Contacts of the helix formed by residues 235 - 264 (chain F) in PDB entry 4DEM
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 GLY 235 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F ILE 3.6 2.4 - - - -
234F ASP* 1.3 81.6 + - - +
236F GLU* 1.3 67.1 + - - -
237F LYS 3.3 2.5 - - - -
238F GLU* 3.3 23.6 + - - +
239F HIS* 3.0 26.6 + - - -
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Residues in contact with GLU 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234F ASP 3.6 3.5 + - - +
235F GLY* 1.3 73.0 - - - +
237F LYS* 1.3 59.9 + - - +
239F HIS* 3.3 6.5 + - - +
240F ALA* 2.9 30.1 + - - +
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Residues in contact with LYS 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235F GLY 3.3 0.6 - - - -
236F GLU* 1.3 80.2 - - - +
238F GLU* 1.3 62.8 + - - +
240F ALA* 3.4 7.1 + - + +
241F ASN* 3.0 46.0 + - - +
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Residues in contact with GLU 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228F MET* 3.7 7.7 - - + +
233F ILE* 3.9 27.5 - - + +
235F GLY* 3.3 28.3 + - - +
237F LYS* 1.3 80.5 + - - +
239F HIS* 1.3 62.7 + - - +
241F ASN* 3.5 7.3 + - - +
242F ALA* 3.0 24.9 + - - +
349F PRO* 4.7 24.0 - - + +
350F LEU* 5.4 5.9 - - + +
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Residues in contact with HIS 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221F TYR* 2.7 31.2 + - - +
225F ALA* 3.7 21.4 - - + +
228F MET* 3.8 19.7 - - + +
229F TYR* 3.4 37.0 + + - +
233F ILE 2.8 26.9 + - - -
234F ASP 3.8 10.1 - - - -
235F GLY 3.0 27.7 + - - +
236F GLU* 3.8 4.9 - - - +
238F GLU* 1.3 77.8 - - + +
240F ALA* 1.3 61.3 + - - +
242F ALA* 3.5 3.1 + - - +
243F LYS* 2.9 26.5 + - - +
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Residues in contact with ALA 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236F GLU 2.9 16.9 + - - +
237F LYS* 3.8 7.6 - - + +
239F HIS* 1.3 78.1 - - - +
241F ASN* 1.3 65.4 + - - +
243F LYS* 3.3 11.3 + - - +
244F LYS* 3.2 36.1 + - - +
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Residues in contact with ASN 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F LYS* 3.0 35.9 + - - +
238F GLU* 3.9 6.3 - - - +
239F HIS 3.4 0.2 - - - -
240F ALA* 1.3 74.8 - - - +
242F ALA* 1.3 67.2 + - - +
244F LYS* 3.3 21.5 + - - +
245F ILE* 3.5 4.7 + - - +
346F TYR* 3.4 55.4 + - + +
348F ALA 4.5 12.4 + - - +
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Residues in contact with ALA 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221F TYR* 5.0 2.9 - - + -
224F ILE* 4.9 0.2 - - + -
228F MET* 3.9 23.6 - - + -
238F GLU 3.0 17.9 + - - +
239F HIS* 3.7 4.0 - - - +
241F ASN* 1.3 74.9 - - - +
243F LYS* 1.3 64.9 + - - +
245F ILE* 3.1 5.9 + - - +
246F LEU* 2.9 40.2 + - + +
346F TYR 4.9 0.8 + - - -
350F LEU* 4.9 2.2 - - + -
355F PHE* 4.2 22.0 - - + -
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Residues in contact with LYS 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180F GLN* 5.2 4.2 - - - +
217F PHE* 4.3 15.7 - - + -
221F TYR* 3.7 49.7 + - + -
239F HIS 2.9 17.5 + - - +
240F ALA* 3.5 10.3 - - - +
242F ALA* 1.3 77.4 - - - +
244F LYS* 1.3 55.8 + - - +
246F LEU* 4.4 2.2 - - - +
247F LEU* 2.8 63.5 + - + +
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Residues in contact with LYS 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240F ALA* 3.2 27.9 + - - +
241F ASN* 3.3 12.3 + - - +
243F LYS* 1.3 74.8 - - - +
245F ILE* 1.3 61.6 + - - +
247F LEU* 4.8 1.5 - - - +
248F GLU* 3.5 23.0 + - - +
342F LEU* 4.0 6.9 - - + +
346F TYR* 3.7 48.7 + - + +
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Residues in contact with ILE 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F ASN 3.5 4.2 + - - +
242F ALA 3.1 5.4 + - - +
244F LYS* 1.3 77.1 - - - +
246F LEU* 1.3 64.9 + - - +
248F GLU* 3.2 6.1 + - - +
249F MET* 3.0 41.2 + - + +
339F ILE* 4.9 6.1 - - + +
342F LEU* 3.7 31.5 - - + +
343F ILE* 4.0 15.0 - - + -
346F TYR* 3.7 26.2 - - + +
347F ALA* 3.8 14.6 - - - +
355F PHE* 3.7 42.4 - - + -
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Residues in contact with LEU 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216F ALA 4.7 0.2 - - - +
220F PHE* 3.4 33.3 - - + +
221F TYR* 3.9 18.6 - - + +
224F ILE* 3.6 34.3 - - + -
242F ALA* 2.9 31.9 + - + +
243F LYS* 4.1 3.1 - - - +
245F ILE* 1.3 79.5 - - - +
247F LEU* 1.3 57.6 + - - +
249F MET* 3.2 13.9 + - - +
250F GLY* 2.9 23.9 + - - -
355F PHE* 4.0 13.5 - - + -
358F LEU* 3.6 31.6 - - + -
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Residues in contact with LEU 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212F LYS* 4.3 20.4 - - + +
216F ALA* 3.7 38.5 - - + +
217F PHE* 3.9 38.1 - - + +
221F TYR* 4.4 5.2 - - + -
243F LYS* 2.8 41.4 + - + +
244F LYS* 4.9 1.8 - - - +
246F LEU* 1.3 75.9 - - - +
248F GLU* 1.3 65.0 + - + +
250F GLY 3.2 0.7 + - - -
251F GLU* 3.0 22.0 + - - +
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Residues in contact with GLU 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208F LYS* 5.7 3.0 - - - -
244F LYS 3.5 9.1 + - - +
245F ILE 3.2 8.8 + - - +
247F LEU* 1.3 77.4 - - + +
249F MET* 1.3 64.8 + - - +
251F GLU* 3.3 25.0 + - - +
252F PHE* 3.2 16.6 + - - +
335F SER* 5.3 0.3 + - - -
338F HIS* 3.0 25.8 + - + -
339F ILE* 3.9 14.3 - - + +
342F LEU* 3.5 28.5 - - + -
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Residues in contact with MET 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220F PHE* 4.0 14.8 - - + -
245F ILE* 3.0 28.0 + - + +
246F LEU* 3.5 30.7 - - - +
248F GLU* 1.3 75.8 - - - +
250F GLY* 1.3 58.8 + - - +
252F PHE* 3.2 4.3 + - - +
253F PHE* 2.9 27.9 + - - +
339F ILE* 3.5 40.4 - - + -
343F ILE* 3.9 7.0 - - + -
355F PHE* 3.5 27.1 - - + +
358F LEU* 4.1 15.0 - - - -
359F ALA* 4.1 10.8 - - + +
362F ILE* 3.9 10.7 - - + +
363F TYR* 5.5 0.2 - - + -
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Residues in contact with GLY 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211F VAL 5.2 0.8 - - - +
215F THR* 4.1 5.1 - - - +
216F ALA* 3.7 17.5 - - - -
220F PHE* 3.4 25.8 - - - -
246F LEU 2.9 11.1 + - - -
247F LEU 3.2 4.2 + - - -
248F GLU 3.2 0.4 - - - -
249F MET* 1.3 75.8 - - - +
251F GLU* 1.3 64.0 + - - +
253F PHE* 3.3 1.4 + - - +
254F GLN* 3.0 24.3 + - - +
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Residues in contact with GLU 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F TYR* 5.1 1.6 - - + -
208F LYS* 3.4 55.4 + - - +
211F VAL* 4.0 23.1 - - + +
212F LYS* 5.9 1.6 - - - +
216F ALA* 4.2 2.1 - - + +
247F LEU 3.0 12.9 + - - +
248F GLU* 3.6 27.8 - - - +
249F MET 3.3 0.2 - - - -
250F GLY* 1.3 76.3 - - - +
252F PHE* 1.3 62.5 + - - +
254F GLN* 3.2 4.0 + - - +
255F ILE* 3.0 39.0 + - + +
331F TYR* 3.6 14.7 + - - +
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Residues in contact with PHE 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F GLU 3.2 9.8 + - - +
249F MET 3.2 7.8 + - - +
251F GLU* 1.3 75.8 - - - +
253F PHE* 1.3 68.4 + - - +
255F ILE* 3.1 8.2 + - + +
256F GLN* 2.9 49.3 + - + +
328F PHE* 4.2 13.9 - + - -
331F TYR* 4.0 15.4 + + - +
332F GLU* 3.6 48.0 - - + -
335F SER* 3.4 18.2 - - - +
362F ILE* 3.9 19.7 - - + -
363F TYR* 3.4 39.3 - + - +
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Residues in contact with PHE 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F ASN* 5.7 7.4 - - + -
74F ARG* 3.8 30.1 - - - -
215F THR* 3.7 23.1 - - + -
219F SER* 5.7 0.2 - - - -
220F PHE* 3.5 36.1 - + + -
249F MET 2.9 10.0 + - - +
250F GLY 3.6 2.0 - - - +
252F PHE* 1.3 85.1 - - - +
254F GLN* 1.3 59.2 + - - +
256F GLN* 3.4 21.0 + - - +
257F ASP* 2.8 36.5 + - + +
362F ILE* 4.3 17.0 - - + -
367F LYS 5.5 5.4 - - - -
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Residues in contact with GLN 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F TYR* 3.5 3.6 - - - +
211F VAL* 3.4 39.0 - - + -
214F LYS* 3.8 12.7 - - - +
215F THR* 2.7 32.8 + - - +
250F GLY 3.0 16.0 + - - +
251F GLU 3.2 1.5 + - - +
253F PHE* 1.3 75.9 - - - +
255F ILE* 1.3 60.4 + - - +
257F ASP* 3.0 25.7 + - - +
258F ASP* 2.8 52.3 + - - +
401F YS4 3.8 16.3 + - - -
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Residues in contact with ILE 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F TYR* 3.4 23.3 - - + +
251F GLU* 3.0 30.4 + - + +
252F PHE* 3.1 6.0 + - + +
254F GLN* 1.3 76.5 - - - +
256F GLN* 1.3 63.3 + - - +
258F ASP* 3.2 3.8 + - - +
259F TYR* 2.9 21.3 + - - +
283F TRP* 3.5 46.5 - - + +
328F PHE* 3.9 17.3 - - + -
331F TYR* 3.0 45.3 - - + +
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Residues in contact with GLN 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F PHE* 2.9 34.0 + - + +
253F PHE* 3.4 28.8 + - - +
255F ILE* 1.3 78.6 - - - +
257F ASP* 1.3 62.3 + - - +
259F TYR* 3.2 1.7 + - - +
260F LEU* 2.9 39.1 + - + +
328F PHE* 3.9 19.8 - - + -
332F GLU* 4.2 3.5 - - - +
362F ILE* 3.3 12.2 + - - +
365F ARG* 3.0 49.0 + - - +
367F LYS 4.3 5.7 + - - -
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Residues in contact with ASP 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253F PHE* 2.8 28.9 + - + +
254F GLN* 3.0 31.7 + - - +
256F GLN* 1.3 75.9 - - - +
258F ASP* 1.3 56.4 + - - +
260F LEU* 3.4 9.7 + - - +
261F ASP* 3.0 26.3 + - - +
271F LYS* 2.8 28.5 + - - -
401F YS4 3.2 6.0 + - - -
404F MG 2.2 29.3 - - - -
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Residues in contact with ASP 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F TYR* 2.6 27.9 + - - -
214F LYS* 4.9 2.6 + - - -
254F GLN* 2.8 36.9 + - - +
255F ILE 3.2 6.7 + - - +
257F ASP* 1.3 74.5 - - - +
259F TYR* 1.3 68.9 + - - +
261F ASP* 3.3 15.4 + - - +
275F ASP* 4.0 13.4 - - - +
281F CYS 4.5 0.2 - - - +
282F SER* 3.3 25.9 + - - +
283F TRP* 3.0 19.9 + - + +
284F LEU* 3.6 14.0 - - - +
401F YS4 4.5 1.9 + - - -
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Residues in contact with TYR 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255F ILE 2.9 13.4 + - - +
256F GLN 3.5 6.3 - - - +
258F ASP* 1.3 80.0 - - - +
260F LEU* 1.3 78.4 + - + +
262F LEU* 3.3 1.4 + - - +
263F PHE* 2.9 72.4 + + + +
283F TRP* 5.4 1.5 - - + -
284F LEU* 4.0 18.1 - - + +
325F PRO* 3.9 32.6 + - + +
328F PHE* 3.6 51.6 - + + -
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Residues in contact with LEU 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F GLN* 2.9 44.0 + - + +
257F ASP* 3.8 8.3 - - - +
259F TYR* 1.3 91.0 - - + +
261F ASP* 1.3 65.4 + - - +
264F GLY* 2.9 40.2 + - - +
269F THR* 4.3 14.2 + - + +
271F LYS* 6.5 0.4 - - - -
365F ARG 4.4 2.7 - - - +
366F ARG* 3.7 39.7 - - + +
367F LYS* 4.1 13.5 - - - +
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Residues in contact with ASP 261 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257F ASP* 3.0 14.2 + - - +
258F ASP 3.3 13.2 - - - +
259F TYR 3.3 0.2 - - - -
260F LEU* 1.3 76.6 - - - +
262F LEU* 1.3 60.9 + - + +
271F LYS* 5.5 8.3 - - - +
272F ILE 4.7 0.5 - - - +
273F GLY* 3.2 42.8 + - - +
274F THR* 3.2 6.8 + - - -
275F ASP* 2.9 53.9 + - + +
276F ILE* 4.7 0.3 + - - +
401F YS4 4.7 2.1 + - - -
404F MG 4.0 8.8 - - - -
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Residues in contact with LEU 262 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258F ASP 4.8 0.2 - - - +
259F TYR 3.3 1.8 + - - -
260F LEU 3.1 0.2 - - - -
261F ASP* 1.3 83.7 - - + +
263F PHE* 1.3 76.4 + - + +
264F GLY 3.5 4.7 - - - +
276F ILE* 3.7 26.7 - - + -
284F LEU* 3.9 14.1 - - + -
312F VAL* 5.0 7.0 - - + -
316F LYS* 3.6 45.5 + - + -
319F TYR* 3.4 38.1 - - + -
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Residues in contact with PHE 263 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259F TYR* 2.9 57.7 + + + +
260F LEU* 4.5 0.4 - - - -
262F LEU* 1.3 93.6 - - + +
264F GLY* 1.3 65.3 + - - +
265F ASP 3.8 0.7 + - - -
284F LEU* 4.1 20.6 - - + -
316F LYS* 3.8 19.3 - - + +
319F TYR* 4.2 14.6 - + + -
320F GLU* 3.7 35.0 - - + -
325F PRO* 4.0 24.9 - - + -
----------------------------------------------------------
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Residues in contact with GLY 264 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260F LEU* 2.9 46.1 + - - +
262F LEU 3.5 4.0 - - - +
263F PHE* 1.3 82.0 - - - +
265F ASP* 1.3 64.6 + - - -
266F PRO* 3.4 9.4 - - - +
269F THR* 4.0 5.8 + - - -
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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