Contacts of the strand formed by residues 259 - 264 (chain C) in PDB entry 1OHV
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 VAL 259 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C TYR* 4.1 8.5 + - - -
181C SER* 3.3 16.2 - - - +
183C LEU* 3.7 20.4 - - + +
216C PRO* 3.7 18.8 - - + -
249C ILE* 3.9 27.4 + - + +
252C TYR* 3.9 15.0 - - + +
253C ARG* 5.2 1.2 - - - +
258C THR* 1.3 73.2 - - - +
260C ALA* 1.3 60.8 + - - +
261C GLY 3.3 25.1 - - - +
262C ILE* 4.5 1.8 - - + -
291C HIS 5.2 0.9 - - - +
293C CYS* 3.4 29.6 - - - -
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Residues in contact with ALA 260 (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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147C ILE* 3.4 14.9 - - + +
148C PHE* 3.9 24.0 - - + -
150C TRP* 3.7 6.8 - - - -
151C TYR* 3.7 32.0 - - + -
180C TYR* 4.4 4.0 - - + -
181C SER 2.9 12.9 + - - +
258C THR 3.1 6.6 + - - +
259C VAL* 1.3 73.9 - - - +
261C GLY* 1.3 57.1 + - - +
293C CYS* 3.5 3.1 - - - -
294C ALA* 2.9 20.1 + - - +
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Residues in contact with GLY 261 (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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147C ILE* 4.0 12.9 - - - +
181C SER 3.8 2.6 + - - -
182C ILE* 3.4 11.4 - - - +
183C LEU 2.9 23.6 + - - -
259C VAL* 3.3 8.7 - - - +
260C ALA* 1.3 81.3 - - - +
262C ILE* 1.3 63.9 + - - -
293C CYS* 4.1 1.8 - - - -
294C ALA 3.1 15.0 - - - -
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Residues in contact with ILE 262 (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 ILE* 4.7 0.4 - - - -
183C LEU* 3.5 24.9 - - + +
185C PHE* 4.1 23.3 - - + -
245C VAL* 4.4 10.8 - - + -
249C ILE* 3.9 24.9 - - + -
259C VAL* 4.5 2.9 - - + -
261C GLY* 1.3 77.9 - - - +
263C ILE* 1.3 64.3 + - - +
284C LEU* 4.7 7.6 - - + -
287C ILE* 4.9 0.2 - - + -
288C SER* 3.8 28.3 - - - +
293C CYS* 4.2 6.5 - - + -
294C ALA 2.7 10.6 + - - +
295C PHE* 3.8 21.3 - - + -
296C LEU* 2.8 31.9 + - - +
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Residues in contact with ILE 263 (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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140C ASN* 3.9 16.4 - - - +
144C PHE* 3.8 11.0 - - + -
182C ILE* 3.9 14.9 - - + +
183C LEU 3.0 19.3 + - - +
184C SER* 3.9 4.5 - - - -
185C PHE* 3.6 16.6 - - - -
190C HIS* 3.4 48.3 + - + +
199C THR* 3.9 11.2 - - - -
262C ILE* 1.3 74.2 - - - +
264C VAL* 1.3 66.9 + - - +
296C LEU* 3.2 37.0 - - + +
298C ASP* 4.2 7.2 - - + -
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Residues in contact with VAL 264 (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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185C PHE* 3.9 27.1 - - + -
190C HIS* 4.1 7.6 - - - -
220C PHE* 3.9 14.6 - - + -
263C ILE* 1.3 77.4 - - - +
265C GLU* 1.3 76.9 + - - +
266C PRO 4.1 0.5 - - - -
268C GLN* 5.7 1.1 - - - +
281C PHE* 3.8 22.4 - - + -
284C LEU* 4.1 4.0 - - + -
295C PHE* 3.8 33.7 - - + -
296C LEU 3.2 6.1 + - - +
297C VAL* 3.6 6.9 - - + -
298C ASP 2.9 23.2 + - - -
316C TRP* 5.2 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