Contacts of the helix formed by residues 2 - 19 (chain N) in PDB entry 2WQT
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 THR 2 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0N LEU 5.0 3.1 + - - -
1N MET* 1.3 82.2 + - + +
3N LYS* 1.3 59.4 + - - +
4N HIS 3.3 2.0 - - - -
5N THR* 3.1 16.0 + - - +
6N LEU* 2.9 47.5 + - + +
29N LEU 6.1 0.9 - - - +
30N ILE* 6.6 0.2 - - - -
34N ASN* 5.6 8.1 + - - +
37N ALA* 5.7 2.1 - - - +
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Residues in contact with LYS 3 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F GLN* 2.8 32.5 + - - +
53F GLY* 4.7 4.8 - - - -
0N LEU* 3.8 37.8 - - + +
1N MET 3.2 2.6 - - - -
2N THR* 1.3 79.2 + - - +
4N HIS* 1.3 62.8 + - - +
6N LEU* 3.2 14.2 + - + +
7N GLU* 3.0 44.0 + - + +
44N ILE* 4.8 9.6 - - + -
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Residues in contact with HIS 4 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F ASP* 3.5 29.2 + - - -
52F GLN* 4.6 7.8 + - - +
54F ARG* 3.4 50.0 + - + +
85F ASP* 3.9 14.4 - - - +
98F ARG* 5.1 6.7 - - - -
1265F K 4.3 6.5 - - - -
1312F NA 4.1 10.0 - - - -
0N LEU 4.8 1.4 + - - -
1N MET 4.4 2.1 + - - +
2N THR 3.3 0.4 - - - -
3N LYS* 1.3 78.5 - - - +
5N THR* 1.3 65.2 - - - +
7N GLU* 3.3 9.1 + - - +
8N GLN* 3.1 53.2 + - + +
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Residues in contact with THR 5 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F ARG* 5.1 17.9 + - - -
1N MET 4.4 2.6 + - - -
2N THR* 3.1 22.9 + - - +
4N HIS* 1.3 79.1 - - - +
6N LEU* 1.3 62.9 + - + +
8N GLN* 3.2 19.8 + - + +
9N LEU* 3.0 47.3 + - + +
29N LEU* 4.9 20.6 - - + +
30N ILE* 5.7 0.9 - - + -
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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
----------------------------------------------------------
2N THR* 2.9 34.3 + - + +
3N LYS* 3.2 17.7 + - + +
5N THR* 1.3 78.4 - - - +
7N GLU* 1.3 60.0 + - - +
9N LEU* 3.3 2.1 + - - +
10N ALA* 2.9 31.2 + - - +
30N ILE* 4.1 25.1 - - + -
37N ALA* 4.1 20.2 - - + +
40N ALA* 4.0 21.5 - - + -
41N ILE* 3.9 23.3 - - + +
44N ILE* 5.0 12.1 - - + -
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Residues in contact with GLU 7 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F GLU* 5.0 0.6 - - - +
52F GLN* 3.3 46.5 - - + +
1265F K 4.5 3.6 - - - -
3N LYS* 3.0 45.3 + - + +
4N HIS* 3.3 9.2 + - - +
6N LEU* 1.3 74.9 - - - +
8N GLN* 1.3 62.4 + - - +
10N ALA* 3.5 5.4 + - - +
11N ALA* 3.0 23.6 + - - +
14N ARG* 5.2 2.8 + - - -
44N ILE* 3.6 31.5 - - + +
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Residues in contact with GLN 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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14F ARG 5.1 0.2 + - - -
17F ALA* 3.7 35.7 + - - +
18F GLU* 3.8 28.4 - - + +
1265F K 4.5 4.7 - - - -
4N HIS* 3.1 44.2 + - + +
5N THR* 3.2 23.3 + - + +
7N GLU* 1.3 76.1 - - - +
9N LEU* 1.3 59.3 + - + +
11N ALA* 3.3 4.7 + - - +
12N ASP* 3.0 34.3 + - - +
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Residues in contact with LEU 9 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F GLU 5.6 0.2 - - - +
5N THR* 3.0 28.2 + - + +
6N LEU 3.9 3.8 - - - +
8N GLN* 1.3 73.5 - - + +
10N ALA* 1.3 65.7 + - - +
12N ASP* 3.1 18.8 + - - +
13N LEU* 3.0 25.9 + - - +
23N ILE* 5.3 0.2 - - - +
26N LEU* 3.9 32.8 - - + +
29N LEU* 4.2 30.5 - - + -
30N ILE* 3.4 32.3 - - + -
41N ILE* 3.9 17.9 - - + -
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Residues in contact with ALA 10 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6N LEU 2.9 17.7 + - - +
7N GLU 3.6 4.5 - - - +
8N GLN 3.3 0.2 - - - -
9N LEU* 1.3 76.3 - - - +
11N ALA* 1.3 57.0 + - - +
13N LEU* 3.3 1.8 + - - -
14N ARG* 3.0 23.7 + - - +
41N ILE* 3.8 18.5 - - + +
44N ILE* 3.8 27.1 - - + -
45N ASN* 3.2 31.5 + - - +
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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
----------------------------------------------------------
18F GLU* 3.5 27.1 - - - +
1262F PO4 5.1 4.5 + - - +
7N GLU 3.0 15.3 + - - +
8N GLN 3.5 7.6 - - - +
10N ALA* 1.3 73.8 - - - +
12N ASP* 1.3 60.5 + - - +
14N ARG* 3.1 28.5 + - - +
15N ARG* 2.9 34.5 + - - +
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Residues in contact with ASP 12 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F GLU* 2.8 31.9 - - - +
19F GLN* 4.2 3.2 - - - +
8N GLN 3.0 17.4 + - - +
9N LEU* 3.1 25.1 + - + +
11N ALA* 1.3 74.0 - - - +
13N LEU* 1.3 56.9 + - - +
15N ARG* 2.6 36.5 + - - +
16N ALA* 2.9 29.6 + - - +
23N ILE* 4.0 25.1 - - + +
26N LEU* 5.7 0.2 - - - +
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Residues in contact with LEU 13 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N LEU 3.0 9.7 + - - +
10N ALA 3.4 8.1 - - - +
11N ALA 3.2 0.2 - - - -
12N ASP* 1.3 74.7 - - - +
14N ARG* 1.3 64.3 + - - +
16N ALA* 3.4 4.5 + - - +
17N ALA* 3.2 21.5 + - - +
23N ILE* 3.7 22.9 - - + -
26N LEU* 3.7 28.3 - - + -
41N ILE* 3.8 17.7 - - + -
45N ASN* 3.8 8.5 - - - +
143N ARG* 3.9 23.3 - - + +
144N ILE* 4.7 4.7 - - + -
156N ALA 3.6 24.9 - - - +
157N ASP* 4.0 18.8 - - - +
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Residues in contact with ARG 14 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E GLN* 5.1 0.2 + - - -
7N GLU* 5.2 2.4 + - - -
10N ALA* 3.0 17.1 + - - +
11N ALA* 3.5 30.4 - - - +
13N LEU* 1.3 72.6 - - - +
15N ARG* 1.3 60.4 - - - +
17N ALA* 3.3 6.9 + - - +
18N GLU* 3.0 41.2 + - - +
44N ILE* 4.5 7.5 - - - +
45N ASN* 2.8 49.5 + - - +
48N HIS* 3.7 52.2 + - - +
49N ASP* 4.8 4.3 - - - -
1263N K 4.5 8.3 - - - -
1315N NA 4.2 8.1 - - - -
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Residues in contact with ARG 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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15E ARG* 3.7 15.3 - - - +
15F ARG* 3.6 8.9 - - - +
18F GLU* 3.2 21.4 + - - +
19F GLN* 3.0 32.2 - - - +
1262F PO4 3.0 40.7 + - - +
1263F PO4 3.3 23.6 - - - -
11N ALA 2.9 14.1 + - - +
12N ASP* 2.6 36.9 + - - +
14N ARG* 1.3 72.7 - - - +
16N ALA* 1.3 66.9 + - - +
18N GLU* 3.3 10.3 + - - +
19N GLN* 3.0 43.7 + - - +
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Residues in contact with ALA 16 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N ASP 2.9 18.8 + - - +
13N LEU* 3.5 9.2 - - - +
15N ARG* 1.3 76.1 - - - +
17N ALA* 1.3 56.6 + - - +
19N GLN* 5.0 2.0 - - - -
20N GLY* 3.0 25.1 + - - -
21N GLU 3.2 30.3 + - - +
23N ILE* 4.1 11.6 - - + +
100N LEU* 4.2 2.0 - - - +
143N ARG* 3.8 27.8 - - + +
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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
----------------------------------------------------------
8E GLN* 4.0 18.0 + - - +
13N LEU 3.2 9.7 + - - +
14N ARG* 3.6 9.4 - - - +
15N ARG 3.2 0.2 - - - -
16N ALA* 1.3 77.5 - - - +
18N GLU* 1.3 65.9 + - - +
19N GLN 3.2 0.7 + - - -
20N GLY* 3.4 10.2 + - - -
100N LEU* 5.4 2.5 - - - -
143N ARG* 3.8 20.8 - - + +
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Residues in contact with GLU 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E GLN* 3.8 35.7 - - + +
9E LEU* 5.8 0.2 - - - +
11E ALA* 3.8 22.4 - - - +
12E ASP* 3.1 31.2 - - - +
15E ARG* 3.2 27.7 + - - +
1262F PO4 4.1 4.3 + - - -
14N ARG* 3.0 27.5 + - - +
15N ARG* 3.3 7.7 + - - +
17N ALA* 1.3 75.9 - - - +
19N GLN* 1.3 58.6 + - - +
1263N K 3.4 18.5 - - - -
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Residues in contact with GLN 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ASP* 4.4 2.5 - - - +
15E ARG* 3.3 31.1 - - - +
19E GLN* 5.4 0.2 + - - -
19F GLN* 5.1 0.7 + - - -
1263F PO4 2.6 40.9 + - - -
15N ARG* 3.0 29.2 + - - +
16N ALA* 4.1 1.7 - - - +
18N GLU* 1.3 76.2 - - - +
20N GLY* 1.3 63.0 + - - +
21N GLU* 3.9 34.1 + - + +
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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) + - + + + + + -
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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