Contacts of the helix formed by residues 228 - 256 (chain B) in PDB entry 4O6M
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 SER 228 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ASN* 4.6 7.1 + - - -
226B MET 3.6 4.2 + - - -
227B GLU* 1.3 77.6 - - - +
229B LYS* 1.3 64.1 + - - +
230B TYR* 3.8 6.5 + - - +
231B GLY* 2.9 28.6 + - - -
232B ALA* 3.1 22.5 + - - +
422B C5P 3.1 9.6 + - - +
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Residues in contact with LYS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ALA* 3.6 27.9 + - - +
286A TYR* 3.6 50.8 + - + +
287A MET* 5.3 4.4 - - - +
288A ARG* 5.3 5.6 - - - +
228B SER* 1.3 72.4 - - - +
230B TYR* 1.3 62.2 + - - +
232B ALA* 3.3 7.0 + - - +
233B TRP* 3.0 22.7 + - - +
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Residues in contact with TYR 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A TYR* 3.2 17.8 + - - +
336A ILE* 3.0 23.4 + - - +
339A LEU* 3.5 26.9 - - + +
340A ARG* 3.5 29.7 - - + +
175B ASN* 4.0 13.9 - - - -
228B SER* 3.3 6.1 + - - +
229B LYS* 1.3 78.2 - - - +
231B GLY* 1.3 54.4 + - - +
233B TRP* 3.2 17.5 + + - +
234B LEU* 2.7 65.9 + - + +
407B MPG 3.5 30.2 - - + +
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Residues in contact with GLY 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ASN* 3.4 15.3 - - - -
228B SER* 2.9 16.5 + - - -
230B TYR* 1.3 78.2 - - - +
232B ALA* 1.3 56.2 + - - +
234B LEU* 4.0 1.9 - - - +
235B ASP* 3.0 31.4 + - - +
422B C5P 3.2 29.5 + - - -
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LYS* 3.6 15.3 + - - +
285A ALA* 4.5 10.3 - - + -
228B SER 3.1 11.5 + - - +
229B LYS* 3.7 8.3 - - - +
231B GLY* 1.3 72.1 - - - +
233B TRP* 1.3 65.3 + - - +
235B ASP* 3.9 1.7 - - - +
236B GLY 3.3 16.3 + - - -
422B C5P 3.3 41.5 + - - +
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Residues in contact with TRP 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A THR* 3.0 42.2 + - + +
281A LYS* 3.6 18.9 - - + +
282A PHE* 3.4 31.8 - - + +
285A ALA* 4.2 4.6 - - + +
286A TYR* 4.2 13.2 - + + -
335A ARG* 4.0 2.9 - - + -
336A ILE* 3.7 47.3 - - + -
339A LEU* 3.5 23.8 - - + +
229B LYS 3.0 16.7 + - - +
230B TYR* 3.6 24.5 - + - +
232B ALA* 1.3 77.8 - - - +
234B LEU* 1.3 78.0 + - + +
236B GLY* 3.3 2.9 + - - -
237B VAL* 2.9 47.9 + - + +
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ILE* 4.0 19.7 - - + -
175B ASN* 4.5 10.8 - - - +
178B THR* 4.2 15.3 - - + -
179B VAL* 4.5 5.2 - - + -
230B TYR* 2.7 57.2 + - + +
231B GLY 4.0 2.7 - - - +
233B TRP* 1.3 82.4 - - + +
235B ASP* 1.3 58.6 + - - +
237B VAL* 4.4 2.5 - - + -
238B LEU* 2.8 57.4 + - + +
407B MPG 4.1 23.3 - - + -
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Residues in contact with ASP 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B THR* 3.7 12.5 - - + +
214B ASP* 3.1 12.0 - - - +
217B ASP* 2.9 15.5 - - - +
231B GLY 3.0 19.5 + - - +
232B ALA* 3.9 4.5 - - - +
233B TRP 3.3 0.2 - - - -
234B LEU* 1.3 77.6 - - - +
236B GLY* 1.3 62.3 + - - +
238B LEU* 4.0 0.7 - - - +
239B ASP* 3.0 37.1 + - - +
401B CA 2.3 30.6 - - - -
422B C5P 3.3 28.2 + - + +
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Residues in contact with GLY 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TYR* 3.6 18.6 - - - -
281A LYS* 4.2 7.9 - - - -
232B ALA 3.3 11.5 + - - -
233B TRP 3.7 2.7 - - - -
234B LEU 3.3 0.4 - - - -
235B ASP* 1.3 78.7 - - - +
237B VAL* 1.3 61.2 + - - +
239B ASP* 3.3 2.3 + - - -
240B ARG* 3.2 37.6 + - - -
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Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A MET* 4.1 6.1 - - + -
277A TYR* 3.8 18.1 - - + -
278A THR* 4.0 12.6 - - + -
336A ILE* 4.0 21.5 - - + -
233B TRP* 2.9 53.3 + - + +
234B LEU* 3.7 6.5 - - + +
236B GLY* 1.3 75.3 - - - +
238B LEU* 1.3 65.3 + - + +
240B ARG* 3.1 6.8 + - - +
241B TYR* 3.1 42.3 + - + -
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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
----------------------------------------------------------
336A ILE* 4.6 10.8 - - + -
178B THR* 4.1 16.6 - - + +
179B VAL* 4.6 5.6 - - + -
182B PHE* 3.7 48.5 - - + -
234B LEU* 2.8 51.5 + - + +
235B ASP 4.3 2.0 - - - +
237B VAL* 1.3 71.7 - - + +
239B ASP* 1.3 63.7 + - - +
241B TYR* 3.2 14.1 + - + +
242B SER* 2.8 32.8 + - - -
407B MPG 4.5 19.1 - - + -
412B MPG 4.6 2.0 - - + -
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B THR* 5.9 0.2 - - - +
210B HIS* 4.8 3.5 - - - -
214B ASP* 3.0 34.9 - - - +
235B ASP* 3.0 31.8 + - - +
236B GLY* 3.6 6.3 - - - +
237B VAL 3.2 0.4 - - - -
238B LEU* 1.3 79.5 - - - +
240B ARG* 1.3 77.1 + - - +
242B SER* 3.4 1.2 + - - -
243B ASP* 2.9 35.3 + - - +
301B ARG* 3.5 28.3 + - - +
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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
----------------------------------------------------------
270A PHE* 4.1 2.0 - - - -
274A MET* 3.7 22.7 - - + -
277A TYR* 3.3 37.4 + - + -
146B TYR* 3.8 12.1 + - - -
236B GLY* 3.2 29.8 + - - +
237B VAL 3.1 9.8 + - - +
239B ASP* 1.3 86.0 + - - +
241B TYR* 1.3 65.2 + - - +
243B ASP* 3.3 22.8 + - - -
244B PHE* 3.1 20.4 + - - +
272B SER 5.2 0.4 + - - -
273B LEU* 3.5 30.3 - - + +
276B ALA* 3.2 27.4 - - + +
301B ARG* 3.6 13.9 - - - +
419B SO4 3.1 21.2 + - - -
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Residues in contact with TYR 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A PHE* 3.6 31.7 - + - -
274A MET* 3.8 21.8 - - + -
278A THR* 5.8 0.2 - - + -
329A ASN* 4.5 7.6 + - - -
332A ALA* 3.3 28.4 - - + +
333A LEU* 4.2 7.4 + - - +
336A ILE* 4.0 14.0 - - + +
182B PHE* 3.6 15.7 - + + -
237B VAL* 3.1 38.9 + - + -
238B LEU* 3.2 13.7 + - + +
240B ARG* 1.3 75.6 - - - +
242B SER* 1.3 58.1 + - - +
244B PHE* 3.7 0.9 - - - +
245B ILE* 2.9 45.6 + - + +
412B MPG 3.9 26.7 - - + -
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Residues in contact with SER 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PHE* 3.2 11.9 - - - -
185B SER* 2.7 35.0 + - - -
210B HIS* 4.0 6.6 - - - -
238B LEU 2.8 18.3 + - - -
239B ASP* 4.3 0.4 - - - -
240B ARG 3.3 0.2 - - - -
241B TYR* 1.3 76.7 - - - +
243B ASP* 1.3 56.7 + - - +
245B ILE* 3.3 3.7 + - - +
246B ILE* 2.9 38.3 + - - +
301B ARG* 3.3 22.7 - - - -
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Residues in contact with ASP 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ASP 2.9 16.3 + - - +
240B ARG* 3.3 18.0 + - - +
242B SER* 1.3 74.5 - - - +
244B PHE* 1.3 62.1 + - - +
246B ILE* 4.0 5.0 - - - +
247B VAL* 3.3 29.6 + - - +
269B ALA* 6.0 0.2 - - - -
272B SER* 4.2 19.9 - - - +
273B LEU* 4.6 3.6 - - + -
301B ARG* 2.8 34.4 + - - +
304B ARG* 2.9 32.5 + - - -
305B LEU* 4.2 9.4 - - - +
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Residues in contact with PHE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PHE* 3.3 37.5 - + - -
267A LEU* 4.4 9.2 - - + -
270A PHE* 3.3 60.8 - + + -
240B ARG 3.1 17.1 + - - +
241B TYR 3.7 0.9 - - - +
243B ASP* 1.3 75.1 - - - +
245B ILE* 1.3 73.2 + - + +
247B VAL* 3.3 5.1 + - - +
248B PHE* 2.8 62.5 + + - +
269B ALA* 4.3 17.0 - - + +
273B LEU* 4.5 11.1 - - + +
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Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PHE* 4.4 6.1 - - + -
185B SER 5.8 0.2 - - - -
186B LEU* 3.7 30.7 - - + -
189B SER* 3.5 22.0 - - - +
241B TYR* 2.9 33.3 + - + +
242B SER* 4.0 3.1 - - - +
244B PHE* 1.3 86.0 - - + +
246B ILE* 1.3 65.5 + - - +
248B PHE* 3.6 8.9 - - + +
249B SER* 3.0 29.0 + - - +
411B MPG 4.1 14.1 - - + -
412B MPG 4.2 24.9 - - + -
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Residues in contact with ILE 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B SER* 4.3 13.2 - - - +
189B SER* 3.3 17.7 - - - +
192B PHE* 4.2 13.4 - - + -
207B ILE* 3.8 23.8 - - + -
210B HIS* 4.8 2.7 - - + -
242B SER* 2.9 29.5 + - - +
243B ASP* 4.0 5.6 - - - +
245B ILE* 1.3 77.8 - - - +
247B VAL* 1.3 61.8 + - - +
249B SER* 3.3 2.6 + - - -
250B ILE* 3.2 34.1 + - + +
305B LEU* 4.2 22.9 - - + -
308B ILE* 3.9 27.4 - - + -
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PHE* 4.9 1.1 - - + -
243B ASP 3.3 17.4 + - - +
244B PHE 3.3 4.1 + - - +
246B ILE* 1.3 76.5 - - + +
248B PHE* 1.3 59.6 + - - +
250B ILE* 3.3 2.1 + - + +
251B THR* 2.7 45.0 + - - +
265B GLY 3.4 26.0 - - - +
268B ALA* 4.2 4.3 - - + -
269B ALA* 3.9 22.7 - - + +
272B SER* 4.6 10.3 - - - +
308B ILE* 5.3 8.3 - - + -
321B LEU* 3.9 25.6 - - + -
324B ILE* 5.5 3.4 - - + -
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Residues in contact with PHE 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ILE* 3.9 27.8 - - + -
266A PHE* 4.0 27.3 - + + -
267A LEU* 4.1 19.3 - - + -
244B PHE* 2.8 51.1 + + + +
245B ILE* 3.6 10.8 - - + +
246B ILE 3.3 0.2 - - - -
247B VAL* 1.3 73.5 - - - +
249B SER* 1.3 56.4 + - - +
251B THR* 3.6 2.8 - - - -
252B TYR* 2.8 33.8 + + + +
262B TRP* 3.9 30.5 - + - -
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Residues in contact with SER 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B SER* 3.4 37.5 + - - -
192B PHE* 4.2 7.9 - - - -
193B LEU* 4.1 13.8 - - - +
245B ILE* 3.0 18.7 + - - +
246B ILE 3.6 4.7 - - - -
248B PHE* 1.3 74.2 - - - +
250B ILE* 1.3 65.7 + - - +
252B TYR* 3.4 3.4 + - - +
253B VAL* 3.2 27.7 + - - +
411B MPG 3.8 13.0 - - - +
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Residues in contact with ILE 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PHE* 3.8 46.7 - - + -
246B ILE* 3.2 25.8 + - + +
247B VAL* 3.8 3.4 - - - +
249B SER* 1.3 76.0 - - - +
251B THR* 1.3 63.4 + - - +
253B VAL* 3.4 4.4 + - - +
254B LEU* 3.1 43.1 + - + +
308B ILE* 4.3 14.4 - - + -
317B PRO* 3.8 24.5 - - + +
320B ALA* 5.6 1.1 - - + -
321B LEU* 3.9 24.5 - - + -
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Residues in contact with THR 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PHE* 4.2 3.8 - - + -
247B VAL* 2.7 26.3 + - - +
248B PHE* 3.6 6.1 - - - -
250B ILE* 1.3 77.6 - - - +
252B TYR* 1.3 56.2 + - - +
254B LEU* 3.3 4.0 + - - +
255B SER* 2.9 28.8 + - - -
261B TYR* 3.4 23.9 - - - +
262B TRP* 3.5 33.9 - - + -
265B GLY* 3.2 24.5 - - - -
321B LEU* 3.6 12.2 - - - +
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Residues in contact with TYR 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ILE* 4.1 24.3 - - + +
193B LEU* 3.9 18.6 - - + -
248B PHE* 2.8 28.1 + + + +
249B SER* 3.7 6.3 - - - +
250B ILE 3.3 0.2 - - - -
251B THR* 1.3 74.0 - - - +
253B VAL* 1.3 63.5 + - + +
255B SER* 2.8 22.6 + - - -
256B ALA* 3.9 3.3 + - - +
262B TRP* 4.0 26.4 - + + -
415B MPG 3.7 28.4 - - + +
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Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PHE* 3.4 24.0 - - + +
193B LEU* 3.7 24.0 - - + +
195B ASN* 3.5 35.5 + - + +
249B SER 3.2 13.9 + - - +
250B ILE* 3.8 8.3 - - - +
252B TYR* 1.3 79.2 - - + +
254B LEU* 1.3 69.5 + - + +
255B SER 3.3 0.7 + - - -
256B ALA* 3.3 20.1 + - - +
257B SER* 4.3 1.6 + - - -
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Residues in contact with LEU 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ILE* 3.1 35.6 + - + +
251B THR 3.8 3.4 - - - +
253B VAL* 1.3 81.7 - - + +
255B SER* 1.3 58.1 + - - +
257B SER* 3.0 26.3 + - - +
258B ASN 3.1 12.4 + - - +
261B TYR* 3.9 28.3 - - + -
317B PRO* 5.1 7.6 - - + -
318B SER* 3.5 45.1 - - - +
321B LEU* 3.9 12.1 - - + -
----------------------------------------------------------
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Residues in contact with SER 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B THR 2.9 15.4 + - - -
252B TYR* 2.8 21.8 + - - -
254B LEU* 1.3 76.0 - - - +
256B ALA* 1.3 62.2 + - - +
257B SER 3.3 0.2 + - - -
258B ASN 3.4 22.9 + - - -
259B PRO* 3.6 9.2 - - - +
261B TYR* 4.5 1.8 - - - +
262B TRP* 3.1 46.3 + - - -
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Residues in contact with ALA 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B TYR 4.8 2.7 - - - +
253B VAL 3.3 13.8 + - - +
254B LEU 3.1 0.4 - - - -
255B SER* 1.3 82.0 + - - +
257B SER* 1.3 60.4 + - - +
259B PRO* 5.8 0.5 - - - +
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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