Contacts of the helix formed by residues 265 - 269 (chain A) in PDB entry 4QA7
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 GLY 265 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LEU 3.9 3.1 - - - +
178A ASP* 3.5 31.9 - - - +
263A GLN* 2.8 15.7 + - - -
264A LEU* 1.3 71.8 - - - +
266A ALA* 1.3 58.5 + - - -
267A ASP* 3.2 13.5 + - - +
268A THR* 3.9 11.1 + - - -
284A ILE* 5.9 0.9 - - - +
303A GLY* 4.0 4.5 - - - -
304A GLY 3.5 12.8 - - - -
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Residues in contact with ALA 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU 3.3 2.5 + - - -
265A GLY* 1.3 69.9 - - - -
267A ASP* 1.3 52.6 + - - -
268A THR 3.1 8.6 + - - -
269A ILE* 3.3 35.4 + - + +
272A ASP* 4.0 5.7 - - - +
304A GLY 2.7 12.0 + - - +
305A GLY* 3.8 5.4 - - - -
311A THR* 3.9 30.1 + - + +
314A CYS* 4.3 7.4 - - + -
315A TRP* 3.8 18.6 - - - +
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Residues in contact with ASP 267 (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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178A ASP* 3.2 7.4 - - - +
179A LEU* 3.1 49.7 + - + +
180A HIS* 3.1 8.5 + - - -
265A GLY 3.5 4.2 - - - +
266A ALA* 1.3 71.7 - - - +
268A THR* 1.3 58.0 + - - +
269A ILE 3.4 0.4 - - - -
272A ASP* 3.3 28.0 - - - +
274A MET* 4.9 0.4 - - - +
275A CYS 5.8 0.2 + - - -
276A SER* 5.6 1.2 + - - -
277A PHE 5.3 1.2 + - - -
304A GLY* 3.7 7.2 - - - -
305A GLY 3.5 12.9 - - - +
306A PHE* 3.7 10.6 - - + -
401A ZN 2.1 34.4 - - - -
505B ALY 3.0 4.2 - - - +
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Residues in contact with THR 268 (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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177A LEU 3.4 24.9 - - - +
178A ASP 3.8 0.9 - - - +
179A LEU* 3.4 25.1 - - - +
240A TYR* 5.1 3.6 - - + +
265A GLY 3.9 8.6 + - - +
267A ASP* 1.3 79.4 - - - +
269A ILE* 1.3 78.4 + - - +
277A PHE* 3.3 47.4 - - + +
279A MET* 3.3 17.6 + - - +
284A ILE* 4.1 13.8 - - - +
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Residues in contact with ILE 269 (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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266A ALA* 3.3 25.2 + - + +
268A THR* 1.3 87.6 - - - +
270A ALA* 1.3 77.6 + - - +
272A ASP* 3.2 23.2 + - - +
277A PHE 4.7 1.0 - - - +
279A MET* 3.5 11.0 - - + +
280A THR 3.7 27.1 - - - +
281A PRO* 3.8 5.6 - - + -
284A ILE* 4.1 8.1 - - + -
310A ASN* 4.6 10.8 - - + +
314A CYS* 3.9 26.2 - - + -
348A ILE* 3.8 26.7 - - + -
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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