Contacts of the strand formed by residues 235 - 242 (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 GLY 235 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184C LEU* 3.7 7.1 - - - +
185C VAL 3.4 11.4 - - - -
186C THR* 4.8 1.8 - - - -
187C VAL* 5.6 0.4 - - - -
208C VAL* 4.3 15.9 - - - +
231C ILE* 5.4 0.2 - - - -
232C GLY* 3.3 28.5 + - - +
233C PRO 3.5 3.8 + - - -
234C GLU* 1.3 80.7 - - - +
236C LEU* 1.3 66.0 + - - -
237C VAL* 3.7 3.6 + - - +
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Residues in contact with LEU 236 (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* 3.5 5.3 - - - +
185C VAL* 3.0 37.5 + - + +
207C ILE* 3.9 32.3 - - + +
208C VAL* 3.9 24.9 - - + +
211C VAL* 4.0 17.9 - - + +
217C ILE* 4.2 22.4 - - + -
228C VAL* 4.2 11.7 - - + -
230C LYS 3.8 2.0 - - - -
231C ILE* 3.9 27.8 - - + -
235C GLY* 1.3 71.8 - - - -
237C VAL* 1.3 63.1 + - - +
238C THR* 3.2 16.5 + - + +
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Residues in contact with VAL 237 (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* 4.2 23.3 - - + -
183C VAL 4.3 2.2 - - - +
184C LEU* 4.7 10.3 - - + +
228C VAL* 3.7 1.9 - - - -
229C GLN* 2.8 31.8 + - + +
230C LYS* 2.6 42.5 + - + +
231C ILE 5.4 2.0 - - - -
232C GLY* 5.9 2.0 - - - -
235C GLY 3.7 5.3 + - - +
236C LEU* 1.3 71.6 - - - +
238C THR* 1.3 60.2 + - - +
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Residues in contact with THR 238 (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* 3.4 11.3 - - - +
183C VAL* 2.4 63.6 + - - +
185C VAL* 4.1 17.3 - - + -
217C ILE* 4.5 5.6 - - + -
226C LEU* 4.0 18.1 - - + +
227C VAL 3.5 8.7 - - - -
228C VAL* 4.2 15.7 - - + +
229C GLN* 4.2 3.8 - - - -
236C LEU* 3.4 24.0 - - + +
237C VAL* 1.3 77.5 - - - +
239C GLN* 1.3 59.9 + - - +
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Residues in contact with GLN 239 (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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180C GLY* 3.7 25.8 + - - +
181C SER 3.3 9.0 - - - +
182C GLN* 4.1 6.3 - - - +
226C LEU* 3.7 2.4 - - - -
227C VAL* 3.0 37.1 + - + +
229C GLN* 3.4 32.3 + - - +
238C THR* 1.3 73.4 - - - +
240C VAL* 1.3 69.8 + - - +
241C GLU* 3.2 1.8 + - - +
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Residues in contact with VAL 240 (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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177C LEU* 3.9 11.9 - - + +
178C VAL 3.2 18.8 - - - +
179C LYS* 3.8 1.3 - - - +
180C GLY* 2.9 27.9 + - - +
181C SER* 2.9 33.8 + - - +
183C VAL* 3.4 27.6 - - + -
224C ILE* 5.4 0.2 - - + -
225C SER 4.1 2.0 - - - +
226C LEU* 3.7 14.4 - - + -
239C GLN* 1.3 71.2 - - - +
241C GLU* 1.3 60.7 + - - +
242C ASN 3.4 23.1 - - - +
243C GLY* 3.7 14.8 - - - +
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Residues in contact with GLU 241 (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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179C LYS* 3.3 29.6 + - - +
216C ARG* 2.6 38.3 + - - -
225C SER* 2.5 38.8 + - - +
227C VAL* 3.5 19.3 - - + +
239C GLN 3.2 2.0 + - - +
240C VAL* 1.3 73.2 - - - +
242C ASN* 1.3 67.6 + - - +
243C GLY 4.1 0.2 - - - -
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Residues in contact with ASN 242 (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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381A PRO* 4.8 14.0 - - + +
179C LYS* 5.1 4.3 + - - +
218C TYR* 6.0 0.8 - - - -
223C LEU 4.1 11.9 - - - +
224C ILE* 3.8 2.9 - - - +
225C SER* 3.0 52.2 + - - +
240C VAL* 3.4 7.3 - - - +
241C GLU* 1.3 87.7 + - - +
243C GLY* 1.3 61.6 + - - +
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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