Contacts of the strand formed by residues 76 - 80 (chain B) in PDB entry 2VSH
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 ILE 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B ILE* 3.8 30.1 - - + -
41B VAL* 5.2 1.1 - - + -
49B ILE* 3.2 17.3 - - + +
51B VAL* 4.2 8.7 - - + -
65B VAL* 3.9 30.2 - - + +
69B LEU* 4.0 13.5 - - + -
72B TYR* 3.5 22.7 - - + +
73B LYS 3.2 16.4 + - - +
74B GLU 3.3 2.0 - - - +
75B ARG* 1.3 84.3 - - + +
77B ILE* 1.3 67.6 + - - +
78B ILE* 3.9 28.2 + - + +
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Residues in contact with ILE 77 (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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48B LYS* 4.0 31.2 - - + -
49B ILE 2.7 9.8 + - - +
50B VAL* 3.3 24.4 - - + +
51B VAL* 2.6 34.1 + - - +
74B GLU 5.6 0.7 - - - +
76B ILE* 1.3 78.1 - - - +
78B ILE* 1.3 70.3 + - - +
79B THR* 4.7 5.4 - - - +
95B ALA* 4.9 10.1 - - + +
96B ILE* 5.9 0.7 - - - -
99B TYR* 4.0 31.6 - - + -
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Residues in contact with ILE 78 (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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33B LEU* 5.7 0.7 - - + -
37B ILE* 5.3 0.9 - - + -
51B VAL* 3.5 32.8 - - + +
53B VAL* 4.0 13.9 - - + -
58B VAL* 3.7 32.9 - - + +
61B ALA* 3.9 21.1 - - + -
62B GLU* 3.8 39.6 + - + +
65B VAL* 4.2 11.2 - - + -
76B ILE* 3.9 16.3 + - + +
77B ILE* 1.3 79.9 - - - +
79B THR* 1.3 62.0 + - - +
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Residues in contact with THR 79 (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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50B VAL* 3.9 21.1 - - + -
51B VAL 2.8 16.3 + - - +
52B GLY* 3.4 8.3 - - - -
53B VAL* 3.0 28.2 + - - +
58B VAL* 4.1 7.2 - - - -
77B ILE* 3.9 4.5 + - - -
78B ILE* 1.3 74.1 - - - +
80B LYS* 1.3 72.1 + - - +
91B ASN* 4.3 7.2 + - + +
92B ILE* 4.3 8.1 - - + +
95B ALA* 3.8 23.4 - - + +
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Residues in contact with LYS 80 (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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53B VAL 3.4 5.2 - - - -
55B GLY* 3.7 30.9 - - - +
58B VAL* 4.1 9.3 - - + +
79B THR* 1.3 77.1 + - - +
81B GLY* 1.3 70.6 + - - +
91B ASN* 3.0 28.8 + - - +
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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