Contacts of the strand formed by residues 182 - 186 (chain C) in PDB entry 2VGB
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 GLN 182 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180C GLY 4.3 3.8 + - - -
181C SER* 1.3 80.1 + - - +
183C VAL* 1.3 62.5 + - - +
184C LEU 4.3 0.2 - - - -
198C ASN* 3.4 29.8 + - - +
229C GLN* 3.4 22.2 + - - -
237C VAL* 4.2 19.1 - - + -
238C THR 3.4 8.1 + - - +
239C GLN* 4.1 10.9 - - - +
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Residues in contact with VAL 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C LEU* 3.9 8.3 - - + -
181C SER* 3.7 2.1 + - - +
182C GLN* 1.3 75.2 - - - +
184C LEU* 1.3 66.6 + - - +
185C VAL* 4.6 1.1 - - + -
197C ALA 3.3 26.2 - - - +
198C ASN* 3.3 4.9 - - - +
200C VAL* 3.8 26.5 - - + +
226C LEU* 4.1 14.8 - - + -
237C VAL* 5.2 0.9 - - - -
238C THR* 2.4 53.5 + - - +
240C VAL* 3.4 29.4 - - + -
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Residues in contact with LEU 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C GLN 4.3 0.4 - - - -
183C VAL* 1.3 71.6 - - - +
185C VAL* 1.3 61.8 + - - +
186C THR* 3.7 22.9 - - + -
198C ASN 2.8 13.4 + - - +
199C THR* 3.5 13.8 - - + +
200C VAL 3.0 24.8 + - - +
234C GLU* 3.8 18.2 - - - +
235C GLY* 3.7 13.5 - - - +
236C LEU 3.5 32.1 - - - +
237C VAL* 4.4 10.1 - - + +
238C THR 4.9 0.4 - - - +
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Residues in contact with VAL 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C VAL* 4.6 0.9 - - + -
184C LEU* 1.3 74.6 - - - +
186C THR* 1.3 61.8 + - - +
200C VAL* 3.2 25.1 - - + +
202C VAL* 4.1 28.5 - - + -
207C ILE* 4.4 18.4 - - + -
208C VAL* 4.8 2.6 - - - +
217C ILE* 4.6 11.7 - - + -
226C LEU* 4.2 15.5 - - + -
235C GLY* 3.4 4.9 - - - -
236C LEU* 3.0 43.4 + - + +
238C THR* 4.1 20.2 - - + +
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Residues in contact with THR 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C LEU* 3.7 24.0 + - + -
185C VAL* 1.3 74.7 - - - +
187C VAL* 1.3 64.5 + - - +
188C ASP* 3.8 13.9 - - + -
191C PHE* 3.7 31.8 - - + +
199C THR* 4.1 9.8 - - + +
200C VAL 3.1 5.7 + - - -
201C TRP* 3.4 11.1 + - - -
202C VAL* 3.1 23.9 + - - -
234C GLU 3.6 23.8 - - - +
235C GLY* 4.8 0.9 - - - -
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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