Contacts of the helix formed by residues 161 - 170 (chain A) in PDB entry 1PQA
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 SER 161 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA* 3.9 27.5 - - - +
159A ILE* 5.4 0.4 - - - -
160A VAL* 1.3 77.5 - - - +
162A ARG* 1.4 65.9 + - - +
163A ALA* 3.8 7.6 + - - +
164A THR* 3.0 26.4 + - - -
165A CYS* 3.0 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASP* 2.8 43.4 + - - -
160A VAL 3.4 2.9 + - - -
161A SER* 1.4 73.9 - - - +
163A ALA* 1.4 57.7 + - - +
165A CYS* 3.6 6.0 - - - +
166A ARG* 2.7 77.3 + - - +
174A ILE* 3.9 11.1 - - + +
175A THR 3.1 16.9 + - - -
176A ASN* 3.6 28.6 + - - -
178A MET 2.8 22.8 + - - -
179A PHE* 3.9 9.0 - - - +
180A CYS* 5.4 2.2 - - - +
227A SER* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A SER* 3.1 7.6 - - - +
162A ARG* 1.4 79.8 - - - +
164A THR* 1.3 63.2 + - - +
166A ARG* 3.3 10.3 + - - +
167A ALA* 3.0 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A VAL* 3.8 14.1 - - + -
161A SER* 3.0 21.4 + - - -
163A ALA* 1.3 78.1 - - - +
165A CYS* 1.3 62.8 + - - +
167A ALA* 3.0 19.3 + - + +
168A GLN* 3.0 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A VAL* 4.3 1.5 - - + +
161A SER 3.0 12.6 + - - +
162A ARG* 3.6 9.6 - - - +
164A THR* 1.3 75.8 - - - +
166A ARG* 1.3 59.2 + - - +
168A GLN* 3.2 10.5 + - - +
169A TYR* 2.9 49.9 + - - +
174A ILE* 3.7 18.2 - - + -
180A CYS* 2.0 50.7 - - + -
222A SER* 4.1 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ARG* 2.7 43.6 + - - +
163A ALA* 3.5 8.2 - - - +
165A CYS* 1.3 75.0 - - - +
167A ALA* 1.3 59.4 + - - +
170A GLY* 2.7 35.7 + - - -
171A THR* 3.6 39.7 + - - +
174A ILE* 2.9 38.7 + - + -
175A THR* 3.9 3.6 - - - +
176A ASN* 3.3 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ALA 3.0 11.7 + - - +
164A THR* 3.0 15.1 + - + +
166A ARG* 1.3 76.0 - - - +
168A GLN* 1.3 63.5 + - + +
170A GLY 4.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A VAL* 4.8 1.0 - - - +
164A THR* 3.0 34.4 + - + +
165A CYS* 3.4 8.8 - - - +
166A ARG 3.1 0.2 - - - -
167A ALA* 1.3 81.8 - - + +
169A TYR* 1.3 67.0 + - + +
184A SER* 5.7 3.8 - - - +
220A ASN* 3.1 48.2 + - + +
221A TYR* 3.3 21.5 + - + -
222A SER* 2.8 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A CYS* 2.9 24.1 + - - +
168A GLN* 1.3 83.9 - - + +
170A GLY* 1.3 60.1 + - - +
173A ALA* 3.6 23.5 - - + +
174A ILE* 3.8 16.8 - - + -
212A TRP* 3.5 27.1 - + - -
213A GLY* 3.7 1.0 - - - -
214A ASN* 3.5 31.7 + - + -
221A TYR* 3.5 25.0 + + - +
222A SER 2.5 40.5 + - - -
224A VAL* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ARG* 2.7 26.9 + - - +
167A ALA 4.4 1.6 + - - -
168A GLN 3.7 1.2 - - - -
169A TYR* 1.3 75.5 - - - +
171A THR* 1.4 66.2 + - - +
172A SER* 3.4 2.9 - - - -
173A ALA* 3.1 13.5 + - - +
174A ILE* 3.7 4.7 + - - +
----------------------------------------------------------
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