Contacts of the helix formed by residues 236 - 258 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D THR* 3.7 22.1 - - + +
233D ASN* 2.9 32.2 + - - +
234D GLY 3.3 0.4 - - - -
235D LYS* 1.3 75.3 - - - +
237D MET* 1.3 64.5 + - - +
238D PRO* 3.3 14.4 - - - +
239D ALA* 2.8 36.9 + - + +
240D ARG* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLU* 3.7 20.4 - - + +
177D PRO* 4.2 22.0 - - - -
178D LEU* 3.3 35.2 - - + -
181D VAL* 4.2 19.7 - - + -
235D LYS 2.9 11.0 + - - +
236D ASP* 1.3 70.3 - - - +
238D PRO* 1.3 67.0 - - + +
240D ARG* 3.2 3.8 + - - -
241D GLU* 2.8 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ASN* 4.2 3.0 - - - +
236D ASP* 3.3 16.2 - - - +
237D MET* 1.3 96.5 - - + +
239D ALA* 1.3 55.3 + - - +
241D GLU* 3.9 4.9 - - + +
242D ALA* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ASN* 3.6 18.5 - - - +
229D THR* 3.7 24.5 - - + -
230D ALA* 3.8 17.5 - - - +
236D ASP* 2.8 26.4 + - + +
238D PRO* 1.3 72.8 - - - +
240D ARG* 1.3 60.6 + - - +
242D ALA* 3.3 2.3 + - - +
243D MET* 3.0 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D ALA* 5.4 0.4 - - - +
177D PRO* 4.0 19.5 - - + +
180D MET* 3.3 30.7 + - + +
181D VAL* 3.3 18.6 + - + +
183D MET* 2.8 38.7 + - - +
188D THR* 2.8 34.7 + - - +
230D ALA* 4.2 13.2 + - + +
233D ASN 5.4 0.2 - - - +
234D GLY* 2.8 44.3 + - - +
236D ASP 3.0 18.8 + - - +
237D MET* 3.6 10.1 - - - +
239D ALA* 1.3 77.0 - - - +
241D GLU* 1.3 60.9 + - - +
243D MET* 3.4 7.1 + - - +
244D ALA* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ALA* 5.0 17.5 - - - +
15D GLY* 3.7 6.7 - - - -
16D GLU* 3.4 28.9 + - - +
177D PRO* 3.8 21.5 - - + +
237D MET* 2.8 25.2 + - + +
238D PRO* 4.0 5.2 - - + +
240D ARG* 1.3 70.8 - - - +
242D ALA* 1.3 65.3 + - - +
244D ALA* 3.2 4.7 + - + +
245D TYR* 3.1 47.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D MET* 3.6 22.8 - - + +
226D ASN* 3.3 35.0 - - - +
238D PRO 3.0 19.9 + - - +
239D ALA 3.6 0.7 - - - +
241D GLU* 1.3 77.6 - - - +
243D MET* 1.3 56.8 + - - +
245D TYR* 3.3 3.0 + - - -
246D ALA* 2.9 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D ALA* 3.8 24.4 - - + +
188D THR* 6.1 0.7 - - + -
192D GLY* 3.7 30.7 - - - +
195D ALA* 5.0 2.0 - - + -
222D MET 4.7 0.4 - - - +
223D ILE* 4.0 33.2 - - + -
226D ASN* 4.3 8.1 - - + -
227D LEU* 3.8 30.1 - - + -
230D ALA* 4.4 16.2 - - + -
239D ALA 3.0 20.5 + - - +
240D ARG* 3.8 7.2 - - - +
242D ALA* 1.3 73.9 - - - +
244D ALA* 1.3 61.1 + - - +
246D ALA* 3.7 3.3 - - + +
247D GLN* 2.8 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D MET* 6.2 0.9 - - + -
15D GLY 6.0 0.9 - - - +
140D ALA* 4.5 0.4 - - - +
175D ASN* 4.5 17.7 - - + +
177D PRO* 4.7 6.5 - - + -
180D MET* 3.7 28.7 - - + -
240D ARG 3.1 13.7 + - - +
241D GLU* 3.2 13.7 + - + +
243D MET* 1.3 76.4 - - - +
245D TYR* 1.3 63.0 + - + +
247D GLN* 3.3 14.1 + - - +
248D PHE* 3.2 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ALA 4.5 7.1 + - - -
4C SER* 2.6 28.3 + - - -
209C THR* 4.2 9.0 - - - +
210C PRO* 4.1 30.7 - - + -
211C ILE* 4.0 18.3 - - + +
14D MET* 3.6 40.4 + - + +
15D GLY* 4.5 3.0 + - - -
222D MET* 3.8 13.5 - - + -
241D GLU* 3.1 45.3 + - + -
242D ALA* 3.6 8.5 - - - +
244D ALA* 1.3 78.8 - - + +
246D ALA* 1.3 60.8 + - - +
248D PHE* 3.1 7.0 + - - +
249D LEU* 2.8 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D ALA* 3.4 12.4 - - - +
222D MET* 3.7 23.3 - - + -
223D ILE* 3.9 23.1 - - + +
242D ALA 2.9 16.9 + - - +
243D MET* 3.7 9.2 - - + +
245D TYR* 1.3 77.2 - - - +
247D GLN* 1.3 58.6 + - - +
249D LEU* 3.2 12.0 + - - -
250D ALA* 2.8 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D ASN* 3.5 12.7 + - - +
140D ALA* 3.7 16.6 - - - +
141D GLY* 3.5 26.9 + - - +
143D ALA* 2.9 37.9 + - - +
145D GLU* 2.7 25.8 + - - -
175D ASN* 3.2 17.4 + - - +
195D ALA* 4.0 13.2 - - + +
243D MET* 2.8 19.7 + - + +
244D ALA* 3.3 16.5 + - - +
246D ALA* 1.3 73.7 - - - +
248D PHE* 1.3 71.0 + - - +
250D ALA* 3.4 3.2 + - - +
251D GLY 3.1 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PHE* 5.1 2.0 - + - -
211C ILE* 3.7 7.0 - - + -
8D ILE* 4.1 11.2 - - + -
12D ASN* 3.4 26.2 - - - -
14D MET* 3.5 27.4 - - + -
143D ALA* 4.7 2.9 - - - +
145D GLU* 4.1 1.3 - - - -
146D MET* 3.7 24.2 - - + +
173D SER* 3.6 21.5 - - - -
175D ASN* 3.4 20.9 - - - +
244D ALA 3.2 14.1 + - - +
245D TYR* 3.1 12.0 + - - +
247D GLN* 1.3 78.9 - - - +
249D LEU* 1.3 60.6 + - - +
251D GLY* 2.9 3.6 + - - -
252D MET* 2.8 56.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C PRO* 4.7 4.3 - - + +
211C ILE* 4.0 33.9 - - + -
214C ALA* 4.7 3.8 - - + -
215D CYS* 3.6 46.3 - - + +
218D LYS* 3.5 31.0 - - + -
219D ALA* 3.9 5.6 - - + +
222D MET* 3.7 18.8 - - - -
245D TYR 2.8 20.4 + - - +
246D ALA* 3.4 7.4 - - - +
248D PHE* 1.3 76.9 - - - +
250D ALA* 1.3 63.2 + - - +
252D MET* 3.1 21.4 + - - +
253D ALA* 3.1 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D ALA* 3.5 28.0 - - - +
198D HIS* 3.8 13.4 - - + +
199D ALA* 4.3 5.2 - - - +
219D ALA* 3.6 13.2 - - + +
223D ILE* 5.4 0.2 - - + -
246D ALA 2.8 15.4 + - - +
247D GLN* 3.6 10.8 - - - +
248D PHE 3.2 0.2 - - - -
249D LEU* 1.3 77.1 - - - +
251D GLY* 1.3 57.1 - - - +
253D ALA* 3.2 8.4 + - - +
254D PHE* 3.0 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D ALA* 3.6 19.9 - - - +
146D MET* 3.7 9.0 - - - -
247D GLN 3.1 6.9 + - - -
248D PHE 2.9 8.0 + - - -
250D ALA* 1.3 73.8 - - - +
252D MET* 1.3 65.0 + - - +
253D ALA 2.9 1.8 - - - -
254D PHE* 3.5 14.4 - - - -
255D ASN* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PHE* 4.2 10.1 - - + -
211C ILE* 3.9 26.2 - - + -
215C CYS* 4.9 0.2 - - - -
252C MET* 3.4 33.4 - - + -
6D PHE* 3.3 17.8 - - + -
8D ILE* 4.2 9.4 - - + -
146D MET* 3.8 8.9 - - + +
212D THR* 4.1 1.2 - - - +
215D CYS* 3.8 24.0 - - - -
248D PHE* 2.8 50.1 + - + +
249D LEU* 3.1 16.1 + - - +
251D GLY* 1.3 71.0 - - - +
253D ALA* 1.3 59.2 + - - +
256D ASN* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D HIS 5.2 0.4 - - - +
199D ALA* 5.4 0.2 - - - -
202D ALA* 3.6 18.4 - - + -
212D THR* 3.3 37.3 - - - +
215D CYS* 4.3 1.1 - - + +
216D ALA* 3.9 13.0 - - + +
249D LEU 3.1 9.9 + - - +
250D ALA* 3.3 9.4 - - - +
251D GLY 2.9 1.6 - - - -
252D MET* 1.3 77.5 - - - +
254D PHE* 1.3 61.0 + - - +
256D ASN 3.2 2.1 + - - -
257D ALA* 2.8 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D THR 3.3 27.4 - - - -
143D ALA* 4.1 1.3 - - + -
144D SER* 5.8 0.2 - - - -
147D THR* 3.8 12.6 - - + -
149D PHE* 3.8 27.3 - + - -
198D HIS* 3.5 28.7 - + - +
202D ALA* 3.8 7.2 - - + -
250D ALA 3.0 28.9 + - - +
251D GLY* 3.5 17.7 - - - -
253D ALA* 1.3 69.6 - - - +
255D ASN* 1.3 61.4 + - - +
256D ASN 2.9 2.5 - - - -
258D SER* 2.8 36.5 + - - +
259D LEU* 3.2 48.2 - - + -
1385D NAD 3.9 13.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D TYR* 3.0 41.2 + - - +
146D MET* 3.7 16.0 + - + +
147D THR* 3.3 21.3 - - + +
148D ARG* 2.8 59.1 + - - +
149D PHE* 3.6 13.1 - - - -
169D THR* 5.5 0.2 + - - -
251D GLY 2.9 20.8 + - - +
254D PHE* 1.3 79.9 - - - +
256D ASN* 1.3 59.9 + - - +
258D SER 4.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D THR 3.3 14.2 - - - +
6D PHE* 3.1 26.1 - - + -
7D TYR* 2.5 52.2 + - - +
148D ARG* 4.6 8.5 + - - +
207D ALA* 4.5 7.3 - - - +
209D THR* 5.7 3.2 - - + +
212D THR* 3.8 18.4 - - + -
252D MET* 2.9 22.4 + - - +
253D ALA 3.2 1.4 + - - -
254D PHE 2.9 0.2 - - - -
255D ASN* 1.3 84.7 - - - +
257D ALA* 1.3 60.4 + - - +
258D SER* 3.3 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D ALA* 3.7 24.2 - - - +
205D SER* 2.6 25.6 + - - +
207D ALA* 3.4 17.3 - - - +
208D ALA* 3.9 12.3 - - - +
212D THR* 3.8 17.3 - - + +
253D ALA 2.8 18.3 + - - +
256D ASN* 1.3 73.2 - - - +
258D SER* 1.3 69.3 + - - +
365D THR* 3.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D ARG* 6.3 0.7 - - - -
149D PHE* 4.9 12.6 - - - -
202D ALA* 3.6 19.6 - - - -
205D SER* 4.2 0.3 - - - -
254D PHE* 2.8 21.2 + - - -
255D ASN 4.5 0.2 - - - -
256D ASN 3.3 2.0 - - - -
257D ALA* 1.3 87.2 - - - +
259D LEU* 1.3 75.4 + - - +
361D ALA 4.9 3.1 + - - -
362D CYS* 4.5 12.8 - - - -
365D THR* 3.5 20.2 + - - +
----------------------------------------------------------
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