Contacts of the helix formed by residues 230 - 249 (chain B) in PDB entry 1OH7
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 ALA 230 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 4.5 5.4 - - + -
159B GLU* 2.8 24.6 - - - +
227B VAL* 3.2 23.1 + - + +
228B GLU 3.3 1.8 - - - -
229B ASN* 1.3 79.4 - - - +
231B PRO* 1.3 58.0 - - - +
233B GLY 3.1 0.7 + - - -
234B LEU* 2.9 26.8 + - + +
260B MET* 3.9 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B GLU* 3.9 3.6 - - - +
206B ILE* 3.3 30.3 - - + +
210B ARG* 4.3 9.0 - - - +
228B GLU 4.8 1.1 - - - +
229B ASN* 3.3 10.5 - - - +
230B ALA* 1.3 86.6 - - - +
232B ARG* 1.3 67.5 + - + +
234B LEU* 3.1 4.2 + - + -
235B CYS* 3.1 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B TRP* 3.3 35.7 - - - +
139B ASP* 3.5 24.6 + - - -
141B LYS* 3.9 12.3 - - - +
142B GLY* 3.3 28.1 - - - +
143B PHE 3.1 31.5 + - - +
144B GLY* 3.6 21.4 - - - +
159B GLU* 3.0 39.6 + - + +
160B PRO 3.8 7.7 + - - -
161B ALA* 5.0 4.2 - - - +
231B PRO* 1.3 81.8 - - + +
233B GLY* 1.3 61.6 + - - +
235B CYS* 3.6 0.4 + - - -
236B ALA 3.5 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLY* 4.1 4.0 - - - -
145B TYR 4.4 1.8 - - - -
157B LEU* 4.1 18.8 - - - +
158B SER 3.9 19.5 - - - -
159B GLU* 3.0 15.5 + - - +
230B ALA 3.5 3.6 - - - -
232B ARG* 1.3 72.6 - - - +
234B LEU* 1.3 65.5 + - - +
236B ALA* 3.1 5.7 + - - +
237B ALA* 3.0 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 4.5 5.1 - - + +
206B ILE* 3.8 8.1 - - + -
209B ALA* 3.6 11.0 - - + +
210B ARG* 3.6 34.8 - - + +
213B LEU* 3.3 31.1 - - + +
222B LEU* 3.4 20.9 - - + -
227B VAL* 3.3 36.1 - - + +
228B GLU 3.9 2.0 - - - +
230B ALA 2.9 18.1 + - - +
231B PRO* 3.1 8.3 + - + +
233B GLY* 1.3 76.0 - - - +
235B CYS* 1.3 53.2 + - - +
237B ALA* 3.1 5.8 + - - +
238B GLY* 2.8 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B TRP* 3.9 20.9 - - + +
204B PHE* 2.9 46.1 - - + +
206B ILE* 3.7 28.7 - - - -
209B ALA* 4.2 6.6 - - - +
231B PRO 3.1 17.3 + - - -
232B ARG 3.7 9.0 - - - +
233B GLY 3.2 0.2 - - - -
234B LEU* 1.3 75.7 - - - +
236B ALA* 1.3 63.4 + - - +
238B GLY* 3.3 1.0 + - - -
239B CYS* 3.2 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ALA* 3.3 35.5 - - + +
137B TRP* 4.6 5.6 - - + -
144B GLY 3.9 6.7 - - - +
145B TYR 3.9 17.5 - - - +
146B ALA* 3.9 7.2 - - - +
204B PHE* 4.2 10.5 - - - -
232B ARG 3.5 3.6 + - - +
233B GLY 3.1 9.6 + - - +
235B CYS* 1.3 79.5 - - - +
237B ALA* 1.3 56.7 + - - +
239B CYS* 3.2 2.9 + - - +
240B LEU 3.0 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ALA* 3.6 16.5 - - + +
155B PHE* 3.5 23.6 - - + -
157B LEU* 4.7 1.3 - - + -
213B LEU* 3.9 10.9 - - + +
233B GLY 3.0 12.7 + - - +
234B LEU* 3.1 8.7 + - - +
236B ALA* 1.3 76.3 - - - +
238B GLY* 1.3 56.7 + - - +
240B LEU* 3.8 2.2 - - - -
241B LEU* 3.2 27.0 + - - +
258B ILE* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLU 4.3 4.3 - - - -
209B ALA* 4.0 25.8 - - - -
212B GLN* 5.2 6.4 - - - +
213B LEU* 4.7 4.3 - - - -
234B LEU 2.8 14.3 + - - -
235B CYS 3.3 2.2 + - - -
236B ALA 3.2 0.4 - - - -
237B ALA* 1.3 75.7 - - - +
239B CYS* 1.3 63.8 + - - +
241B LEU* 4.2 2.4 - - - +
242B GLN* 3.3 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ALA* 4.5 0.7 - - + -
179B LEU* 3.6 26.0 - - - -
199B ARG* 4.2 2.9 - - - -
203B GLU* 3.4 39.7 + - - +
204B PHE* 3.4 37.2 - - + -
235B CYS 3.2 5.1 + - - +
236B ALA 3.2 9.1 + - - +
238B GLY* 1.3 74.5 - - - +
240B LEU* 1.3 66.8 + - - +
242B GLN* 2.9 17.7 + - - +
243B TYR* 3.0 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 3.6 27.1 - - + +
134B ALA* 3.8 7.0 - - - -
135B ALA* 3.8 5.1 - - + +
146B ALA* 3.5 33.2 - - + +
147B THR 3.8 0.9 - - - +
148B LEU* 3.4 49.8 - - + +
155B PHE* 4.2 9.0 - - + -
179B LEU* 3.9 11.2 - - - +
236B ALA 3.0 12.6 + - - +
237B ALA* 3.9 7.9 - - - +
239B CYS* 1.3 79.6 - - - +
241B LEU* 1.3 60.8 + - - +
243B TYR* 3.2 4.0 + - - +
244B ALA* 2.9 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 5.8 1.3 - - + -
155B PHE* 4.4 14.1 - - + -
212B GLN* 4.3 12.1 - - + +
213B LEU* 3.6 33.9 - - + +
216B GLN* 3.7 41.3 - - + +
237B ALA 3.2 14.6 + - - +
238B GLY 4.2 2.9 - - - +
239B CYS 3.2 0.4 - - - -
240B LEU* 1.3 78.3 - - - +
242B GLN* 1.3 68.4 + - - +
244B ALA* 3.3 5.9 + - + +
245B LYS* 3.0 46.8 + - + +
252B LEU* 4.7 9.0 - - + -
255B ILE* 4.9 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B TRP* 4.3 18.3 - - - -
203B GLU* 3.5 48.4 + - - +
208B THR* 5.2 10.9 - - + +
212B GLN* 4.9 20.3 - - + +
238B GLY 3.3 11.9 + - - +
239B CYS* 2.9 10.0 + - - +
241B LEU* 1.3 81.1 - - - +
243B TYR* 1.3 61.6 + - - +
245B LYS* 3.4 7.0 + - - +
246B ASP* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B SER* 4.5 1.4 + - - -
115B THR* 3.8 14.1 - - - +
118B THR* 4.2 2.7 - - + -
133B LEU* 3.9 17.0 - - + -
177B GLU* 2.6 36.9 + - - -
179B LEU* 3.5 40.6 - - + -
197B ARG* 3.8 11.3 + - + -
199B ARG* 3.6 34.5 - - - +
203B GLU* 5.5 2.9 + - - +
239B CYS* 3.0 7.1 + - - +
240B LEU 3.2 2.4 + - - +
242B GLN* 1.3 72.5 - - - +
244B ALA* 1.3 68.2 + - - +
246B ASP* 3.0 13.2 + - - +
247B THR* 2.9 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B THR* 4.5 2.5 - - - -
133B LEU* 4.2 10.7 - - + +
148B LEU* 4.0 25.8 - - + -
150B ILE* 4.7 6.3 - - + -
240B LEU 2.9 16.1 + - - +
241B LEU* 3.6 8.3 - - + +
243B TYR* 1.3 76.0 - - - +
245B LYS* 1.3 62.4 + - - +
247B THR* 2.7 23.1 + - - -
248B GLN* 3.2 16.1 + - - +
252B LEU* 4.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLN* 4.5 27.7 + - - +
215B LEU* 5.3 8.3 - - - +
216B GLN* 3.7 29.4 + - - +
241B LEU* 3.0 34.5 + - + +
242B GLN* 3.7 7.0 - - - +
244B ALA* 1.3 76.1 - - - +
246B ASP* 1.3 57.4 + - - +
248B GLN* 4.0 2.3 - - - +
249B ARG* 3.0 29.6 + - - -
250B THR 4.2 14.1 + - - +
251B THR* 5.8 0.9 - - - -
252B LEU* 4.0 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ARG* 5.5 4.0 + - - -
242B GLN 3.1 17.2 + - - +
243B TYR* 3.0 15.7 + - - +
245B LYS* 1.3 76.2 - - - +
247B THR* 1.3 64.9 + - + +
249B ARG* 2.9 56.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 4.4 14.3 - - - +
115B THR* 3.6 20.9 - - + -
118B THR* 3.3 18.9 - - + +
243B TYR* 2.9 49.0 + - + +
244B ALA 2.7 18.9 + - - -
246B ASP* 1.3 79.6 - - + +
248B GLN* 1.3 75.4 + - - +
249B ARG* 4.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B THR* 3.4 22.5 + - - +
120B SER* 5.1 2.8 + - - -
150B ILE* 3.8 15.9 - - + +
244B ALA 3.2 16.0 + - - +
245B LYS 4.0 2.2 - - - +
247B THR* 1.3 101.1 + - - +
249B ARG* 1.3 70.3 + - - +
250B THR* 3.4 23.4 + - - +
252B LEU* 3.7 23.3 - - + -
357B LEU* 4.2 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B HIS* 6.3 0.8 - - - -
245B LYS 3.0 12.5 + - - -
246B ASP* 2.9 46.5 + - - +
247B THR 4.9 1.1 - - - +
248B GLN* 1.3 79.8 - - - +
250B THR* 1.3 66.0 + - - +
----------------------------------------------------------
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