Contacts of the helix formed by residues 235 - 262 (chain F) in PDB entry 2AJQ
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 235 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234F PHE* 1.3 72.5 - - - +
236F THR* 1.3 63.3 + - - +
237F LYS* 3.6 9.5 + - - +
238F ALA* 3.3 27.9 + - + +
239F ILE* 3.2 22.5 + - - +
453F ALA 6.0 0.2 - - - -
454F ALA* 2.8 18.8 + - - +
459F HIS* 3.1 41.0 - - + +
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Residues in contact with THR 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234F PHE* 3.2 14.9 + - - -
235F ASP* 1.3 69.4 + - - +
237F LYS* 1.3 56.0 + - - +
239F ILE* 3.1 2.6 + - - +
240F GLU* 2.7 53.3 + - - +
407F LEU* 3.8 18.1 - - + +
410F VAL* 3.6 29.4 - - + +
414F GLY* 5.6 1.2 - - - -
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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 ASP* 3.5 7.3 + - - +
236F THR* 1.3 77.7 - - - +
238F ALA* 1.3 61.3 + - - +
240F GLU* 3.3 9.3 + - - +
241F GLU* 2.5 67.8 + - + +
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Residues in contact with ALA 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235F ASP* 3.3 33.2 + - + +
236F THR 3.2 0.6 - - - -
237F LYS* 1.3 80.2 - - - +
239F ILE* 1.3 62.0 - - + +
241F GLU* 3.2 9.3 + - - +
242F LEU* 2.9 28.6 + - - +
450F GLN* 5.5 3.5 + - - +
454F ALA* 5.0 7.9 - - + -
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Residues in contact with ILE 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234F PHE* 3.3 35.9 - - + -
235F ASP 3.2 2.1 + - - +
236F THR 3.1 5.4 + - - +
238F ALA* 1.3 78.4 - - + +
240F GLU* 1.3 63.5 + - - +
242F LEU* 3.7 19.0 - - + +
243F TYR* 3.0 23.0 + - - +
399F SER* 4.0 24.1 + - - +
400F ALA* 5.6 0.4 - - + -
406F TRP* 4.1 17.5 - - + -
407F LEU* 3.9 24.5 - - + -
450F GLN 4.6 2.7 - - - +
451F CYS* 4.6 7.0 - - - -
454F ALA* 3.5 23.8 - - + -
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Residues in contact with GLU 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLY* 4.8 12.0 - - - +
112A SER* 4.4 17.5 + - - +
236F THR* 2.7 34.9 + - - +
237F LYS* 3.6 9.5 - - - +
239F ILE* 1.3 77.4 - - - +
241F GLU* 1.3 62.3 + - + +
243F TYR* 3.4 11.6 + - + +
244F VAL* 3.3 26.3 + - + +
407F LEU* 4.6 16.0 - - + +
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Residues in contact with GLU 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F LYS* 2.5 67.4 + - + +
238F ALA* 3.6 7.4 - - - +
240F GLU* 1.3 76.5 - - + +
242F LEU* 1.3 64.3 + - - +
244F VAL* 3.2 11.2 + - - +
245F GLU* 3.2 18.9 + - - +
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Residues in contact with LEU 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238F ALA 2.9 17.0 + - - +
239F ILE* 3.7 22.9 - - + +
241F GLU* 1.3 76.2 - - - +
243F TYR* 1.3 57.4 + - - +
245F GLU* 3.0 11.5 + - - +
246F LEU* 2.8 48.5 + - + +
395F ARG* 5.9 0.7 - - + -
399F SER* 5.0 7.6 - - - +
447F TYR* 3.8 29.2 - - + -
450F GLN* 3.3 38.1 - - + +
451F CYS* 4.3 20.6 - - - -
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Residues in contact with TYR 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER* 4.9 28.9 + - - -
239F ILE 3.0 17.4 + - - +
240F GLU* 3.5 11.7 - - + +
241F GLU 3.2 0.2 - - - -
242F LEU* 1.3 77.6 - - - +
244F VAL* 1.3 59.2 + - + +
246F LEU* 4.5 6.7 - - - +
247F ALA* 2.8 42.7 + - + +
250F ARG* 4.1 2.7 + - - -
396F ILE* 3.8 25.8 - - + -
399F SER* 5.3 3.6 + - - +
400F ALA* 4.0 26.9 - - + -
401F GLU* 2.5 36.3 + - + +
407F LEU* 4.9 6.3 - - + -
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Residues in contact with VAL 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ARG* 3.8 52.0 - - + +
112A SER* 4.5 8.3 - - - +
240F GLU* 3.3 17.2 + - + +
241F GLU* 3.2 10.5 + - - +
242F LEU 3.2 0.4 - - - -
243F TYR* 1.3 78.9 - - + +
245F GLU* 1.3 64.8 + - - +
247F ALA* 3.9 4.8 - - - +
248F ALA* 3.1 25.7 + - + +
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Residues in contact with GLU 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F GLU 3.2 8.9 + - - +
242F LEU* 3.0 13.8 + - - +
244F VAL* 1.3 80.3 - - - +
246F LEU* 1.3 64.3 + - - +
248F ALA* 3.3 7.2 + - + +
249F ARG* 3.0 26.3 + - - +
447F TYR* 3.5 34.1 + - - -
450F GLN* 4.3 11.3 + - - +
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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
----------------------------------------------------------
242F LEU* 2.8 50.1 + - + +
243F TYR* 4.0 4.7 - - - +
245F GLU* 1.3 74.1 - - - +
247F ALA* 1.3 51.4 + - - +
249F ARG* 3.1 7.2 + - + +
250F ARG* 2.7 34.5 + - - +
392F ILE* 3.6 17.9 - - + +
395F ARG* 4.1 23.8 - - + -
396F ILE* 3.8 25.8 - - + +
399F SER* 4.8 2.7 - - - +
447F TYR* 3.5 47.8 - - + +
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Residues in contact with ALA 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER 5.7 4.5 - - - +
243F TYR* 2.8 41.0 + - + +
244F VAL* 3.9 5.4 - - - +
246F LEU* 1.3 73.7 - - - +
248F ALA* 1.3 57.8 + - - +
250F ARG* 3.2 20.6 + - - +
251F SER* 2.9 29.6 + - - -
396F ILE* 4.0 5.2 - - - +
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Residues in contact with ALA 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F VAL* 3.1 19.9 + - + +
245F GLU* 3.7 6.1 - - - +
246F LEU 3.3 0.2 - - - -
247F ALA* 1.3 77.3 - - - +
249F ARG* 1.3 58.2 + - - +
251F SER* 3.5 7.3 + - - -
252F GLU* 3.1 27.7 + - - +
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Residues in contact with ARG 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245F GLU* 3.0 18.8 + - + +
246F LEU* 3.5 10.5 - - - +
248F ALA* 1.3 74.3 - - - +
250F ARG* 1.3 67.4 + - - +
252F GLU* 3.3 20.0 + - - +
253F LEU* 2.9 46.7 + - + +
256F LYS* 5.0 6.3 - - - +
385F LEU* 4.8 6.1 - - - +
388F GLU* 2.7 42.2 + - - +
392F ILE* 4.3 16.2 - - + -
447F TYR* 5.1 4.5 - - - +
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Residues in contact with ARG 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243F TYR* 4.1 7.7 + - - -
246F LEU 2.7 14.0 + - - +
247F ALA* 3.2 16.6 + - - +
249F ARG* 1.3 77.2 - - - +
251F SER* 1.3 57.1 + - - +
253F LEU* 3.3 7.4 + - - +
254F LEU* 2.9 30.6 + - + +
389F TYR* 3.7 23.9 - - + +
392F ILE* 4.2 14.5 - - + +
393F GLN* 3.2 35.4 + - - +
396F ILE* 3.8 17.9 - - + +
401F GLU* 2.8 43.2 + - - -
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Residues in contact with SER 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247F ALA 2.9 17.0 + - - -
248F ALA* 3.7 8.1 - - - -
249F ARG 3.2 0.2 - - - -
250F ARG* 1.3 74.7 - - - +
252F GLU* 1.3 65.4 + - - +
254F LEU* 3.4 8.6 + - - +
255F ARG* 3.1 22.7 + - - +
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Residues in contact with GLU 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F ALA 3.1 17.9 + - - +
249F ARG* 3.8 18.6 - - - +
251F SER* 1.3 77.5 + - - +
253F LEU* 1.3 63.3 + - - +
255F ARG* 2.5 47.4 + - - +
256F LYS* 3.2 45.3 + - - +
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Residues in contact with LEU 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249F ARG* 2.9 41.1 + - - +
250F ARG* 3.7 3.8 - - - +
252F GLU* 1.3 75.2 - - - +
254F LEU* 1.3 66.1 - - - +
256F LYS* 3.4 6.0 + - + +
257F LEU* 3.0 30.5 + - + +
385F LEU* 3.8 44.6 - - + +
388F GLU* 3.7 33.0 - - + +
389F TYR* 3.8 31.4 - - + +
392F ILE* 4.4 6.5 - - + -
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Residues in contact with LEU 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250F ARG* 2.9 19.7 + - + +
251F SER* 3.7 8.3 - - - +
253F LEU* 1.3 76.1 - - - +
255F ARG* 1.3 66.0 + - - +
257F LEU* 3.7 3.0 - - - -
258F THR* 2.9 44.5 + - + +
334F PHE 4.2 5.2 - - - +
335F ASN* 5.3 0.4 - - - -
336F PRO* 3.8 28.3 - - + -
389F TYR* 4.4 17.2 - - + +
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Residues in contact with ARG 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251F SER 3.1 11.3 + - - +
252F GLU* 2.5 40.8 + - - +
254F LEU* 1.3 78.8 - - - +
256F LYS* 1.3 90.9 + - - +
258F THR* 2.7 22.4 + - - +
259F GLU* 3.2 14.2 + - + +
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Residues in contact with LYS 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249F ARG* 5.0 6.8 - - - +
252F GLU* 3.2 48.2 + - - +
253F LEU* 4.0 8.3 - - + +
255F ARG* 1.3 97.8 - - - +
257F LEU* 1.3 62.8 + - - +
259F GLU* 3.3 9.8 + - - +
260F THR* 3.2 25.8 + - - -
385F LEU* 4.6 22.7 - - + -
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Residues in contact with LEU 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253F LEU* 3.0 21.4 + - + +
254F LEU 3.9 2.2 - - - +
256F LYS* 1.3 73.2 - - - +
258F THR* 1.3 61.8 + - - +
260F THR* 3.2 4.1 + - - +
261F PHE* 2.9 41.0 + - + +
334F PHE* 4.0 14.1 - - + -
336F PRO* 3.6 31.9 - - + -
382F ALA* 3.9 36.6 - - + +
385F LEU* 4.0 34.5 - - + +
386F ILE* 4.0 13.2 - - + -
389F TYR* 4.5 4.3 - - + -
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Residues in contact with THR 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254F LEU* 2.9 40.1 + - + +
255F ARG* 2.7 24.0 + - - +
257F LEU* 1.3 75.2 - - + +
259F GLU* 1.3 59.3 + - - +
262F GLY* 2.7 35.9 + - - +
333F VAL* 5.5 6.3 - - + -
334F PHE* 4.2 20.9 - - + +
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Residues in contact with GLU 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255F ARG* 3.2 13.9 + - + +
256F LYS* 3.6 12.6 - - - +
257F LEU 3.2 0.2 - - - -
258F THR* 1.3 83.5 + - - +
260F THR* 1.3 64.1 + - - +
262F GLY* 4.5 1.6 + - - -
378F GLU* 4.7 6.4 - - - +
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Residues in contact with THR 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F LYS 3.2 15.1 + - - -
257F LEU* 3.2 9.7 + - - +
259F GLU* 1.3 83.2 - - - +
261F PHE* 1.3 71.4 + - + +
378F GLU* 3.2 36.3 + - + +
379F LYS* 4.3 24.0 - - + -
382F ALA* 4.1 25.3 - - + +
385F LEU* 5.9 1.7 - - - +
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Residues in contact with PHE 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257F LEU* 2.9 20.1 + - + +
260F THR* 1.3 80.7 - - + +
262F GLY* 1.3 67.0 + - - +
263F SER 3.6 2.4 + - - +
264F TRP* 4.1 9.9 - - - -
334F PHE* 3.5 48.7 - + + -
345F LYS* 3.6 42.2 + - + +
346F LEU* 4.6 13.7 - - + -
348F GLU* 5.9 0.2 - - - -
349F ALA* 6.0 0.2 - - + -
379F LYS* 3.8 35.4 - - + -
382F ALA* 4.0 28.0 - - + -
386F ILE* 4.0 9.9 - - + -
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Residues in contact with GLY 262 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258F THR* 2.7 31.0 + - - +
259F GLU 4.4 1.5 + - - -
260F THR 3.7 1.0 - - - -
261F PHE* 1.3 77.9 - - - +
263F SER* 1.3 59.8 + - - -
264F TRP* 3.6 1.9 - - - -
333F VAL* 4.9 0.7 - - - -
334F PHE* 3.1 26.7 + - - +
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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