Contacts of the helix formed by residues 225 - 239 (chain A) in PDB entry 1OE4
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 GLY 225 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A GLY 3.8 1.6 - - - +
224A VAL* 1.3 76.6 - - - +
226A ARG* 1.3 65.2 + - - -
227A PHE* 3.3 3.1 - - - -
228A SER 3.5 1.7 + - - -
229A GLU* 3.1 24.3 + - - +
248A ILE 3.0 19.9 + - - -
250A HIS* 3.7 13.7 - - - +
282E C 3.2 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLY* 1.3 69.3 - - - -
227A PHE* 1.3 67.1 + - - +
229A GLU* 3.3 29.2 + - - -
230A GLN* 2.9 47.5 + - - +
247A GLY* 5.5 3.4 - - - -
248A ILE 6.0 0.9 - - - -
269A GLN* 6.0 2.2 - - - +
1284A GOL 4.0 6.5 - - - +
282E C 2.9 42.9 + - - +
283E C 3.8 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A MET* 3.6 44.4 - - + -
175A HIS* 5.1 7.0 - + + -
190A PRO* 4.5 6.5 - - + -
191A THR* 3.4 25.1 - - - +
198A ARG* 5.9 1.3 - - - -
202A LEU* 3.9 37.0 - - + -
225A GLY 3.3 0.2 - - - -
226A ARG* 1.3 78.3 - - - +
228A SER* 1.3 66.4 + - - +
230A GLN* 4.0 1.0 - - - +
231A ARG* 3.0 51.4 + - + +
1284A GOL 3.9 33.9 + - - -
282E C 3.2 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 3.4 28.4 + - - +
94A GLY 3.2 5.9 + - - -
95A MET* 3.1 35.0 + - - +
175A HIS* 5.6 2.0 - - - -
223A GLY* 4.1 3.4 - - - -
224A VAL 3.7 11.9 + - - -
225A GLY 3.5 3.0 + - - -
226A ARG 3.4 0.4 - - - -
227A PHE* 1.3 80.8 - - - +
229A GLU* 1.3 61.8 + - - +
231A ARG* 3.9 2.4 - - - +
232A ALA* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A GLY* 3.9 10.9 - - - -
225A GLY 3.1 17.3 + - - +
226A ARG* 3.3 37.5 + - - +
228A SER* 1.3 78.4 - - - +
230A GLN* 1.3 60.1 + - + +
232A ALA* 3.4 0.4 + - - -
233A ARG* 2.8 62.2 + - - +
245A VAL* 3.6 7.5 - - + +
246A LYS* 3.6 15.5 - - - +
247A GLY* 3.5 25.4 + - - -
248A ILE 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ARG* 2.9 30.2 + - - +
227A PHE 4.1 1.8 - - - +
229A GLU* 1.3 78.0 - - + +
231A ARG* 1.3 63.5 + - - +
233A ARG* 3.4 12.2 + - - +
234A LYS* 2.7 49.9 + - - +
1284A GOL 3.0 45.3 + - - +
283E C 4.7 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A HIS* 3.5 25.4 - - + +
198A ARG* 5.9 0.2 - - - +
199A ASP* 5.2 9.3 + - - +
202A LEU* 3.5 41.8 + - - +
203A GLU* 4.1 9.7 - - - +
206A ASP* 3.0 29.5 + - - +
227A PHE* 3.0 43.5 + - + +
228A SER* 3.9 5.2 - - - +
230A GLN* 1.3 78.7 - - - +
232A ALA* 1.3 62.2 + - - +
234A LYS* 3.5 5.1 + - - +
235A ALA* 3.1 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 3.8 21.1 - - + -
175A HIS* 5.1 0.6 + - - -
209A LEU* 4.0 17.0 - - + +
221A VAL* 4.2 17.5 - - + -
228A SER 2.9 19.2 + - - +
229A GLU* 3.8 2.9 - - - +
231A ARG* 1.3 75.1 - - - +
233A ARG* 1.3 64.9 + - - +
235A ALA* 4.6 0.2 - - - -
236A LEU* 3.0 34.9 + - + +
245A VAL* 4.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLU* 2.8 59.7 + - - +
230A GLN* 3.8 16.3 - - - +
231A ARG 3.3 0.2 - - - -
232A ALA* 1.3 77.8 - - - +
234A LYS* 1.3 68.3 + - - +
236A LEU* 4.1 0.3 - - - +
237A MET* 3.0 49.7 + - + +
245A VAL* 3.0 43.9 + - + +
246A LYS* 4.2 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASP* 6.1 0.2 - - - +
230A GLN* 2.7 52.9 + - - +
231A ARG* 3.9 5.4 - - - +
233A ARG* 1.3 93.9 - - - +
235A ALA* 1.3 62.0 + - - +
237A MET* 4.0 2.5 - - - +
238A ALA* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASP* 3.6 46.1 + - + +
209A LEU* 4.6 9.2 - - + -
210A CYS* 3.5 13.9 - - - -
231A ARG 3.1 18.0 + - - +
232A ALA 4.0 2.9 - - - +
234A LYS* 1.3 76.9 - - - +
236A LEU* 1.3 61.8 + - - +
238A ALA* 3.6 5.8 + - - +
239A GLU* 3.5 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 4.4 9.6 - - + -
210A CYS* 4.0 29.6 - - - +
213A VAL* 3.8 26.9 - - + -
221A VAL* 3.9 21.5 - - + -
232A ALA* 3.0 29.6 + - + +
235A ALA* 1.3 76.3 - - - +
237A MET* 1.3 65.3 + - + +
239A GLU 3.5 1.2 + - - -
240A GLY 3.1 6.8 + - - -
241A ILE* 3.0 37.9 + - + +
243A VAL* 4.0 17.5 - - + -
245A VAL* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ARG* 3.0 36.5 + - + +
234A LYS* 4.3 2.5 - - - -
236A LEU* 1.3 89.0 - - + +
238A ALA* 1.3 65.7 + - - +
240A GLY* 3.2 14.1 - - - +
241A ILE 3.8 13.7 - - - +
243A VAL* 3.5 26.2 - - + +
245A VAL* 4.9 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LYS 3.1 20.3 + - - +
235A ALA* 3.7 7.0 - - - +
236A LEU 3.3 0.2 - - - -
237A MET* 1.3 77.7 + - - +
239A GLU* 1.3 69.6 + - - +
240A GLY 3.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A CYS* 3.7 27.4 - - + -
214A ARG* 4.0 24.1 + - - +
235A ALA 3.5 4.6 + - - +
236A LEU 3.5 2.0 + - - -
237A MET 3.3 0.4 + - - -
238A ALA* 1.3 86.3 - - - +
240A GLY* 1.3 63.9 + - - +
241A ILE* 3.5 13.3 + - + +
----------------------------------------------------------
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