Contacts of the strand formed by residues 233 - 237 (chain A) in PDB entry 2Z1Z
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 ILE 233 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PHE* 4.1 19.7 - - + -
200A ASP 2.8 6.7 + - - -
201A ILE* 3.3 17.5 - - + +
202A ILE* 2.8 32.6 + - - +
232A SER* 1.3 74.0 - - - +
234A ILE* 1.3 66.8 + - - +
235A VAL* 4.4 2.0 - - + -
261A VAL 3.2 5.6 - - - +
263A MET* 4.1 21.3 - - + -
288A LEU* 3.7 22.4 - - + -
290A TYR* 4.4 0.4 - - + -
296A VAL* 4.4 16.8 - - + -
22B THR* 4.0 10.5 - - + +
24B VAL* 3.6 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ILE* 3.1 20.2 - - + +
204A PHE* 4.2 6.1 - - + -
223A LEU* 3.9 39.5 - - + +
224A VAL* 4.2 16.6 - - + +
227A ALA* 3.7 29.4 - - + -
233A ILE* 1.3 73.9 - - - +
235A VAL* 1.3 74.5 + - - +
236A TYR* 3.9 15.9 - - + +
252A ILE* 4.6 2.5 - - + -
261A VAL* 2.7 22.0 + - + +
262A ALA* 3.4 11.1 - - + -
263A MET* 2.8 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 6.1 1.8 - - + -
135A LEU* 4.1 13.9 - - + -
139A PHE* 3.9 20.2 - - + -
155A TYR* 6.4 0.2 - - + -
201A ILE* 3.8 24.9 - - + -
202A ILE 2.6 9.9 + - - +
203A PHE* 3.5 27.5 - - + +
204A PHE 2.8 26.7 + - - +
233A ILE* 4.4 1.3 - - + -
234A ILE* 1.3 78.1 - - - +
236A TYR* 1.3 60.1 + - - +
237A ASP* 3.9 2.6 + - + +
263A MET* 4.0 18.2 - - + +
265A THR* 3.8 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A PHE* 3.2 28.7 - + + -
206A SER* 3.3 39.3 + - - -
220A LEU* 3.7 20.3 - - + +
234A ILE* 4.0 7.2 - - + -
235A VAL* 1.3 74.2 - - - +
237A ASP* 1.3 60.0 + - - +
238A SER* 4.0 11.0 - - - -
249A PRO 4.2 10.0 + - - -
250A ARG 4.0 12.8 + - - -
251A SER 4.7 0.3 - - - -
252A ILE* 3.7 51.1 - - + -
263A MET 3.0 19.2 + - - +
264A GLU* 3.3 25.0 - - - +
265A THR 2.8 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA* 5.0 1.7 - - - +
132A ILE* 4.3 3.6 - - - +
155A TYR* 2.8 38.4 + - + +
204A PHE 2.7 13.4 + - - +
205A CYS* 3.5 6.0 - - - -
206A SER 3.0 29.6 + - - +
207A PRO 4.6 0.2 - - - +
235A VAL* 5.1 2.9 - - + +
236A TYR* 1.3 72.6 - - - +
238A SER* 1.3 59.2 + - - +
239A ALA* 3.1 30.3 + - - +
265A THR* 3.4 17.0 - - - +
266A ALA* 4.8 0.5 - - - -
500A PLP 2.9 29.8 + - - -
----------------------------------------------------------
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