Contacts of the helix formed by residues 209 - 233 (chain B) 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 THR 209 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A TYR* 4.4 9.5 - - - +
4B SER* 3.9 28.7 - - - +
6B PHE* 5.6 1.0 - - - -
207B ALA 3.5 11.4 - - - +
208B ALA* 1.3 78.6 - - - +
210B PRO* 1.3 77.2 - - - +
211B ILE* 3.1 18.4 + - - +
212B THR* 2.8 22.6 + - + +
213B ASP* 2.9 27.4 + - - -
256B ASN* 5.7 2.9 - - + +
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Residues in contact with PRO 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LYS* 3.5 20.4 - - - +
222A MET* 3.7 38.6 - - + -
245A TYR* 4.0 31.6 - - + -
249A LEU* 4.8 2.2 - - + -
209B THR* 1.3 88.7 - - - +
211B ILE* 1.3 61.5 + - - +
213B ASP* 3.7 6.1 - - + +
214B ALA* 3.3 19.1 + - - +
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Residues in contact with ILE 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A MET* 3.6 39.9 - - + -
245A TYR* 4.0 14.4 - - + -
248A PHE* 3.8 17.7 - - + -
249A LEU* 4.0 24.0 - - + -
252A MET* 4.1 17.3 - - + -
6B PHE* 3.5 35.0 - - + -
209B THR* 3.1 7.0 + - - +
210B PRO* 1.3 75.4 - - - +
212B THR* 1.3 65.7 + - - +
214B ALA* 3.4 3.3 + - - +
215B CYS* 3.2 25.5 + - - -
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Residues in contact with THR 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 4.7 4.7 - - + -
202B ALA 4.9 3.3 + - - -
208B ALA* 3.5 9.7 - - - +
209B THR* 2.8 40.8 + - + +
211B ILE* 1.3 76.0 - - - +
213B ASP* 1.3 57.2 + - - +
215B CYS* 4.5 1.3 - - - -
216B ALA* 2.8 32.8 + - - +
252B MET 4.1 2.2 - - - +
253B ALA* 3.4 36.8 - - - +
256B ASN* 3.8 22.4 - - + -
257B ALA* 3.8 11.2 - - + +
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Residues in contact with ASP 213 (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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218A LYS* 4.7 10.2 + - - +
202B ALA 4.9 0.2 - - - +
203B TYR* 3.4 22.3 + - + +
208B ALA* 3.6 11.6 - - - +
209B THR 2.9 23.2 + - - +
210B PRO* 3.7 8.7 - - + +
212B THR* 1.3 78.5 + - - +
214B ALA* 1.3 63.6 + - - +
216B ALA* 3.7 1.0 - - - +
217B LEU* 3.0 31.6 + - + +
299B ARG* 2.4 40.4 + - - -
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Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ALA* 4.2 15.3 - - + +
215A CYS* 5.5 0.9 - - - -
218A LYS* 3.7 39.6 - - + +
249A LEU* 5.0 4.7 - - + -
210B PRO 3.3 7.3 + - - +
211B ILE* 3.8 5.6 - - - +
212B THR 3.3 0.2 - - - -
213B ASP* 1.3 79.1 - - - +
215B CYS* 1.3 64.2 + - - +
217B LEU* 4.0 6.0 - - - +
218B LYS* 3.1 24.3 + - - +
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Residues in contact with CYS 215 (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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214A ALA* 5.3 0.9 - - - -
215A CYS* 5.0 9.4 - - - -
211B ILE* 3.2 29.8 + - - +
212B THR 3.8 2.9 - - - +
214B ALA* 1.3 77.3 - - - +
216B ALA* 1.3 61.8 + - - +
218B LYS* 3.4 2.3 + - - +
219B ALA* 2.9 30.3 + - - +
249B LEU* 3.4 37.1 - - + +
252B MET* 3.8 39.7 - - + -
253B ALA 4.1 4.3 - - - +
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Residues in contact with ALA 216 (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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199B ALA* 3.5 35.0 - - - +
203B TYR* 4.1 18.8 - - + +
212B THR 2.8 18.8 + - - +
213B ASP 3.7 3.6 - - - +
215B CYS* 1.3 76.5 - - - +
217B LEU* 1.3 58.5 + - - +
219B ALA* 3.1 6.6 + - - +
220B ALA* 2.9 25.9 + - - +
253B ALA* 3.7 15.8 - - + +
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Residues in contact with LEU 217 (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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218A LYS* 6.2 2.0 - - - +
203B TYR* 3.3 57.4 - - + +
213B ASP* 3.0 17.4 + - + +
214B ALA* 4.0 5.4 - - - +
216B ALA* 1.3 77.6 - - - +
218B LYS* 1.3 58.5 + - - +
220B ALA* 3.4 3.3 + - + +
221B SER* 3.0 28.6 + - - -
302B ASP* 4.5 6.5 - - + +
303B VAL* 4.2 23.1 - - + +
306B ALA* 3.6 21.2 - - + +
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Residues in contact with LYS 218 (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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210A PRO* 3.4 24.8 - - - +
213A ASP* 4.5 13.9 + - - +
214A ALA* 3.7 21.3 - - + +
214B ALA 3.1 19.8 + - - +
215B CYS* 3.8 3.6 - - - +
216B ALA 3.3 0.2 - - - -
217B LEU* 1.3 72.8 - - - +
219B ALA* 1.3 66.5 + - - +
221B SER* 3.3 10.0 + - - +
222B MET* 3.0 49.7 + - + +
249B LEU* 3.5 20.6 - - + -
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Residues in contact with ALA 219 (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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199B ALA* 4.2 4.7 - - + -
215B CYS 2.9 14.9 + - - +
216B ALA 3.4 8.3 - - - +
218B LYS* 1.3 76.3 - - - +
220B ALA* 1.3 58.3 + - - +
222B MET* 3.3 2.8 + - - +
223B ILE* 2.9 38.3 + - + +
246B ALA* 3.3 30.9 - - - +
249B LEU* 4.0 4.6 - - + +
250B ALA* 3.6 22.2 - - + +
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Residues in contact with ALA 220 (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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196B LEU* 4.1 19.0 - - + +
199B ALA* 4.3 5.8 - - + +
216B ALA 2.9 15.4 + - - +
217B LEU* 3.7 7.2 - - - +
219B ALA* 1.3 76.0 - - - +
221B SER* 1.3 63.6 + - - +
223B ILE* 3.8 1.1 - - - +
224B ALA* 3.0 26.5 + - - +
303B VAL* 3.8 31.6 - - + +
306B ALA* 4.8 0.4 - - + -
307B MET* 3.7 11.9 - - + +
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Residues in contact with SER 221 (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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217B LEU 3.0 16.3 + - - -
218B LYS* 3.6 13.9 + - - +
219B ALA 3.3 0.2 - - - -
220B ALA* 1.3 78.5 - - - +
222B MET* 1.3 63.7 + - - +
224B ALA* 3.6 1.9 + - - +
225B LYS* 3.1 46.8 + - - +
306B ALA* 3.0 29.9 + - - +
307B MET* 4.4 0.9 - - - +
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Residues in contact with MET 222 (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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210A PRO* 3.7 39.5 - - + -
218B LYS* 3.0 28.6 + - + +
221B SER* 1.3 75.1 - - - +
223B ILE* 1.3 61.1 + - - +
225B LYS* 3.2 4.1 + - - +
226B ASN* 2.9 43.6 + - - +
242B ALA* 3.4 35.9 - - + +
243B MET* 5.1 0.4 - - - -
245B TYR* 4.0 3.8 - - + -
246B ALA* 3.7 18.4 - - + -
249B LEU* 3.8 21.5 - - - -
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Residues in contact with ILE 223 (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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192B GLY 4.2 4.3 - - - +
195B ALA* 3.8 16.6 - - + +
196B LEU* 3.5 51.8 - - + +
219B ALA* 2.9 28.9 + - + +
220B ALA* 3.8 4.0 - - - +
222B MET* 1.3 75.1 - - - +
224B ALA* 1.3 67.3 + - - +
227B LEU* 2.9 54.0 + - + +
228B LYS 4.7 0.2 + - - -
243B MET* 4.0 15.5 - - + -
246B ALA* 3.9 15.0 - - + -
330B LEU* 4.8 2.8 - - + +
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Residues in contact with ALA 224 (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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220B ALA 3.0 18.0 + - - +
221B SER 3.9 2.7 - - - +
223B ILE* 1.3 79.3 - - - +
225B LYS* 1.3 61.7 - - + +
227B LEU 5.1 0.3 + - - -
228B LYS* 5.6 5.4 + - - +
307B MET* 3.6 50.5 - - + +
330B LEU* 5.0 10.3 - - + +
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Residues in contact with LYS 225 (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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221B SER* 3.1 36.3 + - - +
222B MET* 3.2 6.8 + - + +
223B ILE 3.0 0.8 - - - -
224B ALA* 1.3 83.8 - - + +
226B ASN* 1.3 68.5 + - - +
228B LYS* 5.6 1.5 - - - +
229B THR* 4.1 10.2 + - - -
306B ALA 5.0 3.8 - - - -
307B MET 5.6 5.2 - - - +
308B GLY* 6.0 2.9 - - - +
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Residues in contact with ASN 226 (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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222B MET* 2.9 31.9 + - - +
225B LYS* 1.3 89.6 - - - +
227B LEU* 1.3 65.9 + - - +
228B LYS 3.4 2.7 - - - -
229B THR* 3.1 10.1 + - - +
230B ALA* 2.8 23.2 + - - +
238B PRO 4.7 0.9 - - - +
239B ALA* 3.9 20.4 - - - +
242B ALA* 3.3 35.0 - - + +
243B MET* 4.2 7.9 - - - -
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Residues in contact with LEU 227 (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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188B THR* 3.7 28.5 - - + +
189B ALA* 4.5 0.4 - - - -
192B GLY* 3.8 23.8 - - - -
193B MET* 4.1 10.3 - - - +
223B ILE* 2.9 37.4 + - + +
226B ASN* 1.3 71.1 - - - +
228B LYS* 1.3 64.2 + - - +
230B ALA* 3.1 2.3 + - - +
231B CYS* 2.9 29.8 + - - -
243B MET* 3.7 25.5 - - + -
330B LEU* 4.5 9.2 - - + -
334B ILE* 3.9 26.0 - - + -
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Residues in contact with LYS 228 (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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223B ILE 4.7 0.6 + - - -
224B ALA 5.6 5.7 + - - +
225B LYS 6.1 1.1 - - - +
226B ASN 3.4 0.6 - - - +
227B LEU* 1.3 77.1 - - - +
229B THR* 1.3 58.7 + - - +
231B CYS* 3.3 1.6 + - - +
232B ASP* 2.7 77.5 + - - +
330B LEU* 4.5 11.2 - - + +
333B SER* 3.8 45.8 + - - +
334B ILE* 4.2 13.2 - - + +
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Residues in contact with THR 229 (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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225B LYS 4.1 12.0 + - - -
226B ASN* 3.1 12.9 + - - +
228B LYS* 1.3 78.5 - - - +
230B ALA* 1.3 57.8 + - - +
232B ASP* 3.4 6.3 + - - +
233B ASN* 3.0 31.6 + - + +
236B ASP* 3.1 28.3 - - + +
239B ALA* 3.9 8.1 - - + -
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Residues in contact with ALA 230 (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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188B THR* 3.9 20.4 + - + +
226B ASN 2.8 15.7 + - - +
227B LEU 3.1 4.7 + - - +
229B THR* 1.3 76.7 - - - +
231B CYS* 1.3 63.6 + - - +
233B ASN 3.5 5.8 - - - -
234B GLY* 3.4 23.9 + - - -
239B ALA* 4.1 14.1 - - + -
240B ARG* 4.3 14.0 + - - +
243B MET* 4.1 19.3 - - + -
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Residues in contact with CYS 231 (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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185B LYS* 3.5 41.9 - - + +
188B THR* 3.7 10.3 - - - -
189B ALA* 3.6 43.1 - - - -
227B LEU* 2.9 23.9 + - - +
228B LYS 3.6 4.7 - - - +
230B ALA* 1.3 77.1 - - - +
232B ASP* 1.3 66.3 + - - +
233B ASN* 3.2 1.2 + - - -
234B GLY 4.4 1.7 + - - -
334B ILE* 3.8 19.5 - - + -
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Residues in contact with ASP 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LYS* 4.1 15.1 + - - +
228B LYS* 2.7 60.9 + - - +
229B THR* 3.9 5.8 - - - +
231B CYS* 1.3 78.5 - - - +
233B ASN* 1.3 60.7 + - + +
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Residues in contact with ASN 233 (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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229B THR* 3.0 15.4 + - + +
230B ALA* 3.5 5.9 - - - +
231B CYS 3.2 0.8 - - - -
232B ASP* 1.3 81.8 - - + +
234B GLY* 1.3 63.0 + - - +
235B LYS* 3.1 25.0 + - - +
236B ASP* 3.2 36.3 + - + +
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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
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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