Contacts of the strand formed by residues 310 - 314 (chain D) in PDB entry 2OHI
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 ALA 310 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258D ARG 3.6 2.6 + - - -
259D VAL* 3.3 21.6 - - + -
260D THR 3.1 21.0 + - - -
308D SER* 3.3 4.4 - - - -
309D GLY* 1.3 81.6 - - - +
311D ILE* 1.3 68.7 + - - +
345D LYS* 3.2 11.9 - - + +
398D LEU* 3.4 30.1 - - + -
402D ILE* 4.2 10.5 - - + -
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Residues in contact with ILE 311 (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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259D VAL* 4.6 0.7 - - - -
260D THR* 3.2 12.1 - - - +
262D ILE* 4.8 16.2 - - + -
305D ILE* 4.2 25.4 - - + -
308D SER* 4.9 5.2 - - - -
310D ALA* 1.3 81.5 - - - +
312D ALA* 1.3 58.4 + - - +
313D LEU* 4.9 6.3 - - + +
329D LEU* 6.5 0.2 - - + -
333D LEU* 5.1 2.2 - - + -
344D ARG* 5.0 2.5 - - + -
345D LYS 3.0 6.1 + - - +
346D ALA* 3.1 17.8 - - + -
347D LEU 2.7 30.1 + - - -
366D LEU* 3.9 24.5 - - + -
371D PHE* 3.6 38.8 - - + -
398D LEU* 3.8 7.1 - - - +
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Residues in contact with ALA 312 (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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259D VAL* 4.7 0.9 - - + +
260D THR 2.9 9.3 + - - +
261D VAL* 4.4 7.4 - - + -
262D ILE* 2.6 37.0 + - - +
277D ILE* 4.2 21.3 - - + -
311D ILE* 1.3 76.3 - - - +
313D LEU* 1.3 57.3 + - - +
347D LEU* 3.1 20.9 - - + +
349D PHE* 3.9 15.7 - - + -
398D LEU* 4.3 4.0 - - + -
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Residues in contact with LEU 313 (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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262D ILE* 3.1 37.0 - - + +
293D LEU* 4.3 11.0 - - + -
311D ILE* 4.3 8.6 - - + +
312D ALA* 1.3 73.2 - - - +
314D GLY* 1.3 59.4 + - - +
326D VAL* 3.8 25.8 - - + -
329D LEU* 3.9 15.9 - - + -
330D LEU* 4.0 22.9 - - + -
347D LEU 2.9 7.8 + - - +
348D VAL* 3.4 11.8 - - + +
349D PHE* 3.2 22.1 + - - -
362D MET* 4.1 16.1 - - + +
366D LEU* 4.4 21.3 - - + -
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Residues in contact with GLY 314 (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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262D ILE 2.8 11.7 + - - -
263D TYR* 3.2 2.3 - - - -
264D ASP 3.0 24.4 + - - -
270D THR* 3.7 6.1 - - - -
313D LEU* 1.3 76.3 - - - +
315D ALA* 1.3 63.1 + - - +
326D VAL* 4.4 3.6 - - - +
349D PHE* 3.0 31.9 - - - -
362D MET* 4.4 2.0 - - - -
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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