Contacts of the strand formed by residues 226 - 231 (chain D) in PDB entry 3V56
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 LEU 226 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D GLN* 3.6 36.6 - - + +
214D ARG 3.4 7.0 - - - +
215D LYS* 3.8 31.6 - - + +
224D LEU* 3.6 17.1 - - - +
225D SER* 1.3 80.5 - - - +
227D VAL* 1.3 66.3 + - - +
260D GLN* 4.1 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D GLN* 3.1 7.7 - - - -
214D ARG* 2.8 70.6 + - + +
216D LYS* 6.1 2.2 - - + -
224D LEU* 3.8 31.0 - - + +
225D SER 5.0 0.9 - - - +
226D LEU* 1.3 79.7 - - - +
228D THR* 1.3 65.1 + - - +
229D LEU* 3.5 10.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D LEU* 3.8 30.3 - - + +
212D ILE 3.8 2.9 - - - +
213D GLN* 3.4 20.9 + - - -
227D VAL* 1.3 72.7 - - - +
229D LEU* 1.3 61.0 + - - +
230D PHE 3.7 22.9 - - - +
231D ARG* 4.1 0.2 - - + -
275E ASP* 3.5 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D ILE* 4.4 6.3 - - + -
212D ILE* 2.7 21.3 + - + +
214D ARG* 3.9 39.0 - - + +
227D VAL* 3.5 7.4 + - + +
228D THR* 1.3 72.1 - - - +
230D PHE* 1.4 85.8 + - + +
251D ALA* 4.0 29.2 - - + -
252D LYS 5.8 0.4 - - - +
253D LEU* 4.2 2.5 - - + -
259D LEU* 3.9 19.3 - - + -
274E GLY 4.6 1.4 - - - +
275E ASP* 3.4 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D ILE* 4.3 18.8 - - + -
210D HIS* 4.1 0.7 - - - +
211D LEU* 3.5 2.8 - - - -
212D ILE* 2.8 52.1 + - + +
228D THR* 3.7 3.9 - - - +
229D LEU* 1.4 104.1 - - + +
231D ARG* 1.3 61.6 + - - +
247D SER* 3.9 20.2 - - - +
248D ALA 4.5 1.3 - - - +
249D GLY* 3.4 47.1 - - - -
250D ILE 3.7 15.9 - - - -
251D ALA* 4.6 2.0 - - + -
148E GLN* 4.4 11.4 - - - -
274E GLY 6.0 0.2 - - - -
275E ASP 3.2 5.4 - - - +
278E PHE* 3.8 26.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D HIS 3.4 5.2 - - - -
211D LEU* 3.6 28.7 - - + -
228D THR* 4.1 0.4 - - + -
230D PHE* 1.3 75.5 - - - +
232D CYS* 1.4 63.7 + - - +
233D ILE* 3.7 14.4 - - + +
247D SER* 4.6 4.3 - - - -
198E GLN* 2.9 27.6 + - - -
200E LEU* 4.4 4.2 - - - +
271E SER* 4.6 0.4 + - - -
273E ASP* 3.1 29.9 + - - +
275E ASP* 2.8 52.9 + - - +
276E VAL* 3.4 25.1 - - + +
27J LEU 5.3 1.3 - - - -
28J LEU* 2.8 39.4 + - + +
29J VAL 4.2 11.3 + - - -
30J ARG* 4.2 16.5 - - - +
----------------------------------------------------------
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