Contacts of the helix formed by residues 291 - 295 (chain C) in PDB entry 2O2C
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 SER 291 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192C HIS* 3.6 22.9 - - - -
277C LEU* 4.0 7.4 - - - +
278C LEU* 3.8 15.4 - - - +
281C LEU* 3.7 27.9 - - - +
288C GLU 2.7 21.8 + - - -
289C LYS 3.4 1.6 + - - -
290C GLY* 1.3 75.2 - - - +
292C VAL* 1.3 63.8 + - - +
294C LYS* 3.1 3.7 + - - +
295C HIS* 3.1 33.1 + - - +
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Residues in contact with VAL 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C ARG* 4.3 30.3 - - + -
277C LEU* 4.6 3.8 - - + -
278C LEU* 4.6 11.9 - - + -
288C GLU 5.6 0.7 - - - +
290C GLY* 3.5 0.6 - - - -
291C SER* 1.3 82.4 - - - +
293C ALA* 1.3 56.3 + - - +
296C PHE* 2.9 56.8 + - + +
309C PHE* 5.5 0.9 - - + -
310C GLY* 3.7 27.1 - - - +
311C ILE* 4.5 4.8 - - + +
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Residues in contact with ALA 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C TRP* 3.6 9.0 - - - -
290C GLY* 3.6 15.6 + - - +
291C SER 3.2 1.0 - - - -
292C VAL* 1.3 77.6 - - - +
294C LYS* 1.3 59.8 + - + +
296C PHE 4.7 0.2 - - - -
311C ILE* 6.3 0.4 - - - +
312C ASP* 3.7 33.4 + - - +
315C ASN* 2.8 31.0 + - - +
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Residues in contact with LYS 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C TRP* 2.8 33.0 + - - +
190C LYS 3.9 15.5 - - - +
191C GLY* 4.2 6.4 + - - +
192C HIS* 3.3 48.2 + - - +
197C ILE* 5.0 1.9 - - - +
253C LEU* 4.4 3.2 - - - +
289C LYS 5.3 0.2 - - - -
290C GLY* 3.1 25.8 - - - +
291C SER 3.1 4.4 + - - +
293C ALA* 1.3 82.9 - - + +
295C HIS* 1.3 68.6 + - + +
296C PHE 3.7 0.4 - - - -
297C VAL* 6.5 0.2 - - - -
315C ASN* 5.5 0.2 - - - -
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Residues in contact with HIS 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C GLY* 3.7 7.6 - - - -
192C HIS* 2.9 36.4 + - + +
197C ILE* 5.2 0.6 - - + +
249C ILE 3.4 14.4 + - - -
250C GLU* 3.4 28.2 - - - -
252C THR 2.8 24.2 + - - +
253C LEU* 3.9 6.1 - - - -
254C PHE* 2.7 39.5 + - + +
277C LEU* 3.7 33.8 - - + +
281C LEU* 6.1 0.2 - - - +
291C SER 3.1 24.1 + - - +
294C LYS* 1.3 81.7 + - + +
296C PHE* 1.3 59.4 + - + +
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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