Contacts of the strand formed by residues 181 - 188 (chain D) in PDB entry 1PZY
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 LYS 181 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D SER 5.0 9.9 - - - +
179D PRO 3.6 1.9 + - - +
180D HIS* 1.3 71.8 - - - +
182D VAL* 1.3 60.4 + - - +
212D ASP* 3.3 23.8 - - + +
243D TYR* 3.7 24.5 + - + -
244D ASP* 3.4 49.1 + - - +
245D TYR* 3.6 8.0 - - - -
246D ASN* 3.1 42.3 + - - +
247D CYS 3.1 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D HIS* 3.9 22.9 - - + +
181D LYS* 1.3 75.9 - - - +
183D ALA* 1.3 69.0 + - - +
184D ILE* 4.0 6.5 + - + -
211D LEU* 4.4 5.6 - - + -
212D ASP 2.9 10.1 + - - +
213D TYR* 3.0 34.3 - - + +
214D GLY 3.1 4.3 + - - -
245D TYR* 3.5 5.0 - - - -
247D CYS* 3.4 27.8 - - + +
249D VAL* 3.5 32.8 - - + +
264D TYR 3.8 17.0 - - - +
265D ARG* 4.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D VAL* 1.3 71.6 - - - +
184D ILE* 1.3 61.1 + - - +
185D ILE* 3.1 10.3 - - + +
214D GLY 3.7 5.2 - - - -
216D TYR* 4.2 2.9 - - + -
239D ALA* 3.9 12.1 - - + -
245D TYR* 3.5 32.7 - - + -
247D CYS 3.0 6.1 + - - -
248D PHE* 3.5 23.1 - - + -
249D VAL 3.0 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D VAL* 4.2 11.4 - - + +
183D ALA* 1.3 74.4 - - - +
185D ILE* 1.3 58.2 + - - +
186D ILE* 4.6 4.6 - - + +
198D TRP* 3.9 24.2 - - + -
206D LEU* 3.3 46.4 - - + -
211D LEU* 5.7 0.2 - - + -
213D TYR* 4.6 6.7 - - + -
214D GLY 2.9 11.8 + - - +
215D ILE* 3.6 11.0 - - + +
216D TYR* 2.8 32.9 + - - +
249D VAL* 3.3 29.4 - - + +
251D SER* 4.4 8.7 - - - -
264D TYR* 4.4 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D ALA* 3.1 27.6 - - + +
184D ILE* 1.3 73.7 - - - +
186D ILE* 1.3 64.5 + - - +
187D PRO* 3.7 2.6 - - - +
216D TYR* 3.4 8.5 - - + -
218D ILE* 3.8 23.3 - - + -
232D LEU* 3.8 25.7 - - + +
235D GLY* 3.8 27.8 - - - +
236D PHE 4.1 1.1 - - - +
239D ALA* 4.8 0.7 - - + -
248D PHE* 3.7 23.6 - - + -
249D VAL 2.8 11.6 + - - +
250D PHE* 3.6 17.2 - - + -
251D SER 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ILE* 4.6 6.5 - - + +
185D ILE* 1.3 81.1 - - - +
187D PRO* 1.3 63.9 - - - +
188D PHE* 3.4 2.8 + - + +
195D LEU* 4.5 5.8 - - + -
198D TRP* 3.8 51.8 - - + -
215D ILE* 4.2 9.9 - - + -
216D TYR 2.7 15.7 + - - +
217D VAL* 3.5 15.0 - - + -
218D ILE 2.9 26.7 + - - -
251D SER 3.3 17.3 - - - +
253D VAL* 2.9 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D ILE 3.7 0.4 - - - +
186D ILE* 1.3 86.6 - - - +
188D PHE* 1.3 58.5 + - - +
218D ILE* 3.9 5.4 - - + +
226D PHE* 4.0 16.4 - - + -
228D ARG* 4.1 30.7 - - + +
231D LEU* 4.2 9.2 - - + -
232D LEU* 3.7 21.0 - - + -
251D SER 3.0 17.0 - - - +
252D ASP* 4.0 14.6 - - - +
253D VAL* 3.6 0.5 - - - +
409D UDP 3.0 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D ILE 3.8 0.4 - - - +
187D PRO* 1.3 77.6 - - - +
189D ARG* 1.3 74.1 - - - +
190D ASN* 3.9 7.2 - - - -
191D ARG* 3.3 40.4 - - + -
192D GLN* 3.6 24.7 - - + -
195D LEU* 4.2 12.1 - - + -
217D VAL* 3.4 31.2 - - + -
218D ILE 2.9 12.1 + - - +
219D ASN* 3.3 22.8 - - + -
220D GLN 3.0 26.7 + - - -
226D PHE* 3.7 6.8 - - - -
231D LEU* 3.9 3.6 - - - +
253D VAL* 3.9 18.4 - - + -
393D LYS* 3.9 18.8 - - - -
409D UDP 3.2 7.4 - - - -
----------------------------------------------------------
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