Contacts of the helix formed by residues 236 - 249 (chain D) in PDB entry 3OLJ
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 PHE 236 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D PHE* 4.0 6.3 - + - -
134D PHE* 3.7 24.2 - + + -
137D SER* 3.4 35.9 - - - -
138D ASP* 4.1 17.0 - - - -
141D VAL* 4.5 6.7 - - + -
231D VAL* 3.4 22.0 + - + -
232D GLU* 3.6 28.7 - - + +
234D ILE 3.1 1.2 - - - +
235D PHE* 1.3 83.8 - - + +
237D SER* 1.3 60.8 + - - +
238D GLY 3.4 1.3 - - - -
239D SER* 3.2 5.8 + - - -
240D PHE* 2.8 50.8 + + + -
266D GLU* 3.5 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D GLY 3.4 21.3 + - - -
234D ILE* 2.7 20.3 + - - -
236D PHE* 1.3 77.9 - - - +
238D GLY* 1.3 57.9 + - - +
240D PHE* 3.4 10.7 + - - +
241D ALA* 2.9 30.7 + - - +
323D TYR* 3.6 9.5 + - - -
324D ILE* 3.4 16.5 - - - +
327D VAL* 4.0 23.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D SER* 1.3 82.2 + - - +
239D SER* 1.3 59.0 + - - +
241D ALA* 3.5 0.7 + - - -
242D SER* 2.9 30.1 + - - -
300D GLU* 3.0 16.8 + - - -
304D LEU* 3.5 22.9 - - - -
320D MET* 3.6 11.9 - - - +
324D ILE* 3.8 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D VAL* 3.9 16.3 - - - +
133D PHE* 3.9 12.7 - - - -
134D PHE* 3.3 31.4 - - - -
206D LYS* 4.7 0.2 + - - -
235D PHE 4.7 1.4 + - - -
236D PHE 3.2 6.2 + - - -
238D GLY* 1.3 73.4 - - - +
240D PHE* 1.3 66.5 + - - +
242D SER* 3.3 9.3 - - - -
243D ILE* 3.2 26.2 + - - +
300D GLU* 4.0 2.2 + - - -
303D PHE* 3.8 23.6 - - - -
304D LEU* 4.3 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D PHE* 3.6 17.3 - + - -
176D TYR* 3.9 11.7 - - - -
232D GLU 4.4 2.7 - - - -
236D PHE* 2.8 46.2 + + + +
237D SER* 3.7 8.3 - - - +
239D SER* 1.3 76.1 - - - +
241D ALA* 1.3 62.3 + - - +
243D ILE 3.2 1.9 + - - -
244D PHE* 3.1 28.9 + - + -
259D ASN* 3.2 26.1 + - - +
262D ILE* 4.1 2.9 - - + -
263D SER* 3.6 45.1 - - - -
266D GLU* 3.8 27.8 - - + -
350D MET* 4.8 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D SER 2.9 16.9 + - - +
238D GLY 3.7 4.7 - - - +
240D PHE* 1.3 77.0 - - - +
242D SER* 1.3 57.4 + - - +
244D PHE* 3.1 2.9 + - - +
245D TRP* 2.8 27.5 + - - +
315D MET* 4.7 0.2 - - - -
320D MET* 3.9 15.7 - - + -
323D TYR* 3.7 22.0 - - + -
347D PHE* 4.5 5.6 - - + -
349D PHE* 3.6 6.9 - - + -
350D MET* 3.8 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D PHE* 3.4 37.6 - - - -
130D VAL* 5.2 0.7 - - - -
238D GLY 2.9 18.8 + - - -
239D SER* 3.3 12.4 - - - -
241D ALA* 1.3 75.2 - - - +
243D ILE* 1.3 62.5 + - - +
245D TRP* 3.2 5.5 - - - +
246D LEU* 3.1 27.8 + - - +
304D LEU* 4.6 0.2 - - - +
310D VAL* 3.7 13.5 - - - +
313D ILE* 3.5 5.2 - - - +
315D MET* 3.8 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D PHE* 6.1 0.9 - - + -
127D ILE* 6.1 2.0 - - + -
130D VAL* 4.1 22.4 - - + -
131D LEU* 5.0 2.9 - - + -
134D PHE* 4.1 9.9 - - + -
176D TYR* 5.5 2.5 - - + -
239D SER 3.2 11.9 + - - +
240D PHE 3.2 2.2 + - - +
242D SER* 1.3 77.0 - - - +
244D PHE* 1.3 64.5 + - - +
246D LEU* 3.2 16.0 + - + +
247D LYS 3.0 17.2 + - - -
255D LEU* 3.8 41.3 - - + +
256D THR* 3.7 12.4 - - + +
259D ASN* 3.6 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D PHE 3.1 23.9 + - - -
241D ALA 3.1 6.9 + - - +
243D ILE* 1.3 78.5 - - - +
245D TRP* 1.3 55.3 + - - +
247D LYS* 3.1 23.1 + - + +
248D LYS* 3.0 27.4 + - - +
256D THR* 5.4 0.9 - - - -
259D ASN* 3.3 17.5 - - - -
260D GLU* 3.9 33.7 - - + -
263D SER* 3.7 23.1 - - - -
349D PHE* 3.9 21.1 - - + +
350D MET* 3.6 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D ALA 2.8 12.9 + - - +
242D SER 3.2 9.2 - - - +
243D ILE 3.2 0.2 - - - -
244D PHE* 1.3 77.4 - - - +
246D LEU* 1.3 62.4 + - + +
248D LYS* 3.1 25.2 + - + +
249D ARG* 3.1 44.0 + - + +
313D ILE* 3.0 35.9 + - + -
314D GLY* 3.6 18.1 - - - -
315D MET* 3.5 34.1 - - + +
347D PHE* 5.9 1.8 - + - -
349D PHE* 3.6 34.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D LEU* 5.4 2.7 - - + -
123D GLU* 5.6 0.2 - - - +
126D PHE* 5.9 1.1 - - + -
127D ILE* 3.7 37.7 - - + -
242D SER 3.1 14.6 + - - +
243D ILE* 3.2 16.8 + - + +
245D TRP* 1.3 77.5 - - - +
247D LYS* 1.3 61.6 + - - +
249D ARG* 3.1 32.8 + - - +
251D LEU* 3.0 47.6 + - + +
252D MET* 5.6 2.0 - - - -
255D LEU* 3.8 21.5 - - + -
256D THR* 4.5 2.7 - - + -
313D ILE* 4.4 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLU* 3.9 19.5 + - - +
243D ILE 3.0 8.6 + - - +
244D PHE* 3.1 29.9 + - + +
246D LEU* 1.3 76.6 - - - +
248D LYS* 1.3 54.3 + - - +
250D GLY* 2.7 25.5 + - - +
251D LEU 4.5 1.3 - - - +
256D THR* 3.7 29.6 - - + +
260D GLU* 2.7 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D PHE 3.0 11.8 + - - +
245D TRP* 3.4 28.7 - - + +
247D LYS* 1.3 76.2 - - - +
249D ARG* 1.3 60.7 + - + +
250D GLY 3.4 0.7 + - - -
348D ASP* 4.0 24.5 - - - -
349D PHE* 4.0 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D LEU* 4.6 0.8 - - - +
120D LYS* 5.9 0.6 - - - +
123D GLU* 2.7 35.1 + - - -
245D TRP* 3.1 42.9 + - + +
246D LEU* 3.6 20.0 - - - +
247D LYS 3.1 0.8 - - - -
248D LYS* 1.3 76.3 - - + +
250D GLY* 1.3 61.4 + - - +
251D LEU* 3.3 35.5 + - + +
313D ILE* 3.1 22.8 + - - +
314D GLY* 5.2 0.2 - - - -
----------------------------------------------------------
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