Contacts of the helix formed by residues 288 - 293 (chain F) in PDB entry 2OX4
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 288 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F GLY* 4.3 16.2 - - - +
264F GLY 4.3 2.8 + - - -
265F GLU* 4.9 4.7 - - - +
286F GLN 3.5 2.0 + - - -
287F PRO* 1.3 71.9 - - - +
289F LEU* 1.3 60.5 + - - +
290F GLY* 2.7 30.4 + - - -
291F THR* 3.5 21.7 + - + +
292F CYS* 2.8 34.1 + - - +
315F HIS* 2.7 49.6 + - + +
317F ALA 4.6 4.9 + - - -
322F ALA* 5.7 4.9 - - - +
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Residues in contact with LEU 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F SER* 3.3 4.2 - - - -
98F ILE* 3.9 12.7 - - + +
287F PRO 4.0 2.0 + - - -
288F ASP* 1.3 74.2 + - - +
290F GLY* 1.3 56.6 + - - +
292F CYS* 4.2 4.3 - - - -
294F GLY* 3.0 46.5 + - - +
295F PHE* 3.6 20.2 - - + +
298F PHE* 3.5 37.9 - - + -
314F ALA* 5.5 2.7 - - + +
315F HIS 4.5 2.4 + - - -
322F ALA* 4.9 3.1 - - + +
325F ALA* 3.5 45.8 - - + +
326F SER* 3.6 14.1 - - - +
329F ALA* 4.0 6.3 - - + -
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Residues in contact with GLY 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F GLU* 3.5 21.8 - - - -
38F ALA* 3.6 2.4 - - - -
39F GLY* 2.8 26.1 + - - -
91F SER* 3.3 15.8 + - - -
94F SER* 3.4 10.2 - - - -
98F ILE* 4.2 2.2 - - - +
288F ASP* 2.7 18.8 + - - -
289F LEU* 1.3 71.9 - - - +
291F THR* 1.3 54.9 + - - -
322F ALA* 6.4 0.4 - - - +
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Residues in contact with THR 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F GLY* 3.4 28.0 - - - +
40F ILE* 4.4 3.4 - - + -
87F THR* 4.8 2.2 - - + +
90F PHE* 3.2 27.7 - - - +
91F SER* 3.1 24.2 - - - +
94F SER* 3.2 3.6 - - - -
265F GLU 3.9 4.9 + - - -
267F ILE 5.0 0.5 + - - -
268F TYR* 3.6 33.1 - - + -
288F ASP* 3.0 20.6 + - + +
290F GLY* 1.3 80.9 - - - +
292F CYS* 1.3 61.0 + - - +
293F GLY 3.2 3.1 - - - -
81H TRP* 4.8 7.0 - - + -
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Residues in contact with CYS 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F PHE* 4.8 2.1 - - - -
267F ILE 4.6 4.7 - - - +
268F TYR* 4.2 3.8 - - - +
269F SER* 3.0 27.0 + - - +
287F PRO* 3.8 25.4 - - + -
288F ASP 2.8 30.2 + - - +
289F LEU* 4.2 0.7 - - - -
291F THR* 1.3 73.8 + - - +
293F GLY* 1.3 58.3 + - - +
294F GLY 4.0 5.2 - - - -
297F GLU* 3.2 13.7 - - - +
298F PHE* 3.8 38.8 - - - -
301F ILE* 3.8 9.9 - - + -
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Residues in contact with GLY 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F TRP* 2.9 36.0 + - - -
90F PHE* 4.3 5.8 - - - -
93F ILE* 4.7 1.3 - - - -
94F SER* 2.7 26.9 + - - -
97F ASP* 4.0 4.0 - - - +
291F THR 3.2 0.8 + - - -
292F CYS* 1.3 74.5 - - - +
294F GLY* 1.3 63.2 + - - +
297F GLU* 3.5 13.9 + - - +
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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