Contacts of the strand formed by residues 5 - 13 (chain A) in PDB entry 2WP9
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 VAL 5 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.8 27.1 - - + -
3A LEU 3.5 14.6 - - - +
4A PRO* 1.3 73.8 - - - +
6A ARG* 1.3 65.5 + - - +
7A GLU* 4.0 5.1 + - + +
192A TYR* 3.5 21.5 - - + +
194A LYS* 3.9 33.2 - - + -
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Residues in contact with ARG 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PRO* 5.3 4.0 - - + +
5A VAL* 1.3 76.4 - - - +
7A GLU* 1.3 59.1 + - - +
8A PHE* 3.5 23.2 - - + -
161A PHE* 3.7 25.8 - - - -
164A TRP* 5.0 7.9 - - - -
189A GLU* 5.4 5.9 + - - -
191A VAL* 3.9 23.3 - - + +
192A TYR 2.9 10.1 + - - +
193A PHE* 3.4 32.6 - - + -
194A LYS* 2.9 22.5 + - - -
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Residues in contact with GLU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 4.0 6.0 + - + +
6A ARG* 1.3 69.5 - - - +
8A PHE* 1.3 83.5 + - - +
32A THR* 4.9 0.7 + - - -
194A LYS* 3.3 49.0 + - + +
195A ALA* 5.7 0.4 - - - -
196A ARG* 6.0 2.3 - - - -
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Residues in contact with PHE 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ARG* 3.5 35.9 - - + -
7A GLU* 1.3 86.3 - - - +
9A ASP* 1.3 66.8 + - - +
10A ALA 3.4 19.3 - - - +
11A VAL* 4.4 7.0 - - + -
32A THR* 3.6 13.5 - - - +
33A CYS 4.0 8.3 - - - -
34A ALA* 3.6 38.6 - - + -
159A THR* 4.3 13.7 - - + -
161A PHE* 3.8 17.3 - + - -
193A PHE* 4.0 6.3 - + - -
194A LYS 2.9 16.3 + - - +
195A ALA* 3.2 7.1 - - - -
196A ARG* 3.7 2.6 + - - -
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Residues in contact with ASP 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 1.3 70.6 - - - +
10A ALA* 1.3 60.0 + - + +
31A GLN* 3.4 24.6 - - + +
32A THR* 2.9 40.5 + - - +
196A ARG* 2.9 63.8 + - - +
197A ALA* 3.1 8.7 + - - +
423A ILE* 4.7 3.5 - - + +
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 3.4 6.5 - - - +
9A ASP* 1.3 79.1 - - + +
11A VAL* 1.3 65.3 + - - +
12A VAL* 4.1 0.7 - - + -
26A ILE* 4.1 21.1 - - + -
32A THR 3.0 10.1 + - - +
33A CYS* 3.3 6.3 - - - -
34A ALA 3.0 23.2 + - - -
195A ALA* 4.3 0.2 - - - -
197A ALA* 3.2 10.3 - - + +
199A VAL* 5.1 1.3 - - + -
419A LEU* 3.9 26.2 - - + -
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Residues in contact with VAL 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 4.4 11.7 - - + -
10A ALA* 1.3 76.6 - - - +
12A VAL* 1.3 62.8 + - - +
13A ILE* 3.9 18.2 + - + -
34A ALA* 3.4 5.6 - - + -
36A LEU* 4.1 26.5 - - + -
179A GLY* 5.8 0.2 - - - -
180A CYS* 4.7 5.2 - - - +
193A PHE* 4.0 26.7 - - + +
194A LYS 4.4 4.7 - - - +
195A ALA* 3.5 22.6 - - + +
197A ALA 3.0 7.1 + - - +
198A THR* 3.5 7.5 - - + +
199A VAL* 2.9 24.6 + - - +
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Residues in contact with VAL 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 1.3 75.7 - - - +
13A ILE* 1.3 59.7 + - - +
14A GLY 3.3 21.7 + - - +
19A GLY* 3.7 17.3 - - - +
22A ALA* 4.8 2.0 - - + -
23A ALA* 4.5 7.4 - - - +
26A ILE* 3.8 28.5 - - + -
33A CYS* 3.8 14.8 - - - -
34A ALA 2.8 11.4 + - - +
35A LEU* 3.6 15.1 - - + +
36A LEU* 2.9 28.2 + - - +
199A VAL* 3.5 22.0 - - + +
201A ALA* 4.4 4.7 - - + -
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Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 4.1 15.0 - - + -
12A VAL* 1.3 72.3 - - - +
14A GLY* 1.3 57.9 + - - +
36A LEU* 4.0 10.3 - - + +
166A ALA* 3.7 25.4 - - + +
169A LEU* 4.6 0.2 - - + -
180A CYS* 3.7 26.9 - - + -
198A THR* 3.8 20.4 - - + -
199A VAL 2.7 15.8 + - - +
200A LEU* 4.0 17.7 - - + -
201A ALA* 2.8 27.9 + - - -
202A THR* 3.4 20.8 - - + +
225A MET* 4.2 8.3 - - + -
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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