Contacts of the strand formed by residues 252 - 257 (chain A) in PDB entry 2OA2
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 TRP 252 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 4.0 16.4 - - + -
206A GLU* 3.3 26.2 - - - -
207A ILE* 3.4 41.2 - - + +
226A MSE 3.1 5.1 - - - -
227A GLY 2.8 34.3 + - - +
228A HIS 3.3 25.7 + - - -
229A ARG* 3.6 1.5 - - - +
230A GLN* 3.4 61.7 - - + +
233A LEU* 3.9 16.4 - - + -
250A GLY 4.7 0.2 - - - -
251A THR* 1.3 73.7 - - - +
253A HIS* 1.3 58.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ILE* 6.2 5.6 - - + -
204A GLY 3.7 2.3 - - - +
205A LEU* 3.3 9.7 - - - +
206A GLU* 2.9 61.5 + - + +
207A ILE* 3.9 2.9 - - - -
208A HIS* 3.9 22.1 + - + -
213A GLN* 3.9 14.3 + - + -
224A VAL* 6.2 0.2 - - + -
225A GLN 3.1 7.0 - - - -
226A MSE 3.8 16.6 - - + -
247A ILE* 3.5 37.6 - - + +
251A THR 2.9 22.3 + - - -
252A TRP* 1.3 75.3 - - - +
254A ASN* 1.3 65.4 + - - +
255A VAL* 6.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ASP* 2.8 26.6 + - - -
203A ILE* 3.6 1.2 + - - -
204A GLY 2.8 24.1 + - - -
205A LEU* 3.6 27.5 - - + +
223A LEU 4.4 0.4 - - - -
224A VAL* 3.5 1.7 - - - +
225A GLN* 2.9 45.2 + - + +
233A LEU* 5.3 1.1 - - + -
253A HIS* 1.3 77.9 - - - +
255A VAL* 1.3 80.4 + - - +
256A ARG* 3.5 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 5.1 1.7 - - - +
202A ASP* 3.2 2.1 - - - -
203A ILE* 2.9 53.7 + - + +
215A LEU* 4.7 7.9 - - + -
223A LEU 3.3 10.1 - - - +
224A VAL* 4.3 13.9 - - + -
239A VAL* 5.0 3.4 - - + -
245A ILE* 4.3 22.0 - - + -
247A ILE* 5.2 9.6 - - + -
253A HIS* 6.0 2.0 - - + -
254A ASN* 1.3 83.0 + - - +
256A ARG* 1.3 65.6 + - - +
263A LEU* 4.0 25.4 - - + -
265A LEU* 4.7 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLU 3.7 5.4 - - - +
202A ASP* 3.3 30.6 + - + +
222A GLY* 3.0 5.5 - - - -
223A LEU* 2.8 51.3 + - + +
225A GLN* 2.8 35.8 + - - +
254A ASN* 3.5 18.6 - - - +
255A VAL* 1.3 78.1 - - - +
257A ASN* 1.3 64.5 - - - +
258A THR* 3.3 4.3 + - + +
263A LEU* 4.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 3.0 26.3 + - + +
198A GLN 3.2 25.8 + - - +
199A VAL* 3.4 6.5 - - - +
200A GLY* 3.8 18.4 + - - -
201A GLU 2.8 13.7 + - - +
221A ARG 3.0 10.2 + - - +
255A VAL 4.3 0.4 + - - -
256A ARG* 1.3 73.3 - - - +
258A THR* 1.3 60.6 + - - +
259A GLY* 2.9 20.9 + - - +
261A ARG 3.0 23.7 + - - +
263A LEU* 3.3 21.1 - - + +
----------------------------------------------------------
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