Contacts of the strand formed by residues 296 - 300 (chain A) 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 PHE 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A ILE* 4.8 0.7 - - + -
253A LEU* 4.6 0.2 - - - +
254A PHE* 3.4 42.6 - + + -
256A VAL* 3.9 17.0 - - + -
270A ALA 4.0 14.6 - - - -
273A ALA* 3.7 6.5 - - + -
274A ARG* 3.5 35.4 - - + -
277A LEU* 3.9 18.6 - - + -
292A VAL* 2.8 38.0 + - + +
293A ALA* 4.1 9.9 - - - +
294A LYS 3.7 0.8 - - - -
295A HIS* 1.3 80.2 - - + +
297A VAL* 1.3 67.7 + - - +
309A PHE* 3.8 17.3 - + - -
311A ILE* 3.9 28.1 - - + +
315A ASN* 4.3 1.9 + - - +
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Residues in contact with VAL 297 (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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180A PHE* 3.6 36.8 - - + -
189A TRP* 5.1 3.4 - - + -
253A LEU* 4.3 10.1 - - + -
254A PHE 3.1 5.0 + - - +
255A ILE* 3.8 33.0 - - + -
256A VAL* 2.9 25.6 + - - +
296A PHE* 1.3 77.6 - - - +
298A ALA* 1.3 60.1 + - - +
299A LEU* 5.3 0.2 - - + -
311A ILE* 3.9 8.9 - - - +
315A ASN* 3.5 28.0 - - + +
317A PHE* 4.0 7.6 - - + -
335A LEU* 4.4 6.1 - - + -
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Residues in contact with ALA 298 (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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256A VAL 3.4 3.8 - - - -
261A PHE* 3.8 16.6 - - + -
297A VAL* 1.3 75.6 - - - +
299A LEU* 1.3 60.4 + - - +
300A SER 3.9 0.4 - - - -
306A VAL* 3.6 33.7 - - + -
311A ILE* 3.8 12.7 - - + +
315A ASN 3.1 8.4 + - - +
316A MET* 3.4 2.8 - - - -
317A PHE* 2.8 35.7 + - - -
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Residues in contact with LEU 299 (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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255A ILE* 3.6 27.8 - - + -
256A VAL 3.0 8.0 + - - +
257A ALA* 3.8 14.6 - - + -
258A SER 3.0 26.7 + - - +
297A VAL* 5.3 0.2 - - + -
298A ALA* 1.3 79.0 - - - +
300A SER* 1.3 60.3 + - - +
317A PHE* 3.4 19.3 - - + +
319A PHE* 3.8 5.1 - - - -
332A ALA* 3.3 30.3 - - + +
333A ILE* 3.7 27.4 - - + +
335A LEU* 3.7 25.8 - - + -
336A PRO* 4.1 6.5 - - + -
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Residues in contact with SER 300 (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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258A SER 2.8 21.5 + - - -
259A LYS 3.3 4.0 + - - -
261A PHE* 3.6 25.5 - - - +
298A ALA 3.9 1.2 - - - -
299A LEU* 1.3 74.9 - - - +
301A THR* 1.3 69.6 + - - +
302A ASN* 3.2 10.4 + - - +
306A VAL* 3.9 17.0 - - - -
316A MET* 3.6 8.0 - - - +
317A PHE 3.2 5.5 + - - -
318A GLN* 3.5 8.7 - - - -
319A PHE* 3.3 27.4 + - - -
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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