Contacts of the strand formed by residues 259 - 263 (chain B) in PDB entry 2OIB
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 CYS 259 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B PHE* 4.0 13.0 - - - -
173B LEU* 3.5 20.2 - - + -
180B PHE* 4.2 7.4 - - - -
212B VAL* 4.5 4.3 - - + -
213B LYS 3.2 6.5 - - - +
214B LYS* 3.9 20.2 - - - -
230B PHE* 3.3 11.7 - - - -
251B PHE* 3.5 3.7 - - - -
252B SER* 3.3 43.6 + - - +
256B ASP* 3.9 14.4 - - - -
258B LEU* 1.3 80.8 - - - +
260B LEU* 1.3 64.2 + - - +
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ALA 3.4 3.6 - - - +
212B VAL* 3.5 1.3 - - - -
213B LYS* 2.8 42.0 + - + +
215B LEU* 4.5 20.4 - - + -
229B GLN 5.4 0.2 - - - +
230B PHE* 3.7 33.4 - - + +
233B GLU* 3.6 19.3 - - + -
234B ILE* 3.7 26.0 - - + -
248B LEU* 3.9 13.0 - - + -
250B GLY 3.9 1.8 - - - -
251B PHE* 4.5 2.0 - - + -
259B CYS* 1.3 76.2 - - - +
261B VAL* 1.3 62.6 + - - +
262B TYR* 3.4 34.2 - - + +
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PHE* 4.0 23.3 - - + -
173B LEU* 3.6 38.8 - - + -
205B VAL* 5.3 0.7 - - + -
210B VAL* 3.8 35.2 - - + -
211B ALA 3.4 2.9 - - - +
212B VAL* 4.3 7.2 - - + -
248B LEU* 3.5 4.9 - - - +
249B LEU* 2.7 36.9 + - + -
250B GLY 2.9 23.4 + - - +
251B PHE* 4.7 0.9 - - - +
260B LEU* 1.3 78.4 - - - +
262B TYR* 1.3 57.1 + - - +
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Residues in contact with TYR 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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200B VAL* 6.0 0.7 - - + -
210B VAL* 3.3 9.9 - - - +
211B ALA* 2.8 51.0 + - + +
213B LYS* 3.6 29.3 + - + -
233B GLU* 2.9 37.7 + - - -
237B MET* 5.1 0.4 - - - -
246B VAL* 4.2 25.6 - - + -
247B GLU 3.3 15.3 - - - +
248B LEU* 3.8 16.8 - - + -
249B LEU* 3.7 6.5 - - - +
260B LEU* 3.4 40.7 - - + +
261B VAL* 1.3 73.5 - - - +
263B VAL* 1.3 69.0 + - - +
328B SER* 6.2 0.2 - - - -
329B ASP 5.9 1.3 + - - -
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Residues in contact with VAL 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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208B THR* 5.7 4.5 - - + -
209B THR 4.3 4.9 - - - +
211B ALA* 4.4 2.5 - - - +
246B VAL* 5.7 2.6 - - - +
247B GLU* 3.1 34.6 + - + +
249B LEU* 3.6 33.1 - - + +
262B TYR* 1.3 80.6 - - - +
264B TYR* 1.3 75.0 + - - +
265B MET* 3.6 18.9 + - - +
286D HIS* 4.7 6.7 - - + -
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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