Contacts of the helix formed by residues 223 - 229 (chain A) in PDB entry 4ZVN
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 223 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TRP* 3.7 6.7 - - - -
173A HIS* 5.1 1.8 - - - -
177A HIS* 5.8 1.6 - - + -
221A PRO* 2.8 27.9 + - + +
222A CYS* 1.3 80.3 - - - +
224A ALA* 1.3 64.9 + - - +
225A HIS* 3.5 10.4 + - - +
226A TRP* 3.2 21.5 + - - +
227A HIS* 2.9 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TRP* 3.6 25.8 - - + -
223A THR* 1.3 72.8 - - - +
225A HIS* 1.3 58.7 + - - +
227A HIS 3.2 0.5 + - - -
228A PHE* 2.8 45.1 + - + +
229A GLY 4.7 0.4 - - - +
157B LYS* 4.6 15.3 - - + +
162B GLY* 5.7 1.1 - - - -
166B TYR* 4.4 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A THR* 3.1 9.7 + - - +
224A ALA* 1.3 78.1 - - - +
226A TRP* 1.3 63.7 + - - +
229A GLY* 2.8 49.8 + - - -
230A GLN 3.8 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ARG* 2.9 82.7 + - + +
168A LEU* 4.1 4.3 - - + -
172A GLN* 3.4 27.6 - - - -
185A ALA* 5.3 1.6 - - + -
186A PRO* 3.9 20.9 - - + -
220A ILE* 3.8 29.6 - - + +
221A PRO* 3.0 47.5 - - + +
223A THR* 3.2 10.6 + - - +
225A HIS* 1.3 84.3 + - - +
227A HIS* 1.3 85.2 + + - +
229A GLY 4.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASP* 4.6 1.2 - - - +
165A ARG* 3.3 40.4 - - - +
166A TYR* 3.5 15.2 - - - -
168A LEU* 4.1 1.1 - - + -
169A TRP* 3.3 38.7 - + - -
172A GLN* 3.1 25.4 + - + +
173A HIS* 4.5 0.4 - - + -
222A CYS* 3.8 25.4 - - - -
223A THR 2.9 23.9 + - - +
225A HIS 3.2 0.4 - - - -
226A TRP* 1.3 101.4 - + - +
228A PHE* 1.3 81.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LYS* 5.1 5.2 + - - -
166A TYR* 3.6 43.6 + + + -
169A TRP* 3.5 45.8 - + + -
224A ALA* 2.8 30.4 + - + +
227A HIS* 1.3 77.4 - - + +
229A GLY* 1.3 62.9 + - - +
230A GLN* 4.0 5.9 + - - +
166B TYR* 3.4 47.1 - + + +
228B PHE* 3.2 42.8 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ALA 4.7 0.2 - - - +
225A HIS* 2.8 45.6 + - - -
226A TRP 4.7 0.6 + - - -
227A HIS 3.9 0.4 - - - -
228A PHE* 1.3 76.6 - - - +
230A GLN* 1.3 74.6 + - - +
157B LYS* 5.7 3.6 + - - -
----------------------------------------------------------
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