Contacts of the strand formed by residues 259 - 264 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151D TYR* 3.9 10.4 + - - -
181D SER* 3.3 15.7 - - - +
183D LEU* 3.6 19.5 - - + +
216D PRO* 3.7 19.5 - - + -
249D ILE* 4.0 27.0 + - + +
252D TYR* 3.9 13.7 - - + -
253D ARG* 5.1 1.2 - - - +
258D THR* 1.3 73.5 - - - +
260D ALA* 1.3 61.5 + - - +
261D GLY 3.2 24.5 - - - +
262D ILE* 4.4 2.2 - - + -
291D HIS 5.2 0.3 - - - +
293D CYS* 3.4 30.4 - - - -
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Residues in contact with ALA 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ILE* 3.4 14.6 - - + +
148D PHE* 3.8 25.1 - - + -
150D TRP* 3.7 0.5 - - - -
151D TYR* 3.5 38.3 - - + -
180D TYR* 4.4 7.4 - - + -
181D SER 2.9 12.7 + - - +
258D THR 3.2 2.6 + - - +
259D VAL* 1.3 74.3 - - - +
261D GLY* 1.3 57.0 + - - +
293D CYS* 3.5 3.1 - - - -
294D ALA* 2.8 19.8 + - - +
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Residues in contact with GLY 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ILE* 3.9 14.2 - - - +
181D SER 3.7 2.6 + - - -
182D ILE* 3.4 10.6 - - - +
183D LEU 2.9 23.7 + - - -
259D VAL* 3.2 6.9 - - - +
260D ALA* 1.3 82.0 - - - +
262D ILE* 1.3 64.3 + - - -
293D CYS* 4.1 1.6 - - - -
294D ALA 3.1 14.4 - - - -
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Residues in contact with ILE 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D ILE* 4.7 0.4 - - - -
183D LEU* 3.5 24.5 - - + +
185D PHE* 4.1 22.9 - - + -
245D VAL* 4.4 11.2 - - + -
249D ILE* 3.9 25.1 - - + -
259D VAL* 4.4 2.7 - - + -
261D GLY* 1.3 79.2 - - - +
263D ILE* 1.3 60.7 + - - +
284D LEU* 4.7 7.9 - - + -
288D SER* 3.7 31.6 - - - +
293D CYS* 4.2 5.8 - - + -
294D ALA 2.7 10.2 + - - +
295D PHE* 3.8 17.9 - - + -
296D LEU* 2.8 35.8 + - - +
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Residues in contact with ILE 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D ASN* 4.0 17.3 - - - +
144D PHE* 3.8 10.3 - - + -
182D ILE* 3.9 14.9 - - + +
183D LEU 3.0 19.0 + - - +
184D SER* 3.9 4.5 - - - -
185D PHE* 3.6 16.3 - - - -
190D HIS* 3.3 48.9 + - + +
199D THR* 4.0 11.9 - - - -
262D ILE* 1.3 74.7 - - - +
264D VAL* 1.3 67.2 + - - +
296D LEU* 3.2 36.3 - - + +
298D ASP* 4.2 7.6 - - + -
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Residues in contact with VAL 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D PHE* 3.9 27.6 - - + -
190D HIS* 4.1 6.5 - - - -
220D PHE* 3.9 13.9 - - + -
263D ILE* 1.3 77.0 - - - +
265D GLU* 1.3 77.4 + - - +
266D PRO 4.0 0.4 - - - -
268D GLN* 5.7 1.3 - - - +
281D PHE* 3.8 22.7 - - + -
284D LEU* 4.1 4.5 - - + -
295D PHE* 3.8 32.8 - - + -
296D LEU 3.2 5.8 + - - +
297D VAL* 3.6 7.6 - - + +
298D ASP 2.9 22.8 + - - -
316D TRP* 5.2 0.4 - - + -
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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