Contacts of the helix formed by residues 2 - 19 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0E LEU 5.5 1.6 + - - -
1E MET* 1.3 83.4 + - + +
3E LYS* 1.3 65.1 + - - +
4E HIS 3.3 1.8 - - - -
5E THR* 3.1 17.2 + - - +
6E LEU* 2.9 41.8 + - - +
29E LEU 6.1 0.9 - - - +
30E ILE* 6.6 0.2 - - - -
34E ASN* 5.6 8.9 + - - +
37E ALA* 5.7 2.0 - - - +
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Residues in contact with LYS 3 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0E LEU* 3.8 40.3 + - + +
1E MET 3.2 2.4 - - - -
2E THR* 1.3 77.7 + - - +
4E HIS* 1.3 63.7 + - - +
6E LEU* 3.2 14.8 + - + +
7E GLU* 3.0 42.2 + - + +
44E ILE* 4.8 10.3 - - + -
52N GLN* 3.0 30.6 + - - +
53N GLY* 5.0 2.2 - - - -
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Residues in contact with HIS 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0E LEU 4.8 1.6 + - - +
1E MET 4.5 1.9 + - - +
2E THR 3.3 0.6 - - - -
3E LYS* 1.3 78.2 - - - +
5E THR* 1.3 65.7 + - - +
7E GLU* 3.3 8.2 + - - +
8E GLN* 3.1 53.1 + - + +
49N ASP* 3.6 29.9 + - - -
52N GLN* 4.3 9.4 + - - +
54N ARG* 3.6 48.6 + - + +
85N ASP* 4.1 14.4 - - - +
98N ARG* 5.4 4.9 - - - -
1263N K 4.3 7.2 - - - -
1315N NA 4.4 4.9 - - - -
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Residues in contact with THR 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MET 4.4 3.1 + - - -
2E THR* 3.1 23.5 + - - +
4E HIS* 1.3 79.1 - - - +
6E LEU* 1.3 61.2 + - + +
8E GLN* 3.1 20.0 + - - +
9E LEU* 2.9 46.6 + - + +
29E LEU* 4.9 19.7 - - + +
30E ILE* 5.7 0.7 - - + -
98N ARG* 5.5 10.4 + - - -
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Residues in contact with LEU 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E THR* 2.9 35.0 + - - +
3E LYS* 3.2 17.0 + - + +
5E THR* 1.3 79.5 - - - +
7E GLU* 1.3 55.2 + - - +
9E LEU* 3.3 2.6 + - - +
10E ALA* 2.9 32.2 + - - +
30E ILE* 4.1 25.4 - - + -
37E ALA* 4.2 19.1 - - + +
40E ALA* 4.0 22.0 - - + -
41E ILE* 3.9 23.0 - - + +
44E ILE* 5.1 11.9 - - + -
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Residues in contact with GLU 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E LYS* 3.0 46.4 + - + +
4E HIS* 3.5 9.2 - - - +
6E LEU* 1.3 74.9 - - - +
8E GLN* 1.3 62.1 + - + +
10E ALA* 3.5 5.3 + - - +
11E ALA* 3.0 25.0 + - - +
14E ARG* 5.3 2.1 + - - -
44E ILE* 3.6 31.4 - - + +
18N GLU* 5.6 0.4 - - - -
52N GLN* 3.4 46.7 - - + +
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Residues in contact with GLN 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E HIS* 3.1 44.5 + - + +
5E THR* 3.1 23.9 + - + +
7E GLU* 1.3 75.9 - - - +
9E LEU* 1.3 60.1 + - + +
11E ALA* 3.3 5.1 + - - +
12E ASP* 3.0 34.2 + - - +
14N ARG 5.1 0.2 + - - -
17N ALA* 4.0 16.6 + - - +
18N GLU* 3.8 46.7 - - + +
1263N K 4.5 4.7 - - - -
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Residues in contact with LEU 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E THR* 2.9 28.8 + - + +
6E LEU 3.9 3.4 - - - +
8E GLN* 1.3 72.7 - - + +
10E ALA* 1.3 66.8 + - - +
12E ASP* 3.1 19.2 + - - +
13E LEU* 3.0 25.9 + - - +
26E LEU* 4.0 31.9 - - + +
29E LEU* 4.2 30.3 - - + -
30E ILE* 3.4 32.8 - - + -
41E ILE* 4.0 18.4 - - + -
18N GLU 5.8 0.2 - - - +
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Residues in contact with ALA 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E LEU 2.9 18.3 + - - +
7E GLU 3.6 4.9 - - - +
9E LEU* 1.3 76.3 - - - +
11E ALA* 1.3 56.8 + - - +
13E LEU 3.3 1.6 + - - -
14E ARG* 3.0 24.7 + - - +
41E ILE* 3.8 13.6 - - + +
44E ILE* 3.8 26.5 - - + -
45E ASN* 3.2 36.6 + - - +
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Residues in contact with ALA 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E GLU 3.0 17.3 + - - +
8E GLN 3.5 4.9 - - - +
9E LEU 3.2 0.2 - - - -
10E ALA* 1.3 73.1 - - - +
12E ASP* 1.3 60.9 + - - +
14E ARG* 3.2 27.4 + - - +
15E ARG* 2.9 33.9 + - - +
1262F PO4 4.8 7.6 + - - +
18N GLU* 3.8 25.4 - - - +
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Residues in contact with ASP 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E GLN* 3.0 21.0 + - - +
9E LEU* 3.1 25.5 + - + +
11E ALA* 1.3 75.8 - - - +
13E LEU* 1.3 56.3 + - - +
15E ARG* 2.6 35.3 + - - +
16E ALA* 2.9 29.1 + - - +
23E ILE* 3.9 28.0 - - + +
18N GLU* 3.1 28.9 - - - +
19N GLN* 4.4 2.7 - - - +
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Residues in contact with LEU 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E LEU 3.0 9.7 + - - +
10E ALA 3.4 8.1 - - - +
12E ASP* 1.3 75.2 - - - +
14E ARG* 1.3 63.6 + - - +
16E ALA* 3.5 3.9 + - - +
17E ALA* 3.2 21.5 + - - +
23E ILE* 3.7 23.1 - - + -
26E LEU* 3.7 28.5 - - + -
41E ILE* 3.8 17.5 - - + -
45E ASN* 3.8 9.2 - - - +
143E ARG* 3.9 22.8 - - + +
144E ILE* 4.7 4.9 - - + -
156E ALA 3.7 25.6 - - - +
157E ASP* 4.0 18.6 - - - +
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Residues in contact with ARG 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E GLU* 5.3 2.6 + - - -
10E ALA* 3.0 17.7 + - - +
11E ALA* 3.2 29.2 + - - +
13E LEU* 1.3 74.7 - - - +
15E ARG* 1.3 60.0 + - - +
17E ALA* 3.2 7.2 + - - +
18E GLU* 3.0 40.1 + - - +
44E ILE* 4.5 7.1 - - - +
45E ASN* 2.8 48.5 + - - +
48E HIS* 3.7 53.1 + - - +
49E ASP* 4.7 4.3 - - - -
1263E K 4.5 8.5 - - - -
1311E NA 4.6 7.9 - - - -
8F GLN* 5.1 0.2 + - - -
1262F PO4 5.7 1.6 + - - -
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Residues in contact with ARG 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ALA 2.9 13.8 + - - +
12E ASP* 2.6 36.5 + - - +
14E ARG* 1.3 72.4 - - - +
16E ALA* 1.3 66.5 + - - +
18E GLU* 3.3 10.3 + - - +
19E GLN* 3.0 46.1 + - - +
15F ARG* 3.7 14.4 - - - +
1262F PO4 2.8 49.7 + - - +
1263F PO4 3.4 21.5 - - - -
15N ARG* 3.7 11.3 - - - +
18N GLU* 3.2 19.0 + - - +
19N GLN* 3.3 27.8 - - - +
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Residues in contact with ALA 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E ASP 2.9 18.0 + - - +
13E LEU* 3.5 8.7 - - - +
15E ARG* 1.3 76.0 - - - +
17E ALA* 1.3 57.1 + - - +
19E GLN* 5.0 1.8 - - - -
20E GLY* 3.0 24.8 + - - -
21E GLU 3.2 30.1 + - - +
23E ILE* 4.1 15.0 - - + -
100E LEU* 4.1 2.1 - - - +
143E ARG* 3.8 24.9 - - + +
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Residues in contact with ALA 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E LEU 3.2 10.8 + - - +
14E ARG* 3.6 8.7 - - - +
15E ARG 3.2 0.4 - - - -
16E ALA* 1.3 76.3 - - - +
18E GLU* 1.3 65.6 + - - +
19E GLN 3.2 0.7 + - - -
20E GLY* 3.4 10.3 + - - -
100E LEU* 5.3 2.5 - - - -
143E ARG* 3.8 20.6 - - + +
8F GLN* 4.0 18.5 + - - +
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Residues in contact with GLU 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E ARG* 3.0 29.2 + - - +
15E ARG* 3.7 7.6 - - - +
17E ALA* 1.3 76.7 - - - +
19E GLN* 1.3 59.6 + - - +
1263E K 3.7 16.5 - - - -
8F GLN* 3.8 35.6 - - + +
9F LEU* 5.7 0.5 - - - +
11F ALA* 3.7 23.0 - - - +
12F ASP* 3.1 30.2 - - - +
15F ARG* 3.1 29.7 + - - +
1262F PO4 4.1 3.2 + - - -
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Residues in contact with GLN 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ARG* 3.0 31.3 + - - +
16E ALA* 4.2 0.9 - - - +
18E GLU* 1.3 76.8 - - - +
20E GLY* 1.3 63.7 - - - +
21E GLU* 3.4 34.3 + - + +
12F ASP* 4.5 2.7 - - - +
15F ARG* 3.4 33.6 - - - +
19F GLN* 5.3 0.6 + - - -
1263F PO4 2.8 33.9 + - - -
19N GLN* 5.4 0.2 + - - -
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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