Contacts of the helix formed by residues 2 - 24 (chain N) in PDB entry 6O3N
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 LYS 2 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16L LYS* 4.8 5.5 - - - +
19L GLU* 5.3 14.4 - - + +
20L LEU* 5.9 5.3 - - - +
1N SER* 1.3 75.8 - - - +
3N LEU* 1.3 59.4 + - - +
5N GLU* 3.1 11.5 + - - +
6N LEU* 3.1 25.3 + - - +
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Residues in contact with LEU 3 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L LEU* 3.8 33.7 - - + -
3M LEU* 5.9 8.5 - - + -
7M LEU* 5.3 5.4 - - + -
1N SER 3.3 5.5 - - - +
2N LYS* 1.3 74.9 - - - +
4N LEU* 1.3 67.3 + - + +
6N LEU* 3.4 28.6 + - + +
7N LEU* 3.1 32.4 - - + +
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Residues in contact with LEU 4 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3M LEU* 6.2 2.9 - - + -
1N SER* 3.5 23.7 + - - +
2N LYS 3.3 0.2 - - - -
3N LEU* 1.3 81.9 - - + +
5N GLU* 1.3 57.0 + - - +
7N LEU* 3.2 23.4 + - + +
8N ARG* 3.1 27.5 + - - +
18P ILE* 5.4 0.5 - - - +
21P LEU* 5.0 10.1 - - + +
22P GLU* 3.3 52.3 - - + +
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Residues in contact with GLU 5 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L LYS* 3.9 6.4 - - + +
1N SER 3.1 14.3 + - - +
2N LYS* 3.1 17.7 + - - +
4N LEU* 1.3 72.6 - - - +
6N LEU* 1.3 63.1 + - - +
8N ARG* 3.5 9.1 + - - +
9N LYS* 3.2 21.7 + - - +
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Residues in contact with LEU 6 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K ILE* 6.0 2.9 - - + -
21K LEU* 5.9 0.4 - - + -
13L ALA 4.0 9.6 - - - +
16L LYS* 2.9 23.7 - - + +
17L ALA* 3.8 27.1 - - + +
20L LEU* 4.0 24.5 - - + -
7M LEU* 3.9 30.5 - - + -
2N LYS 3.1 9.6 + - - +
3N LEU* 3.4 19.3 - - + +
5N GLU* 1.3 75.6 - - - +
7N LEU* 1.3 63.9 + - + +
9N LYS* 3.2 5.4 + - - +
10N LEU* 2.9 41.0 + - + +
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Residues in contact with LEU 7 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3M LEU* 5.6 11.9 - - + +
6M LEU* 5.7 8.7 - - + -
7M LEU* 5.1 13.2 - - + +
10M LEU* 4.9 6.9 - - + +
3N LEU* 3.1 27.4 - - + +
4N LEU* 3.2 29.4 + - + +
5N GLU 3.2 0.6 - - - -
6N LEU* 1.3 82.1 - - + +
8N ARG* 1.3 66.5 - - - +
10N LEU* 3.3 25.0 - - + +
11N ALA* 3.3 20.8 + - - +
20O LEU* 6.3 2.2 - - + -
18P ILE* 4.5 26.4 - - + +
21P LEU* 5.9 4.5 - - + -
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Residues in contact with ARG 8 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N LEU 3.1 12.1 + - - +
5N GLU* 3.6 12.3 - - - +
7N LEU* 1.3 74.7 - - - +
9N LYS* 1.3 56.7 + - - +
11N ALA* 3.3 9.7 - - - +
12N GLU* 3.1 25.9 + - - +
18P ILE* 4.8 8.2 - - + +
19P GLU* 6.4 2.0 - - - -
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Residues in contact with LYS 9 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L LYS 4.3 3.8 - - - +
12L GLU* 3.5 39.7 - - + +
13L ALA* 3.8 4.5 - - - +
16L LYS* 4.4 2.7 - - + -
5N GLU 3.2 9.9 + - - +
6N LEU 3.2 10.9 + - - +
8N ARG* 1.3 76.7 - - - +
10N LEU* 1.3 57.9 + - - +
12N GLU* 3.1 8.9 + - - +
13N ALA* 3.0 30.8 + - - +
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Residues in contact with LEU 10 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K LEU* 6.6 0.2 - - + -
18K ILE* 5.1 9.6 - - + -
13L ALA* 4.9 11.2 - - + +
7M LEU* 3.8 29.6 - - + +
10M LEU* 3.7 50.9 - - + +
11M ALA* 4.4 11.4 - - - +
14M LEU* 4.8 9.1 - - + +
6N LEU* 2.9 23.5 + - + +
7N LEU* 3.3 26.5 - - + +
9N LYS* 1.3 70.9 - - - +
11N ALA* 1.3 63.9 + - - +
13N ALA* 3.5 7.7 - - - +
14N LEU* 3.5 20.3 + - - +
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Residues in contact with ALA 11 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M LEU* 4.2 7.3 - - + +
7N LEU 3.3 8.1 + - - +
8N ARG* 3.3 12.3 - - - +
10N LEU* 1.3 76.7 - - - +
12N GLU* 1.3 66.5 + - - +
14N LEU* 3.3 10.0 + - - +
15N HIS* 3.1 22.9 + - - +
11P ALA 4.8 3.6 - - - +
14P LEU* 4.7 8.5 - - + +
15P HIS* 3.7 36.5 - - + +
18P ILE* 5.7 4.9 - - + -
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Residues in contact with GLU 12 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L LYS* 4.0 11.6 - - + +
12L GLU* 5.5 3.4 - - + -
8N ARG 3.1 13.6 + - - +
9N LYS* 3.1 14.5 + - - +
11N ALA* 1.3 74.9 - - - +
13N ALA* 1.3 64.0 + - - +
15N HIS* 3.2 9.0 + - - +
16N LYS* 3.0 24.9 + - - +
15P HIS* 5.2 2.7 - - - +
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Residues in contact with ALA 13 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L LEU* 4.0 6.3 - - + +
9L LYS* 3.4 26.2 - - + +
10L LEU* 4.8 2.5 - - - +
13L ALA* 4.6 7.4 - - + -
14M LEU* 3.4 28.0 - - + -
9N LYS 3.0 11.9 + - - +
10N LEU* 3.5 9.6 - - - +
12N GLU* 1.3 76.5 - - - +
14N LEU* 1.3 49.9 - - - +
16N LYS* 3.4 3.3 + - - +
17N ALA* 2.8 37.1 + - - +
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Residues in contact with LEU 14 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M LEU* 4.0 25.1 - - + +
13M ALA* 4.8 10.5 - - + -
14M LEU* 3.7 27.3 - - + +
17M ALA* 4.6 5.6 - - + -
10N LEU 3.5 6.5 + - - +
11N ALA* 3.3 12.1 - - - +
13N ALA* 1.3 77.4 - - - +
15N HIS* 1.3 53.1 + - - +
17N ALA* 3.4 1.7 - - + +
18N ILE* 2.7 46.1 + - + +
6O LEU* 4.1 23.1 - - + -
10O LEU* 4.3 24.5 - - + -
11P ALA* 4.1 15.3 - - + -
14P LEU* 5.6 3.6 - - + -
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Residues in contact with HIS 15 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N ALA 3.1 9.2 + - - +
12N GLU* 3.5 11.9 - - - +
14N LEU* 1.3 76.1 - - - +
16N LYS* 1.3 60.1 + - - +
18N ILE* 4.3 1.6 - - - +
19N GLU* 3.0 29.8 + - - +
8P ARG 5.7 0.2 - - - -
11P ALA* 4.0 21.5 - - + +
12P GLU* 4.9 4.7 - - + +
15P HIS* 5.2 6.1 - - + -
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Residues in contact with LYS 16 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L LYS 3.8 6.2 - - - +
5L GLU* 3.6 42.9 - - + +
6L LEU* 3.6 4.9 - - - +
9L LYS* 3.9 4.3 - - + -
12N GLU 3.0 13.3 + - - +
13N ALA 3.7 6.5 - - - +
15N HIS* 1.3 73.7 - - - +
17N ALA* 1.3 62.2 + - - +
19N GLU* 3.5 7.4 - - - +
20N LEU* 3.2 22.7 + - - +
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Residues in contact with ALA 17 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L LEU* 3.7 21.3 - - + +
14M LEU* 4.0 12.1 - - + -
17M ALA* 5.5 2.2 - - + -
18M ILE* 4.5 0.2 - - + -
21M LEU* 3.4 24.4 - - + +
13N ALA 2.8 19.5 + - - +
14N LEU* 3.4 12.6 - - + +
16N LYS* 1.3 74.3 - - - +
18N ILE* 1.3 60.7 + - + +
20N LEU* 3.2 6.6 + - - +
21N LEU* 3.0 22.8 + - - +
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Residues in contact with ILE 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M ALA* 5.7 0.9 - - + -
14N LEU* 2.7 28.4 + - + +
15N HIS 4.3 2.5 - - - +
17N ALA* 1.3 71.6 - - + +
19N GLU* 1.3 60.3 - - - +
21N LEU* 3.2 8.8 + - + +
22N GLU* 2.9 34.8 + - + +
6O LEU* 3.8 38.8 - - + -
10O LEU* 4.0 2.7 - - + -
4P LEU* 4.2 7.9 - - + +
7P LEU* 2.9 32.1 - - + +
8P ARG* 2.9 45.5 - - + +
11P ALA* 3.9 12.3 - - + -
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Residues in contact with GLU 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L LYS* 4.7 4.0 - - + -
5L GLU* 6.2 1.1 - - + -
15N HIS 3.0 19.5 + - - +
16N LYS* 3.5 10.1 - - - +
18N ILE* 1.3 76.8 - - - +
20N LEU* 1.3 54.7 + - - +
22N GLU* 3.8 5.1 - - - +
23N LYS* 3.0 29.0 + - - +
8P ARG* 5.4 2.9 - - - +
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Residues in contact with LEU 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L LYS* 3.2 35.8 - - + +
3L LEU* 3.7 20.0 - - + +
6L LEU* 3.0 40.2 - - + -
21M LEU* 3.3 33.9 - - + +
16N LYS 3.2 11.2 + - - +
17N ALA 3.3 4.7 - - - +
18N ILE 3.1 0.2 - - - -
19N GLU* 1.3 73.9 - - - +
21N LEU* 1.3 64.1 + - - +
23N LYS* 3.2 4.7 + - - +
24N TRP* 3.2 24.3 + - + +
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Residues in contact with LEU 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M ALA* 4.5 14.8 - - + +
20M LEU* 4.9 8.5 - - + -
21M LEU* 4.1 30.1 - - + +
17N ALA 3.0 10.5 + - - +
18N ILE* 3.3 19.1 - - + +
20N LEU* 1.3 76.6 - - - +
22N GLU* 1.3 59.8 + - - +
24N TRP* 3.4 20.6 + - - +
3O LEU* 4.2 16.4 - - + -
6O LEU* 3.8 29.4 - - + -
4P LEU* 3.4 32.7 - - + +
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Residues in contact with GLU 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18N ILE* 2.9 18.9 + - + +
19N GLU* 3.9 5.2 - - - +
21N LEU* 1.3 70.0 - - - +
23N LYS* 1.3 64.2 + - - +
24N TRP 3.1 11.5 - - - +
4P LEU* 3.2 36.5 - - + +
5P GLU* 6.0 0.7 - - - -
8P ARG* 5.0 4.7 - - + -
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Residues in contact with LYS 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L LYS* 4.3 11.0 - - + -
19N GLU 3.0 16.3 + - - +
20N LEU* 3.2 14.3 + - - +
22N GLU* 1.3 76.0 - - - +
24N TRP* 1.3 60.2 + - - +
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Residues in contact with TRP 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M TRP* 5.4 12.3 - - + -
20N LEU* 3.2 11.4 + - + +
21N LEU* 3.6 17.4 - - - +
22N GLU* 3.1 14.7 - - - +
23N LYS* 1.3 78.4 - - - +
4P LEU* 4.9 5.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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