Contacts of the helix formed by residues 4 - 15 (chain J) in PDB entry 2WWB
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 LEU 4 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1J MET* 3.6 32.5 - - + -
2J ALA* 3.1 17.8 - - - +
3J ASN* 1.4 79.1 - - + +
5J ARG* 1.4 57.7 + - - +
6J THR* 3.3 1.3 - - + -
7J GLN* 3.8 27.8 - - + +
8J LYS* 3.1 27.8 + - + +
24J LEU* 4.0 24.0 - - + -
29J THR* 4.3 19.3 - - - +
32J ILE* 4.6 1.6 - - + -
33J ALA* 3.8 26.9 - - + +
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Residues in contact with ARG 5 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1654F C 4.4 0.8 + - - -
1655F C 3.8 20.2 + - - -
1656F A 5.3 7.9 + - - -
1671F G 3.1 56.6 + - - +
1672F G 2.9 21.6 + - - -
3J ASN* 3.2 5.7 + - - +
4J LEU* 1.4 75.1 - - - +
6J THR* 1.4 61.0 + - - +
8J LYS* 3.5 5.9 + - - +
9J ARG* 3.1 33.9 + - + +
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Residues in contact with THR 6 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1656F A 3.4 21.4 + - - -
1657F C 2.9 37.8 + - - +
3J ASN* 3.6 21.5 + - - +
4J LEU* 5.4 0.9 - - + -
5J ARG* 1.4 84.6 - - - +
7J GLN* 1.4 67.5 + - + +
9J ARG* 3.4 7.0 + - - +
10J LEU* 2.9 39.1 + - - +
36J ASN* 5.3 1.3 - - - +
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Residues in contact with GLN 7 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J LEU* 3.7 38.4 + - + -
5J ARG 3.3 0.8 - - - -
6J THR* 1.4 82.3 - - + +
8J LYS* 1.4 58.7 + - - +
10J LEU* 3.6 17.0 - - - +
11J ALA* 3.0 34.6 + - - +
24J LEU* 4.8 8.5 - - + +
32J ILE* 3.8 18.0 + - + +
33J ALA* 4.6 4.3 - - - +
35J ALA* 3.4 24.9 - - + +
36J ASN* 3.1 29.1 + - - +
41J ILE* 3.4 18.2 - - - +
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Residues in contact with LYS 8 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J LEU* 3.1 22.4 + - + +
5J ARG* 3.8 5.8 - - - +
7J GLN* 1.4 74.7 - - - +
9J ARG* 1.4 57.6 + - - +
11J ALA* 4.8 1.8 - - - -
12J ALA* 3.1 30.0 + - - +
19J LYS* 2.9 34.9 + - + +
20J ARG* 3.9 6.5 + - - +
22J VAL* 2.9 38.1 + - + +
23J TRP* 5.2 0.2 - - - +
24J LEU* 4.3 21.0 - - + +
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Residues in contact with ARG 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1655F C 3.2 48.7 + - - -
1656F A 3.1 33.2 + - - -
5J ARG* 3.1 23.5 + - + +
6J THR* 3.5 7.0 - - - +
7J GLN 3.3 0.2 - - - -
8J LYS* 1.4 77.7 - - - +
10J LEU* 1.4 65.9 + - - +
12J ALA* 3.8 2.3 - - - +
13J SER* 3.1 29.1 + - - -
19J LYS* 4.5 24.9 - - + +
38J ARG* 4.3 9.9 - - - +
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Residues in contact with LEU 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1655F C 5.1 0.2 - - - +
1656F A 3.4 29.4 - - - +
1657F C 4.7 2.5 - - - +
6J THR* 2.9 37.5 + - - +
7J GLN* 3.6 22.7 - - - +
9J ARG* 1.4 75.5 - - - +
11J ALA* 1.4 60.9 + - - +
13J SER* 3.2 5.7 + - - -
14J VAL* 3.1 22.5 + - - +
36J ASN* 4.0 21.8 - - - +
37J SER 5.9 0.4 - - - -
38J ARG* 3.5 36.0 + - + +
41J ILE* 3.4 19.6 - - + +
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Residues in contact with ALA 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J GLN* 3.0 24.4 + - - +
8J LYS 4.4 1.6 - - - +
10J LEU* 1.4 73.1 - - - +
12J ALA* 1.4 63.3 + - - +
14J VAL* 3.4 8.7 - - + +
15J VAL* 3.4 25.8 + - - +
22J VAL* 4.2 16.3 - - + +
24J LEU* 4.8 7.6 - - + -
32J ILE* 6.3 0.2 - - + -
41J ILE* 4.2 9.8 - - - +
50J ILE* 4.2 26.7 - - + -
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Residues in contact with ALA 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J LYS 3.1 19.6 + - - +
9J ARG 3.8 2.9 - - - +
11J ALA* 1.4 78.7 - - - +
13J SER* 1.4 55.7 + - - +
15J VAL* 3.4 2.2 + - - -
16J GLY 2.9 23.6 + - - -
17J VAL* 2.9 39.4 + - + +
19J LYS* 3.4 28.7 - - + -
22J VAL* 4.1 4.4 - - + +
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Residues in contact with SER 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J ARG* 3.1 23.7 + - - -
10J LEU 3.2 6.7 + - - -
12J ALA* 1.4 76.4 - - - +
14J VAL* 1.4 59.6 + - - +
16J GLY* 3.4 11.2 + - - -
17J VAL 5.2 0.9 - - - +
38J ARG* 3.2 34.7 + - - -
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Residues in contact with VAL 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J LEU 3.1 5.6 + - - +
11J ALA* 3.4 14.1 - - - +
13J SER* 1.4 76.0 - - - +
15J VAL* 1.4 68.4 + - + +
16J GLY 3.4 0.7 - - - -
38J ARG* 4.3 18.3 - - + +
41J ILE* 3.6 31.9 - - + +
42J ARG* 4.2 34.3 - - + +
45J VAL* 4.7 9.4 - - + -
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Residues in contact with VAL 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J ALA 3.4 18.8 + - - +
12J ALA* 3.7 7.4 - - - +
13J SER 3.3 0.2 - - - -
14J VAL* 1.4 86.7 - - + +
16J GLY* 1.4 62.5 + - - +
17J VAL* 3.8 21.3 - - + +
22J VAL* 4.2 13.9 - - + -
45J VAL* 4.3 22.2 - - + -
50J ILE* 5.3 2.2 - - + -
51J VAL 5.8 1.1 - - - +
52J LYS* 4.3 37.3 + - + +
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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