Contacts of the strand formed by residues 8 - 17 (chain A) in PDB entry 2W5H
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 TYR 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A SER 5.1 0.2 - - - -
4A ARG 3.6 13.9 - - - -
5A ALA 3.2 12.4 + - - +
6A GLU* 3.1 5.9 - - - +
7A ASP* 1.3 88.5 - - + +
9A GLU* 1.3 62.4 + - - +
10A VAL 4.2 0.4 + - - -
25A ILE* 4.0 21.3 - - + -
26A ARG 3.4 7.2 - - - +
27A ARG* 3.7 44.3 + - + -
28A LYS* 4.2 7.9 - - - -
34A LEU* 4.1 14.4 - - + -
36A TRP* 4.0 19.0 - + + -
72A ASP* 2.7 31.7 + - - +
74A ILE* 3.4 28.3 - - + -
85A VAL* 4.1 12.9 - - + +
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Residues in contact with GLU 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 TYR* 1.3 75.0 - - - +
10A VAL* 1.3 75.9 + - - +
11A LEU* 3.2 12.0 + - - +
25A ILE* 3.3 3.3 - - - -
26A ARG* 2.8 57.4 + - + +
28A LYS* 4.7 14.6 - - + -
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Residues in contact with VAL 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 TYR 4.2 0.8 + - - -
9A GLU* 1.3 84.0 - - - +
11A LEU* 1.3 63.7 + - - +
12A TYR* 3.6 17.7 - - - +
23A GLN* 3.7 32.5 - - + +
24A LYS 4.2 2.7 - - - +
25A ILE* 3.8 9.4 - - + -
36A TRP* 3.3 34.5 - - + -
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Residues in contact with LEU 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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9A GLU* 3.2 18.7 + - - +
10A VAL* 1.3 75.9 - - - +
12A TYR* 1.3 80.8 + - + +
24A LYS* 2.8 36.7 + - + +
25A ILE 4.5 1.8 - - - -
26A ARG* 4.4 11.7 - - + +
33A ILE* 3.7 30.3 - - + -
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Residues in contact with TYR 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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10A VAL* 3.6 11.7 - - - +
11A LEU* 1.3 94.6 - - + +
13A THR* 1.3 75.8 + - - +
14A ILE* 4.2 15.6 - - + +
23A GLN* 3.6 0.5 - - - -
24A LYS* 2.8 68.5 + - + +
88A TYR* 4.6 2.1 + - - -
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Residues in contact with THR 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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10A VAL* 4.9 0.2 - - - +
12A TYR* 1.3 81.9 - - - +
14A ILE* 1.3 65.7 + - - +
15A GLY* 3.9 17.3 - - - +
16A THR* 4.5 4.7 - - - +
21A ARG* 3.9 30.4 + - + -
22A CYS 3.6 12.6 - - - +
23A GLN* 3.3 21.6 + - + -
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Residues in contact with ILE 14 (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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12A TYR* 4.2 12.3 - - + +
13A THR* 1.3 75.4 - - - +
15A GLY* 1.3 60.9 + - - +
22A CYS* 2.9 22.8 + - - +
23A GLN 4.3 1.1 - - - -
24A LYS* 3.7 29.8 - - + +
35A VAL* 3.6 30.5 - - + -
88A TYR* 3.9 17.3 - - + -
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Residues in contact with GLY 15 (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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13A THR* 3.6 7.1 - - - -
14A ILE* 1.3 86.3 - - - +
16A THR* 1.3 64.2 + - - -
17A GLY 3.5 0.4 + - - -
22A CYS* 2.8 31.6 + - - +
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Residues in contact with THR 16 (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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13A THR* 4.5 5.2 - - - +
15A GLY* 1.3 70.9 - - - -
17A GLY* 1.3 72.5 + - - +
20A GLY* 4.0 7.6 - - - +
21A ARG* 4.0 27.9 - - + +
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Residues in contact with GLY 17 (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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15A GLY 3.5 4.0 + - - -
16A THR* 1.3 87.3 - - - +
18A SER* 1.3 62.8 + - - -
19A TYR 3.0 7.0 + - - -
20A GLY 2.6 23.9 + - - +
22A CYS* 4.5 2.3 - - - +
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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