Contacts of the helix formed by residues 225 - 246 (chain B) in PDB entry 2BTO
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 THR 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B SER 4.0 8.5 - - - +
224B PRO* 1.3 76.3 - - - +
226B VAL* 1.3 65.6 + - - +
227B ASP* 3.6 15.8 + - - +
228B ASP* 2.9 32.8 + - - +
229B LEU* 3.3 17.7 + - - +
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Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLN* 3.9 13.9 - - - +
225B THR* 1.3 73.5 - - - +
227B ASP* 1.3 72.7 + - - +
229B LEU* 3.3 12.9 + - + +
230B ASN* 2.9 37.0 + - - +
1433B GTP 3.4 49.6 - - + +
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Residues in contact with ASP 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 5.9 2.8 - - - +
17B GLN* 5.9 1.4 - - - -
225B THR* 3.2 11.5 + - - +
226B VAL* 1.3 87.8 - - - +
228B ASP* 1.3 64.5 + - - +
230B ASN* 3.3 10.8 + - - +
231B LEU* 3.2 27.8 + - - +
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Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ALA* 4.5 16.6 - - + -
219B TRP* 3.7 16.6 - - + -
221B ILE* 3.7 19.6 - - - +
224B PRO* 3.4 8.2 - - + +
225B THR* 2.9 36.6 + - - +
227B ASP* 1.3 77.0 - - - +
229B LEU* 1.3 66.5 + - - +
231B LEU* 3.3 28.6 + - - +
232B LEU* 3.6 5.3 + - - +
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ASN* 3.7 32.3 - - + +
211B LEU* 3.7 38.6 - - + +
212B PHE* 3.7 18.2 - - + +
215B ALA* 4.2 11.0 - - + -
224B PRO* 4.5 6.5 - - + -
225B THR 3.3 16.3 + - - +
226B VAL* 3.3 13.9 + - + +
228B ASP* 1.3 76.5 - - - +
230B ASN* 1.3 61.7 + - - +
232B LEU* 3.4 12.2 + - - +
233B ILE* 3.3 23.8 + - - +
1433B GTP 3.7 17.3 - - + +
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Residues in contact with ASN 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLN* 4.0 18.4 + - - +
18B ILE* 3.2 22.4 - - + +
21B SER* 4.7 10.3 - - - +
226B VAL* 2.9 23.6 + - - +
227B ASP* 3.7 11.0 + - - +
228B ASP 3.2 0.4 - - - -
229B LEU* 1.3 75.8 - - - +
231B LEU* 1.3 57.3 + - + +
233B ILE* 3.3 6.0 + - - +
234B THR* 2.6 41.3 + - - +
1433B GTP 2.6 45.4 + - - -
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Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B SER* 4.8 10.1 - - - +
219B TRP* 4.2 21.8 - - + -
227B ASP 3.2 17.2 + - - +
228B ASP* 3.3 17.7 + - - +
230B ASN* 1.3 77.2 - - + +
232B LEU* 1.3 61.6 + - - +
234B THR* 3.3 5.1 + - + -
235B GLU* 3.1 32.9 + - + +
282B PRO* 4.5 16.8 - - + -
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LEU* 3.7 42.4 - - + +
214B LEU* 4.2 13.0 - - + -
215B ALA* 4.6 6.1 - - + +
219B TRP* 3.7 31.9 - - + -
228B ASP 3.6 5.8 + - - +
229B LEU* 3.4 11.1 + - - +
230B ASN 3.3 0.4 - - - -
231B LEU* 1.3 79.2 - - - +
233B ILE* 1.3 62.9 + - - +
235B GLU* 3.6 10.6 + - - +
236B ALA 3.3 15.4 + - - -
279B LEU* 3.6 31.4 - - + -
306B PHE* 3.3 28.7 - - + -
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Residues in contact with ILE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 3.8 30.5 - - + -
173B VAL* 4.2 10.5 - - + -
206B PHE* 3.8 34.8 - - + -
211B LEU* 3.7 27.6 - - + -
229B LEU 3.3 12.4 + - - +
230B ASN* 3.3 8.0 + - - +
231B LEU 3.3 0.4 - - - -
232B LEU* 1.3 76.1 - - - +
234B THR* 1.3 56.8 + - - +
236B ALA* 3.2 3.6 + - - +
237B LEU* 2.9 46.7 + - + +
1433B GTP 3.8 18.2 - - - +
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Residues in contact with THR 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 4.5 5.7 + - - +
21B SER* 2.9 35.1 + - - +
22B PHE* 3.9 13.8 + - + +
25B THR* 3.4 30.5 - - + +
230B ASN* 2.6 24.9 + - - +
231B LEU* 3.7 6.3 - - + -
232B LEU 3.3 0.2 - - - -
233B ILE* 1.3 73.9 - - - +
235B GLU* 1.3 56.6 + - - +
237B LEU* 3.3 8.6 + - - +
238B ALA* 2.8 34.1 + - - +
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Residues in contact with GLU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B THR* 6.2 0.4 - - - -
219B TRP* 5.0 9.4 - - - -
231B LEU* 3.1 20.8 + - + +
232B LEU* 3.7 18.4 - - - +
234B THR* 1.3 77.1 - - - +
236B ALA* 1.3 56.3 + - - +
238B ALA* 3.4 6.3 + - - +
239B GLY* 2.9 26.5 + - - -
276B PHE* 3.3 38.6 - - + +
278B PRO 4.8 1.0 - - - +
279B LEU* 5.2 0.3 - - - +
282B PRO* 6.1 1.0 - - - +
365B SER* 4.1 10.2 + - - +
366B HIS* 2.6 36.4 - - + +
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Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B PHE* 4.2 14.4 - - + -
232B LEU 3.3 9.7 + - - +
233B ILE 3.2 8.5 + - - +
235B GLU* 1.3 80.1 - - - +
237B LEU* 1.3 57.0 + - - +
239B GLY* 3.3 1.2 + - - -
240B ILE* 2.8 37.5 + - + +
274B CYS* 4.3 10.3 - - - -
276B PHE* 4.2 8.0 - - + -
306B PHE* 4.0 16.6 - - + -
371B VAL* 3.8 16.7 - - + +
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Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 4.0 16.8 - - + -
22B PHE* 3.7 24.7 - - + -
138B ILE* 5.7 3.6 - - + -
140B LEU* 4.0 22.4 - - + -
171B CYS* 3.8 27.6 - - + -
206B PHE* 4.1 14.1 - - + -
233B ILE* 2.9 37.5 + - + +
234B THR* 3.8 2.2 - - - +
236B ALA* 1.3 73.5 - - - +
238B ALA* 1.3 57.3 + - - +
240B ILE* 3.4 10.4 + - + +
241B THR* 2.8 42.1 + - + +
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Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B PHE* 4.3 7.1 - - + -
25B THR* 4.2 15.3 - - + -
26B VAL* 5.3 2.0 - - + -
29B GLU* 3.5 23.1 - - - +
234B THR* 2.8 21.2 + - + +
235B GLU* 3.6 7.2 - - - +
237B LEU* 1.3 72.0 - - - +
239B GLY* 1.3 57.7 + - - +
241B THR* 3.2 6.0 + - - -
242B ALA* 2.9 17.2 + - - +
245B ARG* 2.9 23.0 + - - +
324B ARG* 4.0 5.2 - - - +
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Residues in contact with GLY 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B GLU 2.9 15.3 + - - -
236B ALA 3.6 3.4 - - - -
238B ALA* 1.3 74.8 - - - +
240B ILE* 1.3 63.2 + - - +
242B ALA* 3.5 13.7 + - - +
243B SER* 4.6 2.4 + - - -
276B PHE* 5.6 1.1 - - - -
322B LEU* 4.5 11.4 - - - +
324B ARG* 4.3 20.1 - - - +
359B VAL* 5.8 0.3 - - - +
369B SER* 5.9 0.2 - - - -
371B VAL* 4.0 16.2 - - - -
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Residues in contact with ILE 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ILE* 6.4 0.9 - - + -
169B LEU* 5.7 9.2 - - + -
204B LEU* 3.7 29.6 - - + -
236B ALA* 2.8 33.5 + - + +
237B LEU* 4.0 10.5 - - + +
239B GLY* 1.3 73.9 - - - +
241B THR* 1.3 65.3 - - + +
242B ALA 3.5 0.3 + - - -
243B SER* 3.7 12.1 + - - -
244B MET* 3.6 15.9 - - + +
259B LEU* 4.0 24.7 - - + +
274B CYS* 5.2 0.7 - - + -
322B LEU* 3.9 15.7 - - + +
371B VAL* 3.8 18.8 - - + -
373B LEU* 3.8 14.8 - - + -
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Residues in contact with THR 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B PHE* 3.8 12.0 - - + -
52B PHE* 3.8 27.1 - - + -
138B ILE* 4.2 19.1 - - + -
237B LEU* 2.8 28.0 + - + +
238B ALA* 3.2 5.9 + - - -
240B ILE* 1.3 82.6 - - + +
242B ALA* 1.3 63.6 + - - +
243B SER 3.3 0.7 - - - -
244B MET* 2.9 25.2 + - + +
245B ARG* 3.1 32.9 + - - +
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Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B ALA 2.9 16.4 + - - +
239B GLY 3.6 9.2 - - - +
240B ILE 3.3 1.2 - - - -
241B THR* 1.3 77.3 - - - +
243B SER* 1.3 61.0 + - - +
244B MET 3.1 1.4 + - - -
245B ARG* 3.1 17.2 + - - +
246B PHE* 3.3 18.5 + - + +
324B ARG* 3.8 33.7 - - + +
359B VAL* 3.7 20.9 - - + +
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Residues in contact with SER 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B GLY 4.6 2.5 + - - -
240B ILE 3.7 13.1 + - - -
241B THR 3.3 0.6 - - - -
242B ALA* 1.3 74.4 - - - +
244B MET* 1.3 60.4 + - - +
245B ARG 3.5 0.2 - - - -
246B PHE 4.1 7.1 - - - +
251B THR* 5.5 1.1 - - - +
252B VAL 4.1 8.3 - - - -
253B GLU* 3.6 10.6 - - - +
254B ILE* 3.3 48.4 + - - +
259B LEU* 5.9 1.2 - - - +
322B LEU* 4.4 17.5 - - - +
357B GLY* 6.0 0.2 - - - -
359B VAL* 3.6 15.5 - - - +
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Residues in contact with MET 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B VAL* 5.4 2.1 - - - +
4B ASN* 5.0 5.1 - - + +
6B THR* 4.5 10.5 - - - +
48B ASN* 4.6 5.6 + - - +
51B SER* 3.2 20.8 + - - -
52B PHE* 4.3 21.3 - - + -
138B ILE* 5.4 4.5 - - + -
240B ILE* 3.6 24.0 - - + +
241B THR* 2.9 20.3 + - + +
243B SER* 1.3 80.0 - - - +
245B ARG* 1.3 60.1 + - - +
246B PHE 3.6 1.8 - - - -
254B ILE 3.4 17.9 - - - +
255B SER* 4.7 1.6 - - - -
256B LEU* 4.0 42.6 - - + +
259B LEU* 4.2 15.0 - - + -
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Residues in contact with ARG 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 4.0 19.0 - - - +
29B GLU* 2.8 36.8 + - - +
30B HIS* 3.1 47.5 + - + +
48B ASN* 2.9 25.3 + - - -
51B SER* 3.7 7.0 - - - +
52B PHE* 3.4 40.4 - - + -
238B ALA* 2.9 31.3 + - - +
241B THR* 3.1 25.1 + - - +
242B ALA* 3.1 8.6 + - - +
244B MET* 1.3 79.3 - - - +
246B PHE* 1.3 73.1 + - + +
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Residues in contact with PHE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLU* 3.4 27.1 - - + -
30B HIS* 3.9 15.7 - + - -
46B ARG* 4.6 3.1 - - + -
47B GLY* 3.7 18.4 - - - -
48B ASN* 3.5 12.8 + - - +
242B ALA* 3.3 19.4 + - - +
243B SER 4.1 7.3 - - - +
244B MET 3.6 1.1 - - - -
245B ARG* 1.3 114.6 - - + +
247B SER* 1.3 65.1 + - - +
251B THR* 3.8 12.7 - - + +
253B GLU* 3.9 9.4 - - - +
324B ARG* 3.8 7.2 - - - -
359B VAL* 4.0 17.7 - - + -
361B GLN* 3.7 42.8 - - + +
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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) + - + + + + + -
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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