Contacts of the strand formed by residues 202 - 206 (chain B) in PDB entry 1WYK
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 ARG 202 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B GLN 3.3 3.3 - - - +
198B TYR* 3.3 6.0 - - - -
199B SER 2.9 33.2 + - - +
200B GLY* 3.9 15.5 - - - -
201B GLY* 1.3 83.9 - - - +
203B PHE* 1.3 64.4 + - - +
204B THR* 3.8 16.5 + - + +
236B GLU* 2.7 40.4 + - - -
241B ALA* 3.5 16.8 - - + +
242B LEU 5.9 2.0 - - - +
256B THR* 5.4 7.9 - - + -
258B PRO* 4.2 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B HIS* 4.8 8.5 - + + -
189B TYR* 4.2 7.0 - + - -
196B VAL* 3.8 24.5 - - + -
197B GLN 3.1 5.6 - - - -
198B TYR* 3.5 46.2 - + + -
201B GLY 5.7 0.2 - - - -
202B ARG* 1.3 72.8 - - - +
204B THR* 1.3 61.6 + - - +
219B ILE* 4.0 16.6 - - + -
227B VAL* 4.0 32.8 - - + -
228B ALA* 3.8 17.0 - - + -
241B ALA* 3.7 0.9 - - - +
242B LEU* 2.9 40.3 + - + +
244B VAL* 3.9 26.0 - - + -
246B THR* 4.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B VAL* 3.3 1.2 - - - -
197B GLN* 2.9 47.2 + - - +
199B SER* 6.1 0.3 - - - -
202B ARG* 4.5 20.4 + - + +
203B PHE* 1.3 77.6 - - - +
205B ILE* 1.3 71.6 + - - +
236B GLU* 5.5 0.4 - - - +
239B ARG* 2.7 37.9 + - + -
240B THR 3.2 14.1 - - - +
241B ALA* 4.0 13.7 - - + -
242B LEU 4.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B TRP* 3.6 33.7 - - + +
195B ALA 3.8 13.5 - - - +
196B VAL* 3.9 20.0 - - + -
204B THR* 1.3 81.0 - - - +
206B PRO* 1.3 82.2 - - + +
209B VAL* 4.4 2.7 - - + -
210B GLY* 3.8 21.8 - - - +
239B ARG* 3.3 12.7 - - - +
240B THR* 2.9 34.3 + - - +
242B LEU* 3.9 24.0 - - + -
264B TRP* 4.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B TRP* 6.2 0.2 - - - +
195B ALA* 4.3 9.6 - - + +
205B ILE* 1.3 101.1 - - + +
207B ARG* 1.3 67.6 + - - +
209B VAL* 3.5 33.8 + - + +
210B GLY 4.8 0.2 + - - -
238B THR 4.0 4.7 - - - +
239B ARG* 3.6 20.9 - - - +
240B THR* 4.3 1.7 + - - -
----------------------------------------------------------
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