Contacts of the helix formed by residues 205 - 208 (chain B) 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 ILE 205 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B GLY* 1.3 74.2 - - - +
206B GLY* 1.3 68.7 + - - +
207B GLY 3.2 1.4 + - - -
208B SER* 3.1 15.2 + - - -
209B ASP* 3.8 3.6 - - - -
233B SER 3.3 26.0 - - - +
234B ASN* 4.5 0.2 - - - -
263B THR* 3.8 22.4 - - + -
265B GLU* 3.9 8.5 - - + -
266B THR* 3.6 15.7 + - - +
5002B G6Q 3.4 14.8 - - - +
438C THR* 3.7 23.6 - - - +
439C ASN* 4.0 24.7 - - - +
442C HIS* 3.7 28.9 - - + +
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Residues in contact with GLY 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B ILE* 1.3 75.7 - - - +
207B GLY* 1.3 57.9 + - - -
208B SER 3.1 0.4 - - - -
209B ASP* 3.0 7.8 + - - +
210B LEU* 2.8 36.9 + - - +
407B GLN* 3.3 13.6 - - - +
5002B G6Q 3.6 9.6 - - - -
439C ASN* 5.1 4.1 + - - +
442C HIS* 3.7 18.4 - - - -
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Residues in contact with GLY 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLY* 1.3 71.4 - - - -
208B SER* 1.3 57.3 + - - +
209B ASP 3.3 2.3 + - - -
210B LEU* 4.8 1.8 - - - -
211B GLY* 4.8 2.7 + - - -
212B PRO* 4.6 4.7 - - - +
325B GLY* 3.3 24.3 - - - +
326B ARG* 4.2 1.3 - - - -
328B SER* 3.1 20.0 + - - -
329B MET 5.3 0.5 + - - -
333B ILE* 3.7 6.2 - - - +
407B GLN* 3.4 8.0 - - - +
5002B G6Q 2.9 26.8 + - - -
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Residues in contact with SER 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ASN* 3.1 21.3 + - - -
204B GLY* 3.6 5.2 - - - -
205B ILE 3.1 15.9 + - - -
207B GLY* 1.3 77.0 - - - +
209B ASP* 1.3 58.0 + - - +
212B PRO* 4.6 6.1 - - - +
257B ALA* 3.3 31.7 + - - +
258B SER* 3.7 0.3 - - - -
259B LYS* 4.1 0.9 + - - +
319B PHE* 5.3 0.3 - - - -
325B GLY* 6.0 0.2 - - - -
328B SER* 5.4 0.2 + - - -
333B ILE* 3.5 22.8 - - - +
5002B G6Q 2.8 23.9 + - - -
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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