Contacts of the strand formed by residues 259 - 264 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A TYR* 4.0 5.9 + - - -
181A SER* 3.3 16.2 - - - +
183A LEU* 3.7 19.1 - - + +
216A PRO* 3.7 20.2 - - + -
249A ILE* 4.0 26.7 + - + +
252A TYR* 4.0 14.0 - - + +
253A ARG* 5.2 0.6 - - - +
258A THR* 1.3 78.2 - - - +
260A ALA* 1.3 57.8 + - - +
261A GLY 3.2 25.4 - - - +
262A ILE* 4.5 1.8 - - + -
291A HIS 5.1 1.0 - - - +
293A CYS* 3.4 32.7 - - - -
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Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ILE* 3.4 14.2 - - + +
148A PHE* 3.9 25.8 - - + -
150A TRP* 3.7 6.9 - - - -
151A TYR* 3.7 30.1 - - + -
180A TYR* 4.4 8.1 - - + -
181A SER 2.9 12.0 + - - +
258A THR 3.2 2.2 + - - -
259A VAL* 1.3 72.6 - - - +
261A GLY* 1.3 59.7 + - - +
293A CYS* 3.5 4.0 - - - -
294A ALA* 2.9 18.9 + - - +
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Residues in contact with GLY 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ILE* 3.9 12.9 - - - +
181A SER 3.8 2.4 + - - -
182A ILE* 3.4 11.4 - - - +
183A LEU 2.9 23.7 + - - -
259A VAL* 3.2 7.9 - - - +
260A ALA* 1.3 82.3 - - - +
262A ILE* 1.3 64.1 + - - -
293A CYS* 4.1 1.3 - - - -
294A ALA* 3.1 15.7 - - - -
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Residues in contact with ILE 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ILE* 4.7 0.7 - - - -
183A LEU* 3.5 24.7 - - + +
185A PHE* 4.1 17.7 - - + -
245A VAL* 4.4 10.8 - - + -
249A ILE* 3.9 25.4 - - + -
259A VAL* 4.5 2.9 - - + -
261A GLY* 1.3 77.6 - - - +
263A ILE* 1.3 67.1 + - - +
284A LEU* 4.7 8.3 - - + -
287A ILE* 4.9 0.2 - - + -
288A SER* 3.6 31.6 - - - +
293A CYS* 4.2 5.8 - - + -
294A ALA 2.7 11.2 + - - +
295A PHE* 3.8 17.3 - - + -
296A LEU* 2.7 35.9 + - - +
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Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ASN* 4.0 16.6 - - - +
144A PHE* 3.8 10.8 - - + -
182A ILE* 3.9 15.0 - - + +
183A LEU 3.0 19.3 + - - +
184A SER* 4.0 4.4 - - - -
185A PHE* 3.6 17.0 - - - -
190A HIS* 3.3 49.7 + - + +
199A THR* 3.9 10.5 - - + -
262A ILE* 1.3 74.8 - - - +
264A VAL* 1.3 68.4 + - - +
296A LEU* 3.2 37.0 - - + +
298A ASP* 4.2 6.5 - - + -
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Residues in contact with VAL 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A PHE* 3.9 25.1 - - + -
190A HIS* 4.1 8.1 - - - -
220A PHE* 3.9 17.3 - - + -
263A ILE* 1.3 79.0 - - - +
265A GLU* 1.3 75.5 + - - +
266A PRO* 4.0 1.1 - - - +
268A GLN* 5.6 1.3 - - + +
281A PHE* 3.8 22.4 - - + -
284A LEU* 4.1 4.5 - - + -
295A PHE* 3.8 33.7 - - + -
296A LEU 3.2 4.4 + - - +
297A VAL* 3.6 7.6 - - + -
298A ASP 3.0 21.8 + - - -
316A TRP* 5.2 0.7 - - + -
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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