Contacts of the helix formed by residues 243 - 255 (chain D) in PDB entry 2X86
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 PHE 243 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D ASN* 5.2 3.1 - - - -
184D VAL* 3.6 29.6 - - + +
188D LEU* 5.7 0.2 - - - +
200D LEU* 3.9 19.0 - - + +
204D SER* 4.2 10.7 + - - -
207D PHE* 3.4 37.3 + - + -
208D LYS 4.5 0.2 - - - -
209D ARG* 3.7 36.8 - - + -
211D PHE* 3.8 21.5 - + - -
242D SER* 1.3 73.6 - - - +
244D GLN* 1.3 64.1 + - - +
246D VAL* 3.1 7.1 + - + +
247D ALA* 3.0 21.7 + - - +
272D TYR* 3.7 8.5 - - - -
401D ADP 3.5 39.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D LEU* 4.2 13.7 - - + +
204D SER 4.5 7.1 + - - +
205D GLU* 5.6 5.8 - - - -
242D SER* 3.1 13.1 + - - +
243D PHE* 1.3 79.3 - - - +
245D ALA* 1.3 55.6 + - - +
247D ALA* 3.3 7.4 + - - +
248D ASP* 2.8 67.0 + - - +
259D ILE* 4.2 13.4 - - - +
261D TYR* 3.9 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D GLU* 4.1 27.6 - - + +
242D SER* 2.9 22.5 + - - +
244D GLN* 1.3 73.2 - - - +
246D VAL* 1.3 66.3 + - - +
248D ASP* 3.2 13.5 + - - +
249D ALA* 3.0 22.5 + - - +
295D VAL* 4.0 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D VAL* 4.9 6.7 - - + -
185D ALA* 4.2 34.5 - - + +
188D LEU* 4.6 5.6 - - + -
211D PHE* 3.7 47.8 - - + -
242D SER 3.5 2.0 + - - +
243D PHE* 3.1 8.4 + - + +
245D ALA* 1.3 78.0 - - - +
247D ALA* 1.3 63.4 + - - +
249D ALA* 3.2 4.3 + - - +
250D THR* 3.0 26.7 + - - +
295D VAL* 3.8 19.0 - - + +
299D VAL* 4.2 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D LEU* 3.8 18.6 - - + +
200D LEU* 4.3 6.1 - - + -
243D PHE 3.0 11.6 + - - +
244D GLN* 3.4 13.5 - - - +
246D VAL* 1.3 77.2 - - - +
248D ASP* 1.3 54.0 + - - +
250D THR* 3.2 1.9 + - - -
251D LEU* 2.8 40.0 + - + +
259D ILE* 3.4 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D GLN* 2.8 51.7 + - - +
245D ALA* 3.3 12.8 - - - +
247D ALA* 1.3 73.2 - - - +
249D ALA* 1.3 63.0 - - - +
251D LEU* 3.5 4.8 + - - +
252D ALA* 3.0 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D ALA 3.0 9.1 + - - +
246D VAL 3.2 8.0 + - - +
248D ASP* 1.3 80.2 - - - +
250D THR* 1.3 61.3 + - - +
252D ALA* 3.5 6.5 - - - +
253D TYR* 3.2 17.0 + - - +
295D VAL* 4.3 10.1 - - + +
296D ALA* 4.3 16.4 - - + +
299D VAL* 3.7 24.0 - - + +
300D THR* 3.8 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D ALA* 4.6 0.9 - - - -
188D LEU* 4.1 21.4 - - + +
189D ASN 4.5 1.6 - - - +
192D LEU* 3.9 21.5 - - + -
246D VAL* 3.0 17.6 + - - +
247D ALA* 3.5 10.1 - - - -
249D ALA* 1.3 73.5 - - - +
251D LEU* 1.3 67.3 + - + +
252D ALA 3.1 0.9 - - - -
253D TYR* 3.1 4.3 + - - +
254D HIS* 3.1 25.2 + - + +
299D VAL* 3.4 16.9 - - - +
303D MET* 3.6 30.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D LEU* 5.5 0.9 - - + -
192D LEU* 3.8 22.2 - - + -
198D PRO* 3.9 18.8 - - + -
247D ALA* 2.8 28.8 + - + +
248D ASP* 4.2 4.5 - - - +
250D THR* 1.3 75.9 - - + +
252D ALA* 1.3 57.3 + - - +
254D HIS* 3.3 2.9 + - - +
255D LYS* 2.8 26.7 + - - -
256D LYS 3.5 18.1 + - - +
257D GLY 3.0 30.7 - - - +
258D GLN* 4.0 8.1 - - - +
259D ILE* 4.4 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D ASP 3.0 19.8 + - - +
249D ALA* 3.5 8.7 - - - +
251D LEU* 1.3 78.3 - - - +
253D TYR* 1.3 61.6 + - - +
255D LYS* 3.2 25.7 - - - +
300D THR* 5.6 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ALA 3.2 10.0 + - - +
250D THR 3.1 9.0 + - - +
252D ALA* 1.3 82.2 - - - +
254D HIS* 1.3 75.8 + + - +
255D LYS* 3.2 12.0 + - - +
300D THR* 4.3 18.8 - - + +
303D MET* 3.5 40.6 + - + -
304D ALA* 3.4 32.2 + - + +
307D ASN* 4.0 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D ASN* 2.8 32.9 + - - -
192D LEU* 3.8 35.1 - - + +
193D ASN* 3.4 23.9 + - - -
250D THR* 3.1 30.7 + - + +
251D LEU 4.0 3.1 - - - +
253D TYR* 1.3 88.2 - + - +
255D LYS* 1.3 69.6 + - - +
256D LYS* 3.0 28.6 + - + +
303D MET* 3.9 6.5 - - - -
307D ASN* 4.5 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D LEU 2.8 10.2 + - - -
252D ALA* 3.2 24.2 - - - +
253D TYR 3.2 9.7 - - - +
254D HIS* 1.3 79.3 - - - +
256D LYS* 1.3 59.2 + - - +
----------------------------------------------------------
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