Contacts of the strand formed by residues 259 - 263 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A PHE* 4.0 12.6 - - - -
173A LEU* 3.7 25.6 - - + -
180A PHE* 3.8 29.8 - - - -
212A VAL* 4.1 4.5 - - + -
213A LYS 3.1 7.4 - - - +
214A LYS* 4.3 11.0 - - - -
230A PHE* 3.4 9.3 - - - -
251A PHE* 3.3 3.7 - - - -
252A SER* 2.9 32.5 + - - -
257A ASP 3.8 10.8 - - - -
258A LEU* 1.3 80.1 - - - +
260A LEU* 1.3 63.7 + - - +
261A VAL* 5.1 0.2 - - - -
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Residues in contact with LEU 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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212A VAL* 3.4 1.9 - - - -
213A LYS* 2.7 51.0 + - + +
230A PHE* 4.0 28.7 - - + +
233A GLU* 3.4 25.8 - - + +
234A ILE* 3.7 29.2 - - + +
248A LEU* 3.8 16.2 - - + -
250A GLY 3.7 1.8 - - - -
251A PHE* 4.0 6.5 - - + -
259A CYS* 1.3 76.3 - - - +
261A VAL* 1.3 62.1 + - - +
262A TYR* 3.4 34.5 - - + +
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Residues in contact with VAL 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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168A PHE* 3.8 29.2 - - + -
173A LEU* 3.7 34.8 - - + -
210A VAL* 3.8 35.9 - - + -
211A ALA 3.3 4.5 - - - +
212A VAL* 4.4 4.5 - - + -
248A LEU* 3.4 4.0 - - - +
249A LEU* 2.7 35.6 + - + -
250A GLY 2.8 24.9 + - - +
251A PHE* 4.4 0.9 - - - +
260A LEU* 1.3 77.7 - - - +
262A TYR* 1.3 58.1 + - - +
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Residues in contact with TYR 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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200A VAL* 5.9 1.3 - - + -
210A VAL* 3.6 8.3 - - - +
211A ALA* 2.7 50.2 + - + +
213A LYS* 3.8 23.8 + - + -
233A GLU* 2.4 36.7 + - - -
237A MET* 4.2 11.7 - - - -
246A VAL* 3.8 26.5 - - + -
247A GLU 3.5 6.7 - - - +
248A LEU* 3.7 24.2 - - + -
249A LEU* 3.6 6.5 - - - +
260A LEU* 3.4 34.3 - - + +
261A VAL* 1.3 74.5 - - - +
263A VAL* 1.3 64.2 + - - +
264A TYR 3.4 0.7 + - - -
329A ASP* 6.1 4.3 - - - -
330A PHE* 5.8 1.6 - + - -
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Residues in contact with VAL 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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211A ALA* 4.4 3.7 - - - +
246A VAL* 4.1 3.5 - - - +
247A GLU* 3.1 38.4 + - + +
249A LEU* 3.6 27.4 - - + +
262A TYR* 1.3 80.1 - - - +
264A TYR* 1.3 71.4 + - - +
265A MET* 3.6 35.2 + - + +
318A LEU* 5.8 0.5 - - - +
321A GLU* 5.7 2.2 - - - +
286C HIS* 4.7 5.8 - - + -
287C MET* 6.3 3.1 - - + -
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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