Contacts of the strand formed by residues 232 - 236 (chain A) in PDB entry 2OM5
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 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A GLY* 3.4 29.6 - - - -
152A ARG 4.2 2.7 - - - -
153A HIS 4.1 11.7 - - - -
154A PHE* 3.4 41.1 - - + -
163A TYR* 3.6 34.7 - + + -
164A ILE 4.4 0.2 - - - -
165A ALA* 4.0 22.0 - - + -
211A ILE* 3.7 3.5 - - - +
212A LYS* 3.3 4.9 + - - +
213A ALA* 3.2 36.2 + - + +
231A CYS* 1.3 75.3 - - - +
233A ALA* 1.3 83.9 + - - +
234A PHE* 5.7 0.9 - + - -
239A PRO* 6.0 2.5 - - + -
241A ILE* 4.2 10.1 - - + -
259A PRO* 3.8 22.2 - - + -
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Residues in contact with ALA 233 (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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165A ALA* 3.3 13.0 - - - +
209A PRO* 4.3 3.4 - - + -
210A SER 3.3 14.8 - - - +
211A ILE* 3.7 7.2 - - + +
212A LYS 4.4 0.2 - - - +
232A PHE* 1.3 87.5 - - - +
234A PHE* 1.3 67.6 + - - +
239A PRO* 3.3 18.2 - - + +
241A ILE* 4.3 4.5 - - + +
278A ALA* 3.4 34.1 - - + -
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Residues in contact with PHE 234 (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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120A GLY* 3.5 18.8 - - - +
121A VAL* 3.2 40.4 - - - -
122A MET* 3.6 14.1 - - + -
163A TYR* 4.4 15.5 - + + -
164A ILE 3.3 19.3 - - - -
165A ALA* 4.2 3.6 - - - +
208A ALA 4.5 0.2 - - - +
209A PRO* 3.1 4.3 - - - +
210A SER* 2.8 41.2 + - - +
212A LYS* 3.3 41.4 - - + +
232A PHE* 5.7 0.9 - + - -
233A ALA* 1.3 74.3 - - - +
235A GLY* 1.3 57.9 + - - +
239A PRO* 4.2 0.7 - - - -
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Residues in contact with GLY 235 (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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118A GLY 5.3 0.7 - - - -
120A GLY 5.5 0.4 - - - +
165A ALA 2.9 24.9 + - - +
166A ARG* 3.8 5.7 - - - +
207A PHE* 3.9 15.0 - - - -
208A ALA 4.9 0.9 - - - -
209A PRO* 4.2 1.1 - - - -
233A ALA 3.8 2.0 + - - -
234A PHE* 1.3 75.3 - - - +
236A ASN* 1.3 61.9 + - - +
237A PRO 3.7 6.6 - - - +
239A PRO* 3.6 19.0 - - - +
280A ASN* 4.0 4.3 - - - -
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Residues in contact with ASN 236 (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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118A GLY* 4.3 14.4 + - - +
166A ARG* 2.7 41.5 + - - +
203A ASP 5.5 1.4 + - - -
204A THR 4.7 3.0 + - - -
205A ARG 2.8 26.5 + - - -
206A LEU* 3.5 21.3 - - - +
207A PHE* 3.0 45.9 + - + +
235A GLY* 1.3 74.4 - - - +
237A PRO* 1.3 66.6 - - - +
238A VAL 4.1 0.2 - - - +
280A ASN* 3.4 4.1 + - - +
282A LYS* 4.6 1.2 - - - +
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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