Contacts of the helix formed by residues 2 - 19 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0P LEU 4.4 3.7 + - - +
1P MET* 1.3 83.7 + - + +
3P LYS* 1.3 58.8 + - - +
4P HIS 3.3 1.8 - - - -
5P THR* 3.1 15.2 + - + +
6P LEU* 2.8 47.7 + - + +
29P LEU 6.0 1.6 - - - +
30P ILE* 6.6 0.2 - - - -
34P ASN* 5.6 7.9 + - - +
37P ALA* 5.7 2.0 - - - +
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Residues in contact with LYS 3 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0P LEU* 3.8 38.8 - - + +
1P MET 3.2 2.2 - - - -
2P THR* 1.3 79.2 + - - +
4P HIS* 1.3 62.5 + - - +
6P LEU* 3.3 14.6 + - + +
7P GLU* 3.0 46.0 + - + +
44P ILE* 4.8 10.1 - - + -
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Residues in contact with HIS 4 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0P LEU 4.9 1.2 + - - +
1P MET 4.4 6.3 + - - +
2P THR 3.3 0.4 - - - -
3P LYS* 1.3 78.4 - - - +
5P THR* 1.3 65.9 + - - +
7P GLU* 3.3 11.6 + - + +
8P GLN* 3.1 52.3 + - + +
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Residues in contact with THR 5 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1P MET 4.4 3.1 + - - -
2P THR* 3.1 22.6 + - + +
4P HIS* 1.3 80.5 - - - +
6P LEU* 1.3 62.1 + - + +
8P GLN* 3.2 19.5 + - + +
9P LEU* 2.9 47.3 + - + +
29P LEU* 4.9 20.2 - - + +
30P ILE* 5.7 0.4 - - + -
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Residues in contact with LEU 6 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2P THR* 2.8 33.7 + - - +
3P LYS* 3.4 17.7 - - + +
4P HIS 3.2 0.2 - - - -
5P THR* 1.3 78.1 - - - +
7P GLU* 1.3 56.1 + - - +
9P LEU* 3.3 3.6 + - - +
10P ALA* 2.9 30.9 + - - +
30P ILE* 4.1 25.8 - - + -
37P ALA* 4.2 19.1 - - + +
40P ALA* 4.0 21.5 - - + -
41P ILE* 4.0 24.0 - - + +
44P ILE* 5.1 11.7 - - + -
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Residues in contact with GLU 7 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3P LYS* 3.0 46.3 + - + +
4P HIS* 3.5 13.9 - - + +
6P LEU* 1.3 75.4 - - - +
8P GLN* 1.3 61.4 + - + +
10P ALA* 3.4 5.5 + - - +
11P ALA* 3.1 24.1 + - - +
14P ARG* 5.2 2.6 + - - -
44P ILE* 3.6 31.6 - - + +
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Residues in contact with GLN 8 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4P HIS* 3.1 46.0 + - + +
5P THR* 3.2 24.0 + - + +
7P GLU* 1.3 74.5 - - - +
9P LEU* 1.3 62.7 + - + +
11P ALA* 3.3 7.5 + - - +
12P ASP* 3.0 35.1 + - - +
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Residues in contact with LEU 9 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P THR* 2.9 28.4 + - + +
6P LEU 3.8 3.4 - - - +
8P GLN* 1.3 74.1 - - + +
10P ALA* 1.3 66.1 + - - +
12P ASP* 3.1 19.1 + - - +
13P LEU* 3.0 25.5 + - - +
23P ILE* 5.3 0.2 - - - +
26P LEU* 3.9 31.7 - - + +
29P LEU* 4.2 29.8 - - + -
30P ILE* 3.4 32.5 - - + -
41P ILE* 4.0 18.8 - - + -
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Residues in contact with ALA 10 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P LEU 2.9 17.5 + - - +
7P GLU 3.6 5.4 - - - +
9P LEU* 1.3 75.9 - - - +
11P ALA* 1.3 57.1 + - - +
13P LEU 3.2 1.7 + - - -
14P ARG* 3.0 24.8 + - - +
41P ILE* 3.8 17.6 - - + +
44P ILE* 3.9 27.4 - - + -
45P ASN* 3.3 31.9 + - - +
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Residues in contact with ALA 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P GLU 3.1 17.3 + - - +
8P GLN* 3.5 7.2 - - - +
10P ALA* 1.3 74.2 - - - +
12P ASP* 1.3 61.7 + - - +
14P ARG* 3.2 28.2 + - - +
15P ARG* 3.0 36.4 + - - +
1262P PO4 4.8 11.6 + - - +
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Residues in contact with ASP 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P GLN* 3.0 22.0 + - - +
9P LEU* 3.1 25.8 + - + +
11P ALA* 1.3 77.6 - - - +
13P LEU* 1.3 55.9 + - - +
15P ARG* 2.7 35.9 + - - +
16P ALA* 2.9 28.6 + - - +
23P ILE* 3.9 26.7 - - + +
26P LEU* 5.6 0.2 - - - +
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Residues in contact with LEU 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P LEU 3.0 7.8 + - - +
10P ALA 3.2 8.7 + - - +
12P ASP* 1.3 75.5 - - - +
14P ARG* 1.3 63.3 + - - +
16P ALA* 3.4 4.7 + - - +
17P ALA* 3.2 21.1 + - - +
23P ILE* 3.7 23.3 - - + -
26P LEU* 3.7 27.8 - - + -
41P ILE* 3.8 17.7 - - + -
45P ASN* 3.8 8.7 - - - +
143P ARG* 3.9 23.0 - - + +
144P ILE* 4.7 4.5 - - + -
156P ALA 3.6 25.6 - - - +
157P ASP* 4.0 18.4 - - + +
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Residues in contact with ARG 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P GLU* 5.2 2.6 + - - -
10P ALA* 3.0 17.7 + - - +
11P ALA* 3.2 29.6 + - - +
13P LEU* 1.3 75.5 - - - +
15P ARG* 1.3 58.7 + - - +
17P ALA* 3.3 8.5 + - - +
18P GLU* 3.0 40.7 + - - +
44P ILE* 4.5 7.1 - - - +
45P ASN* 2.8 47.4 + - - +
48P HIS* 3.7 54.8 + - - +
49P ASP* 4.7 3.4 - - - -
1265P K 4.3 8.7 - - - -
1317P NA 4.3 9.0 - - - -
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Residues in contact with ARG 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P ALA* 3.0 17.8 + - - +
12P ASP* 2.7 37.5 + - - +
14P ARG* 1.3 72.4 - - - +
16P ALA* 1.3 66.9 + - - +
18P GLU* 3.3 15.1 + - - +
19P GLN* 3.0 45.7 + - + +
1262P PO4 2.8 53.0 + - - +
1264P PO4 3.5 23.6 + - - -
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Residues in contact with ALA 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P ASP 2.9 17.8 + - - +
13P LEU* 3.5 9.2 - - - +
14P ARG 3.3 0.2 - - - -
15P ARG* 1.3 76.8 - - - +
17P ALA* 1.3 57.2 + - - +
19P GLN* 5.0 1.6 - - - -
20P GLY* 3.0 25.5 + - - -
21P GLU 3.2 30.3 + - - +
23P ILE* 4.1 10.3 - - + +
100P LEU* 4.2 1.7 - - - +
143P ARG* 3.8 28.0 - - + +
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Residues in contact with ALA 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P LEU 3.2 10.6 + - - +
14P ARG* 3.6 9.0 - - - +
15P ARG 3.2 0.2 - - - -
16P ALA* 1.3 78.1 - - - +
18P GLU* 1.3 63.5 + - + +
19P GLN 3.3 0.9 + - - -
20P GLY* 3.4 9.8 + - - -
100P LEU* 5.4 2.2 - - - -
143P ARG* 3.8 20.4 - - + +
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Residues in contact with GLU 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P ARG* 3.0 29.4 + - - +
15P ARG* 3.7 15.5 - - - +
17P ALA* 1.3 77.2 - - + +
19P GLN* 1.3 62.7 + - + +
20P GLY 3.9 0.2 + - - -
1262P PO4 4.2 15.1 + - - -
1265P K 3.7 17.7 - - - -
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Residues in contact with GLN 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P ARG* 3.0 35.6 + - + +
16P ALA* 4.1 0.9 - - - +
18P GLU* 1.3 81.2 - - + +
20P GLY* 1.3 62.9 + - - +
21P GLU* 3.4 33.2 + - + +
1264P PO4 3.2 42.9 + - - -
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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
------------------------------------------------------------
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