Contacts of the strand formed by residues 228 - 234 (chain D) in PDB entry 6WNX
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 SER 228 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D HIS* 4.7 3.1 - - - -
206D HIS* 3.2 18.4 + - - -
223D CYS* 3.4 3.8 - - - +
224D SER 3.1 26.2 + - - +
226D ASP* 2.9 22.0 + - - -
227D ARG* 1.3 79.7 - - - +
229D ILE* 1.3 62.0 + - - +
230D ALA 4.3 0.2 - - - -
245D VAL* 3.9 22.7 - - - +
246D LEU 3.8 5.4 - - - -
247D VAL* 5.0 7.6 - - - +
253D VAL* 4.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D VAL* 3.2 34.8 - - + -
222D THR 3.2 6.1 - - - +
223D CYS* 4.1 3.4 - - + -
228D SER* 1.3 79.3 - - - +
230D ALA* 1.3 61.4 + - - +
231D VAL* 4.6 0.9 - - + -
245D VAL* 3.4 6.2 - - - +
246D LEU* 2.9 54.9 + - + +
249D HIS* 4.5 4.5 - - + -
253D VAL* 3.9 17.5 - - + -
256D VAL* 4.2 4.3 - - + -
263D ILE* 5.0 1.3 - - + -
265D SER* 3.3 34.5 - - - +
275D TRP* 3.9 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D HIS* 3.9 19.5 - - + +
206D HIS* 3.8 9.8 - - - +
221D VAL* 3.2 8.1 - - - +
222D THR* 2.8 49.9 + - - +
229D ILE* 1.3 74.7 - - - +
231D VAL* 1.3 61.1 + - - +
232D TRP* 3.4 17.6 - - + +
242D LEU* 4.2 4.0 - - + -
244D ARG 3.8 4.0 - - - -
245D VAL* 4.6 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D LEU* 3.4 27.6 - - + -
220D MET 3.6 2.7 - - - -
221D VAL* 4.5 6.1 - - + +
229D ILE* 4.6 3.6 - - + -
230D ALA* 1.3 75.7 - - - +
232D TRP* 1.3 54.7 + - - +
242D LEU* 3.5 4.5 - - - +
243D ARG* 2.8 42.9 + - + +
244D ARG 2.9 18.9 + - - +
246D LEU* 4.2 17.3 - - + -
263D ILE* 4.2 19.1 - - + -
280D CYS* 4.0 30.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D VAL* 6.0 0.7 - - + -
203D LEU* 4.1 36.8 - - + -
204D ILE 5.0 1.8 - - - -
205D HIS* 3.8 31.2 - + + -
206D HIS* 5.1 1.8 - + - -
219D LEU* 3.0 12.6 - - - +
220D MET* 2.7 58.6 + - + +
222D THR* 3.2 33.4 + - + +
230D ALA* 3.4 25.2 - - + +
231D VAL* 1.3 76.9 - - - +
233D ASP* 1.3 59.6 + - - +
240D ILE* 3.9 26.2 - - + -
241D THR* 3.2 9.0 - - - +
242D LEU* 3.5 36.6 - - + -
243D ARG* 4.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D GLY 3.6 6.1 - - - +
219D LEU* 5.4 0.9 - - - +
232D TRP* 1.3 71.5 - - - +
234D MET* 1.3 57.6 + - - +
235D ALA* 3.7 2.9 - - + +
239D ASP 3.8 1.6 - - - +
240D ILE* 3.3 5.5 - - - +
241D THR* 2.9 47.6 + - - +
242D LEU 5.3 0.2 - - - -
243D ARG* 3.4 46.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 234 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D ARG* 3.8 28.3 + - - +
179D VAL* 5.1 4.9 - - + -
181D VAL* 5.0 6.1 - - - -
191D VAL* 6.1 0.7 - - - -
215D PHE* 3.5 49.1 - - + -
216D SER 6.3 0.2 - - - -
218D GLY* 2.6 44.4 + - - +
219D LEU 4.1 1.8 - - - +
220D MET* 4.2 20.2 - - + +
232D TRP 3.7 0.2 + - - -
233D ASP* 1.3 70.8 - - - +
235D ALA* 1.3 64.0 + - - +
236D SER 3.3 4.2 + - - +
237D ALA* 6.2 1.1 - - - -
239D ASP 3.9 2.7 - - - -
240D ILE* 3.6 32.5 - - + -
----------------------------------------------------------
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