - - -
27I ILE* 4.6 20.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LYS* 5.8 11.0 - - - +
18C ALA* 5.9 4.6 - - - +
24H ILE* 3.0 20.2 + - + +
25H ALA* 3.7 12.1 - - - +
27H ILE* 1.3 77.0 - - - +
29H GLN* 1.3 60.9 + - - +
30H GLY 4.4 2.1 - - - +
23I GLU* 2.7 34.7 + - - +
27I ILE* 3.9 31.6 - - + -
31L TYR* 6.4 0.2 - - - -
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Residues in contact with GLN 29 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LYS* 6.4 0.2 - - - +
25H ALA* 3.2 23.0 + - - +
26H ALA* 3.5 16.4 - - - +
27H ILE 3.1 0.6 - - - -
28H LYS* 1.3 78.8 - - + +
30H GLY* 1.3 64.5 + - - +
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Residues in contact with GLY 30 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H ALA 3.2 7.2 + - - -
27H ILE* 3.1 17.1 + - - +
28H LYS 4.4 2.6 - - - +
29H GLN* 1.3 86.1 - - - +
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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