Contacts of the helix formed by residues 227 - 254 (chain W) in PDB entry 4BOG
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 PHE 227 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225W PRO* 4.2 8.7 - - + -
226W LEU* 1.3 105.8 - - + +
228W TYR* 1.4 68.8 + - - +
229W VAL* 3.1 1.3 - - - +
230W ILE* 2.5 48.2 - - + +
231W ASN* 3.4 1.9 + - - +
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Residues in contact with TYR 228 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224W LYS* 4.1 22.4 + - + +
225W PRO* 3.2 47.6 - - + +
227W PHE* 1.4 78.2 - - - +
229W VAL* 1.3 94.6 + - + +
230W ILE 3.1 0.5 + - - -
231W ASN* 3.6 0.8 + - - -
232W PHE* 2.9 52.7 + + + +
287W LEU* 5.6 10.1 - - + -
291W TYR* 5.1 6.8 - - - -
295W ILE* 5.9 8.3 - - + -
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Residues in contact with VAL 229 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225W PRO 3.6 0.7 - - - +
226W LEU* 3.2 44.6 - - + +
227W PHE 3.4 0.2 - - - +
228W TYR* 1.3 98.2 - - + +
230W ILE* 1.3 63.2 + - + +
233W ILE* 2.6 49.0 + - + +
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Residues in contact with ILE 230 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226W LEU 2.9 27.4 - - - +
227W PHE* 2.5 42.2 + - + +
229W VAL* 1.3 82.0 - - + +
231W ASN* 1.3 86.1 + - - +
233W ILE* 4.8 0.2 - - - +
234W THR* 2.4 33.7 + - - -
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Residues in contact with ASN 231 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227W PHE 3.4 3.2 + - - +
228W TYR* 4.8 0.7 - - - +
230W ILE* 1.3 119.3 - - + +
232W PHE* 1.3 65.7 + - + +
234W THR* 4.0 8.2 - - - +
235W PRO* 2.9 20.2 - - - +
261X VAL* 4.4 17.9 - - + +
265X PRO* 5.9 1.3 - - - +
278X MET* 4.9 3.6 - - - +
282X MET* 3.9 29.3 - - - +
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Residues in contact with PHE 232 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228W TYR* 2.9 37.5 + + + +
231W ASN* 1.3 84.1 - - + +
233W ILE* 1.3 63.2 + - + +
235W PRO* 2.9 26.9 - - + +
236W CYS* 4.0 10.2 + - - -
274W THR* 4.4 29.8 - - + -
277W ARG* 4.7 16.2 - - + -
278W LEU* 4.8 21.8 - - + -
281W THR* 6.1 2.0 - - + -
295W ILE* 5.4 10.1 - - + -
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Residues in contact with ILE 233 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229W VAL* 2.6 47.0 + - + +
232W PHE* 1.3 82.5 - - + +
234W THR* 1.3 66.8 + - - +
235W PRO* 3.1 1.1 - - - -
236W CYS* 2.9 23.8 + - + +
237W VAL* 3.1 24.8 + - + +
471W PHE* 5.3 18.2 - - + -
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Residues in contact with THR 234 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230W ILE* 2.4 27.5 + - - -
231W ASN* 4.0 8.6 - - - +
233W ILE* 1.3 79.3 - - - +
235W PRO* 1.3 69.8 - - + +
237W VAL* 3.5 5.7 - - - +
238W LEU* 3.1 46.2 + - + +
282X MET* 5.3 13.5 - - + -
286X ILE* 5.7 6.5 - - + -
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Residues in contact with PRO 235 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231W ASN 2.9 23.6 - - - +
232W PHE* 2.9 25.4 - - + +
233W ILE 3.1 0.2 - - - -
234W THR* 1.3 93.3 - - + +
236W CYS* 1.3 56.0 + - - +
238W LEU* 4.0 8.3 - - + -
239W ILE* 2.3 50.3 + - + +
274W THR* 5.8 4.0 - - - +
258X LEU* 5.8 8.1 - - + -
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Residues in contact with CYS 236 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232W PHE 4.0 11.4 - - - -
233W ILE* 2.9 23.2 + - + +
235W PRO* 1.3 84.4 - - - +
237W VAL* 1.3 52.6 + - + +
239W ILE* 4.3 5.6 - - - +
240W SER* 2.5 45.7 + - - +
295W ILE* 5.9 3.1 - - - -
298W LEU* 6.0 5.2 - - - -
299W VAL* 5.2 22.0 - - - -
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Residues in contact with VAL 237 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233W ILE* 3.1 20.8 + - + +
234W THR* 3.5 13.5 - - - +
236W CYS* 1.3 74.1 - - + +
238W LEU* 1.3 75.2 + - + +
240W SER* 4.0 5.6 - - - -
241W PHE* 3.0 29.3 + - - +
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Residues in contact with LEU 238 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234W THR* 3.1 37.5 + - + +
235W PRO* 3.7 7.0 - - + +
237W VAL* 1.3 91.3 - - + +
239W ILE* 1.3 66.8 + - + +
241W PHE* 2.8 49.0 - - + -
242W LEU* 3.3 1.4 + - - +
286X ILE* 4.0 19.3 - - + -
289X ILE* 3.6 36.8 - - + -
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Residues in contact with ILE 239 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235W PRO* 2.3 46.1 + - + +
236W CYS* 4.0 4.9 - - - +
238W LEU* 1.3 68.0 - - + +
240W SER* 1.3 57.1 + - - +
242W LEU* 2.6 45.4 + - + +
243W ALA* 3.1 4.7 + - + -
267W GLN* 4.9 20.8 + - + +
270W PHE* 4.4 29.2 - - + -
299W VAL* 5.9 5.2 - - + -
302W VAL* 4.8 19.1 - - + -
258X LEU* 5.6 6.7 - - + -
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Residues in contact with SER 240 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236W CYS* 2.5 32.6 + - - +
237W VAL* 4.0 6.5 - - - -
239W ILE* 1.3 75.8 - - - +
241W PHE* 1.3 51.6 + - - +
243W ALA* 3.1 7.6 + - - +
244W ALA* 2.4 40.8 + - - +
302W VAL* 4.7 12.1 - - - +
464W VAL* 5.8 8.9 - - - +
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Residues in contact with PHE 241 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237W VAL 3.0 14.6 + - - +
238W LEU* 2.8 49.1 + - + -
240W SER* 1.3 75.3 - - - +
242W LEU* 1.3 68.0 + - + +
244W ALA* 3.4 9.2 - - + -
245W LEU* 2.3 76.4 + - + +
289X ILE* 4.6 5.2 - - + -
292X THR* 6.1 0.7 - - + -
293X VAL* 2.9 41.1 - - + -
297X ASN* 5.1 0.4 - - - -
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Residues in contact with LEU 242 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238W LEU 3.3 2.4 + - - +
239W ILE* 2.6 32.4 + - + +
241W PHE* 1.3 94.6 - - + +
243W ALA* 1.3 49.6 + - - +
245W LEU* 3.3 5.7 - - + +
246W ALA* 2.3 35.6 + - + +
249W LEU* 4.5 6.8 - - + +
263W VAL* 3.2 35.0 - - + -
267W GLN* 4.5 20.9 - - + +
270W PHE* 6.5 1.1 - - + -
251X LEU* 5.8 2.9 - - + -
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Residues in contact with ALA 243 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239W ILE* 3.1 7.0 + - + +
240W SER* 3.8 3.4 - - - +
242W LEU* 1.3 75.9 - - - +
244W ALA* 1.3 63.7 + - - +
246W ALA* 2.7 25.4 - - + +
247W PHE* 3.3 11.1 + - - +
267W GLN* 4.7 15.2 - - - +
302W VAL* 3.3 34.8 - - + +
305W ASN* 5.9 4.5 - - + -
306W CYS* 5.6 0.7 - - - -
309W VAL* 5.3 6.6 - - + +
460W ILE* 5.5 1.2 - - - +
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Residues in contact with ALA 244 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240W SER* 2.4 34.2 + - - +
241W PHE* 3.3 12.3 - - + +
243W ALA* 1.3 68.0 - - - +
245W LEU* 1.3 59.5 + - + +
247W PHE* 3.2 11.3 + - - +
248W TYR* 2.4 40.2 + - + -
460W ILE* 4.8 10.0 - - + +
464W VAL* 6.2 4.5 - - + -
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Residues in contact with LEU 245 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241W PHE* 2.3 73.1 + - + +
242W LEU* 3.6 4.7 - - + +
244W ALA* 1.3 68.6 - - + +
246W ALA* 1.3 56.3 + - - +
248W TYR* 2.7 15.5 + - + -
249W LEU* 2.4 58.7 + - + +
293X VAL* 4.8 4.0 - - + -
297X ASN* 3.0 41.1 - - - +
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Residues in contact with ALA 246 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242W LEU* 2.3 29.1 + - + +
243W ALA* 2.7 26.2 - - - +
245W LEU* 1.3 69.4 - - - +
247W PHE* 1.3 50.9 + - + +
249W LEU* 3.4 10.3 + - - +
250W PRO* 2.5 30.5 - - - +
267W GLN* 5.5 3.4 - - - +
309W VAL* 4.2 22.9 - - + -
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Residues in contact with PHE 247 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243W ALA 3.3 8.3 + - - +
244W ALA 3.2 9.5 + - - +
245W LEU 3.0 0.6 - - - -
246W ALA* 1.3 82.6 - - + +
248W TYR* 1.3 51.8 + - - +
250W PRO* 2.5 33.3 - - + +
251W ALA* 4.9 2.3 - - - +
305W ASN* 4.5 3.4 - - + -
308W ILE* 3.6 24.9 - - + -
309W VAL* 4.2 14.1 - - + -
312W PHE* 3.5 54.3 - + + -
313W HIS* 6.3 0.7 - - + -
453W ILE* 5.6 0.7 - - - +
456W LEU* 4.1 11.0 - - + -
457W SER* 2.4 33.5 + - - +
460W ILE* 3.4 43.3 - - + -
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Residues in contact with TYR 248 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244W ALA* 2.4 48.7 - - + -
245W LEU* 2.7 21.6 + - + +
247W PHE* 1.3 71.3 - - - +
249W LEU* 1.3 66.4 + - + +
250W PRO* 3.0 4.7 - - - -
251W ALA* 3.4 8.4 + - - +
252W GLU* 3.3 20.4 + - - +
457W SER* 4.1 16.6 - - - -
460W ILE* 4.6 7.1 - - + +
461W ILE* 2.7 43.0 - - + +
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Residues in contact with LEU 249 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242W LEU* 4.5 7.6 - - + +
245W LEU* 2.4 67.5 + - + +
246W ALA* 3.7 9.4 - - - +
248W TYR* 1.3 75.3 - - + +
250W PRO* 1.4 58.0 - - - +
251W ALA 2.9 5.8 - - - -
252W GLU* 3.9 9.5 - - + +
253W SER 3.0 33.4 + - - +
256W LYS* 3.3 23.5 + - - +
297X ASN* 4.3 18.2 - - - +
300X HIS* 6.0 8.3 - - + -
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Residues in contact with PRO 250 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246W ALA 2.5 20.4 - - - +
247W PHE* 2.5 35.2 - - + +
248W TYR 3.0 0.9 - - - -
249W LEU 1.4 92.7 - - - +
251W ALA* 1.3 59.0 + - + +
254W GLY* 3.2 27.8 + - - -
256W LYS* 5.3 0.4 - - - +
312W PHE 6.0 0.9 - - - +
313W HIS* 5.5 15.5 - - + +
315W ARG* 6.1 3.1 - - - +
453W ILE* 5.3 3.6 - - + -
456W LEU* 6.3 3.1 - - + -
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Residues in contact with ALA 251 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247W PHE 4.9 1.1 - - - +
248W TYR* 3.5 11.0 - - - +
249W LEU 2.9 0.2 - - - -
250W PRO* 1.3 83.6 - - + +
252W GLU* 1.3 57.1 + - - +
253W SER* 2.8 16.1 + - - -
254W GLY 4.2 0.3 + - - -
453W ILE* 2.8 41.7 - - + -
303X PRO 4.3 5.4 - - - +
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Residues in contact with GLU 252 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248W TYR 3.3 12.6 + - - +
249W LEU* 3.6 9.6 + - + +
251W ALA* 1.3 79.2 - - - +
253W SER* 1.3 64.8 + - - +
297X ASN 5.1 1.6 - - - +
300X HIS* 3.1 26.5 - - + +
301X ARG* 2.9 34.1 - - - +
302X SER 3.2 18.1 - - - +
303X PRO* 3.0 27.6 - - - +
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Residues in contact with SER 253 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249W LEU 3.0 7.7 + - - -
251W ALA 2.8 4.7 + - - -
252W GLU* 1.3 84.7 - - - +
254W GLY* 1.3 57.5 + - - +
255W GLU* 3.0 8.6 + - - +
256W LYS* 3.0 41.2 + - - +
300X HIS* 4.5 4.0 - - - -
303X PRO 4.6 3.8 - - - -
304X SER* 5.9 0.7 - - - +
306X HIS* 2.6 44.4 + - - +
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Residues in contact with GLY 254 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250W PRO* 3.2 30.9 + - - -
251W ALA 4.2 1.2 + - - -
253W SER* 1.3 70.1 - - - +
255W GLU* 1.3 57.2 + - - +
256W LYS* 3.0 13.4 + - - -
257W MET* 3.5 24.8 + - - +
313W HIS* 4.5 8.5 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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