Contacts of the strand formed by residues 259 - 264 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B TYR* 4.1 8.7 + - - -
181B SER* 3.3 17.0 - - - +
183B LEU* 3.7 19.5 - - + +
216B PRO* 3.7 19.1 - - + -
249B ILE* 4.0 28.1 + - + +
252B TYR* 3.9 14.6 - - + +
253B ARG* 5.2 1.6 - - - +
258B THR* 1.3 72.5 - - - +
260B ALA* 1.3 60.4 + - - +
261B GLY 3.3 24.0 - - - +
262B ILE* 4.4 2.0 - - + -
291B HIS 5.2 0.3 - - - +
293B CYS* 3.4 30.3 - - - -
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Residues in contact with ALA 260 (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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147B ILE* 3.4 16.4 - - + +
148B PHE* 3.8 25.6 - - + -
150B TRP* 3.7 6.4 - - - -
151B TYR* 3.6 30.0 - - + -
180B TYR* 4.4 4.3 - - + -
181B SER 2.8 12.8 + - - +
258B THR 3.1 5.4 + - - +
259B VAL* 1.3 75.0 - - - +
261B GLY* 1.3 57.5 + - - +
293B CYS* 3.5 3.0 - - - -
294B ALA* 2.9 19.8 + - - +
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Residues in contact with GLY 261 (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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147B ILE* 3.9 13.1 - - - +
181B SER 3.8 3.0 + - - -
182B ILE* 3.4 10.6 - - - +
183B LEU 2.9 23.0 + - - -
259B VAL* 3.3 8.3 - - - +
260B ALA* 1.3 81.7 - - - +
262B ILE* 1.3 64.1 + - - -
293B CYS* 4.1 1.3 - - - -
294B ALA 3.1 15.7 - - - -
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Residues in contact with ILE 262 (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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182B ILE* 4.7 0.4 - - - -
183B LEU* 3.5 24.5 - - + +
185B PHE* 4.1 23.1 - - + -
245B VAL* 4.4 10.8 - - + -
249B ILE* 3.9 25.1 - - + -
259B VAL* 4.4 2.7 - - + -
261B GLY* 1.3 78.1 - - - +
263B ILE* 1.3 60.6 + - - +
284B LEU* 4.7 8.5 - - + -
288B SER* 3.7 31.9 - - - +
293B CYS* 4.2 5.6 - - + -
294B ALA 2.7 11.0 + - - +
295B PHE* 3.8 18.2 - - + -
296B LEU* 2.7 35.4 + - - +
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Residues in contact with ILE 263 (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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140B ASN* 4.0 15.9 - - - +
144B PHE* 3.8 11.4 - - + -
182B ILE* 3.9 14.9 - - + +
183B LEU 3.0 20.2 + - - +
184B SER* 3.9 4.5 - - - -
185B PHE* 3.6 16.1 - - - -
190B HIS* 3.3 48.1 + - + +
199B THR* 3.9 11.4 - - + -
262B ILE* 1.3 75.0 - - - +
264B VAL* 1.3 66.4 + - - +
296B LEU* 3.2 35.7 - - + +
298B ASP* 4.2 7.0 - - + -
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Residues in contact with VAL 264 (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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185B PHE* 3.9 24.7 - - + -
190B HIS* 4.1 7.2 - - - -
220B PHE* 3.9 17.3 - - + -
263B ILE* 1.3 77.1 - - - +
265B GLU* 1.3 74.5 + - - +
266B PRO* 4.0 0.5 - - - +
268B GLN* 5.6 1.3 - - - +
281B PHE* 3.8 23.3 - - + -
284B LEU* 4.1 3.8 - - + -
295B PHE* 3.8 33.7 - - + -
296B LEU 3.1 4.8 + - - +
297B VAL* 3.6 8.1 - - + -
298B ASP 3.0 22.3 + - - -
316B 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