Contacts of the helix formed by residues 236 - 258 (chain B) in PDB entry 3OX4
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 ASP 236 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B THR* 3.1 25.5 - - + +
233B ASN* 3.2 29.8 + - - +
234B GLY 3.2 0.2 - - - -
235B LYS* 1.3 75.7 - - - +
237B MET* 1.3 62.0 + - - +
238B PRO* 2.9 23.8 - - - +
239B ALA* 3.3 18.9 + - + +
240B ARG* 3.0 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU* 3.6 25.4 - - - +
177B PRO* 3.9 26.5 - - + -
178B LEU* 3.6 27.6 - - + -
181B VAL* 3.2 33.7 - - - -
235B LYS 3.0 13.5 + - - +
236B ASP* 1.3 68.3 - - - +
238B PRO* 1.3 76.5 - - + +
240B ARG* 3.0 4.7 + - - +
241B GLU* 2.7 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ASN* 5.0 1.3 - - - -
236B ASP* 2.9 19.5 - - - +
237B MET* 1.3 86.8 - - + +
239B ALA* 1.3 56.5 + - - +
241B GLU* 3.3 6.1 + - + +
242B ALA* 2.8 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ASN* 3.9 17.2 - - - +
229B THR* 3.9 17.3 - - + -
230B ALA* 4.1 16.8 - - + +
236B ASP* 3.3 31.8 + - + +
237B MET 3.2 0.6 - - - -
238B PRO* 1.3 79.3 - - - +
240B ARG* 1.3 57.4 + - - +
242B ALA* 3.2 2.9 + - - +
243B MET* 2.9 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ALA* 5.3 0.2 - - - +
177B PRO* 4.1 19.5 - - + +
180B MET* 3.2 24.0 + - + +
181B VAL* 3.0 28.8 + - + +
183B MET* 2.9 45.7 + - - +
188B THR* 2.8 31.7 + - - +
230B ALA* 4.3 11.8 + - - +
234B GLY* 2.9 38.1 + - - +
236B ASP 3.0 21.1 + - - +
237B MET* 3.5 7.9 - - - +
239B ALA* 1.3 75.4 - - - +
241B GLU* 1.3 57.8 + - - +
243B MET* 3.2 8.7 + - - +
244B ALA* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA* 2.6 41.2 + - - +
15B GLY* 4.1 3.6 - - - +
16B GLU* 3.5 26.7 + - - +
177B PRO* 3.8 19.6 - - + +
237B MET* 2.7 20.7 + - + +
238B PRO* 3.7 7.0 - - + +
240B ARG* 1.3 73.5 - - - +
242B ALA* 1.3 62.4 + - - +
244B ALA* 3.2 5.4 + - + +
245B TYR* 3.0 37.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B MET* 3.4 19.7 - - + +
226B ASN* 3.3 38.6 - - - +
238B PRO 2.8 15.9 + - - +
239B ALA 3.6 0.2 - - - +
241B GLU* 1.3 77.5 - - - +
243B MET* 1.3 58.5 + - - +
245B TYR* 3.3 2.8 + - - -
246B ALA* 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ALA* 3.9 25.3 - - + +
188B THR* 5.5 1.1 - - + +
192B GLY* 3.8 28.9 - - - +
195B ALA* 5.2 2.0 - - + -
222B MET 4.7 0.4 - - - +
223B ILE* 4.0 31.9 - - + -
226B ASN* 4.2 7.4 - - + -
227B LEU* 3.7 32.8 - - + -
230B ALA* 4.1 21.1 - - + -
239B ALA 2.9 19.0 + - - +
240B ARG* 3.2 8.3 + - - +
242B ALA* 1.3 77.4 - - - +
244B ALA* 1.3 57.2 + - - +
246B ALA* 3.6 2.3 - - + +
247B GLN* 2.9 32.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
14B MET* 6.2 0.2 - - - -
15B GLY 6.1 0.4 - - - +
140B ALA* 4.6 0.8 - - - +
175B ASN* 4.6 19.0 - - + +
177B PRO* 4.9 4.0 - - + -
180B MET* 3.8 27.8 - - + -
240B ARG 2.9 13.1 + - - +
241B GLU* 3.4 12.3 - - + +
242B ALA 3.2 0.2 - - - -
243B MET* 1.3 75.3 - - - +
245B TYR* 1.3 66.2 + - + +
247B GLN* 3.2 14.3 + - - +
248B PHE* 3.2 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA* 2.8 30.3 + - + +
4A SER* 2.7 25.6 + - - -
209A THR* 3.9 13.0 - - - +
210A PRO* 4.0 34.3 - - + -
211A ILE* 3.9 17.7 - - + -
14B MET* 3.5 37.5 - - + +
15B GLY 5.1 0.7 - - - -
222B MET* 4.0 11.9 - - + -
241B GLU* 3.0 36.2 + - + -
242B ALA* 3.8 6.5 - - - +
244B ALA* 1.3 76.3 - - + +
246B ALA* 1.3 58.2 + - - +
248B PHE* 3.2 6.4 + - - +
249B LEU* 2.8 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ALA* 3.3 14.9 - - - +
222B MET* 3.7 29.7 - - + -
223B ILE* 3.9 23.1 - - + +
242B ALA 2.9 18.0 + - - +
243B MET* 3.6 8.7 - - + +
245B TYR* 1.3 76.9 - - - +
247B GLN* 1.3 56.8 + - - +
249B LEU* 3.2 4.6 + - - -
250B ALA* 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ASN* 3.5 11.4 + - - +
140B ALA* 3.7 7.9 - - - -
141B GLY* 3.5 28.6 + - - +
142B THR 3.4 6.9 + - - -
143B ALA* 2.8 39.4 + - - +
145B GLU* 2.7 25.9 + - - -
175B ASN* 3.1 19.8 + - - +
195B ALA* 4.0 13.7 - - + +
243B MET* 2.9 19.3 + - + +
244B ALA* 3.2 13.7 + - - +
246B ALA* 1.3 71.3 - - - +
248B PHE* 1.3 74.4 + - - +
250B ALA* 3.4 3.5 + - - +
251B GLY 3.0 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 5.0 2.5 - + - -
211A ILE* 3.7 7.2 - - + -
8B ILE* 4.1 11.9 - - + -
12B ASN* 3.4 30.5 - - - -
14B MET* 3.4 31.9 - - + -
143B ALA* 4.6 2.5 - - - -
145B GLU* 4.1 1.3 - - - -
146B MET* 3.7 26.3 - - + +
173B SER* 3.7 11.4 - - - -
175B ASN* 3.4 22.0 - - + +
244B ALA 3.2 13.1 + - - +
245B TYR* 3.4 10.5 - - - +
246B ALA 3.2 0.2 - - - -
247B GLN* 1.3 83.0 - - - +
249B LEU* 1.3 59.2 + - - +
251B GLY* 2.8 5.2 + - - -
252B MET* 2.8 54.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A PRO* 4.3 6.1 - - + +
211A ILE* 3.9 31.2 - - + -
214A ALA* 4.5 9.2 - - + -
215A CYS* 6.0 0.2 - - - -
215B CYS* 3.4 39.9 - - - +
218B LYS* 3.5 24.7 - - + -
219B ALA* 4.0 2.7 - - + +
222B MET* 3.8 17.9 - - - -
245B TYR 2.8 21.2 + - - +
246B ALA* 3.6 5.2 - - - +
248B PHE* 1.3 77.2 - - - +
250B ALA* 1.3 61.7 + - - +
252B MET* 3.2 27.2 + - - +
253B ALA* 3.1 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ALA* 3.4 29.8 - - + +
198B HIS* 3.9 11.9 - - + +
199B ALA* 4.3 4.7 - - - +
216B ALA* 5.2 0.2 - - - +
219B ALA* 3.6 13.4 - - + +
246B ALA 2.9 13.5 + - - +
247B GLN* 3.6 11.7 - - - +
248B PHE 3.1 0.2 - - - -
249B LEU* 1.3 76.1 - - - +
251B GLY* 1.3 58.8 + - - +
253B ALA* 3.1 8.8 + - - +
254B PHE* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ALA* 3.6 4.5 - - - -
146B MET* 3.0 29.4 - - - -
247B GLN 3.0 7.3 + - - -
248B PHE 2.8 6.2 + - - -
250B ALA* 1.3 73.8 - - - +
252B MET* 1.3 64.9 + - - +
253B ALA 3.0 1.8 - - - -
254B PHE* 3.4 12.3 - - - -
255B ASN* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 4.2 11.2 - - + -
211A ILE* 3.9 19.1 - - + -
215A CYS* 4.9 0.2 - - - -
252A MET* 3.6 31.4 - - + -
6B PHE* 3.5 18.6 - - + -
7B TYR 5.8 0.7 - - - -
8B ILE* 4.3 10.1 - - + -
146B MET* 4.1 4.9 - - - -
212B THR* 4.1 0.5 - - - +
215B CYS* 3.8 19.3 - - - -
248B PHE* 2.8 46.7 + - + +
249B LEU* 3.3 29.2 - - - +
251B GLY* 1.3 75.5 - - - +
253B ALA* 1.3 60.2 + - - +
256B ASN* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B HIS 5.2 0.2 - - - +
199B ALA* 5.4 0.2 - - - -
202B ALA* 3.6 17.9 - - + -
212B THR* 3.4 37.9 - - - +
215B CYS* 4.1 0.9 - - + +
216B ALA* 3.7 17.7 - - + +
249B LEU 3.1 6.8 + - - +
250B ALA 3.3 9.0 - - - +
251B GLY 3.0 0.2 - - - -
252B MET* 1.3 77.7 - - - +
254B PHE* 1.3 59.2 + - - +
256B ASN 3.3 1.6 + - - -
257B ALA* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B THR 3.6 10.8 - - - -
143B ALA* 4.1 1.8 - - + -
146B MET* 4.2 1.3 - - + -
147B THR* 3.8 4.0 - - + -
149B PHE* 3.5 24.9 - + - -
198B HIS* 3.5 35.4 - + - +
202B ALA* 3.9 4.9 - - - -
250B ALA 2.8 28.7 + - - +
251B GLY* 3.4 18.4 - - - -
253B ALA* 1.3 69.9 - - - +
255B ASN* 1.3 57.1 + - - +
256B ASN 2.9 5.6 - - - -
258B SER* 2.8 32.8 + - - +
259B LEU* 3.5 46.9 - - + -
1385B NAD 3.3 39.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 3.0 42.2 + - - +
146B MET* 3.8 7.8 + - - -
147B THR* 3.2 31.2 - - + +
148B ARG* 2.8 68.5 + - - +
149B PHE* 3.6 11.9 - - - -
251B GLY 2.8 24.4 + - - +
252B MET* 5.1 0.2 - - - -
254B PHE* 1.3 76.5 - - - +
256B ASN* 1.3 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B THR 3.4 13.7 - - - +
6B PHE* 3.1 28.5 - - + -
7B TYR* 2.6 51.2 + - - +
148B ARG* 4.3 9.0 + - - +
207B ALA* 4.5 7.0 - - - +
209B THR* 5.7 2.5 - - + +
212B THR* 3.8 18.6 - - + -
252B MET* 2.9 21.6 + - - +
253B ALA 3.3 1.4 + - - -
254B PHE 2.9 1.6 - - - -
255B ASN* 1.3 83.1 - - - +
257B ALA* 1.3 59.9 + - - +
258B SER* 3.3 1.9 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
202B ALA* 3.9 15.9 - - - +
205B SER* 2.5 26.6 + - - +
207B ALA* 3.6 29.6 - - - +
208B ALA* 3.8 8.7 - - - +
212B THR* 3.8 18.8 - - - +
253B ALA 2.9 17.2 + - - +
256B ASN* 1.3 72.8 - - - +
258B SER* 1.3 68.1 + - - +
365B THR* 3.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ARG* 6.1 2.0 - - - -
149B PHE* 4.7 13.2 - - - -
201B GLU 4.1 0.7 - - - +
202B ALA* 3.7 19.8 - - - -
207B ALA* 5.5 0.4 - - - -
254B PHE* 2.8 23.1 + - - +
255B ASN 4.5 0.2 - - - -
256B ASN 3.3 2.4 - - - -
257B ALA* 1.3 86.1 - - - +
259B LEU* 1.3 72.0 + - - +
361B ALA 4.9 2.9 + - - -
362B CYS* 4.6 11.4 - - - -
365B THR* 3.6 20.3 + - - +
----------------------------------------------------------
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