Contacts of the helix formed by residues 244 - 264 (chain B) in PDB entry 2OR2
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 SER 244 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PRO* 3.9 20.0 - - - -
236B SER* 3.4 17.2 + - - -
237B SER 3.2 19.6 + - - -
242B ALA* 2.7 17.2 + - - -
243B ASN* 1.3 70.0 - - - +
245B PRO* 1.3 67.6 - - - +
246B TYR 3.3 2.5 - - - -
247B TYR* 3.1 9.2 + - - +
248B TYR* 3.0 38.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLY* 4.7 9.9 - - - -
49B MET 3.8 21.5 - - - +
50B THR* 4.5 5.4 - - + -
235B LEU 3.3 20.0 + - - +
236B SER* 4.6 13.7 - - - -
242B ALA 4.6 0.9 - - - +
243B ASN* 3.2 19.7 - - - +
244B SER* 1.3 95.0 - - - +
246B TYR* 1.3 58.4 + - - +
248B TYR* 3.5 1.2 + - - +
249B ALA* 2.9 30.5 + - - +
274B ASP* 3.9 14.9 - - - +
275B TYR* 4.0 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TYR* 3.8 25.8 - + - -
247A TYR* 3.7 40.2 - + + -
250A SER* 2.8 29.5 + - - -
251A TYR* 3.7 2.8 - - - -
52B GLU* 4.5 5.2 - - - -
243B ASN* 4.4 9.7 + - - +
244B SER 3.3 0.6 - - - -
245B PRO* 1.3 77.7 - - - +
247B TYR* 1.3 71.2 + - - +
249B ALA* 3.2 1.0 + - - +
250B SER* 2.8 22.5 + - - -
275B TYR* 3.5 45.9 - + + +
277B ASN* 4.9 0.4 - - - -
279B LYS* 3.4 23.6 + - - +
280B TRP* 3.7 25.2 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLN* 3.4 25.2 + - - -
42A PRO* 3.5 35.4 - - + -
52A GLU* 2.6 33.5 + - - +
246A TYR* 3.6 46.6 - + + -
204B TYR* 6.3 0.7 - + - -
243B ASN 4.9 1.7 + - - +
244B SER* 3.1 15.7 + - - +
246B TYR* 1.3 79.9 - - - +
248B TYR* 1.3 73.0 + + - +
250B SER* 2.6 21.1 + - - -
251B TYR* 3.5 26.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASN* 4.5 2.3 + - - -
42A PRO* 3.2 32.4 - - + +
43A ILE* 4.2 6.6 + - - +
203B ASN* 5.3 0.7 - - - -
204B TYR* 3.7 39.6 + + + +
235B LEU* 3.6 38.8 - - + +
237B SER* 3.3 39.2 + - - -
244B SER* 3.0 32.5 + - - +
245B PRO 3.9 2.7 - - - +
247B TYR* 1.3 87.5 - + - +
249B ALA* 1.3 53.3 + - - +
251B TYR* 3.1 6.1 + + - +
252B ILE* 2.7 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B THR 5.9 0.9 - - - -
234B SER* 6.3 1.8 - - - +
235B LEU 6.0 0.4 - - - +
245B PRO 2.9 18.7 + - - +
246B TYR 3.8 3.1 - - - +
248B TYR* 1.3 76.4 - - - +
250B SER* 1.3 59.9 + - - +
251B TYR 3.0 0.2 - - - -
252B ILE* 4.3 6.3 - - - +
253B ASN* 2.9 53.0 + - - +
274B ASP* 4.1 11.9 - - + +
275B TYR* 4.0 21.8 - - + -
280B TRP* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TYR* 2.7 33.7 + - - -
250A SER* 5.9 1.6 - - - -
279A LYS* 2.9 27.4 + - - -
246B TYR* 2.8 18.3 + - - -
247B TYR 2.6 18.9 + - - -
249B ALA* 1.3 76.0 - - - +
251B TYR* 1.3 58.8 + - - +
254B PRO* 3.2 15.5 - - - +
280B TRP* 3.5 25.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU* 2.7 35.4 + - - -
53A TYR* 4.9 6.0 + - - -
246A TYR* 3.6 14.6 - - - -
277A ASN* 3.8 6.2 + - - +
279A LYS* 3.6 31.6 - - + +
204B TYR* 3.5 25.0 + + + +
247B TYR* 3.5 35.4 - + - -
248B TYR* 3.1 6.3 + - - +
249B ALA 3.0 0.2 - - - -
250B SER* 1.3 83.1 + - - +
252B ILE* 1.3 66.4 + - - +
253B ASN 3.4 0.2 - - - -
254B PRO* 3.2 3.8 - - - +
255B GLU* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B TYR* 3.5 24.7 - - + +
207B LYS* 4.0 21.8 - - + -
208B VAL* 4.5 5.8 - - + -
211B ILE* 3.9 8.3 - - + -
233B THR* 3.6 34.5 - - - +
235B LEU* 4.1 21.3 - - + -
248B TYR* 2.7 27.1 + - + +
249B ALA* 4.4 2.9 - - - -
251B TYR* 1.3 70.8 - - - +
253B ASN* 1.3 61.5 + - - +
255B GLU* 4.4 2.9 - - - -
256B ILE* 2.9 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B THR* 4.0 6.5 + - - -
249B ALA* 2.9 30.4 + - - +
252B ILE* 1.3 74.7 - - - +
254B PRO* 1.3 59.6 - - + +
256B ILE* 4.2 0.2 - - - -
257B ALA* 3.0 32.0 + - - +
273B GLN* 3.5 19.6 + - - +
274B ASP 3.1 23.3 + - - +
280B TRP* 3.3 30.5 - - + -
282B PRO 5.0 1.3 - - - -
284B LEU* 3.7 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LYS* 4.8 2.5 - - - +
249B ALA 3.6 0.4 - - - +
250B SER 3.2 24.5 - - - +
251B TYR* 3.2 12.8 - - - +
253B ASN* 1.3 96.8 - - + +
255B GLU* 1.3 55.9 + - - +
257B ALA* 3.8 1.0 - - - +
258B ASN* 2.9 32.1 + - - +
280B TRP* 3.6 24.7 - - + -
281B SER 4.3 13.9 - - - +
282B PRO* 4.0 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B TYR* 2.6 31.1 + - - -
208B VAL* 3.2 32.7 - - + +
212B LYS* 3.9 13.8 + - - +
251B TYR* 3.1 15.0 + - - +
252B ILE* 3.8 3.6 - - - +
254B PRO* 1.3 79.9 - - - +
256B ILE* 1.3 61.1 + - + +
258B ASN* 3.4 5.4 + - - +
259B ASP* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL* 4.4 20.0 - - + -
211B ILE* 3.7 31.6 - - + -
212B LYS* 4.4 13.9 - - + -
215B MET* 3.5 32.5 - - + -
233B THR* 4.4 6.1 - - + -
252B ILE* 2.9 38.0 + - + +
255B GLU* 1.3 74.3 - - + +
257B ALA* 1.3 65.7 + - - +
259B ASP* 3.2 5.0 + - + +
260B ILE* 2.9 23.5 + - + +
284B LEU* 3.6 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ASN 3.0 20.9 + - - +
254B PRO 3.8 1.8 - - - +
256B ILE* 1.3 78.1 - - - +
258B ASN* 1.3 59.0 + - - +
260B ILE* 3.4 1.1 + - - +
261B LYS* 3.0 28.2 + - - +
282B PRO* 3.4 30.7 - - + +
283B LEU 3.8 1.3 - - - +
284B LEU* 3.4 28.6 - - - +
287B GLU* 3.6 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B PRO 2.9 17.9 + - - +
255B GLU* 3.6 6.1 - - - +
257B ALA* 1.3 76.5 - - - +
259B ASP* 1.3 59.2 + - - +
261B LYS* 3.3 2.0 + - - +
262B GLN* 2.9 59.8 + - - +
281B SER 4.6 1.8 + - - -
282B PRO* 3.3 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B LYS* 3.9 34.1 + - - +
215B MET* 5.0 9.5 - - - +
255B GLU 2.9 18.0 + - - +
256B ILE* 3.2 11.0 + - + +
258B ASN* 1.3 75.7 - - - +
260B ILE* 1.3 63.5 + - + +
262B GLN* 3.5 4.8 + - - +
263B LYS* 2.8 72.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B MET* 3.4 41.5 - - + -
256B ILE 2.9 19.9 + - - +
257B ALA 3.7 4.3 - - - +
259B ASP* 1.3 74.1 - - - +
261B LYS* 1.3 67.9 + - - +
263B LYS* 3.1 3.0 + - - -
264B ASN* 2.9 19.2 + - - -
265B PRO* 3.0 29.1 - - + +
268B VAL* 4.0 11.0 - - + -
284B LEU* 3.8 19.3 - - + -
287B GLU* 3.7 26.7 - - + +
288B VAL* 3.9 16.4 - - + +
291B ALA* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ALA 3.0 15.9 + - - +
258B ASN* 3.7 6.1 - - - +
260B ILE* 1.3 78.6 - - - +
262B GLN* 1.3 76.8 + - - +
264B ASN* 3.4 17.3 + - - +
282B PRO* 3.9 22.2 - - + +
287B GLU* 3.4 28.1 + - - +
290B ARG* 5.9 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ASN* 2.9 40.4 + - - +
259B ASP* 3.9 5.4 - - - +
261B LYS* 1.3 95.4 - - - +
263B LYS* 1.3 63.6 + - + +
264B ASN* 3.6 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B LYS* 4.6 16.8 + - - +
215B MET* 5.8 4.6 - - + +
216B ASP* 4.0 20.8 + - - +
219B MET* 5.9 0.5 - - - +
259B ASP* 2.8 52.6 + - - +
260B ILE* 3.9 4.0 - - - +
262B GLN* 1.3 78.6 - - + +
264B ASN* 1.3 72.6 + - - +
265B PRO* 3.2 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B MET* 5.4 0.7 - - - +
260B ILE 2.9 5.2 + - - -
261B LYS* 3.4 11.7 + - - +
262B GLN 3.3 3.4 - - - +
263B LYS* 1.3 80.8 - - - +
265B PRO* 1.3 71.7 - - - +
266B THR* 5.1 2.6 - - - +
293B LYS* 3.2 35.3 + - - +
----------------------------------------------------------
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