Contacts of the helix formed by residues 220 - 244 (chain B) in PDB entry 2R9R
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 220 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B GLN* 3.6 10.9 + - - -
212B TYR* 3.4 7.1 - - - -
213B GLN* 2.7 58.0 + - + +
215B SER* 5.1 0.2 + - - -
218B PHE* 3.4 1.1 - - - +
219B THR* 1.3 77.1 - - - +
221B PRO* 1.3 72.5 - - - +
222B PHE* 2.7 40.3 + - - +
223B PHE* 3.1 16.5 + - + +
224B ILE* 3.1 14.8 + - - +
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Residues in contact with PRO 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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219B THR 3.3 11.2 - - - +
220B ASP* 1.3 89.1 - - - +
222B PHE* 1.3 56.0 + - + +
223B PHE 3.3 0.2 - - - -
224B ILE* 3.3 15.2 + - + +
225B VAL* 3.0 36.3 + - + +
509B PGW 3.9 43.5 - - + -
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Residues in contact with PHE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B SER* 3.8 26.9 + - - -
182B LEU* 4.0 12.3 - - + -
183B GLU* 3.6 32.2 - - + +
188B PHE* 3.7 42.4 - + + -
211B GLY 4.5 4.3 - - - +
212B TYR* 3.9 16.7 - - + -
220B ASP* 2.7 25.5 + - - +
221B PRO* 1.3 71.3 - - + +
223B PHE* 1.3 58.9 + - - +
225B VAL* 3.4 3.8 + - - +
226B GLU* 2.9 31.2 + - - +
509B PGW 3.8 40.4 - - + -
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Residues in contact with PHE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B TYR* 3.6 33.6 - + + +
213B GLN 3.2 24.9 - - - +
214B GLN* 4.1 12.1 - - + -
215B SER 3.4 30.1 - - - -
218B PHE* 3.4 33.4 - + - -
220B ASP* 3.1 13.7 + - + +
222B PHE* 1.3 76.5 - - - +
224B ILE* 1.3 60.1 + - - +
226B GLU* 4.5 0.9 - - - -
227B THR* 2.7 51.4 + - - -
266B TYR* 3.4 24.7 - + - -
513B PGW 4.0 19.7 - - + -
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Residues in contact with ILE 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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218B PHE* 3.3 41.1 - - + +
219B THR 4.8 1.8 - - - +
220B ASP 3.1 13.8 + - - +
221B PRO* 3.4 17.9 - - + +
222B PHE 3.1 0.2 - - - -
223B PHE* 1.3 78.1 - - - +
225B VAL* 1.3 61.2 + - + +
227B THR* 3.1 6.2 + - - -
228B LEU* 2.8 51.8 + - + +
515B PGW 4.0 36.3 - - + -
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Residues in contact with VAL 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ILE* 4.0 22.7 - - + -
179B SER* 3.6 32.5 - - - +
221B PRO* 3.0 19.6 + - + +
222B PHE* 3.9 1.6 - - - +
224B ILE* 1.3 78.2 - - + +
226B GLU* 1.3 63.0 + - - +
228B LEU* 3.4 10.3 + - + +
229B CYS* 3.0 33.0 + - - -
509B PGW 4.2 23.6 - - + -
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Residues in contact with GLU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B SER* 5.4 0.2 - - - -
179B SER* 5.0 3.3 + - - +
183B GLU* 5.0 1.1 - - - +
212B TYR* 3.7 24.2 + - + -
222B PHE 2.9 17.9 + - - +
223B PHE* 4.1 3.4 - - - +
225B VAL* 1.3 77.4 - - - +
227B THR* 1.3 58.1 + - - +
229B CYS* 3.7 3.6 - - - +
230B ILE* 2.9 51.2 + - - +
266B TYR* 3.8 21.3 - - + +
296B ARG* 3.0 27.7 + - - +
299B ARG* 2.8 44.6 + - - -
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Residues in contact with THR 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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218B PHE* 3.9 11.4 - - + -
223B PHE* 2.7 37.1 + - - -
224B ILE* 3.5 4.0 - - - -
226B GLU* 1.3 74.0 - - - +
228B LEU* 1.3 60.2 + - - +
230B ILE* 3.2 2.5 + - - +
231B ILE* 2.8 44.6 + - + +
266B TYR* 2.6 32.4 + - - +
513B PGW 4.8 6.1 - - + -
515B PGW 3.9 28.7 - - + -
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ILE* 2.8 37.1 + - + +
225B VAL* 3.7 8.7 - - + +
227B THR* 1.3 72.2 - - - +
229B CYS* 1.3 64.8 + - - +
231B ILE* 2.9 19.3 + - + +
232B TRP* 3.1 13.7 + - - +
515B PGW 4.2 33.7 - - + -
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Residues in contact with CYS 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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172B VAL* 3.9 25.8 - - + -
175B ILE* 4.1 14.8 - - - -
176B SER* 3.8 38.4 - - - -
225B VAL* 3.0 28.0 + - - +
226B GLU* 3.7 5.6 - - - +
228B LEU* 1.3 77.3 - - - +
230B ILE* 1.3 63.7 + - + +
232B TRP* 3.3 3.7 + - - +
233B PHE* 3.0 33.6 + - + -
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Residues in contact with ILE 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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226B GLU* 2.9 53.0 + - - +
227B THR 3.9 3.4 - - - +
229B CYS* 1.3 81.0 - - + +
231B ILE* 1.3 59.8 + - + +
233B PHE* 3.7 15.3 - - + +
234B SER* 2.6 48.2 + - - +
262B ALA 4.6 12.1 - - - +
263B ILE* 4.4 5.8 - - + -
266B TYR* 3.7 47.1 - - + -
267B TYR* 3.8 11.0 - - + +
299B ARG* 4.2 7.9 - - - +
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Residues in contact with ILE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B THR* 2.8 35.6 + - + +
228B LEU* 2.9 13.0 + - + +
230B ILE* 1.3 78.3 - - + +
232B TRP* 1.3 60.7 + - - +
234B SER* 3.5 5.7 - - - -
235B PHE* 2.8 28.4 + - + +
266B TYR* 6.2 0.4 - - + -
267B TYR* 5.3 4.3 - - - +
513B PGW 3.3 34.5 - - + -
515B PGW 4.8 10.1 - - + -
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Residues in contact with TRP 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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153B PHE* 5.2 1.3 - + - -
165B ILE* 3.9 22.9 - - + -
168B VAL* 3.8 31.9 - - + -
169B SER* 3.4 33.9 + - - +
172B VAL* 4.1 22.9 - - + -
228B LEU 3.1 7.6 + - - +
229B CYS 3.7 6.5 - - - +
231B ILE* 1.3 80.4 - - - +
233B PHE* 1.3 78.6 + + - +
235B PHE* 3.1 27.6 + + - +
236B GLU* 3.0 43.4 + - + +
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Residues in contact with PHE 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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169B SER 5.0 0.2 - - - -
172B VAL* 3.6 20.9 - - + -
173B ILE* 3.9 27.8 - - + -
176B SER* 3.6 33.2 - - - -
229B CYS 3.0 22.4 + - - +
230B ILE* 4.1 11.9 - - + +
232B TRP* 1.3 85.0 - + - +
234B SER* 1.3 62.6 + - - +
236B GLU* 3.5 3.1 + - - +
237B PHE* 3.2 23.7 + - - +
259B ASP 5.0 1.1 - - - +
262B ALA* 4.1 21.1 - - + -
263B ILE* 3.5 18.6 - - + +
299B ARG* 4.5 17.0 - - + -
302B LYS* 3.4 30.8 + - + +
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Residues in contact with SER 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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230B ILE* 2.6 25.6 + - - +
231B ILE* 3.5 6.5 - - - -
233B PHE* 1.3 74.3 - - - +
235B PHE* 1.3 66.8 + - - +
237B PHE* 3.5 3.0 + - - +
238B LEU* 3.0 35.9 + - - +
263B ILE* 4.0 13.9 - - - +
267B TYR* 2.7 35.1 + - - -
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Residues in contact with PHE 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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153B PHE* 3.6 29.2 - + - -
231B ILE* 2.8 17.6 + - + +
232B TRP* 3.3 37.5 - + + +
234B SER* 1.3 76.2 - - - +
236B GLU* 1.3 55.6 + - + +
238B LEU* 3.1 9.2 + - + +
239B VAL* 2.8 57.3 + - + +
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Residues in contact with GLU 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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153B PHE* 4.2 19.1 - - + -
165B ILE* 5.4 0.5 - - - +
169B SER* 2.8 25.1 + - - -
173B ILE* 5.8 1.2 - - - +
232B TRP* 3.0 41.8 + - + +
233B PHE* 3.8 4.2 - - - +
235B PHE* 1.3 74.9 - - + +
237B PHE* 1.3 58.5 + - - +
239B VAL* 3.3 5.6 + - - +
240B ARG* 2.8 69.7 + - - +
259B ASP* 4.4 0.8 - - - +
302B LYS* 2.7 32.6 + - - +
305B ARG* 5.3 1.0 - - - -
306B HIS* 5.1 1.9 + - - -
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Residues in contact with PHE 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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233B PHE 3.2 15.7 + - - +
234B SER* 3.8 4.5 - - - +
235B PHE 3.3 0.2 - - - -
236B GLU* 1.3 78.4 - - - +
238B LEU* 1.3 74.3 + - + +
240B ARG* 3.9 6.0 - - - +
241B PHE* 3.0 33.0 + + + +
250B PHE* 3.5 34.0 - + - -
251B PHE* 4.5 8.5 - + - -
256B ASN 5.0 0.2 - - - -
259B ASP* 4.6 21.9 + - + +
260B ILE* 3.5 33.4 - - + -
263B ILE* 4.1 24.9 - - + -
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Residues in contact with LEU 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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234B SER* 3.0 28.0 + - - +
235B PHE* 3.5 6.7 - - + +
237B PHE* 1.3 91.8 - - + +
239B VAL* 1.3 68.1 + - + +
241B PHE* 3.0 16.5 + - + -
242B PHE* 3.1 45.4 + - + -
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Residues in contact with VAL 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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149B VAL* 3.5 17.9 - - + -
153B PHE* 3.4 38.6 - - + -
235B PHE* 2.8 61.1 + - + +
236B GLU* 3.8 4.0 - - - +
238B LEU* 1.3 73.3 - - + +
240B ARG* 1.3 60.7 + - - +
242B PHE* 3.7 3.2 + - - +
243B ALA* 3.2 24.3 + - + +
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Residues in contact with ARG 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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150B TRP* 3.4 21.9 - - + -
153B PHE* 3.1 41.0 + - + +
154B GLU* 5.2 1.9 + - - +
236B GLU* 2.8 66.8 + - - +
237B PHE* 3.9 5.1 - - - +
239B VAL* 1.3 73.0 - - - +
241B PHE* 1.3 63.1 + - - +
244B CYS* 3.2 29.3 + - - +
250B PHE* 4.1 10.7 - - + -
256B ASN* 4.4 8.3 - - - -
259B ASP* 4.2 12.9 + - - -
305B ARG* 3.2 53.4 - - - +
306B HIS* 5.5 2.0 - - - -
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Residues in contact with PHE 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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237B PHE* 3.0 24.7 + + + +
238B LEU* 3.0 10.1 + - + +
240B ARG* 1.3 77.5 - - - +
242B PHE* 1.3 85.0 + + - +
244B CYS* 3.6 1.3 - - - -
247B LYS* 2.7 57.0 + - + +
250B PHE* 3.7 41.9 - + + -
251B PHE* 4.4 17.5 - + - -
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Residues in contact with PHE 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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146B GLN* 3.5 16.8 + - - +
238B LEU* 3.1 45.5 + - + +
239B VAL* 4.5 3.6 - - - +
241B PHE* 1.3 105.9 - + - +
243B ALA* 1.3 58.3 + - - +
247B LYS* 3.1 19.9 + - - +
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Residues in contact with ALA 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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140B LEU* 5.5 1.7 - - - -
146B GLN* 4.0 20.5 - - + +
149B VAL* 4.0 26.9 - - + -
150B TRP* 3.2 38.2 - - + +
153B PHE* 6.3 0.2 - - + -
239B VAL* 3.2 19.8 + - + +
240B ARG 3.6 0.2 + - - -
242B PHE* 1.3 78.4 - - - +
244B CYS* 1.3 61.4 + - - +
245B PRO* 3.9 1.6 - - - +
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Residues in contact with CYS 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLN* 3.8 5.9 - - - +
150B TRP* 3.5 20.6 - - + -
240B ARG 3.2 15.1 + - - +
241B PHE 3.6 9.4 - - - -
243B ALA* 1.3 80.2 - - - +
245B PRO* 1.3 69.9 - - + +
246B SER 3.0 25.1 - - - +
247B LYS* 3.4 34.4 + - - -
250B PHE* 4.3 14.4 - - + -
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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