Contacts of the helix formed by residues 164 - 171 (chain A) in PDB entry 2A0M
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 164 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ASP 3.6 2.7 - - - -
152A ARG 3.2 21.3 - - - +
153A PRO 3.4 9.9 - - - +
154A PRO* 3.9 8.1 - - + -
160A VAL* 3.5 4.2 - - - +
161A HIS* 3.0 57.2 + - + +
163A GLY* 1.3 75.1 - - - +
165A PRO* 1.4 69.8 - - - +
166A PHE 3.1 3.8 + - - -
167A ARG* 3.1 12.1 + - - +
168A GLN* 3.1 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASN* 3.5 35.4 - - - +
123A ASP* 4.6 3.1 - - - -
125A SER* 4.1 5.2 - - - -
126A ALA* 3.7 26.1 - - + +
150A ASP* 3.9 2.2 - - + +
161A HIS 3.6 7.2 - - - +
162A SER 3.3 13.7 - - - +
163A GLY 3.4 2.5 - - - -
164A THR* 1.4 91.8 - - - +
166A PHE* 1.3 69.5 + - + +
168A GLN* 3.5 15.6 - - - +
169A LEU* 3.3 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASN* 4.2 4.3 - - - -
125A SER* 3.7 14.4 - - - -
142A VAL* 3.7 22.9 - - + -
144A ASN* 3.2 38.8 - - + -
149A LEU 4.3 0.9 - - - +
150A ASP* 3.0 24.0 + - + +
151A VAL* 3.8 7.4 - - + -
165A PRO* 1.3 86.2 - - + +
167A ARG* 1.3 60.4 + - - +
168A GLN 3.3 0.4 - - - -
169A LEU* 3.8 25.7 - - + +
170A LEU* 3.1 32.9 + - - +
180A PHE* 3.7 34.5 - + + -
232A PHE* 4.8 1.3 - + - -
234A SER* 3.5 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ASP 3.5 4.4 + - - -
151A VAL* 2.9 47.4 + - - +
152A ARG 3.4 13.5 - - - +
153A PRO* 3.9 27.1 - - - +
154A PRO* 4.9 6.0 - - - +
164A THR* 3.1 10.8 + - - +
166A PHE* 1.3 75.2 - - - +
168A GLN* 1.3 65.5 + - + +
170A LEU 3.3 0.9 + - - -
171A GLU* 3.1 46.3 + - - +
194A HIS* 4.3 10.5 - - - -
197A TYR* 3.5 48.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
123A ASP* 6.1 1.2 - - - +
126A ALA* 3.7 15.7 - - + +
130A ARG* 3.4 28.5 - - - +
160A VAL* 3.6 30.3 - - + +
161A HIS 5.1 0.2 - - - +
164A THR* 3.1 32.6 + - - +
165A PRO* 3.5 14.1 - - - +
167A ARG* 1.3 79.5 - - + +
169A LEU* 1.3 63.1 + - + +
171A GLU* 3.3 20.0 + - - +
172A GLU* 3.5 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A SER 3.9 16.2 - - - +
126A ALA* 3.6 26.5 - - + +
129A GLY* 3.8 23.1 - - - -
130A ARG* 3.9 10.1 - - + +
133A LEU* 4.6 9.2 - - + -
142A VAL* 4.8 13.2 - - + -
165A PRO 3.3 13.4 + - - +
166A PHE* 3.6 33.8 + - + +
167A ARG 3.3 0.6 - - - -
168A GLN* 1.3 77.9 - - + +
170A LEU* 1.3 58.1 + - + +
172A GLU* 3.0 28.4 + - + +
175A PHE* 3.6 23.2 - - + +
180A PHE* 6.4 0.4 - - + -
232A PHE* 4.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A VAL* 4.1 7.0 - - + -
166A PHE* 3.1 22.8 + - + +
167A ARG 3.3 3.5 + - - +
169A LEU* 1.3 77.3 - - + +
171A GLU* 1.3 59.7 + - - +
172A GLU 3.3 5.4 + - - +
175A PHE* 3.9 27.3 - - + +
177A GLY* 4.1 17.7 - - - +
180A PHE* 4.0 32.5 - - + -
197A TYR* 3.7 30.3 - - + +
198A VAL* 4.5 7.2 - - + +
201A HIS* 3.8 35.2 - - + -
203A GLY 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ARG* 3.1 43.7 + - - +
168A GLN* 3.6 14.5 - - - +
169A LEU 3.1 0.8 - - - -
170A LEU* 1.3 76.3 - - - +
172A GLU* 1.3 61.3 + - - +
173A SER* 3.5 2.9 + - - -
197A TYR* 3.4 13.4 + - - +
201A HIS* 5.5 2.2 - - - +
----------------------------------------------------------
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