Contacts of the helix formed by residues 230 - 235 (chain A) in PDB entry 2OR4
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 ASP 230 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ARG* 4.0 7.8 - - - +
228A TYR* 2.6 37.3 + - + +
229A SER* 1.3 73.7 - - - +
231A PRO* 1.4 75.5 - - - +
232A ALA* 3.0 16.8 + - - +
233A ASP* 2.9 21.8 + - - +
234A TYR* 2.9 24.1 + - - +
299A TYR* 4.8 0.2 - - - -
321A GLY* 3.7 6.5 - - - -
322A SER 2.9 23.9 + - - -
323A LEU* 4.1 0.5 - - - +
327A TYR* 2.5 26.6 + - - -
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Residues in contact with PRO 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A SER 3.7 0.2 - - - -
230A ASP* 1.4 93.9 - - - +
232A ALA* 1.3 57.9 + - - +
234A TYR 3.7 1.1 - - - -
235A PHE* 2.9 53.9 + - + +
299A TYR* 3.7 39.9 - - + -
322A SER* 4.2 13.9 - - - +
323A LEU* 3.7 23.1 - - + -
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Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ARG* 3.8 20.2 - - - +
230A ASP* 3.0 17.6 + - - +
231A PRO* 1.3 77.6 - - - +
233A ASP* 1.3 60.5 + - - +
235A PHE 4.9 2.3 - - - +
320A ARG 5.2 0.9 - - - +
321A GLY* 3.9 3.4 - - - -
322A SER* 3.4 26.5 + - - +
544A ASN* 5.0 2.6 - - - +
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Residues in contact with ASP 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A TYR* 2.5 34.2 + - - -
204A ARG* 3.0 33.8 + - - -
205A TYR 4.0 2.8 - - - +
207A LYS* 4.7 3.5 + - - -
230A ASP* 2.9 8.3 + - - +
232A ALA* 1.3 81.6 - - - +
234A TYR* 1.3 84.0 + - + +
235A PHE 3.8 0.9 - - - -
544A ASN* 2.6 40.2 + - - +
547A SER* 5.0 4.8 + - - +
548A GLY 4.8 0.5 - - - +
550A PRO* 5.5 1.4 - - - +
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Residues in contact with TYR 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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205A TYR* 3.5 32.7 - - + +
206A GLY* 3.5 20.4 + - - -
229A SER* 3.8 20.0 - - - -
230A ASP 2.9 16.2 + - - +
231A PRO* 3.9 1.6 - - + -
233A ASP* 1.3 91.8 - - + +
235A PHE* 1.3 59.6 + - - +
236A ALA 4.1 0.7 - - - -
248A LEU* 3.4 32.7 + - + +
254A GLN* 3.6 16.3 + - - -
547A SER* 2.7 34.0 + - - -
548A GLY 3.8 9.4 - - - -
549A TYR 4.0 4.9 - - - -
550A PRO* 3.2 47.3 - - + +
552A TYR* 5.4 1.3 - - + -
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Residues in contact with PHE 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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231A PRO* 2.9 37.5 + - + +
232A ALA 4.9 2.0 - - - +
233A ASP 3.8 1.2 - - - -
234A TYR* 1.3 78.6 - - - +
236A ALA* 1.3 70.6 + - - +
237A PRO* 3.5 9.6 - - + +
238A GLY 5.1 4.3 - - - -
239A VAL 3.4 13.2 - - - -
240A LYS* 5.1 1.1 - - + -
241A SER* 3.4 27.1 - - - -
247A ASN* 3.3 31.6 - - + -
248A LEU 3.6 15.0 - - - +
299A TYR* 3.6 10.5 - - + +
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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