Contacts of the helix formed by residues 222 - 234 (chain B) in PDB entry 4OL0
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 222 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B VAL* 5.6 5.3 - - + +
185B MET* 3.4 34.8 - - - +
215B ASP* 3.8 18.5 + - + +
221B ASN* 1.3 79.2 + - - +
223B LYS* 1.3 85.2 + - - +
224B LEU* 3.3 4.7 + - + +
225B LEU* 3.8 12.9 + - - +
226B ALA* 4.0 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B MET* 4.9 7.4 - - + -
188B VAL* 6.1 5.4 - - + -
222B ASN* 1.3 87.3 + - - +
224B LEU* 1.3 59.2 + - - +
225B LEU 3.3 0.4 - - - -
226B ALA* 3.2 12.8 + - + +
227B LEU* 2.8 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B VAL* 4.0 14.8 - - + +
184B LEU* 3.8 25.8 - - + +
185B MET* 3.8 25.7 - - + +
188B VAL* 4.5 15.5 - - + -
201B VAL* 4.2 22.4 - - + -
202B PHE* 4.8 3.6 - - + -
205B LEU* 3.9 34.4 - - + +
222B ASN* 3.3 3.2 - - + +
223B LYS* 1.3 78.0 - - - +
225B LEU* 1.3 62.0 + - + +
227B LEU* 3.5 11.1 + - + +
228B LEU* 2.8 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 4.9 9.0 - - + -
209B PHE* 3.9 27.1 - - + -
215B ASP 5.2 9.2 - - - +
221B ASN* 3.9 25.6 - - + +
222B ASN 3.8 9.0 + - - +
223B LYS 3.3 0.4 - - - -
224B LEU* 1.3 78.3 - - + +
226B ALA* 1.3 60.6 + - - +
228B LEU* 3.1 10.4 + - + +
229B PHE* 2.8 51.3 + - + -
265B LEU* 3.9 19.7 - - + -
268B GLN* 4.7 9.6 - - + -
269B LEU* 4.0 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ASN 4.0 3.2 + - - +
223B LYS* 3.2 21.3 + - + +
225B LEU* 1.3 80.1 - - - +
227B LEU* 1.3 56.5 + - - +
229B PHE* 3.5 6.0 + - - +
230B GLU* 2.8 32.2 + - - +
233B GLN* 5.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B VAL* 3.9 32.3 - - + -
198B LEU* 4.4 17.3 - - + -
202B PHE* 4.6 9.4 - - + -
223B LYS* 2.8 21.4 + - + +
224B LEU* 3.7 13.5 - - + +
226B ALA* 1.3 73.0 - - - +
228B LEU* 1.3 60.9 + - - +
230B GLU* 3.0 20.8 + - + +
231B VAL* 2.8 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B PHE* 3.5 32.7 - - + -
205B LEU* 4.6 6.5 - - + -
209B PHE* 5.4 2.9 - - + -
224B LEU 2.8 19.2 + - - +
225B LEU* 3.3 18.2 - - + +
227B LEU* 1.3 78.3 - - - +
229B PHE* 1.3 63.4 + - + +
231B VAL* 3.8 3.6 + - - +
232B LEU* 3.6 21.3 + - - +
245B ALA* 3.5 35.8 - - + +
248B CYS* 3.7 23.6 - - + -
249B VAL* 3.7 27.4 - - + +
252B ALA* 6.1 0.4 - - + -
269B LEU* 5.8 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU* 2.8 41.2 + - + +
226B ALA* 4.0 4.5 - - - +
228B LEU* 1.3 76.6 - - + +
230B GLU* 1.3 55.4 + - - +
231B VAL 3.2 0.4 - - - -
232B LEU* 3.0 6.9 + - + +
233B GLN* 2.7 52.6 + - - +
249B VAL* 4.0 30.7 - - + -
268B GLN 4.3 5.8 - - - -
269B LEU* 3.6 36.8 - - + -
272B GLY* 3.6 42.6 - - - +
273B VAL* 3.7 6.5 - - + -
275B THR* 4.9 0.2 - - - +
276B LEU* 4.0 12.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
226B ALA 2.8 21.7 + - - +
227B LEU* 3.0 24.4 + - + +
229B PHE* 1.3 72.4 - - - +
231B VAL* 1.3 63.2 + - - +
233B GLN* 3.1 18.0 + - + +
234B GLN* 3.0 48.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
198B LEU* 5.1 6.3 - - + -
202B PHE* 4.0 19.3 - - + -
227B LEU* 2.8 32.9 + - + +
228B LEU 3.8 5.8 - - - +
230B GLU* 1.3 77.0 - - - +
232B LEU* 1.3 61.9 + - - +
234B GLN* 3.6 9.0 + - - +
237B THR* 2.6 41.5 + - + +
241B LEU* 3.6 37.0 - - + +
242B HIS* 5.2 0.4 - - - +
245B ALA* 4.4 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU 3.6 12.5 + - - +
229B PHE* 3.0 11.0 + - + +
231B VAL* 1.3 76.3 - - - +
233B GLN* 1.3 61.2 + - - +
234B GLN 3.7 2.1 + - - +
242B HIS* 3.7 27.3 + - + +
245B ALA* 3.7 19.7 - - + -
246B SER* 3.6 22.2 - - - +
249B VAL* 3.7 30.1 - - + -
276B LEU* 3.8 21.8 - - + -
279B ALA* 3.6 1.4 - - - +
295B TYR* 2.4 31.2 + - + -
298B ILE* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PHE* 2.7 28.8 + - - +
230B GLU* 3.1 20.4 + - + +
232B LEU* 1.3 79.3 - - - +
234B GLN* 1.3 63.5 + - + +
235B ASP* 3.6 1.6 + - - -
275B THR* 3.1 37.7 + - - +
276B LEU* 3.7 12.3 - - + -
279B ALA* 3.5 21.7 - - + +
282B MET* 5.1 7.1 - - - +
----------------------------------------------------------
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* 3.0 44.7 + - + +
231B VAL* 3.6 7.7 + - - +
232B LEU 3.4 4.0 - - - +
233B GLN* 1.3 79.8 - - + +
235B ASP* 1.3 63.1 + - - +
236B LYS* 3.3 29.5 - - + +
237B THR* 3.0 31.6 + - - +
242B HIS* 5.3 0.3 - - - -
279B ALA* 5.8 0.2 - - - -
291B LYS* 4.2 2.9 + - - -
295B TYR* 5.0 2.0 + - - -
----------------------------------------------------------
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