Contacts of the helix formed by residues 2 - 19 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0O LEU 4.7 4.9 + - - -
1O MET* 1.3 82.5 - - + +
3O LYS* 1.3 65.1 + - - +
4O HIS 3.3 1.6 - - - -
5O THR* 3.1 15.8 + - + +
6O LEU* 2.9 41.8 + - - +
29O LEU 6.1 1.3 - - - +
34O ASN* 5.6 7.9 + - - +
37O ALA* 5.7 2.2 - - - +
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Residues in contact with LYS 3 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0O LEU* 3.9 30.9 - - + +
1O MET 3.2 2.2 - - - -
2O THR* 1.3 79.9 + - - +
4O HIS* 1.3 62.6 + - - +
6O LEU* 3.3 14.4 + - + +
7O GLU* 3.0 47.4 + - + +
44O ILE* 4.8 9.4 - - + -
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Residues in contact with HIS 4 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0O LEU 5.0 1.2 + - - -
1O MET 4.4 6.1 + - - +
2O THR 3.3 0.4 - - - -
3O LYS* 1.3 79.5 - - - +
5O THR* 1.3 66.6 + - - +
7O GLU* 3.3 11.7 + - - +
8O GLN* 3.1 52.0 + - + +
1301O NA 4.3 17.2 - - - -
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Residues in contact with THR 5 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1O MET 4.4 3.3 + - - -
2O THR* 3.1 23.3 + - + +
4O HIS* 1.3 78.9 - - - +
6O LEU* 1.3 62.4 + - + +
8O GLN* 3.2 19.6 + - + +
9O LEU* 3.0 46.8 + - + +
29O LEU* 4.9 20.4 - - + +
30O ILE* 5.7 0.9 - - + -
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Residues in contact with LEU 6 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2O THR* 2.9 33.9 + - - +
3O LYS* 3.4 17.3 - - + +
4O HIS 3.2 0.2 - - - -
5O THR* 1.3 77.6 - - - +
7O GLU* 1.3 59.1 + - - +
9O LEU* 3.3 3.0 + - - +
10O ALA* 2.9 31.5 + - - +
30O ILE* 4.2 18.8 - - + -
37O ALA* 4.1 26.0 - - + +
40O ALA* 4.0 22.2 - - + -
41O ILE* 3.9 22.6 - - + +
44O ILE* 5.1 11.4 - - + -
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Residues in contact with GLU 7 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3O LYS* 3.0 46.0 + - + +
4O HIS* 3.3 13.7 + - - +
6O LEU* 1.3 73.9 - - - +
8O GLN* 1.3 63.7 + - + +
10O ALA* 3.5 5.8 + - - +
11O ALA* 3.0 23.9 + - - +
14O ARG* 5.2 2.3 + - - -
44O ILE* 3.6 30.9 - - + +
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Residues in contact with GLN 8 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4O HIS* 3.1 45.2 + - + +
5O THR* 3.2 24.7 + - + +
7O GLU* 1.3 77.4 - - + +
9O LEU* 1.3 58.6 + - + +
11O ALA* 3.3 7.9 + - - +
12O ASP* 3.0 36.1 + - - +
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Residues in contact with LEU 9 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5O THR* 3.0 28.4 + - + +
6O LEU 3.8 3.1 - - - +
8O GLN* 1.3 73.7 - - + +
10O ALA* 1.3 65.6 + - - +
12O ASP* 3.1 19.2 + - - +
13O LEU* 3.0 25.7 + - - +
26O LEU* 3.9 31.5 - - + +
29O LEU* 4.2 31.2 - - + -
30O ILE* 3.4 33.0 - - + -
41O ILE* 3.9 19.3 - - + -
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Residues in contact with ALA 10 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O LEU 2.9 17.4 + - - +
7O GLU 3.6 5.4 - - - +
9O LEU* 1.3 75.9 - - - +
11O ALA* 1.3 57.6 + - - +
13O LEU* 3.3 1.6 + - - -
14O ARG* 3.0 23.5 + - - +
41O ILE* 3.8 17.4 - - + +
44O ILE* 3.8 26.5 - - + -
45O ASN* 3.2 33.5 + - - +
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Residues in contact with ALA 11 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7O GLU 3.0 17.5 + - - +
8O GLN* 3.5 7.0 - - - +
10O ALA* 1.3 74.0 - - - +
12O ASP* 1.3 61.1 + - - +
14O ARG* 3.2 27.7 + - - +
15O ARG* 2.9 41.2 + - - +
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Residues in contact with ASP 12 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8O GLN* 3.0 20.2 + - - +
9O LEU* 3.1 26.2 + - + +
11O ALA* 1.3 77.4 - - - +
13O LEU* 1.3 56.9 + - - +
15O ARG* 2.7 36.2 + - - +
16O ALA* 2.9 28.8 + - - +
23O ILE* 4.0 27.0 - - + +
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Residues in contact with LEU 13 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O LEU 3.0 9.6 + - - +
10O ALA 3.4 8.5 - - - +
12O ASP* 1.3 74.7 - - - +
14O ARG* 1.3 63.0 + - - +
16O ALA* 3.4 4.2 + - - +
17O ALA* 3.2 21.8 + - - +
23O ILE* 3.7 23.3 - - + -
26O LEU* 3.7 28.0 - - + -
41O ILE* 3.8 17.3 - - + -
45O ASN* 3.8 8.5 - - - +
143O ARG* 3.9 22.5 - - + +
144O ILE* 4.7 4.9 - - + -
156O ALA 3.6 25.1 - - - +
157O ASP* 4.0 18.8 - - - +
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Residues in contact with ARG 14 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7O GLU* 5.2 2.4 + - - -
10O ALA* 3.0 18.3 + - - +
11O ALA* 3.2 29.5 + - - +
13O LEU* 1.3 72.4 - - - +
15O ARG* 1.3 60.9 + - - +
17O ALA* 3.3 6.9 + - - +
18O GLU* 3.0 42.6 + - - +
44O ILE* 4.5 6.7 - - - +
45O ASN* 2.8 47.7 + - - +
48O HIS* 3.7 53.8 + - - +
49O ASP* 4.7 5.4 - - - -
1316O NA 4.4 8.7 - - - -
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Residues in contact with ARG 15 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11O ALA* 2.9 23.0 + - - +
12O ASP* 2.7 38.7 + - - +
14O ARG* 1.3 74.5 - - - +
16O ALA* 1.3 64.6 + - - +
18O GLU* 3.3 15.2 + - - +
19O GLN* 2.9 57.3 + - + +
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Residues in contact with ALA 16 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12O ASP 2.9 18.0 + - - +
13O LEU* 3.5 9.4 - - - +
14O ARG 3.3 0.4 - - - -
15O ARG* 1.3 76.1 - - - +
17O ALA* 1.3 57.0 + - - +
19O GLN* 5.0 1.8 - - - +
20O GLY* 3.0 24.9 + - - -
21O GLU 3.2 31.2 + - - +
23O ILE* 4.1 10.7 - - + +
100O LEU* 4.2 1.6 - - - +
143O ARG* 3.8 27.6 - - + +
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Residues in contact with ALA 17 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13O LEU 3.2 10.5 + - - +
14O ARG* 3.6 9.0 - - - +
15O ARG 3.2 0.4 - - - -
16O ALA* 1.3 76.9 - - - +
18O GLU* 1.3 65.3 + - - +
19O GLN 3.3 0.5 + - - -
20O GLY* 3.4 9.8 + - - -
100O LEU* 5.4 2.7 - - - -
143O ARG* 3.8 20.6 - - + +
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Residues in contact with GLU 18 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14O ARG* 3.0 33.0 + - - +
15O ARG* 3.3 17.1 + - - +
17O ALA* 1.3 76.5 - - + +
19O GLN* 1.3 62.7 + - + +
48O HIS* 6.0 0.2 + - - -
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Residues in contact with GLN 19 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15O ARG* 2.9 45.7 + - + +
16O ALA* 5.2 1.0 - - - +
18O GLU* 1.3 80.9 - - + +
20O GLY* 1.3 63.1 + - - +
21O GLU* 3.4 39.1 + - + +
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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
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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