Contacts of the helix formed by residues 328 - 332 (chain A) in PDB entry 2B9S
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 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A LEU* 5.2 2.2 - - - -
314A ARG* 3.6 13.0 - - - -
316A GLY* 3.5 17.6 - - - -
327A VAL* 1.3 75.3 - - - +
329A CYS* 1.3 69.9 + - - +
330A CYS 3.5 1.8 - - - -
331A SER* 3.1 14.3 + - - -
332A LEU* 3.2 17.0 + - - +
349A PHE* 5.0 6.1 - - - -
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Residues in contact with CYS 329 (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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304A ALA* 3.6 44.2 - - - -
307A PHE* 4.0 15.9 - - - -
308A ILE* 4.0 17.7 - - + -
313A LEU* 4.1 11.2 - - + +
314A ARG 2.7 19.7 + - - +
315A VAL 3.5 4.8 + - - +
328A GLY* 1.3 74.1 - - - +
330A CYS* 1.3 62.5 + - - +
331A SER 3.1 0.5 + - - -
332A LEU* 3.2 22.8 + - - +
385A PHE* 3.4 17.4 - - - -
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Residues in contact with CYS 330 (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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304A ALA* 4.9 0.7 - - - -
315A VAL* 2.8 39.9 + - - +
316A GLY 3.8 7.2 - - - +
329A CYS* 1.3 76.9 - - - +
331A SER* 1.3 56.8 - - - +
332A LEU 3.6 0.6 + - - +
383A ASP* 5.1 5.0 - - - +
385A PHE* 4.1 23.8 + - - +
388A LEU* 4.0 40.9 - - - +
389A ASN 4.2 1.6 - - - -
390A PRO* 4.0 23.1 - - + -
393A LEU* 4.4 8.7 - - - -
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Residues in contact with SER 331 (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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316A GLY* 3.5 15.8 + - - -
317A ASN 4.4 8.1 + - - -
318A GLU* 5.3 5.2 - - - -
326A THR 4.5 1.2 + - - -
327A VAL* 3.4 23.9 - - - +
328A GLY 3.1 23.3 + - - -
329A CYS 3.1 0.8 + - - -
330A CYS* 1.3 78.3 - - - +
332A LEU* 1.3 66.2 + - - +
333A ARG* 3.4 10.7 + - - +
383A ASP* 4.4 9.9 - - - +
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Residues in contact with LEU 332 (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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307A PHE* 4.4 12.3 - - + -
313A LEU* 4.2 14.4 - - + -
327A VAL* 3.9 11.7 - - + -
328A GLY 3.2 11.5 + - - +
329A CYS* 3.2 26.5 + - - +
330A CYS 3.6 0.6 - - - -
331A SER* 1.3 78.9 - - - +
333A ARG* 1.3 60.1 + - - +
336A HIS* 3.8 10.5 - - + +
337A ILE* 5.0 1.6 - - + -
347A PHE* 4.3 16.6 - - + -
349A PHE* 3.6 37.2 - - + -
383A ASP* 3.7 4.0 - - - +
384A ILE* 3.0 40.5 + - + +
385A PHE* 4.3 7.2 + - + -
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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