Contacts of the helix formed by residues 136 - 140 (chain B) in PDB entry 2OR0
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 136 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 5.9 1.6 - - - -
77B VAL* 4.1 19.4 - - - +
81B VAL* 4.6 4.7 - - - -
107B TRP* 5.2 1.0 - - - -
134B SER 3.4 0.2 + - - -
135B SER* 1.3 73.1 - - - +
137B THR* 1.3 63.4 + - - +
138B ASP 3.3 2.5 - - - -
139B HIS* 2.9 27.0 + - - +
140B CYS* 3.4 13.3 - - - -
186B THR 2.8 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ALA* 3.8 15.8 - - - +
134B SER* 3.2 34.8 + - - +
135B SER 3.2 0.8 - - - -
136B GLY* 1.3 76.1 - - - +
138B ASP* 1.3 66.7 + - - +
140B CYS* 3.1 20.2 + - - +
168B ARG* 3.6 3.8 + - - -
171B TYR* 4.6 4.0 + - - -
173B ILE* 3.8 34.9 - - + +
187B GLY 3.8 12.7 + - - +
189B LYS* 4.3 8.3 - - + +
191B LEU* 3.4 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ARG* 3.5 45.2 + - + +
136B GLY 3.1 1.2 + - - -
137B THR* 1.3 78.5 - - - +
139B HIS* 1.3 60.9 + - + +
140B CYS 3.4 0.7 - - - -
141B GLN* 5.1 0.5 + - - -
168B ARG* 2.8 27.9 + - - +
173B ILE* 4.1 13.4 - - - +
175B GLU* 4.0 8.8 - - - +
187B GLY* 4.6 4.9 - - - +
189B LYS* 2.8 37.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ARG* 3.5 28.8 + - + +
28B LEU* 2.7 51.0 + - + +
29B THR 4.0 0.9 - - - -
30B ASP* 3.6 10.5 - - - -
33B ALA* 3.5 23.7 - - + +
107B TRP* 3.6 24.9 + - + +
136B GLY* 2.9 15.6 + - - +
138B ASP* 1.3 83.6 + - + +
140B CYS* 1.3 59.7 + - - +
141B GLN* 4.4 4.7 + - - +
168B ARG* 4.7 0.7 - - - -
606B ACT 2.6 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 4.0 10.1 - - - -
107B TRP* 3.4 24.7 - - - +
108B MSE 3.5 9.0 - - - -
109B ALA* 3.5 38.1 - - + +
136B GLY 3.4 19.1 - - - -
137B THR 3.1 10.0 + - - +
139B HIS* 1.3 80.3 - - - +
141B GLN* 1.3 62.5 + - - +
142B TRP 3.5 3.6 - - - +
168B ARG* 3.0 27.3 + - - -
171B TYR* 4.2 2.3 + - - +
----------------------------------------------------------
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