Contacts of the helix formed by residues 232 - 241 (chain B) in PDB entry 4OMD
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 THR 232 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ASP* 3.8 19.9 + - - +
230B GLU* 3.2 39.4 + - + +
231B VAL* 1.3 76.7 - - - +
233B ASP* 1.3 65.2 + - - +
234B ALA* 3.6 3.8 + - - +
235B VAL* 3.0 26.0 + - + +
236B GLU* 3.0 25.5 + - - +
1I HY1 5.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A ARG* 5.6 0.2 + - - -
530A ASP* 5.0 4.7 - - - +
565A LYS* 6.3 3.6 - - + -
232B THR* 1.3 74.1 - - - +
234B ALA* 1.3 58.3 + - - +
236B GLU* 3.2 10.0 + - - +
237B ALA* 2.8 28.3 + - - +
267B ALA* 3.1 34.5 + - + +
268B ARG* 3.7 2.4 + - - +
269B LEU* 2.9 33.4 + - + +
270B ALA* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ILE* 3.9 22.4 - - + -
453A ASP* 3.8 32.3 - - + +
567A THR* 4.7 2.0 - - + +
232B THR* 3.2 1.9 + - - +
233B ASP* 1.3 78.6 - - - +
235B VAL* 1.3 62.9 + - + +
237B ALA* 3.7 2.1 - - - +
238B ARG* 3.0 35.6 + - + +
269B LEU* 4.0 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B VAL* 3.9 23.5 - - + +
176B ASN* 4.5 4.9 - - - +
226B MET* 3.7 39.7 - - + +
230B GLU 3.4 18.2 - - - +
231B VAL* 4.3 7.4 - - + -
232B THR* 3.0 32.0 + - + +
234B ALA* 1.3 77.8 - - + +
236B GLU* 1.3 62.8 + - - +
238B ARG* 3.4 2.1 + - - +
239B SER* 2.8 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B MET* 4.3 5.2 - - + -
231B VAL* 3.7 13.8 - - + +
232B THR 3.0 18.8 + - - +
233B ASP* 3.6 9.6 - - - +
235B VAL* 1.3 76.6 - - - +
237B ALA* 1.3 58.6 + - - +
239B SER* 3.1 5.8 + - - -
240B LEU* 2.8 38.9 + - + +
254B TRP* 3.7 21.6 - - + -
266B PRO* 4.4 0.7 - - - +
267B ALA 4.8 0.5 + - - -
270B ALA* 3.8 16.9 - - + +
308B TYR* 2.6 28.7 + - - -
2I ARG* 2.9 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ILE* 3.7 16.8 - - + +
233B ASP 2.8 20.7 + - - +
234B ALA 3.7 4.3 - - - +
235B VAL 3.3 0.2 - - - -
236B GLU* 1.3 73.3 - - - +
238B ARG* 1.3 57.1 + - - +
241B GLY* 2.9 26.7 + - - -
269B LEU* 3.6 36.1 - - + +
270B ALA* 4.3 2.8 - - - +
273B ALA* 3.8 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ILE* 3.9 40.8 + - + +
474A CYS* 5.1 4.9 - - - -
477A GLU* 3.3 34.4 + - - -
479A ASN* 5.9 1.0 + - - -
173B PHE* 4.1 18.8 - - - -
175B VAL* 4.0 24.0 - - + +
178B GLN* 3.1 35.1 + - - +
234B ALA* 3.0 22.2 + - - +
235B VAL 4.0 3.4 - - - +
237B ALA* 1.3 76.7 - - - +
239B SER* 1.3 60.7 + - - +
241B GLY* 3.7 1.7 - - - -
242B LEU* 3.2 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 3.8 21.1 - - - +
175B VAL* 3.8 3.6 - - - +
224B VAL* 3.6 22.4 - - - +
226B MET* 3.2 34.1 - - - +
235B VAL 2.8 18.7 + - - -
236B GLU 3.1 7.3 + - - -
238B ARG* 1.3 75.6 - - - +
240B LEU* 1.3 65.2 + - - +
241B GLY 3.3 0.9 + - - -
242B LEU* 3.3 16.6 + - - +
250B TYR* 3.7 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 3.5 22.9 - - + -
236B GLU* 2.8 31.7 + - + +
239B SER* 1.3 72.0 - - - +
241B GLY* 1.3 57.8 + - - +
242B LEU 3.4 0.2 - - - -
250B TYR* 3.3 21.3 + - + -
254B TRP* 5.2 2.7 - - + -
270B ALA* 4.2 20.6 - - + +
273B ALA* 4.0 12.8 - - + +
274B PHE* 3.8 28.3 - - + -
277B GLY* 5.9 0.9 - - - -
287B SER* 5.4 0.2 + - - -
289B PHE* 3.7 33.2 - - + -
291B TRP* 3.9 27.6 - - + -
308B TYR* 5.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A ASN* 5.7 1.0 - - - +
237B ALA 2.9 16.7 + - - -
238B ARG* 3.7 4.3 - - - -
240B LEU* 1.3 78.7 - - - +
242B LEU* 1.3 60.0 + - - +
243B ASN 3.4 0.9 + - - -
244B PRO* 3.4 24.7 - - - +
250B TYR* 4.4 0.2 - - - -
273B ALA* 4.4 8.9 - - - +
----------------------------------------------------------
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