Contacts of the helix formed by residues 230 - 238 (chain D) in PDB entry 1PV2
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 TYR 230 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D ASP* 3.6 36.8 - - + +
214D ASP* 3.9 21.8 + - + -
215D LYS* 3.4 44.2 - - + +
226D HIS* 4.1 11.1 + - - +
227D LEU* 3.9 40.6 + - + -
228D THR 5.4 0.2 - - - -
229D TRP* 1.3 85.0 - - - +
231D PHE* 1.3 67.3 + + - +
232D GLY 3.3 1.0 + - - -
233D GLU* 3.4 14.9 + - + +
234D GLU* 3.2 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D LEU* 4.1 7.8 - - + +
185D CYS 3.6 21.8 - - - -
186D HIS* 3.4 35.2 - + - -
188D PRO* 4.5 1.6 - - + -
189D ALA* 3.7 28.7 - - + -
192D LEU* 4.0 3.8 - - + -
208D ALA* 4.1 10.5 - - + -
209D PHE 3.2 28.3 - - - -
211D ASP* 3.9 8.5 - - - -
214D ASP* 4.3 5.2 - - - -
227D LEU* 6.0 2.0 - - + -
229D TRP* 3.6 25.4 + - + -
230D TYR* 1.3 72.3 - + - +
232D GLY* 1.3 65.8 + - - +
234D GLU* 3.2 4.0 + - - +
235D LEU* 2.9 56.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D PHE 5.5 0.9 - - - -
211D ASP* 3.2 21.2 + - - -
231D PHE* 1.3 89.5 - - - +
233D GLU* 1.3 64.9 + - - +
235D LEU* 4.6 1.3 - - - -
236D LYS* 3.2 23.5 + - - -
242D ILE* 3.2 24.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D ASP* 2.9 13.7 + - - +
230D TYR* 3.5 15.3 - - + +
231D PHE 3.3 0.2 - - - -
232D GLY* 1.3 74.4 - - - +
234D GLU* 1.3 56.7 + - + +
236D LYS* 3.1 24.3 + - - +
237D LYS* 2.8 49.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 234 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D LEU* 3.8 20.5 - - + +
195D ARG* 5.4 9.3 - - - +
229D TRP* 4.1 24.2 - - + +
230D TYR 3.2 21.4 + - - +
231D PHE* 3.2 5.5 + - - +
233D GLU* 1.3 75.9 - - - +
235D LEU* 1.3 61.5 + - - +
237D LYS* 3.1 33.8 + - - +
238D MET* 2.8 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D PRO* 3.5 38.8 - - + +
191D PHE* 3.9 6.1 - - + -
192D LEU* 3.3 24.0 - - + +
206D ILE* 4.2 11.0 - - + -
208D ALA* 5.3 0.2 - - + -
231D PHE* 2.9 40.7 + - + +
232D GLY* 3.8 6.5 - - - +
233D GLU 3.3 0.2 - - - -
234D GLU* 1.3 77.1 - - - +
236D LYS* 1.3 59.8 + - - +
238D MET* 3.6 4.6 + - + -
239D GLY 3.3 4.0 + - - -
240D MET* 2.8 57.8 + - + +
242D ILE* 4.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D ASP* 5.5 0.8 + - - -
232D GLY* 3.2 19.4 + - - +
233D GLU* 3.1 22.8 + - - +
235D LEU* 1.3 75.7 - - - +
237D LYS* 1.3 66.2 + - - +
239D GLY* 3.0 14.9 + - - -
240D MET 3.8 15.2 - - - +
241D ASN* 5.8 1.8 - - - +
242D ILE* 3.4 42.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D GLU* 2.8 28.4 + - - +
234D GLU* 3.3 34.2 + - - +
236D LYS* 1.3 78.9 - - - +
238D MET* 1.3 57.6 + - + +
239D GLY 3.5 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D PHE* 3.3 30.1 - - + +
192D LEU* 4.3 6.3 - - + -
194D LEU* 4.3 7.2 - - + -
195D ARG* 4.1 39.7 - - + +
199D ASN* 2.8 58.0 + - - +
201D LEU* 4.5 1.1 - - + -
202D ASN* 4.1 1.4 - - - +
234D GLU 2.8 20.6 + - - +
235D LEU* 3.9 11.7 - - + +
236D LYS 3.2 0.2 - - - -
237D LYS* 1.3 72.5 - - + +
239D GLY* 1.3 57.1 + - - +
240D MET* 3.9 23.3 + - + -
----------------------------------------------------------
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