Contacts of the helix formed by residues 229 - 243 (chain B) in PDB entry 2W5X
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 ASN 229 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ARG 3.7 0.6 + - - -
228B GLY* 1.3 70.1 - - - -
230B PHE* 1.3 63.6 + - - +
231B LEU 3.3 2.5 - - - -
232B SER* 3.5 17.8 + - - +
233B ALA* 2.9 29.5 + - - +
276B ASP* 4.4 9.2 - - - +
279B ASP* 5.7 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 4.3 8.1 - - + -
129B ALA 3.2 31.4 - - - -
130B THR* 3.9 15.0 - - + -
167B ALA* 4.0 12.1 - - + -
168B GLY* 4.0 18.2 - - - -
199B LEU* 3.9 15.9 - - + -
215B LEU* 4.0 17.0 - - + -
220B MET* 3.8 26.2 - - + -
227B ARG* 3.7 28.8 + - + +
228B GLY 3.1 4.4 + - - -
229B ASN* 1.3 75.5 - - - +
231B LEU* 1.3 58.6 + - - +
233B ALA* 3.7 4.8 - - - +
234B ALA* 2.7 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 4.0 19.5 - - + -
129B ALA* 5.1 0.2 - - - -
130B THR* 4.2 14.1 - - + -
227B ARG* 5.0 0.8 - - - +
228B GLY 4.9 0.2 + - - -
229B ASN* 3.3 1.0 - - - +
230B PHE* 1.3 83.5 - - - +
232B SER* 1.3 59.9 + - - +
234B ALA* 4.0 1.8 - - - +
235B THR* 2.6 38.3 + - - +
253B SER* 4.4 3.4 - - - -
254B GLU 3.6 25.6 - - - +
255B GLY* 4.0 23.3 - - - +
273B GLU 5.9 0.2 - - - +
276B ASP* 3.7 26.5 + - - +
277B PHE* 4.0 14.6 - - + -
280B ALA* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ASN* 3.5 21.0 + - - +
230B PHE 3.4 0.2 - - - -
231B LEU* 1.3 77.4 - - - +
233B ALA* 1.3 59.1 + - - +
235B THR* 3.3 4.4 + - - -
236B ASP* 2.9 31.5 + - - +
276B ASP* 4.4 2.6 + - - -
279B ASP* 3.3 15.0 + - - +
280B ALA* 3.2 31.5 + - - +
283B THR* 3.4 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU* 3.8 15.5 - - + -
229B ASN* 2.9 33.6 + - - +
230B PHE* 3.8 2.7 - - - +
232B SER* 1.3 77.1 - - - +
234B ALA* 1.3 56.7 + - - +
236B ASP* 3.3 7.7 + - - +
237B LEU* 2.8 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 3.8 23.8 - - + -
165B PHE* 4.0 4.6 - - + -
167B ALA* 4.0 11.9 - - + -
199B LEU* 3.6 18.3 - - + +
230B PHE* 2.7 31.5 + - + +
231B LEU 4.1 0.2 - - - +
233B ALA* 1.3 70.2 - - - +
235B THR* 1.3 60.6 + - - +
237B LEU* 3.3 6.6 + - - +
238B ALA* 2.8 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 5.0 6.1 - - + -
40B LEU* 4.7 9.6 - - + -
128B VAL* 4.5 1.8 - - - +
231B LEU* 2.6 27.1 + - - +
232B SER* 3.6 6.2 - - - -
234B ALA* 1.3 76.3 - - - +
236B ASP* 1.3 61.1 + - - +
238B ALA* 3.3 7.5 + - - +
239B ILE* 3.0 40.3 + - + +
251B ILE* 4.9 7.0 - - + -
253B SER* 3.0 34.4 + - - +
280B ALA* 4.8 7.6 - - - +
283B THR* 4.7 8.7 - - + -
284B ALA* 5.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B SER 2.9 16.4 + - - +
233B ALA* 3.4 8.7 - - - +
235B THR* 1.3 75.3 - - - +
237B LEU* 1.3 64.3 + - - +
239B ILE* 3.3 11.6 + - - +
240B GLN* 3.2 41.6 + - - +
283B THR* 4.0 19.0 - - + +
287B PHE* 5.9 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PHE* 4.2 5.6 - - + -
199B LEU* 3.8 18.4 - - + -
200B THR 3.4 26.7 - - - +
201B ASP* 3.8 1.3 - - - -
202B PHE* 3.7 33.0 - - + +
205B ILE* 3.9 15.9 - - + -
213B PHE* 3.7 31.6 - - + -
233B ALA 2.8 16.7 + - - +
234B ALA 3.5 6.1 - - - +
236B ASP* 1.3 75.9 + - - +
238B ALA* 1.3 62.2 + - - +
240B GLN* 3.2 10.4 + - - +
241B PHE* 2.9 25.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
126B GLY* 5.5 0.4 - - - -
128B VAL* 4.6 6.7 - - + -
165B PHE* 3.6 33.6 - - + -
234B ALA 2.8 20.6 + - - +
235B THR* 3.3 7.8 + - - +
237B LEU* 1.3 73.9 - - - +
239B ILE* 1.3 56.3 + - - +
242B LEU* 2.8 38.4 + - + +
251B ILE* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 3.8 24.2 - - + -
235B THR* 3.0 25.9 + - + +
236B ASP* 3.6 13.9 - - - +
238B ALA* 1.3 75.8 - - - +
240B GLN* 1.3 59.2 + - + +
242B LEU* 3.9 0.7 - - - +
243B SER* 2.5 37.3 + - - +
249B PHE* 4.0 7.2 - - + -
251B ILE* 3.6 19.7 - - + -
283B THR* 4.9 4.3 - - + +
284B ALA* 4.8 5.6 - - - -
287B PHE* 3.5 56.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B PHE* 3.6 55.3 - - + +
236B ASP* 3.2 32.3 + - - +
237B LEU* 3.6 14.0 - - - +
239B ILE* 1.3 83.2 - - + +
241B PHE* 1.3 64.3 + - - +
243B SER* 3.5 12.5 + - - -
244B LYS* 3.5 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LYS* 6.0 2.8 - - + +
164B ASP* 3.5 24.2 - - + -
165B PHE* 3.8 23.3 - + + -
202B PHE* 3.7 9.1 - + + -
205B ILE* 3.6 38.1 - - + -
208B ASN* 3.3 29.8 - - + -
209B ARG 3.5 18.8 - - - -
210B LYS* 3.8 8.3 - - - -
211B MET* 4.0 6.3 - - + -
237B LEU 2.9 16.6 + - - +
238B ALA 3.9 1.8 - - - +
240B GLN* 1.3 76.4 - - - +
242B LEU* 1.3 73.8 + - + +
244B LYS* 3.3 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LYS* 3.6 31.6 - - + +
125B THR 3.6 17.0 - - - +
126B GLY* 3.5 27.1 - - - +
164B ASP* 3.7 19.7 - - + -
165B PHE* 3.8 13.2 - - + -
238B ALA* 2.8 21.8 + - + +
241B PHE* 1.3 82.8 - - + +
243B SER* 1.3 58.0 + - - +
244B LYS* 3.3 2.1 + - - -
247B SER* 3.6 14.4 - - - +
249B PHE* 3.6 20.8 - - + +
250B PHE 4.1 2.5 - - - +
251B ILE* 3.5 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASN* 6.1 0.4 - - - -
239B ILE* 2.5 29.3 + - - +
240B GLN* 3.5 8.9 + - - -
241B PHE 3.3 0.2 - - - -
242B LEU* 1.3 76.4 - - - +
244B LYS* 1.3 67.6 + - - +
246B ASN* 3.3 13.4 + - - -
247B SER 3.6 12.3 + - - -
249B PHE* 4.0 17.5 - - - -
287B PHE* 5.1 6.4 - - - -
----------------------------------------------------------
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