Contacts of the helix formed by residues 173 - 182 (chain A) in PDB entry 2OZ6
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 173 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ILE* 1.3 83.1 - - - +
174A ARG* 1.3 63.5 + - - +
175A GLN* 3.4 21.6 + - - +
176A GLU* 3.1 23.6 + - - +
177A ILE* 3.3 27.8 + - - +
179A ARG* 4.1 3.8 + - - -
206A LYS* 3.9 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A THR* 1.3 74.6 - - - +
175A GLN* 1.3 70.4 + - - +
177A ILE* 3.3 4.6 + - - +
178A GLY* 2.9 24.1 + - - -
185A ARG* 3.7 51.8 + - + +
186A GLU* 4.4 6.3 - - - +
188A VAL* 3.7 29.6 - - + +
189A GLY* 4.0 17.9 - - - -
192A LEU* 4.1 13.7 - - + -
206A LYS* 5.6 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A THR* 3.4 16.3 + - - +
174A ARG* 1.3 99.4 + - - +
176A GLU* 1.3 56.6 + - - +
178A GLY 3.2 1.0 + - - -
179A ARG* 2.9 50.9 + - - +
185A ARG* 3.9 25.8 - - - +
206A LYS* 5.1 6.9 + - - +
302A CMP 3.2 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A THR* 4.9 2.4 + - - +
62A ILE* 3.1 18.4 - - - +
65A TYR* 2.6 30.9 + - - +
92A ARG* 5.5 2.1 + - - -
94A LYS* 4.9 5.2 - - - +
172A ILE* 3.3 30.1 - - + -
173A THR* 3.1 19.6 + - - +
175A GLN* 1.3 75.7 - - - +
177A ILE* 1.3 62.2 + - - +
179A ARG* 2.6 45.0 + - - +
180A ILE* 3.0 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL* 4.2 23.8 - - + -
151A THR* 4.6 6.7 - - + -
152A LEU* 3.8 25.6 - - + -
155A LEU* 4.7 4.0 - - + -
172A ILE* 3.6 20.0 - - + -
173A THR 3.3 17.8 + - - +
174A ARG* 3.6 5.8 - - - +
176A GLU* 1.3 72.9 - - - +
178A GLY* 1.3 61.1 + - - +
180A ILE* 3.1 9.2 + - - +
181A VAL* 2.8 37.9 + - + +
188A VAL* 3.8 28.3 - - + -
192A LEU* 4.5 6.3 - - + -
208A MET* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ARG 2.9 12.2 + - - -
175A GLN 3.2 4.0 + - - -
177A ILE* 1.3 78.0 - - - +
179A ARG* 1.3 53.7 + - - +
181A VAL* 3.9 2.7 - - - -
182A GLY* 2.6 31.2 + - - -
183A CYS 3.2 23.7 + - - -
188A VAL* 3.7 14.5 - - - +
302A CMP 3.3 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 4.9 2.5 - - - -
60A GLU* 3.4 42.6 + - - +
61A MET* 3.2 14.4 - - - +
62A ILE* 3.0 36.8 + - + +
92A ARG* 5.0 8.0 - - - +
173A THR* 4.1 3.8 + - - -
175A GLN* 2.9 34.8 + - - +
176A GLU* 2.6 51.7 + - - +
177A ILE 3.3 0.2 - - - -
178A GLY* 1.3 77.5 - - - +
180A ILE* 1.3 60.8 + - - +
182A GLY* 4.0 1.6 + - - -
302A CMP 3.1 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A MET* 4.0 2.3 - - - +
62A ILE* 3.7 26.7 - - + +
65A TYR* 3.5 26.2 - - + +
135A LYS* 3.0 38.2 + - - +
139A LEU* 5.6 0.5 - - - +
151A THR* 3.3 39.3 - - + +
155A LEU* 4.0 16.2 - - + -
176A GLU* 3.0 20.1 + - + +
177A ILE* 3.1 5.8 + - - +
179A ARG* 1.3 78.5 - - - +
181A VAL* 1.3 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A MET* 3.8 1.6 - - - -
139A LEU* 3.5 14.5 - - - +
144A VAL* 4.7 1.3 - - + -
147A ARG* 2.4 62.1 + - + +
148A VAL* 3.7 18.2 - - + +
151A THR* 3.4 23.6 - - - +
177A ILE* 2.8 29.1 + - + +
178A GLY* 3.8 1.1 - - - +
180A ILE* 1.3 73.0 - - - +
182A GLY* 1.3 57.8 + - - +
183A CYS* 3.4 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A MET* 3.5 18.1 - - - +
139A LEU* 5.3 0.7 - - - -
144A VAL* 5.6 0.3 - - - +
147A ARG* 4.4 6.1 + - - -
178A GLY 2.6 18.1 + - - -
180A ILE 3.5 1.6 - - - -
181A VAL* 1.3 76.9 - - - +
183A CYS* 1.3 61.1 + - - +
302A CMP 3.5 31.2 + - - -
----------------------------------------------------------
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