Contacts of the helix formed by residues 181 - 191 (chain A) in PDB entry 2OR4
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 ARG 181 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ASN* 3.4 15.4 - - - +
179A TYR* 3.7 31.4 - - + +
180A ALA* 1.3 81.6 - - - +
182A THR* 1.3 67.2 + - - +
183A GLU* 3.2 36.2 + - - +
184A ASP* 2.9 38.0 + - - +
185A PHE* 3.0 22.2 + - - -
207A LYS* 4.0 26.1 - - - +
208A VAL* 3.8 27.6 - - + -
216A ASN* 3.6 3.8 - - - +
318A SER* 5.2 4.6 + - - -
319A TRP* 5.5 0.4 - - - +
697A HIS 5.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ARG* 1.3 73.8 - - - +
183A GLU* 1.3 62.8 + - - +
185A PHE* 3.2 5.6 + - - +
186A PHE* 2.9 58.7 + - + -
216A ASN* 3.4 21.7 + - - +
697A HIS* 2.7 40.2 + - + +
713A PHE* 3.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ARG* 3.5 47.4 + - + +
182A THR* 1.3 77.1 + - - +
184A ASP* 1.3 65.7 + - - +
186A PHE* 3.3 15.4 + - + +
187A LYS* 2.9 29.5 + - - +
697A HIS* 5.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL 3.4 18.6 - - - +
178A ASN* 3.1 15.1 + - - +
179A TYR 3.1 14.0 + - - -
180A ALA* 4.2 0.9 - - - +
181A ARG* 2.9 63.1 + - - +
183A GLU* 1.3 80.7 - - - +
185A PHE* 1.3 57.6 + - - +
187A LYS* 3.4 4.3 + - - +
188A LEU* 3.1 28.1 + - - +
319A TRP* 3.6 21.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL* 3.8 31.0 - - + -
180A ALA* 3.5 29.4 - - + -
181A ARG 3.0 23.8 + - - -
182A THR* 3.8 7.0 - - - +
184A ASP* 1.3 74.2 - - + +
186A PHE* 1.3 67.1 + - + +
188A LEU* 4.2 10.8 - - + -
189A GLU* 3.0 52.5 + - - +
196A CYS* 4.1 10.1 - - + -
201A VAL* 4.9 2.2 - - + -
216A ASN* 3.5 24.9 - - + -
217A ALA* 3.7 23.3 - - + -
220A ALA* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A THR* 2.9 39.9 + - + -
183A GLU* 3.3 16.4 + - + +
185A PHE* 1.3 77.3 - - + +
187A LYS* 1.3 56.2 + - - +
189A GLU* 5.2 0.4 - - - -
190A ARG* 2.8 84.9 + - - +
191A ASP* 5.1 1.1 - - - -
713A PHE* 4.0 18.8 - + - -
714A ASP* 3.5 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLU 2.9 16.5 + - - +
184A ASP* 3.5 6.5 - - - +
185A PHE 3.3 0.2 - - - -
186A PHE* 1.3 75.7 - - - +
188A LEU* 1.3 58.0 + - - +
191A ASP* 3.1 37.4 + - + +
192A MET* 2.9 31.8 + - + +
315A PRO* 4.0 24.2 - - + -
316A ASP* 4.2 19.6 + - - -
319A TRP* 3.9 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL* 4.3 2.0 - - + -
177A VAL* 3.4 38.1 - - + -
184A ASP 3.1 21.4 + - - +
185A PHE* 3.7 16.8 - - + +
186A PHE 3.4 0.2 - - - -
187A LYS* 1.3 76.6 - - - +
189A GLU* 1.3 63.4 + - + +
192A MET* 3.4 10.1 - - - +
193A LYS 2.9 10.7 + - - -
194A ILE* 2.8 48.1 + - + +
196A CYS* 4.5 4.9 - - - -
319A TRP* 3.7 15.5 - - + -
329A VAL* 3.2 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A PHE* 3.0 42.6 + - + +
186A PHE* 4.5 1.0 - - + +
188A LEU* 1.3 81.4 - - + +
190A ARG* 1.3 66.6 + - + +
193A LYS* 3.4 20.4 + - - +
194A ILE 3.7 15.5 - - - +
195A ASN* 5.6 2.2 - - - +
196A CYS* 5.3 6.5 + - - +
220A ALA* 3.7 25.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PHE* 2.8 60.0 + - + +
189A GLU* 1.3 82.2 - - + +
191A ASP* 1.3 65.1 + - - +
193A LYS* 2.9 28.9 + - - +
714A ASP* 2.8 43.0 + - - -
716A GLU* 5.6 0.2 + - - -
717A SER* 3.4 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PHE 4.5 0.7 - - - -
187A LYS* 3.1 47.1 + - + +
190A ARG* 1.3 88.7 - - - +
192A MET* 1.3 61.6 + - + +
193A LYS* 3.3 15.1 - - - +
----------------------------------------------------------
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