Contacts of the helix formed by residues 227 - 239 (chain C) in PDB entry 2OQH
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 VAL 227 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLU* 5.2 13.2 - - + +
200C ALA* 3.5 29.4 + - + +
202C TRP 4.6 0.4 + - - -
204C VAL* 5.3 2.4 - - + +
226C CYS* 1.3 76.3 - - + +
228C GLY* 1.3 69.0 + - - +
231C GLY* 3.7 16.5 + - - -
247C MSE 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLU* 4.8 22.1 - - - +
226C CYS 4.0 1.0 + - - -
227C VAL* 1.3 75.7 - - - +
229C ILE* 1.3 61.0 - - - -
230C GLU* 3.2 3.4 - - - -
231C GLY 4.7 0.2 - - - -
232C MSE 2.9 32.9 + - - +
248C CYS* 3.8 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ILE* 6.4 0.4 - - + -
253A GLU 4.9 5.5 + - - +
257A PRO* 3.9 13.9 - - + -
228C GLY* 1.3 70.9 - - - -
230C GLU* 1.3 63.4 + - - +
233C ALA* 3.0 23.4 + - - +
248C CYS* 3.5 33.8 - - + +
254C ASP* 4.0 28.0 - - + +
257C PRO* 4.4 9.4 - - + -
258C ALA* 4.1 15.9 - - + +
261C LEU* 3.7 28.0 - - + -
263C ALA* 3.7 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLU 5.5 0.6 + - - +
256A ALA* 3.4 35.1 - - + +
257A PRO* 4.2 7.6 - - + +
260A ARG* 2.6 42.1 + - - -
228C GLY* 3.2 1.0 - - - -
229C ILE* 1.3 80.6 - - - +
231C GLY* 1.3 63.7 + - - +
233C ALA* 3.3 6.6 + - - +
234C GLN* 3.0 52.1 + - + +
261C LEU* 5.2 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C VAL* 3.6 23.6 - - - +
226C CYS* 3.5 7.2 - - - -
227C VAL 3.7 12.4 + - - -
228C GLY* 3.4 3.4 + - - -
230C GLU* 1.3 80.4 - - - +
232C MSE 1.3 61.3 + - - +
234C GLN* 2.9 18.7 + - - +
235C VAL* 3.1 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ASP* 3.7 16.4 - - - +
225C PRO* 3.4 28.9 - - - -
226C CYS* 3.5 23.9 - - - +
228C GLY 2.9 21.5 + - - +
229C ILE* 4.0 3.1 - - - +
231C GLY* 1.3 75.0 - - - +
233C ALA* 1.3 62.3 + - - +
235C VAL* 3.2 2.0 + - - -
236C LYS* 3.0 19.2 + - - +
243C LEU* 3.2 34.3 - - + +
244C CYS 3.3 25.8 - - - +
245C THR* 3.9 9.6 - - - -
248C CYS* 4.0 15.7 - - + -
263C ALA* 3.6 12.1 - - + +
264C VAL* 4.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C ILE 3.0 20.2 + - - +
230C GLU* 3.6 7.4 - - - +
231C GLY 3.2 0.2 - - - -
232C MSE 1.3 75.3 - - - +
234C GLN* 1.3 64.9 + - + +
236C LYS* 3.4 2.3 + - - +
237C ALA* 3.0 23.4 + - - +
261C LEU* 3.3 31.2 - - + +
262C ASN 3.9 3.7 - - - +
263C ALA* 3.8 13.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ARG* 3.7 14.3 - - - +
204C VAL* 3.8 20.0 - - + -
208C VAL* 4.8 2.6 - - + +
230C GLU* 3.0 38.2 + - + +
231C GLY* 2.9 9.7 + - - +
233C ALA* 1.3 80.3 - - - +
235C VAL* 1.3 63.0 + - - +
237C ALA* 3.3 17.4 + - - +
238C LYS* 3.4 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 235 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C VAL* 4.2 10.1 - - + +
207C SER* 3.7 28.3 - - - +
208C VAL* 4.6 7.9 - - + -
222C LEU* 4.5 7.0 - - + -
225C PRO* 4.5 13.0 - - + -
226C CYS* 3.8 15.0 - - - -
231C GLY 3.1 13.1 + - - +
232C MSE 3.2 6.5 + - - +
234C GLN* 1.3 77.5 - - - +
236C LYS* 1.3 55.7 + - - +
238C LYS* 3.1 1.4 + - - -
239C VAL* 2.7 54.7 + - + +
243C LEU* 4.3 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 236 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C MSE 3.0 14.8 + - - +
233C ALA 3.8 4.5 - - - +
235C VAL* 1.3 78.0 - - - +
237C ALA* 1.3 63.1 + - - +
238C LYS 3.2 0.7 + - - -
239C VAL 3.6 16.6 - - - +
241C ILE 5.9 0.9 - - - +
243C LEU* 3.9 14.1 - - + +
262C ASN* 3.3 46.3 + - + +
263C ALA 4.2 7.6 - - - +
264C VAL* 3.7 11.8 + - - +
265C ASP* 2.9 38.8 + - - +
292C LEU* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 237 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C ALA 3.0 13.4 + - - +
234C GLN* 3.5 16.8 - - - +
235C VAL 3.2 0.4 - - - -
236C LYS* 1.3 77.3 - - - +
238C LYS* 1.3 64.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C VAL* 4.1 30.0 - - + +
212C ILE* 5.3 7.4 - - + +
215C GLU* 4.1 3.8 - - - +
234C GLN 3.4 9.3 + - - +
235C VAL 3.1 4.9 + - - +
237C ALA* 1.3 85.7 - - + +
239C VAL* 1.3 63.9 + - - +
240C ARG* 3.7 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C VAL* 3.9 22.2 - - - +
211C GLY* 3.8 28.0 - - - +
212C ILE* 4.2 2.9 - - + +
215C GLU* 3.7 3.1 - - - +
222C LEU* 4.5 7.2 - - + -
235C VAL* 2.7 38.3 + - + +
236C LYS* 3.6 17.3 - - - +
238C LYS* 1.3 75.2 - - + +
240C ARG* 1.3 61.8 + - - +
241C ILE* 3.2 45.5 + - + +
----------------------------------------------------------
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