Contacts of the helix formed by residues 205 - 208 (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 ILE 205 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438B THR* 3.5 25.1 - - - +
439B ASN* 3.9 25.6 - - - +
442B HIS* 3.6 40.6 - - + +
204C GLY* 1.3 73.8 - - - +
206C GLY* 1.3 69.7 + - - +
207C GLY 3.2 1.6 + - - -
208C SER* 3.1 14.1 + - - -
209C ASP* 3.8 3.8 - - - -
233C SER* 3.3 25.8 - - - +
263C THR* 3.8 10.3 - - + -
265C GLU* 3.9 8.5 - - + -
266C THR* 3.6 15.7 + - - +
5003C G6Q 3.3 19.3 - - - +
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Residues in contact with GLY 206 (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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439B ASN* 5.1 4.0 + - - +
442B HIS* 3.6 28.7 - - - -
205C ILE* 1.3 75.9 - - - +
207C GLY* 1.3 58.0 + - - -
208C SER 3.1 0.4 - - - -
209C ASP* 3.0 7.6 + - - +
210C LEU* 2.9 36.7 + - - +
407C GLN* 3.3 12.4 - - - +
5003C G6Q 4.2 0.2 - - - -
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Residues in contact with GLY 207 (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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205C ILE 3.2 0.2 + - - -
206C GLY* 1.3 70.0 - - - -
208C SER* 1.3 58.8 + - - +
209C ASP 3.3 2.6 + - - -
210C LEU* 4.8 1.1 - - - -
211C GLY* 4.8 3.8 + - - -
212C PRO* 4.6 4.5 - - - +
325C GLY* 3.2 22.7 - - - +
326C ARG* 4.2 1.3 - - - -
328C SER* 3.1 20.1 + - - -
329C MET 5.3 0.7 + - - -
333C ILE* 3.7 5.7 - - - +
407C GLN* 3.3 11.0 - - - +
5003C G6Q 2.9 23.0 + - - -
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Residues in contact with SER 208 (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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202C ASN* 3.1 21.5 + - - -
204C GLY* 3.6 6.6 - - - -
205C ILE 3.1 14.5 + - - -
207C GLY* 1.3 77.1 - - - +
209C ASP* 1.3 59.0 + - - +
212C PRO* 4.6 6.4 - - - +
257C ALA* 3.3 31.7 + - - +
258C SER* 3.7 1.6 - - - -
259C LYS* 4.1 0.7 + - - +
319C PHE* 5.4 0.2 - - - -
325C GLY* 5.9 0.3 - - - -
328C SER* 5.3 0.3 + - - -
333C ILE* 3.5 22.4 - - - +
5003C G6Q 2.8 25.3 + - - -
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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