Contacts of the helix formed by residues 229 - 244 (chain B) in PDB entry 5WYF
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 PRO 229 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B PRO* 3.6 27.4 - - + -
178B SER* 3.8 19.7 - - - +
187B GLU* 3.6 27.1 - - + +
190B VAL* 4.5 7.6 - - + -
191B SER* 3.3 24.2 - - - +
227B LYS* 3.6 6.5 - - - +
228B ALA* 1.4 85.4 - - + +
230B GLU* 1.4 66.6 + - - +
231B GLU 3.2 0.8 + - - +
232B TYR* 3.2 6.8 + - + +
233B MET* 3.1 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLU* 4.0 8.9 + - - +
227B LYS* 4.2 7.2 + - - +
228B ALA 3.5 2.2 + - - -
229B PRO* 1.4 70.8 - - - +
231B GLU* 1.3 58.6 + - + +
233B MET* 3.3 5.0 + - - +
234B GLN* 2.9 62.8 + - + +
267B GLN 3.7 5.7 - - - +
268B PHE* 3.3 33.1 - - - -
269B LYS* 3.1 20.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLU* 5.1 2.6 + - + +
188B HIS* 3.4 22.6 + - - +
191B SER* 3.9 10.8 + - - +
192B LEU* 3.9 17.8 - - - +
229B PRO* 3.2 1.0 - - - +
230B GLU* 1.3 79.2 - - + +
232B TYR* 1.3 65.9 + - - +
234B GLN* 3.4 7.5 + - + +
235B LEU* 3.0 37.4 + - + +
1005B CD 2.7 29.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TYR* 2.6 37.0 + + - -
174B PRO 4.2 3.3 + - - -
176B PRO* 3.9 25.4 - - + -
191B SER* 3.3 36.9 + - - +
194B TYR* 3.6 19.0 + - + -
195B PHE* 3.5 24.7 - - + -
198B PHE* 3.8 10.6 - - - +
216B ILE* 4.3 9.0 - - + -
228B ALA* 4.2 7.4 - - + -
229B PRO* 3.2 19.2 + - + +
231B GLU* 1.3 79.6 - - - +
233B MET* 1.3 67.4 + - - +
235B LEU* 3.3 6.6 + - - +
236B VAL* 3.1 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ILE* 4.0 25.4 - - + -
218B PRO* 3.8 23.6 - - + -
228B ALA* 3.9 13.7 - - + -
229B PRO 3.1 4.1 + - - +
230B GLU 3.6 7.9 - - - +
231B GLU 3.3 0.2 - - - -
232B TYR* 1.3 84.3 - - - +
234B GLN* 1.3 56.6 + - - +
236B VAL* 3.4 5.0 + - - +
237B TYR* 2.9 30.0 + - - +
247B PHE* 3.8 24.7 - - + -
265B ILE* 4.6 4.0 - - + -
268B PHE* 3.7 42.0 - - + -
271B ILE* 3.7 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B GLU* 2.9 46.7 + - + +
231B GLU* 3.9 7.2 - - + +
233B MET* 1.3 72.1 - - - +
235B LEU* 1.3 61.2 + - + +
237B TYR* 3.6 13.1 - - - +
238B LYS* 2.8 32.7 + - - +
269B LYS* 2.7 38.2 + - - +
270B ASP 5.0 1.0 - - - +
271B ILE* 3.9 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B SER 4.5 4.9 - - - +
192B LEU* 4.3 23.6 - - + -
195B PHE* 3.7 52.7 - - + -
231B GLU* 3.0 30.7 + - + +
232B TYR* 3.4 7.9 - - - +
234B GLN* 1.3 76.7 - - - +
236B VAL* 1.3 52.1 + - - +
238B LYS* 3.4 21.9 + - + +
239B PHE* 2.7 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TYR* 3.8 5.6 - - - +
195B PHE* 4.4 9.9 - - + -
198B PHE* 4.1 21.3 - - + -
214B VAL* 4.3 11.9 - - + -
216B ILE* 5.4 2.9 - - + -
232B TYR* 3.1 47.2 + - + +
233B MET* 3.4 8.9 + - - +
235B LEU* 1.3 73.5 - - - +
237B TYR* 1.3 61.1 + - - +
239B PHE* 3.1 7.2 + - - +
240B CYS* 2.8 38.3 + - - -
247B PHE* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B MET 2.9 17.9 + - - +
234B GLN* 3.6 15.7 - - - +
236B VAL* 1.3 74.8 - - - +
238B LYS* 1.3 66.4 + - + +
240B CYS* 3.2 4.9 + - - +
241B HIS* 3.1 32.9 + + + +
247B PHE* 3.7 35.6 - + + -
270B ASP 3.8 16.6 + - - -
271B ILE* 3.7 31.3 - - + -
272B GLU* 3.1 39.7 + - - +
274B ASP* 6.1 0.2 - - - -
294B LYS* 5.8 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLN 2.8 19.7 + - - +
235B LEU* 3.7 22.1 + - + +
237B TYR* 1.3 77.1 - - + +
239B PHE* 1.3 64.6 + - - +
241B HIS* 3.4 5.6 + - - +
242B GLU* 3.0 53.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B PHE* 4.0 23.3 - + + -
198B PHE* 3.7 16.8 - + + -
199B LYS* 4.4 17.0 - - + -
202B PHE* 3.9 41.3 - + + -
208B ALA* 4.2 4.3 - - + -
235B LEU 2.7 21.5 + - - +
236B VAL* 3.1 5.1 + - - +
238B LYS* 1.3 72.9 - - - +
240B CYS* 1.3 64.1 + - - +
242B GLU* 4.8 3.4 - - - -
243B HIS* 2.6 64.2 + + - -
245B ILE* 3.9 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B VAL* 3.5 37.0 - - - -
236B VAL* 2.8 20.0 + - - -
237B TYR 3.6 7.2 - - - +
238B LYS 3.2 0.2 - - - -
239B PHE* 1.3 78.2 - - - +
241B HIS* 1.3 60.7 + - - +
243B HIS 3.2 1.6 + - - -
244B GLY* 2.9 25.5 + - - -
245B ILE* 2.9 40.2 + - - +
246B LEU 4.2 3.4 - - - -
247B PHE* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B TYR* 3.1 26.2 + + + +
238B LYS* 4.3 4.3 - - - +
240B CYS* 1.3 76.2 - - - +
242B GLU* 1.3 62.6 + - + +
243B HIS 3.4 0.5 + - - -
244B GLY* 3.6 9.1 + - - +
245B ILE 4.9 1.1 - - - -
294B LYS* 5.8 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B LYS* 3.0 53.9 + - + +
239B PHE* 4.0 5.2 - - - +
241B HIS* 1.3 77.9 - - + +
243B HIS* 1.4 75.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ARG* 2.9 26.8 + - - -
208B ALA* 3.7 26.3 - - + +
209B ASP* 4.7 2.6 - - - +
239B PHE* 2.6 60.0 + + - +
242B GLU* 1.4 92.8 - - + +
244B GLY* 1.3 58.4 + - - +
245B ILE* 3.2 17.0 - - + -
1006B CD 2.5 30.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B THR* 4.2 12.5 - - - +
132B ARG* 3.5 18.2 + - - -
240B CYS 2.9 6.0 + - - -
241B HIS* 3.6 10.1 + - - -
242B GLU 3.6 0.6 - - - -
243B HIS* 1.3 78.1 - - - +
245B ILE* 1.3 60.5 + - - +
246B LEU* 3.9 5.3 + - - +
----------------------------------------------------------
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