Contacts of the helix formed by residues 160 - 167 (chain A) in PDB entry 2Q06
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 ASP 160 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 4.0 6.8 - - - +
159A MET* 1.3 76.1 - - - +
161A PRO* 1.4 76.8 - - - +
162A ARG* 3.0 41.9 + - + +
163A MET* 2.9 49.1 + - + +
257A ILE* 5.5 0.4 - - - +
261A ARG* 3.6 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A THR* 3.9 28.5 - - + +
154A LEU* 4.0 18.1 - - + +
155A VAL* 4.2 22.2 - - + -
159A MET 3.7 7.4 - - - +
160A ASP* 1.4 87.4 - - - +
162A ARG* 1.3 55.8 + - - +
163A MET 2.6 16.8 + - - -
164A CYS* 3.4 20.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
160A ASP* 3.0 41.1 + - + +
161A PRO* 1.3 79.3 - - - +
163A MET* 1.3 58.9 + - + +
164A CYS* 3.5 9.1 + - - -
165A SER* 5.0 1.7 + - - -
264A LEU* 4.8 13.0 - - + +
491A ASP* 4.8 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 4.7 7.4 - - + -
159A MET* 4.1 23.1 - - - -
160A ASP* 3.1 31.4 - - + +
161A PRO 2.6 9.0 + - - -
162A ARG* 1.3 78.2 - - + +
164A CYS* 1.3 63.0 + - - +
165A SER 3.2 3.1 - - - -
166A LEU* 3.1 39.3 + - + +
167A MET* 3.5 14.3 - - + +
257A ILE* 4.2 11.9 - - + +
260A ALA* 4.1 4.7 - - - -
261A ARG* 3.4 53.6 - - + +
264A LEU* 4.8 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLN* 3.5 32.8 - - - +
151A THR* 5.4 0.4 - - - -
154A LEU* 4.8 5.4 - - + +
161A PRO 3.4 17.4 + - - -
162A ARG 3.5 6.8 + - - -
163A MET* 1.3 70.7 - - - +
165A SER* 1.3 54.2 + - - +
166A LEU 2.7 1.2 + - - -
167A MET* 2.7 37.0 + - - +
338A PHE* 3.4 22.6 - - + -
489A PHE* 4.1 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ARG 5.0 1.6 + - - -
163A MET* 4.5 0.9 - - - -
164A CYS* 1.3 76.6 - - - +
166A LEU* 1.3 63.6 + - - +
167A MET 3.7 0.3 + - - -
168A GLN* 4.7 0.9 + - - +
264A LEU* 3.4 26.5 - - - +
270A ILE* 5.2 7.8 - - - +
338A PHE* 3.6 41.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A MET* 3.5 37.7 - - + +
164A CYS 2.7 3.2 + - - -
165A SER* 1.3 79.1 - - - +
167A MET* 1.3 57.4 + - - +
168A GLN 3.2 8.5 + - - -
185A GLY* 3.5 10.2 - - - -
186A VAL* 4.8 5.8 - - + +
187A GLY* 2.9 37.3 + - - +
188A THR 3.1 3.8 + - - -
260A ALA 3.7 17.3 - - - +
263A ALA* 3.5 40.8 - - + +
264A LEU* 3.6 24.2 - - + +
267A ARG* 5.6 1.8 - - + -
268A GLY 6.1 0.2 - - - +
270A ILE* 5.8 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASP* 4.3 3.6 - - - +
150A ARG* 5.0 5.4 + - + +
154A LEU* 4.1 34.5 - - + -
159A MET* 5.3 1.1 - - - -
163A MET* 3.5 16.2 - - - +
164A CYS* 2.7 20.3 + - - +
165A SER 3.4 0.4 - - - -
166A LEU* 1.3 69.6 - - - +
168A GLN* 1.3 59.8 + - - +
169A GLY 3.3 1.2 + - - -
170A SER* 3.0 28.6 + - - +
187A GLY* 3.1 37.5 - - - +
188A THR* 3.1 20.9 - - - -
191A MET* 3.9 25.1 - - + -
338A PHE* 4.5 7.3 - - + -
----------------------------------------------------------
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