Contacts of the strand formed by residues 252 - 257 (chain B) in PDB entry 2O2C
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 THR 252 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B ILE* 4.0 4.7 - - - +
199B HIS* 3.3 19.2 - - + +
201B VAL* 3.7 30.5 - - + -
247B ILE* 3.6 7.8 - - + +
248B ASP 3.0 19.9 + - - -
249B ILE* 3.3 17.4 + - - -
250B GLU 3.5 1.4 + - - -
251B ALA* 1.3 77.3 - - - +
253B LEU* 1.3 66.6 + - - +
254B PHE* 3.8 22.8 + - + -
295B HIS* 2.7 32.2 + - - +
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B PHE* 3.7 39.9 - - + -
184B VAL* 4.0 17.9 - - + -
189B TRP* 4.7 2.9 - - + +
197B ILE* 3.9 21.4 - - + +
199B HIS 2.9 7.3 + - - +
200B VAL* 3.5 6.6 - - + +
201B VAL* 2.8 26.2 + - - -
252B THR* 1.3 75.1 - - - +
254B PHE* 1.3 73.1 + - - +
255B ILE* 4.0 11.8 + - + -
294B LYS 4.4 8.7 - - - +
295B HIS* 3.8 16.4 - - - +
297B VAL* 4.2 9.4 - - + -
339B ILE* 4.1 14.4 - - + -
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Residues in contact with PHE 254 (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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201B VAL* 3.4 31.2 - - + +
203B ILE* 4.0 6.7 - - + -
240B ILE* 5.1 3.6 - - + -
243B VAL* 5.5 0.4 - - + -
244B LEU* 4.8 6.5 - - + -
247B ILE* 3.9 15.3 - - + -
249B ILE* 4.1 24.7 - - + -
252B THR* 3.8 28.9 - - + -
253B LEU* 1.3 74.1 - - - +
255B ILE* 1.3 61.1 + - - +
256B VAL 4.0 0.2 - - - -
273B ALA* 4.0 26.2 - - + -
277B LEU* 4.9 4.0 - - + -
295B HIS* 2.8 19.9 + - + +
296B PHE* 3.4 46.1 - + + +
297B VAL* 3.1 27.2 + - - +
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Residues in contact with ILE 255 (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* 3.7 27.1 - - + -
201B VAL 2.8 13.9 + - - +
202B ASN* 3.5 11.8 - - - +
203B ILE* 2.7 34.1 + - - +
253B LEU* 4.2 8.3 - - + -
254B PHE* 1.3 74.3 - - - +
256B VAL* 1.3 59.2 + - - +
257B ALA 3.5 0.9 + - - -
297B VAL* 3.7 19.5 - - + -
299B LEU* 3.5 41.1 - - + -
335B LEU* 4.3 5.2 - - + -
336B PRO* 4.2 18.6 - - + -
339B ILE* 3.9 20.2 - - + -
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Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE* 3.6 9.2 - - + +
255B ILE* 1.3 71.3 - - - +
257B ALA* 1.3 59.6 + - - +
261B PHE* 3.7 32.6 - - + -
266B THR* 4.0 18.8 - - + -
267B ILE* 5.2 1.8 - - + -
270B ALA* 3.8 29.8 - - + -
296B PHE* 3.9 29.4 - - + -
297B VAL 2.9 14.6 + - - +
298B ALA* 3.3 2.6 - - - -
299B LEU 2.9 26.1 + - - +
309B PHE* 4.8 1.8 - - + -
311B ILE* 4.4 6.7 - - + -
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Residues in contact with ALA 257 (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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202B ASN* 3.9 11.2 - - - +
203B ILE 2.8 21.2 + - - +
204B GLY* 3.4 5.9 - - - -
208B SER* 3.3 32.0 - - - +
255B ILE 3.5 0.4 + - - -
256B VAL* 1.3 71.9 - - - +
258B SER* 1.3 64.8 + - - +
266B THR* 3.7 1.7 + - - +
299B LEU* 3.7 20.4 - - + -
333B ILE* 3.8 19.1 - - + -
5002B G6Q 4.6 0.2 + - - -
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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