Contacts of the helix formed by residues 229 - 250 (chain A) in PDB entry 1OL5
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 229 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LYS 4.4 0.2 + - - -
228A PHE* 1.3 73.4 - - - +
230A GLU* 1.3 64.0 + - - +
231A GLN* 2.9 23.3 + - - +
232A ARG* 3.0 17.6 + - - +
233A THR* 2.8 23.8 + - - -
323A LEU* 4.2 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ASP* 1.3 72.8 - - - +
231A GLN* 1.3 65.6 + - - +
233A THR* 3.8 0.5 - - - -
234A ALA* 2.9 27.2 + - - +
323A LEU* 4.3 10.1 - - + +
351A PHE 5.9 0.2 - - - -
352A VAL* 5.6 0.2 - - - -
353A THR* 2.6 47.1 + - - +
356A ALA* 4.2 2.4 - - - +
382A TRP* 2.9 35.6 + - + -
386A ASN* 4.0 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ASP* 2.9 14.1 + - - +
230A GLU* 1.3 75.8 - - - +
232A ARG* 1.3 71.4 + - - +
235A THR* 2.8 59.5 + - - +
386A ASN* 3.3 25.2 + - + +
388A SER 4.2 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLU* 2.5 47.3 + - - +
225A LEU* 3.6 19.5 - - - +
228A PHE* 4.2 16.3 - - + -
229A ASP* 3.0 21.4 + - - +
231A GLN* 1.3 86.5 + - - +
233A THR* 1.3 62.0 + - - +
235A THR* 3.8 4.5 - - - -
236A TYR* 3.2 57.6 + - + -
264A LEU* 5.4 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PHE* 3.2 18.3 - - - +
229A ASP 2.8 20.4 + - - -
230A GLU 3.8 2.5 - - - -
232A ARG* 1.3 76.4 - - - +
234A ALA* 1.3 58.9 + - - +
236A TYR* 3.4 3.0 + - - +
237A ILE* 2.9 33.7 + - + +
319A CYS* 3.9 13.0 - - - +
322A PHE* 3.5 32.2 - - + +
323A LEU* 3.4 29.4 - - + +
382A TRP* 3.9 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLU 2.9 16.6 + - - +
233A THR* 1.3 74.4 - - - +
235A THR* 1.3 60.8 + - - +
237A ILE* 3.8 0.9 - - - +
238A THR* 2.7 35.3 + - - -
382A TRP* 4.0 15.2 - - + -
383A ILE* 4.1 19.1 - - + +
386A ASN* 3.8 30.5 - - + +
387A SER* 3.8 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLN* 2.8 42.8 + - - +
232A ARG* 3.8 7.2 - - - -
233A THR 3.3 0.2 - - - -
234A ALA* 1.3 78.8 - - - +
236A TYR* 1.3 64.6 + - + +
238A THR* 3.3 2.9 + - - -
239A GLU* 3.1 44.9 + - + +
387A SER* 4.0 8.5 - - - -
388A SER 3.4 14.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A VAL* 4.2 7.2 - - + +
221A GLU* 4.5 1.9 - - - +
228A PHE* 3.7 35.0 - + - -
232A ARG* 3.2 51.4 + - + +
233A THR 3.7 3.6 - - - +
235A THR* 1.3 80.5 - - + +
237A ILE* 1.3 66.6 + - - +
239A GLU* 3.2 15.7 + - - -
240A LEU* 2.9 25.9 + - - +
264A LEU* 3.6 41.8 - - + +
268A GLY 3.9 13.3 + - - -
270A LEU* 3.4 19.1 - - + +
322A PHE* 3.9 21.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A THR* 2.9 29.6 + - + +
234A ALA* 3.8 4.9 - - - +
236A TYR* 1.3 74.7 - - - +
238A THR* 1.3 53.2 + - - +
240A LEU* 3.6 3.8 - - + +
241A ALA* 2.6 38.3 + - - +
315A LEU* 4.2 35.6 - - + +
318A LEU* 4.5 2.9 - - + -
319A CYS* 3.9 43.1 - - + +
322A PHE* 4.1 16.2 - - + -
359A LEU* 4.9 5.2 - - + -
363A LEU* 5.9 0.4 - - + -
377A VAL* 4.3 10.8 - - + -
382A TRP* 5.0 0.2 - - + -
383A ILE* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ALA 2.7 16.7 + - - -
235A THR* 3.4 4.5 - - - -
237A ILE* 1.3 75.1 - - - +
239A GLU* 1.3 67.5 + - + +
242A ASN* 3.0 35.9 + - - +
378A LEU* 3.9 18.9 - - + +
383A ILE* 3.3 17.7 - - + +
387A SER* 2.6 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ASN* 3.6 27.4 + - - +
235A THR* 3.1 25.4 + - + +
236A TYR* 3.5 20.8 - - - +
238A THR* 1.3 77.9 - - + +
240A LEU* 1.3 58.9 + - - +
242A ASN* 3.3 9.0 + - - +
243A ALA* 2.9 28.3 + - - +
268A GLY 4.4 0.7 - - - +
269A GLU* 3.4 24.4 - - - +
270A LEU* 3.1 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ASN* 5.7 0.2 - - - -
236A TYR 2.9 16.5 + - - +
237A ILE* 3.7 3.6 - - + +
239A GLU* 1.3 77.8 - - - +
241A ALA* 1.3 57.1 + - - +
243A ALA* 3.1 4.6 + - - +
244A LEU* 2.8 42.7 + - + +
257A ILE* 4.0 16.2 - - + -
262A LEU* 3.8 17.5 - - + -
270A LEU* 3.5 11.8 - - + +
272A ILE* 3.3 36.3 - - + -
315A LEU* 3.3 29.2 - - + -
318A LEU* 3.3 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE 2.6 21.9 + - - +
240A LEU* 1.3 72.6 - - - +
242A ASN* 1.3 57.8 + - - +
244A LEU* 3.9 3.6 - - - +
245A SER* 3.0 29.3 + - - -
315A LEU* 4.5 4.7 - - + +
374A LEU* 4.0 25.7 - - + +
377A VAL* 4.4 13.7 - - + -
378A LEU* 3.3 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A HIS* 3.8 15.9 - - + +
192A ASN* 4.9 3.3 - - - +
238A THR* 3.0 29.3 + - - +
239A GLU* 3.5 7.1 - - - +
241A ALA* 1.3 75.6 - - - +
243A ALA* 1.3 64.4 + - - +
245A SER* 3.4 5.4 + - - -
246A TYR* 3.2 22.2 + - - +
378A LEU* 2.9 34.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A HIS* 3.8 11.2 + - - -
192A ASN* 3.9 21.8 - - + +
193A ILE* 3.9 7.5 - - + +
239A GLU 2.9 14.5 + - - +
240A LEU* 3.1 5.6 + - - +
242A ASN* 1.3 77.8 - - - +
244A LEU* 1.3 61.5 + - - +
246A TYR* 3.3 6.4 + - - +
247A CYS* 3.1 23.8 + - - -
272A ILE* 3.2 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 2.8 33.0 + - + +
241A ALA 3.9 1.6 - - - +
243A ALA* 1.3 69.7 - - - +
245A SER* 1.3 60.9 + - - +
247A CYS* 3.1 8.5 + - + -
248A HIS* 2.8 38.8 + - - +
254A HIS* 4.5 7.6 - - + -
257A ILE* 3.4 35.9 - - + -
272A ILE* 4.0 16.6 - - + -
311A ASP* 4.1 27.1 - - + +
315A LEU* 4.3 11.9 - - + -
374A LEU* 3.6 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ALA 3.0 19.5 + - - -
242A ASN* 3.6 9.2 - - - -
243A ALA 3.3 0.2 - - - -
244A LEU* 1.3 77.0 - - - +
246A TYR* 1.3 60.3 + - - +
248A HIS* 3.4 2.4 + - - +
249A SER* 3.0 24.1 + - - -
374A LEU* 3.5 17.0 - - - +
375A ARG* 5.9 0.7 - - - +
378A LEU* 5.0 6.3 - - - +
1391A SO4 3.4 21.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 3.8 26.8 - - + +
189A ARG 3.0 36.6 + - - -
190A HIS* 3.6 27.8 - - + +
193A ILE* 3.6 18.2 - - + -
242A ASN 3.2 6.0 + - - +
243A ALA 3.5 7.0 - - - +
244A LEU 3.3 0.2 - - - -
245A SER* 1.3 78.6 - - - +
247A CYS* 1.3 64.6 + - - +
249A SER* 2.5 27.9 + - - -
250A LYS* 3.3 24.4 + - + +
32B ASP* 3.0 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 4.5 7.6 - - - -
193A ILE* 3.8 20.0 - - - -
243A ALA 3.1 16.4 + - - +
244A LEU* 3.1 20.4 + - + +
246A TYR* 1.3 81.6 - - - +
248A HIS* 1.3 59.5 + - + +
250A LYS* 3.0 16.3 + - - +
251A ARG 3.1 0.2 + - - -
252A VAL* 2.8 40.9 + - + +
254A HIS* 5.6 3.6 - - - +
272A ILE* 5.1 4.5 - - - -
275A PHE* 4.2 23.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 2.8 23.3 + - + +
245A SER 3.9 3.6 - - - +
247A CYS* 1.3 75.9 - - + +
249A SER* 1.3 57.1 + - - +
250A LYS 2.9 5.4 - - - -
251A ARG* 2.6 27.7 + - - +
252A VAL 3.3 17.7 - - - +
308A GLU* 3.3 64.4 + - + +
311A ASP* 3.2 25.4 + - + +
312A LEU* 4.1 9.7 - - + +
374A LEU* 3.5 22.8 - - + +
1391A SO4 4.4 11.8 + - - +
1394A MG 4.3 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A SER 3.0 13.9 + - - -
246A TYR* 2.5 27.9 + - - -
248A HIS* 1.3 77.2 - - - +
250A LYS* 1.3 78.0 + - - +
251A ARG* 3.3 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 4.5 6.1 - - + -
246A TYR* 3.6 37.0 - - + +
247A CYS 3.0 9.0 + - - +
248A HIS 2.9 0.6 - - - -
249A SER* 1.3 101.5 + - - +
251A ARG* 1.3 70.3 + - - +
252A VAL* 3.3 2.9 + - + +
280A HIS* 3.4 16.8 + - - -
32B ASP* 3.9 33.3 + - - +
33B SER* 6.0 0.6 - - - +
35B PHE* 3.8 31.8 - - + +
36B GLU* 6.0 1.6 - - + +
----------------------------------------------------------
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