Contacts of the helix formed by residues 360 - 366 (chain A) in PDB entry 3OX4
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 360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A ALA* 3.6 16.2 - - + -
267A HIS* 3.2 27.6 + - - +
268A GLN* 3.9 12.9 + - - +
356A HIS 3.2 4.0 + - - -
357A ALA 3.0 14.4 + - - +
358A LEU 4.2 0.9 - - - +
359A LYS* 1.3 79.8 - - - +
361A ALA* 1.3 67.3 + - - +
362A CYS* 2.8 42.3 + - - +
363A ALA* 3.1 18.2 + - - +
364A LEU* 4.2 1.7 + - - +
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Residues in contact with ALA 361 (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* 4.9 4.4 + - - -
359A LYS 3.6 3.3 + - - -
360A ASP* 1.3 75.0 + - - +
362A CYS* 1.3 63.1 + - - +
363A ALA 3.2 0.7 + - - -
364A LEU* 3.5 21.9 + - - +
365A THR* 4.7 1.6 + - - +
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Residues in contact with CYS 362 (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* 4.8 9.4 - - - -
259A LEU* 4.2 18.2 - - + -
260A GLY* 3.3 40.3 - - - +
263A HIS* 4.2 8.3 - - - -
264A ALA 4.0 4.3 - - - +
267A HIS* 4.0 20.2 - - - -
360A ASP* 2.8 18.9 + - - +
361A ALA* 1.3 78.0 - - - +
363A ALA* 1.3 63.9 + - - +
364A LEU 3.3 0.5 + - - -
365A THR* 3.5 11.1 + - - -
1385A NAD 5.1 3.6 - - - -
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Residues in contact with ALA 363 (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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261A TYR* 3.6 26.9 - - + -
264A ALA* 3.8 6.0 - - + +
357A ALA 3.6 18.8 - - - +
358A LEU* 4.0 13.9 - - + +
360A ASP 3.1 15.2 + - - +
362A CYS* 1.3 80.5 - - - +
364A LEU* 1.3 61.4 + - - +
366A ASN* 3.3 9.0 + - - +
369A GLN* 3.2 21.1 + - - +
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Residues in contact with LEU 364 (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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206A THR* 4.2 5.0 + - - +
360A ASP 4.2 0.8 + - - +
361A ALA* 3.5 15.8 + - - +
362A CYS 3.2 0.6 - - - -
363A ALA* 1.3 78.9 - - - +
365A THR* 1.3 67.3 + - + +
366A ASN 3.7 0.9 + - - +
369A GLN* 3.9 15.7 + - - +
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Residues in contact with THR 365 (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 SER* 3.3 25.9 - - - +
206A THR* 3.0 34.8 + - - +
207A ALA* 4.0 11.2 - - + -
257A ALA 4.0 7.6 - - - +
258A SER* 3.6 18.9 + - - +
259A LEU 2.7 22.7 + - - +
361A ALA 5.0 0.8 + - - +
362A CYS* 3.5 5.4 + - - -
363A ALA 3.3 0.4 - - - -
364A LEU* 1.3 86.2 - - + +
366A ASN* 1.3 66.2 + - - +
367A PRO 3.3 1.0 - - - -
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Residues in contact with ASN 366 (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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201A GLU* 4.3 0.9 - - - +
206A THR* 4.0 5.4 - - - +
260A GLY* 3.6 7.3 - - - -
261A TYR* 2.8 60.3 + - + +
292A ASN* 2.9 37.1 + - - -
362A CYS 4.0 1.8 + - - -
363A ALA 3.3 8.4 + - - +
364A LEU 4.4 0.2 - - - +
365A THR* 1.3 79.1 + - - +
367A PRO* 1.3 69.1 - - - +
368A ARG 2.7 26.1 + - - +
369A GLN* 2.9 20.3 + - - +
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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