Contacts of the helix formed by residues 289 - 295 (chain X) 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 ILE 289 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166X TYR* 3.7 39.7 - - + -
171X LEU* 3.6 33.0 - - + -
285X CYS* 4.0 8.3 - - + -
286X ASP* 3.1 41.5 + - + +
287X ILE 3.2 0.6 - - - -
288X ASP* 1.4 76.2 - - + +
290X ARG* 1.3 66.0 + - - +
291X LYS* 3.3 6.3 - - - +
292X ASP* 3.0 18.1 + - - +
293X LEU* 3.3 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 290 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282X ILE* 3.4 35.6 + - + +
283X MET* 3.9 46.2 + - - +
285X CYS* 2.4 32.4 + - + -
286X ASP 3.3 8.8 + - - +
287X ILE* 3.8 11.5 - - - +
288X ASP 3.4 1.6 - - - -
289X ILE* 1.3 78.4 - - - +
291X LYS* 1.4 61.6 + - - +
292X ASP 3.3 0.2 + - - -
293X LEU* 4.1 7.7 - - - +
294X TYR* 3.1 33.0 + - + -
325X MET* 4.7 5.6 - - + -
201Z VAL* 4.5 12.7 - - - +
202Z THR* 2.2 40.5 + - - +
205Z GLU* 5.3 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 291 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287X ILE 4.7 2.5 + - - +
288X ASP* 3.0 29.4 + - - +
289X ILE 3.3 0.6 - - - -
290X ARG* 1.4 76.4 - - - +
292X ASP* 1.4 96.9 + - - +
294X TYR* 3.4 2.8 + - - +
295X ALA* 3.2 23.2 + - - +
325X MET* 3.7 25.4 - - + +
326X LYS* 4.5 2.4 - - - +
204Z ALA* 5.6 4.3 - - + -
243Z PRO* 6.0 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 292 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149X THR* 3.9 22.8 - - + +
166X TYR* 4.0 19.9 + - - -
289X ILE* 3.0 9.8 + - - +
291X LYS* 1.4 103.2 + - - +
293X LEU* 1.3 68.6 + - - +
295X ALA* 3.1 5.7 + - - -
296X ASN* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149X THR* 3.8 22.7 - - + -
150X GLY* 3.8 19.7 - - - +
151X ILE* 3.4 30.4 - - + +
164X PRO* 4.4 5.8 - - + -
165X ILE 4.3 5.2 - - - +
282X ILE* 4.5 17.7 - - + -
285X CYS* 4.0 22.2 - - + -
289X ILE* 3.3 42.7 + - + +
290X ARG* 4.1 6.7 - - - +
292X ASP* 1.3 77.1 - - - +
294X TYR* 1.3 64.2 + - - +
296X ASN 3.0 20.8 + - - -
297X ASN* 3.7 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 294 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279X TYR* 3.4 18.9 - + - -
282X ILE* 3.6 37.9 - - + +
283X MET* 3.4 32.8 - - + +
290X ARG* 3.1 28.4 + - + +
291X LYS 3.7 3.1 - - - +
292X ASP 3.2 1.0 - - - -
293X LEU* 1.3 78.2 - - - +
295X ALA* 1.3 59.7 + - - +
296X ASN 3.1 1.1 + - - -
297X ASN* 4.6 2.2 + - - +
317X ILE* 4.0 18.6 - - + +
321X ALA* 3.6 21.2 - - + +
322X PRO* 4.7 0.2 - - + -
325X MET* 3.4 33.2 - - + -
326X LYS 3.2 15.3 - - - +
327X ILE* 3.4 16.8 - - + -
328X LYS 2.8 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291X LYS 3.2 11.9 + - - +
292X ASP* 3.1 4.1 + - - -
294X TYR* 1.3 77.7 - - - +
296X ASN* 1.4 75.3 + - - +
326X LYS* 3.8 32.5 - - + +
328X LYS* 3.2 33.8 - - + +
330X ILE* 3.8 0.9 - - - +
----------------------------------------------------------
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