Contacts of the helix formed by residues 229 - 245 (chain B) in PDB entry 3IKH
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 GLY 229 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ASN* 4.5 2.2 - - - -
227B THR 3.2 1.0 + - - -
228B THR* 1.3 78.6 - - - +
230B ALA* 1.3 59.0 + - - +
231B GLY 3.3 3.1 - - - -
232B ASP* 3.3 21.8 + - - +
233B THR* 2.9 32.7 + - - -
264B THR* 3.8 3.4 - - - -
274B PHE* 3.9 13.4 - - - -
900B ATP 4.6 7.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B THR* 3.0 22.4 + - + +
228B THR 3.3 0.8 + - - -
229B GLY* 1.3 77.6 - - - +
231B GLY* 1.3 57.8 + - - +
233B THR* 3.2 4.4 + - - -
234B PHE* 2.9 30.0 + - - +
261B ALA* 4.1 3.9 - - - +
264B THR* 4.0 9.6 - - + -
265B VAL* 3.6 27.4 - - + -
900B ATP 3.7 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LYS* 5.2 1.3 - - - -
43B GLN* 5.1 1.1 + - - -
161B ASN* 5.8 1.3 + - - -
180B VAL* 5.9 0.7 - - - +
200B THR* 6.2 0.9 - - - -
229B GLY 3.3 0.2 - - - -
230B ALA* 1.3 79.7 - - - +
232B ASP* 1.3 62.7 + - - +
234B PHE* 3.4 3.1 + - - +
235B LEU* 3.1 24.1 + - - +
900B ATP 3.6 50.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LYS* 2.8 39.4 + - - +
42B ASN* 3.0 46.1 + - + -
43B GLN* 2.9 30.8 + - + +
46B ILE* 4.3 3.3 - - + +
229B GLY* 3.3 15.1 + - - +
230B ALA 3.3 0.4 - - - -
231B GLY* 1.3 73.1 - - - +
233B THR* 1.3 65.8 + - - +
235B LEU* 3.5 0.3 + - - +
236B ALA* 3.0 26.2 + - - +
900B ATP 4.6 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 3.4 24.1 - - + +
229B GLY 2.9 20.5 + - - -
230B ALA 3.5 5.4 - - - -
232B ASP* 1.3 77.6 - - - +
234B PHE* 1.3 64.8 + - - +
236B ALA* 3.8 0.2 - - - +
237B VAL* 3.0 27.8 + - + +
260B ALA* 3.6 35.9 - - + +
261B ALA* 3.7 1.8 - - - +
264B THR* 2.8 30.8 + - - +
274B PHE* 3.7 2.3 - - - -
275B PRO* 4.3 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B VAL* 5.4 2.5 - - + -
198B VAL* 4.1 14.8 - - + -
200B THR* 4.0 21.5 - - + -
206B ALA* 3.7 20.6 - - + -
230B ALA 2.9 17.2 + - - +
231B GLY* 3.6 4.5 - - - +
232B ASP 3.3 0.2 - - - -
233B THR* 1.3 77.1 - - - +
235B LEU* 1.3 66.7 + - - +
238B MSE 2.9 34.2 + - + +
254B LEU* 3.9 21.1 - - + -
257B ALA* 3.2 36.2 - - + +
258B SER* 3.6 16.6 - - - -
261B ALA* 4.4 1.5 - - + +
900B ATP 3.5 46.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLN* 3.6 24.5 - - + +
134B LEU* 4.0 24.2 - - + -
159B VAL* 5.0 3.8 - - + -
161B ASN* 3.6 34.8 - - + -
180B VAL* 3.7 35.2 - - + -
231B GLY 3.1 13.9 + - - +
232B ASP 3.9 2.7 - - - +
234B PHE* 1.3 83.1 - - - +
236B ALA* 1.3 70.3 + - - +
238B MSE 3.7 8.0 - - + +
239B LEU* 2.9 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLN* 3.6 18.4 - - - +
46B ILE* 3.4 33.7 - - + -
47B LEU* 3.5 16.2 - - + +
232B ASP 3.0 16.0 + - - +
233B THR 3.8 0.2 - - - +
235B LEU* 1.3 86.6 - - - +
237B VAL* 1.3 58.0 + - - +
239B LEU* 4.8 0.2 - - - -
240B ALA* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 3.8 19.7 - - + -
50B CYS* 4.3 3.8 - - - -
233B THR* 3.0 18.3 + - + +
236B ALA* 1.3 73.3 - - - +
238B MSE 1.3 62.5 + - - +
240B ALA* 3.7 5.6 - - - +
241B SER* 2.8 28.4 + - - -
256B HIS* 3.8 9.2 - - + +
257B ALA* 3.8 23.8 - - - +
260B ALA* 3.4 24.5 - - + -
280B LEU* 4.2 10.8 - - + -
283B LEU* 4.5 4.0 - - + -
284B LEU* 3.9 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B VAL* 5.9 1.3 - - + -
178B ILE* 4.6 6.1 - - + -
180B VAL* 4.3 20.0 - - + -
198B VAL* 3.6 33.4 - - + -
234B PHE* 2.9 25.9 + - + +
235B LEU* 3.7 9.6 - - + +
237B VAL* 1.3 76.0 - - - +
239B LEU* 1.3 83.5 + - + +
241B SER 3.4 0.2 + - - -
242B ALA* 3.2 20.1 + - - +
249B PRO* 4.1 22.2 - - + -
253B ALA* 3.6 33.4 - - + +
254B LEU* 3.9 17.7 - - + -
257B ALA* 3.7 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL* 4.9 2.5 - - + -
47B LEU* 4.2 21.1 - - + -
132B ILE* 4.4 15.9 - - + -
134B LEU* 4.8 4.7 - - + -
159B VAL* 4.4 19.7 - - + -
178B ILE* 4.4 23.3 - - + -
235B LEU* 2.9 29.8 + - + +
236B ALA 3.8 3.4 - - - +
238B MSE 1.3 90.1 - - + +
240B ALA* 1.3 56.1 + - - +
242B ALA* 3.3 5.4 + - + +
243B LEU* 2.8 57.4 + - + +
249B PRO* 5.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 4.1 3.8 - - + +
50B CYS* 3.6 38.1 - - + -
52B ILE* 3.9 19.1 - - + -
236B ALA 2.9 18.8 + - - +
237B VAL 3.7 2.9 - - - +
239B LEU* 1.3 77.2 - - - +
241B SER* 1.3 54.3 + - - +
243B LEU* 3.2 2.0 + - - +
244B LEU* 2.7 43.3 + - + +
284B LEU* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B VAL 2.8 18.1 + - - -
238B MSE 3.6 4.5 - - - -
240B ALA* 1.3 76.6 - - - +
242B ALA* 1.3 61.8 + - - +
244B LEU* 3.4 4.6 + - - +
245B ARG* 3.0 46.0 + - - +
253B ALA* 3.6 8.3 - - - -
256B HIS* 2.7 37.3 - - - -
284B LEU* 3.9 11.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
238B MSE 3.2 13.8 + - - +
239B LEU* 3.8 5.4 - - + +
241B SER* 1.3 79.2 + - - +
243B LEU* 1.3 63.8 + - + +
245B ARG* 3.3 11.0 + - - +
246B GLY 3.0 4.7 + - - -
247B VAL* 3.0 47.0 + - + +
248B ALA 3.9 1.6 - - - +
249B PRO* 3.8 29.4 - - + -
253B ALA* 4.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1B LEU* 4.2 21.3 - - + -
3B VAL* 3.7 29.4 - - + -
47B LEU* 4.7 1.1 - - + -
52B ILE* 4.0 23.3 - - + -
132B ILE* 3.7 21.8 - - + -
239B LEU* 2.8 40.9 + - + +
240B ALA* 3.4 4.0 - - - +
242B ALA* 1.3 79.1 - - + +
244B LEU* 1.3 62.6 + - - +
246B GLY* 3.1 14.6 + - - -
247B VAL 4.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B CYS* 3.7 23.8 - - + +
51B GLY* 4.7 6.5 - - - +
52B ILE* 3.8 20.9 - - + -
240B ALA 2.7 25.0 + - - +
241B SER* 3.9 5.6 - - - +
243B LEU* 1.3 72.4 - - - +
245B ARG* 1.3 63.0 + - + +
246B GLY 3.4 0.4 + - - -
284B LEU* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B SER* 3.0 41.9 + - - +
242B ALA* 3.8 5.1 - - - +
243B LEU 3.1 0.8 - - - -
244B LEU* 1.3 81.5 - - + +
246B GLY* 1.3 63.4 + - - +
247B VAL* 3.4 19.7 + - + +
250B ASP* 2.8 43.2 + - - -
252B LEU* 3.7 28.7 - - - +
253B ALA* 3.5 11.9 - - - +
256B HIS* 4.5 2.7 + - - -
284B LEU 5.5 4.7 - - - +
----------------------------------------------------------
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