Contacts of the helix formed by residues 252 - 257 (chain V) in PDB entry 1O1F
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 ASN 252 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196V ARG* 3.5 19.2 + - - -
227V MET* 5.7 1.3 - - - -
230V ALA* 3.3 43.4 + - + +
233V SER* 5.0 2.0 + - - -
236V LEU* 3.9 11.6 - - - +
237V GLU* 4.0 9.6 + - - +
251V GLY* 1.3 75.6 - - - +
253V GLU* 1.4 57.2 + - - +
254V ARG* 2.8 16.2 + - - +
255V PHE* 3.1 36.1 + - + -
256V ARG* 3.8 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 253 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189V LEU* 4.6 6.1 - - + +
192V ILE* 3.6 27.9 - - + +
193V LEU* 4.1 17.5 - - + -
196V ARG* 3.3 39.2 + - - +
250V ILE* 3.5 12.0 - - + -
251V GLY 3.0 28.9 + - - -
252V ASN* 1.4 70.5 + - - +
254V ARG* 1.3 65.7 + - - +
255V PHE 3.1 1.3 - - - -
256V ARG* 3.0 44.6 + - - +
257V CYS* 3.1 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 254 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189V LEU* 5.7 0.4 - - - -
215V LYS 5.4 0.4 + - - -
216V LEU* 2.9 33.8 + - + +
217V CYS* 2.9 29.8 - - - +
218V TYR* 3.1 57.3 + - + +
236V LEU 3.1 21.7 + - - -
237V GLU 4.3 0.2 + - - -
238V LYS* 3.5 30.9 - - - +
250V ILE* 3.6 24.3 - - + +
251V GLY 3.1 26.7 - - - +
252V ASN 3.5 0.9 - - - +
253V GLU* 1.3 73.9 - - - +
255V PHE* 1.4 59.7 + - + +
258V PRO* 3.7 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 255 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218V TYR* 3.4 22.9 - - + +
220V ALA* 4.4 3.4 - - + -
223V PHE* 3.0 50.1 - + + -
226V GLU* 3.4 55.4 - - + -
227V MET* 3.3 35.0 - - + -
230V ALA* 4.8 2.0 - - + -
236V LEU* 4.5 9.2 - - + -
251V GLY 5.1 0.9 - - - -
252V ASN* 3.1 29.8 + - - -
253V GLU 3.1 0.2 - - - -
254V ARG* 1.4 80.1 - - + +
256V ARG* 1.3 70.2 + - + +
257V CYS 3.1 2.5 - - - -
258V PRO* 3.6 1.6 - - - +
259V GLU* 3.1 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 256 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188V TYR* 3.3 22.7 + - - +
192V ILE* 3.6 44.6 + - + +
195V GLU* 3.7 13.5 + - - -
196V ARG* 6.2 0.2 - - - +
227V MET* 3.7 33.5 - - + +
252V ASN* 3.8 9.4 - - - +
253V GLU* 3.0 45.3 + - - +
255V PHE* 1.3 85.9 - - + +
257V CYS* 1.3 59.7 + - - +
259V GLU* 4.0 8.1 - - - -
260V THR* 3.4 2.3 + - - -
266V PHE* 3.3 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 257 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185V LEU* 3.2 39.2 - - - +
188V TYR* 3.8 9.6 - - - -
189V LEU* 3.8 18.2 - - + -
192V ILE* 4.0 7.5 - - + +
213V LYS* 4.2 17.7 - - - -
217V CYS* 4.2 9.0 - - - -
253V GLU 3.1 14.0 + - - +
255V PHE 3.1 0.8 - - - -
256V ARG* 1.3 75.5 - - - +
258V PRO* 1.3 69.2 - - + +
260V THR* 2.6 27.7 + - - -
306V TYR* 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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