Contacts of the helix formed by residues 229 - 246 (chain B) in PDB entry 2BEW
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 THR 229 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B HIS* 4.1 11.9 - - + +
4B PHE* 3.8 30.5 - - + -
136B TRP* 4.3 4.6 - - - -
190B PRO* 3.6 18.0 - - - +
192B ILE* 3.5 32.4 - - + +
193B LEU* 3.9 8.3 - - + +
228B GLY* 1.3 72.1 - - - -
230B GLN* 1.3 62.4 + - - +
231B VAL 3.0 0.2 - - - -
232B HIS* 3.0 26.3 + - - +
233B VAL* 3.6 5.1 + - - +
280B GLU* 4.2 15.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B HIS* 4.9 5.4 + - - -
136B TRP* 5.8 1.7 - - + -
226B ALA* 3.8 17.7 - - + -
227B TRP 3.5 11.2 - - - +
228B GLY 3.0 1.8 + - - -
229B THR* 1.3 79.6 - - - +
231B VAL* 1.3 62.9 + - - +
232B HIS 3.2 0.2 - - - -
233B VAL* 3.2 26.3 + - - +
234B ILE* 3.0 22.6 + - - +
278B SER* 2.8 38.3 + - - +
279B HIS* 4.4 7.0 - - - -
280B GLU* 4.4 16.2 + - + +
327B PRO* 2.9 36.5 + - - +
332B CYS* 3.8 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ARG* 3.7 19.5 - - + -
216B ILE* 3.6 29.2 - - + -
226B ALA* 3.7 4.7 - - - +
227B TRP* 3.5 26.9 + - - +
228B GLY 3.5 14.1 - - - +
229B THR 3.0 0.6 - - - -
230B GLN* 1.3 78.9 - - - +
232B HIS* 1.3 57.0 + - + +
234B ILE* 3.3 9.9 + - + +
235B ARG* 2.9 29.1 + - - +
251B VAL* 4.7 5.4 - - + -
252B ILE 5.0 0.2 - - - +
253B ASP* 3.6 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 4.3 12.3 - + + -
5B THR 3.6 25.8 + - - +
6B PHE* 3.5 30.9 - + - -
7B GLN 5.0 0.9 - - - -
166B ARG* 2.7 43.2 + - + +
167B SER* 5.0 0.2 - - - -
193B LEU* 4.5 10.3 - - + +
228B GLY 4.3 1.3 - - - -
229B THR* 3.0 25.6 + - - +
231B VAL* 1.3 74.7 - - - +
233B VAL* 1.3 65.8 + - - +
235B ARG* 2.8 42.3 + - - +
236B GLU* 3.2 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B HIS* 3.8 34.8 - - + +
4B PHE* 4.3 4.5 - - + +
229B THR 4.1 8.3 - - - +
230B GLN* 3.2 41.8 + - - +
232B HIS* 1.3 77.1 - - - +
234B ILE* 1.3 57.7 + - - +
236B GLU* 3.2 7.7 + - - +
237B VAL* 2.9 27.3 + - + +
327B PRO 4.1 0.9 - - - +
328B ASP* 3.8 3.8 - - - +
329B LYS* 3.5 34.7 - - + +
332B CYS* 4.5 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B LEU* 3.6 47.9 - - + +
225B VAL 3.8 0.9 - - - +
226B ALA* 3.6 24.2 - - + +
230B GLN* 3.0 15.1 + - - +
231B VAL* 3.4 15.7 - - - +
233B VAL* 1.3 74.9 - - - +
235B ARG* 1.3 60.8 + - - +
237B VAL* 3.6 7.3 - - + +
238B ALA* 2.9 27.2 + - - +
251B VAL* 3.9 15.1 - - + +
252B ILE 4.1 3.4 - - - +
276B LEU* 5.0 5.2 - - + -
278B SER* 4.2 24.9 - - - -
332B CYS* 4.6 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B THR 3.7 9.9 + - - -
7B GLN* 3.3 50.5 + - - +
166B ARG* 5.1 2.4 - - - +
216B ILE* 3.8 27.4 - - + +
217B GLN* 4.4 16.1 - - - +
231B VAL* 2.9 20.8 + - - +
232B HIS* 2.8 45.9 + - - +
233B VAL 3.2 0.2 - - - -
234B ILE* 1.3 78.7 - - - +
236B GLU* 1.3 60.9 + - - +
238B ALA* 3.3 8.3 + - - +
239B SER* 3.2 18.7 + - - -
251B VAL* 4.4 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B THR* 5.7 8.6 - - - +
7B GLN* 5.2 8.3 + - - -
232B HIS 3.2 11.9 + - - +
233B VAL* 3.2 9.4 + - - +
235B ARG* 1.3 75.0 - - - +
237B VAL* 1.3 60.2 + - - +
239B SER* 3.1 17.6 + - - -
240B MET* 2.9 37.3 + - - +
329B LYS* 3.9 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B LEU* 4.5 8.3 - - + -
233B VAL 2.9 21.6 + - - +
234B ILE* 3.6 11.9 - - + +
235B ARG 3.3 0.2 - - - -
236B GLU* 1.3 75.2 - - - +
238B ALA* 1.3 53.0 + - - +
240B MET* 3.2 9.2 + - - +
241B ALA* 2.8 33.1 + - - +
276B LEU* 6.3 0.9 - - + -
329B LYS* 3.5 32.5 - - + +
332B CYS* 3.6 20.6 - - + +
333B TYR* 4.0 17.5 - - + +
336B LEU* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLN* 4.0 16.7 + - - +
224B LEU* 4.3 0.9 - - + +
234B ILE 2.9 12.9 + - - +
235B ARG 3.3 11.4 - - - +
237B VAL* 1.3 78.6 - - - +
239B SER* 1.3 56.6 + - - +
241B ALA* 3.5 1.7 + - - +
242B LYS* 3.0 28.1 + - - +
247B VAL 4.4 2.3 - - - +
249B CYS* 3.8 25.8 + - + +
251B VAL* 3.7 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLN* 5.6 0.2 + - - -
235B ARG 3.2 8.6 + - - -
236B GLU* 3.1 24.8 + - - -
238B ALA* 1.3 76.4 - - - +
240B MET* 1.3 65.0 + - - +
242B LYS* 3.4 7.3 + - - +
243B GLU* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B GLU* 2.9 30.6 + - - +
237B VAL* 3.5 11.4 - - - +
239B SER* 1.3 76.8 - - - +
241B ALA* 1.3 58.0 + - - +
243B GLU* 4.6 4.7 - - - -
244B LYS* 2.9 47.0 + - - +
329B LYS* 3.9 33.9 - - + +
330B TRP* 3.3 48.7 - - + -
333B TYR* 3.7 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B VAL 2.8 20.3 + - - +
238B ALA 3.9 0.7 - - - +
239B SER 3.3 0.4 - - - -
240B MET* 1.3 70.8 - - - +
242B LYS* 1.3 61.0 + - - +
245B LEU* 2.8 32.5 + - + +
246B GLY 3.1 6.1 + - - -
247B VAL* 3.2 17.5 + - + +
249B CYS* 3.8 25.4 - - - -
333B TYR* 4.2 9.8 - - + -
336B LEU* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ALA 3.0 18.4 + - - +
239B SER* 3.7 6.7 - - - +
241B ALA* 1.3 75.8 - - - +
243B GLU* 1.3 61.2 + - + +
246B GLY* 3.1 23.9 + - - -
247B VAL 3.4 18.5 + - - +
248B SER* 5.8 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B SER* 3.0 17.2 + - - +
240B MET* 3.9 5.2 - - - +
242B LYS* 1.3 84.4 - - + +
244B LYS* 1.3 74.2 + - + +
246B GLY 4.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B MET* 2.9 46.9 + - - +
243B GLU* 1.3 89.3 + - + +
245B LEU* 1.3 66.7 + - + +
330B TRP* 4.3 17.3 - - - -
333B TYR* 3.4 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ALA* 2.8 20.6 + - + +
244B LYS* 1.3 82.0 - - - +
246B GLY* 1.3 63.3 + - - +
247B VAL* 3.4 20.1 + - + +
333B TYR* 3.4 41.7 - - + +
336B LEU* 5.3 1.8 - - + -
337B ARG* 4.2 33.9 - - + +
340B ILE* 5.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ASP* 4.1 5.5 - - - +
242B LYS* 3.1 21.2 + - - -
243B GLU 4.6 1.0 + - - -
244B LYS 3.8 0.8 - - - -
245B LEU* 1.3 79.0 - - - +
247B VAL* 1.3 59.2 + - - +
248B SER* 4.2 0.5 + - - -
----------------------------------------------------------
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