Contacts of the strand formed by residues 53 - 57 (chain B) in PDB entry 1WVV
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 ARG 53 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B SER* 3.2 1.9 - - - -
50B TYR 2.9 26.3 + - - +
51B ASN 3.3 9.9 - - - +
52B GLY* 1.3 84.6 - - - +
54B ASN* 1.3 60.6 + - - +
55B TYR* 3.4 27.2 - - + +
74B ASP* 2.8 40.2 + - - -
76B GLY* 3.2 21.1 - - - +
77B ALA* 3.6 22.5 - - - +
78B CYS* 3.8 6.2 - - - -
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Residues in contact with ASN 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B CYS* 3.3 27.3 - - - +
33B ALA* 2.8 29.1 + - + +
47B THR* 6.2 1.6 - - - -
48B VAL 3.2 5.8 - - - +
49B SER* 3.4 11.1 - - - -
53B ARG* 1.3 71.4 - - - +
55B TYR* 1.3 68.2 + - - +
74B ASP* 3.8 0.9 - - - -
75B LYS* 2.8 41.6 + - + +
76B GLY 2.9 13.2 + - - +
77B ALA 5.4 0.4 + - - -
78B CYS* 3.4 10.6 - - - +
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Residues in contact with TYR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLY 3.9 0.5 - - - +
47B THR* 3.2 5.9 - - - -
48B VAL* 2.9 36.8 + - + +
50B TYR* 3.6 23.3 + + + -
51B ASN* 6.0 0.2 - - - +
53B ARG* 3.4 33.8 - - + +
54B ASN* 1.3 78.2 - - - +
56B THR* 1.3 62.9 + - - +
66B PRO* 3.5 32.3 - - + -
67B GLY* 3.9 18.5 + - - -
72B TRP* 3.6 31.7 - - + -
73B ALA 3.1 7.2 - - - +
74B ASP* 3.8 38.7 + - + -
75B LYS* 4.3 2.0 - - - +
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Residues in contact with THR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B GLY* 3.7 28.3 - - - +
46B GLY 3.3 2.2 - - - -
47B THR* 3.3 16.9 - - + +
55B TYR* 1.3 72.1 - - - +
57B ALA* 1.3 73.8 + - - +
58B LYS* 3.6 1.1 + - + +
72B TRP* 3.7 3.4 - - - -
73B ALA* 2.9 35.4 + - - +
75B LYS* 3.6 27.1 - - - +
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B TYR* 4.3 2.7 - - + -
43B THR 3.6 18.6 - - - +
44B ASN* 3.7 1.8 + - - -
45B GLY 2.8 26.9 + - - -
46B GLY 2.8 11.2 + - - +
56B THR* 1.3 75.4 - - - +
58B LYS* 1.3 60.3 + - - +
59B TRP 3.8 13.5 - - - +
61B THR* 3.9 10.5 - - + -
71B VAL 3.5 6.3 - - - +
72B TRP* 3.3 27.1 - - + -
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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