Contacts of the helix formed by residues 310 - 315 (chain F) in PDB entry 4BQ7
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 GLN 310 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188F PRO 3.7 3.1 - - - -
189F LEU 3.5 9.2 - - - +
190F ILE* 3.8 10.7 - - - +
191F ASP* 3.1 42.1 + - + +
192F ASN* 4.1 6.1 + - - +
303F TYR* 3.3 34.6 - - - -
307F GLN 3.0 23.1 + - - +
308F ASP 3.8 4.0 + - - -
309F LEU* 1.3 80.2 - - - +
311F LEU* 1.3 57.2 + - - +
312F CYS 3.2 2.0 - - - -
313F VAL* 2.8 41.6 + - + +
314F ASN* 3.1 16.0 + - - +
315F GLY 4.0 2.4 + - - -
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Residues in contact with LEU 311 (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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165E LEU* 5.4 4.9 - - + -
171F LEU* 3.4 17.3 - - + +
173F THR* 3.5 1.9 - - - +
183F VAL* 4.1 21.8 - - + -
187F TRP* 3.9 31.6 - - + -
188F PRO 3.1 19.8 + - - +
189F LEU* 3.9 26.2 - - + -
199F VAL* 5.7 0.4 - - + -
309F LEU* 4.3 12.1 - - + -
310F GLN* 1.3 70.9 - - - +
312F CYS* 1.3 57.3 + - - +
315F GLY* 2.9 39.5 + - - +
316F CYS* 3.9 30.5 - - - -
317F PRO* 4.5 0.2 - - + -
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Residues in contact with CYS 312 (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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163E CYS* 2.0 52.7 - - + -
173F THR* 3.4 3.8 - - - +
174F PHE* 2.8 48.8 + - + +
189F LEU* 3.1 40.3 + - - +
190F ILE* 3.9 12.3 - - + -
293F ILE* 4.4 1.8 - - - -
311F LEU* 1.3 75.1 - - - +
313F VAL* 1.3 60.2 + - + +
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Residues in contact with VAL 313 (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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173F THR* 4.4 4.5 - - - -
174F PHE* 4.1 16.4 - - + -
175F LYS* 3.7 32.9 - - - +
177F ASN* 4.8 0.9 - - - +
300F ALA 4.0 17.7 - - - +
301F MET* 4.0 17.9 - - - -
303F TYR* 3.6 23.8 - - + +
310F GLN* 2.8 38.7 + - + +
312F CYS* 1.3 82.2 - - + +
314F ASN* 1.3 74.2 + - - +
315F GLY 3.5 0.8 + - - -
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Residues in contact with ASN 314 (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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173F THR* 4.9 0.9 - - - -
175F LYS* 3.9 12.7 + - - +
177F ASN* 5.2 3.4 - - - +
179F GLN* 4.8 3.8 + - - -
303F TYR* 4.3 9.7 + - - -
308F ASP* 3.5 28.8 + - - +
310F GLN* 3.1 11.7 + - - +
313F VAL* 1.3 93.6 - - - +
315F GLY* 1.3 66.2 + - - +
316F CYS 4.6 3.1 - - - +
321F ARG* 5.0 3.5 + - - -
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Residues in contact with GLY 315 (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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171F LEU* 3.8 1.8 - - - -
173F THR* 3.7 13.4 - - - +
177F ASN* 5.3 0.2 - - - -
179F GLN* 3.4 13.7 - - - -
309F LEU* 5.5 1.9 - - - +
310F GLN 4.3 1.2 - - - +
311F LEU* 2.9 40.1 + - - +
313F VAL 3.5 1.8 + - - -
314F ASN* 1.3 85.1 - - - +
316F CYS* 1.3 60.7 + - - -
317F PRO* 4.2 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