Contacts of the helix formed by residues 221 - 250 (chain F) in PDB entry 4NFI
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 221 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219F ILE* 3.7 2.6 - - - +
220F ASP* 1.3 80.9 + - - +
222F GLU* 1.3 67.3 + - - -
223F LYS 3.2 2.7 - - - -
224F GLU* 3.2 21.2 + - - +
225F HIS* 3.0 26.1 + - - -
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Residues in contact with GLU 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220F ASP 3.5 3.4 + - - -
221F GLY* 1.3 70.9 - - - +
223F LYS* 1.3 57.8 + - - +
225F HIS* 3.3 5.8 + - - +
226F ALA* 2.9 30.9 + - + +
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Residues in contact with LYS 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221F GLY 3.2 1.0 - - - -
222F GLU* 1.3 80.2 - - - +
224F GLU* 1.3 65.3 + - - +
226F ALA* 3.2 6.7 + - + +
227F ASN* 2.9 45.3 + - - +
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Residues in contact with GLU 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214F MET* 3.6 7.4 - - + +
219F ILE* 3.9 29.4 - - + -
221F GLY* 3.2 26.4 + - - +
223F LYS* 1.3 82.2 + - - +
225F HIS* 1.3 63.0 + - - +
227F ASN* 3.6 7.2 + - - +
228F ALA* 3.1 23.6 + - - +
335F PRO* 4.5 28.3 - - + +
336F LEU* 5.3 4.5 - - + +
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Residues in contact with HIS 225 (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 34.1 + - + +
211F ALA* 3.8 20.3 - - + +
214F MET* 3.7 17.4 - - + +
215F TYR* 3.5 37.0 + + - -
219F ILE 2.8 28.1 + - - -
220F ASP 3.9 8.5 - - - -
221F GLY 3.0 29.2 + - - +
222F GLU* 3.8 5.2 - - - +
224F GLU* 1.3 74.1 - - + +
226F ALA* 1.3 63.8 + - - +
228F ALA* 3.3 3.1 + - - +
229F LYS* 3.0 28.8 + - - +
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Residues in contact with ALA 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222F GLU* 2.9 21.0 + - + +
223F LYS* 3.7 7.0 - - + +
225F HIS* 1.3 72.0 - - - +
227F ASN* 1.3 67.2 + - - +
229F LYS* 3.3 13.5 + - - +
230F LYS* 3.1 33.5 + - - +
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Residues in contact with ASN 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223F LYS* 2.9 34.7 + - - +
224F GLU* 3.9 6.9 - - - +
226F ALA* 1.3 79.4 - - - +
228F ALA* 1.3 62.2 + - - +
230F LYS* 3.1 20.4 + - - +
231F ILE* 3.5 4.3 + - - +
332F TYR* 3.4 54.7 + - + +
334F ALA 4.6 11.6 + - - +
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Residues in contact with ALA 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F TYR* 4.9 3.4 - - + -
210F ILE* 4.8 0.2 - - + -
214F MET* 4.0 22.4 - - + -
224F GLU 3.1 18.2 + - - +
225F HIS* 3.3 4.5 + - - +
227F ASN* 1.3 75.7 - - - +
229F LYS* 1.3 59.2 + - - +
231F ILE* 3.1 5.6 + - - +
232F LEU* 2.9 46.5 + - + +
332F TYR 4.9 0.6 + - - -
336F LEU* 5.0 2.2 - - + -
341F PHE* 4.1 22.0 - - + -
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Residues in contact with LYS 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166F GLN* 5.2 4.4 - - - +
203F PHE* 4.3 14.6 - - + -
207F TYR* 3.6 50.4 + - + -
225F HIS* 3.0 19.7 + - - +
226F ALA* 3.4 10.8 - - - +
228F ALA* 1.3 79.0 - - - +
230F LYS* 1.3 57.3 + - + +
232F LEU* 4.3 2.7 - - - +
233F LEU* 2.8 59.9 + - + +
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Residues in contact with LYS 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F ALA* 3.1 23.4 + - - +
227F ASN* 3.1 10.6 + - - +
229F LYS* 1.3 76.0 - - - +
231F ILE* 1.3 61.5 + - - +
233F LEU* 5.5 0.9 - - - -
234F GLU* 3.5 23.2 + - - +
328F LEU* 3.6 7.9 - - + +
332F TYR* 3.7 49.8 + - + +
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Residues in contact with ILE 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227F ASN 4.0 3.6 - - - +
228F ALA 3.1 5.3 + - - +
230F LYS* 1.3 79.2 - - - +
232F LEU* 1.3 60.5 + - - +
234F GLU* 3.3 5.9 + - - +
235F MET* 3.0 38.1 + - + +
325F ILE* 4.7 6.9 - - + +
328F LEU* 3.7 27.6 - - + +
329F ILE* 3.9 22.7 - - + +
332F TYR* 3.7 31.4 - - + +
333F ALA 3.9 2.5 - - - +
341F PHE* 3.6 49.1 - - + -
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Residues in contact with LEU 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F ALA 4.6 0.2 - - - +
206F PHE* 3.3 44.1 - - + +
207F TYR* 3.9 14.8 - - + +
210F ILE* 3.6 30.5 - - + -
228F ALA* 2.9 28.4 + - + +
229F LYS* 4.2 2.7 - - - +
231F ILE* 1.3 77.7 - - - +
233F LEU* 1.3 58.8 + - - +
235F MET* 3.3 14.3 + - - +
236F GLY* 2.9 23.7 + - - -
341F PHE* 4.0 16.4 - - + -
344F LEU* 3.8 25.1 - - + -
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Residues in contact with LEU 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F LYS* 4.6 19.8 - - + +
202F ALA* 3.7 36.6 - - + +
203F PHE* 3.9 38.8 - - + +
207F TYR* 4.4 9.0 - - + -
229F LYS* 2.8 38.7 + - + +
230F LYS* 5.3 1.3 - - - +
232F LEU* 1.3 76.0 - - - +
234F GLU* 1.3 60.1 + - + +
236F GLY* 3.3 1.6 + - - -
237F GLU* 3.0 26.2 + - - +
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Residues in contact with GLU 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194F LYS* 5.8 1.7 - - - -
230F LYS 3.5 14.8 - - - +
231F ILE 3.3 6.9 + - - +
233F LEU* 1.3 78.6 - - + +
235F MET* 1.3 64.0 + - - +
237F GLU* 3.3 24.5 + - - +
238F PHE* 3.2 18.4 + - - +
317F TYR* 5.5 0.2 + - - -
321F SER* 5.2 0.2 + - - -
324F HIS* 3.5 22.2 + - - -
325F ILE* 3.5 22.5 - - + +
328F LEU* 3.5 13.5 - - + -
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Residues in contact with MET 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206F PHE* 3.9 11.2 - - + -
231F ILE* 3.0 23.5 + - + +
232F LEU* 3.4 29.4 - - - +
234F GLU* 1.3 75.0 - - - +
236F GLY* 1.3 58.5 + - - +
238F PHE* 3.2 7.2 + - - +
239F PHE* 2.9 27.4 + - - +
325F ILE* 3.7 32.1 - - + +
329F ILE* 4.3 2.0 - - + -
341F PHE* 3.4 31.0 - - + +
344F LEU* 4.0 16.2 - - + -
345F ALA* 3.8 19.5 - - + +
348F ILE* 4.0 18.9 - - + +
349F TYR* 4.8 0.4 - - + -
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Residues in contact with GLY 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197F VAL 5.2 0.4 - - - +
201F THR* 4.2 5.0 - - - +
202F ALA* 3.8 15.9 - - - -
206F PHE* 3.5 25.3 - - - -
232F LEU 2.9 13.1 + - - -
233F LEU 3.3 4.4 + - - -
234F GLU 3.2 0.2 - - - -
235F MET* 1.3 78.6 - - - +
237F GLU* 1.3 61.4 + - - +
239F PHE* 3.3 2.8 + - - +
240F GLN* 3.1 22.5 + - - +
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Residues in contact with GLU 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193F TYR* 5.1 1.1 - - + -
194F LYS* 3.3 54.8 + - - +
197F VAL* 4.0 24.1 - - + +
198F LYS* 5.9 1.3 - - - +
202F ALA* 4.2 1.9 - - + +
233F LEU 3.0 13.5 + - - +
234F GLU* 3.6 25.8 - - - +
235F MET 3.3 0.4 - - - -
236F GLY* 1.3 73.4 - - - +
238F PHE* 1.3 65.5 + - - +
240F GLN* 3.1 4.2 + - - +
241F ILE* 3.0 39.2 + - + +
317F TYR* 4.3 10.5 + - - +
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Residues in contact with PHE 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234F GLU 3.2 7.1 + - - +
235F MET 3.2 7.0 + - - +
237F GLU* 1.3 79.2 - - - +
239F PHE* 1.3 61.1 + - - +
241F ILE* 3.2 1.8 + - - +
242F GLN* 2.8 55.2 + - + +
314F PHE* 4.2 7.2 - + - -
317F TYR* 3.2 38.3 + + - +
318F GLU* 3.6 42.0 - - + -
321F SER* 3.5 13.0 - - - +
348F ILE* 3.9 16.6 - - + -
349F TYR* 3.2 44.0 - + - +
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Residues in contact with PHE 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F ARG* 3.9 27.6 - - - -
201F THR* 3.8 21.1 - - + -
205F SER* 5.7 0.2 - - - -
206F PHE* 3.6 30.3 - + + -
235F MET 2.9 13.8 + - - +
236F GLY 3.5 7.6 - - - +
238F PHE* 1.3 84.9 - - - +
240F GLN* 1.3 60.9 + - - +
242F GLN* 3.4 21.5 + - - +
243F ASP* 2.8 34.5 + - + +
348F ILE* 4.2 16.4 - - + -
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Residues in contact with GLN 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193F TYR* 3.6 3.4 - - - +
197F VAL* 3.4 39.0 - - + -
200F LYS* 3.7 21.8 - - - +
201F THR* 2.7 34.2 + - + +
236F GLY 3.1 15.8 + - - +
237F GLU 3.9 0.9 - - - +
239F PHE* 1.3 76.4 - - - +
241F ILE* 1.3 61.3 + - - +
243F ASP* 3.0 26.7 + - - +
244F ASP* 2.9 50.5 + - - +
401F JD5 3.8 9.5 + - - -
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Residues in contact with ILE 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193F TYR* 3.4 23.1 - - + +
237F GLU* 3.0 31.1 + - + +
238F PHE 3.5 6.1 - - - +
240F GLN* 1.3 73.6 - - - +
242F GLN* 1.3 65.5 + - - +
244F ASP* 3.1 3.8 + - - +
245F TYR* 3.0 22.2 + - - +
269F TRP* 3.4 49.9 - - + +
314F PHE* 4.0 6.5 - - + -
317F TYR* 2.9 48.2 - - + +
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Residues in contact with GLN 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238F PHE* 2.8 28.0 + - + +
239F PHE* 3.5 29.5 - - - +
241F ILE* 1.3 77.1 - - - +
243F ASP* 1.3 56.4 + - - +
245F TYR* 3.3 1.2 + - - +
246F LEU* 2.9 52.9 + - + +
314F PHE* 3.8 17.4 - - + -
318F GLU* 3.8 12.7 + - - -
348F ILE* 3.1 25.7 + - - +
351F ARG* 3.1 35.0 + - - +
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Residues in contact with ASP 243 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239F PHE* 2.8 27.8 + - + +
240F GLN* 3.0 32.1 + - - +
242F GLN* 1.3 73.9 - - - +
244F ASP* 1.3 58.1 + - - +
246F LEU* 3.3 8.3 + - - +
247F ASP* 2.9 27.4 + - - +
257F LYS* 3.7 14.0 + - - -
401F JD5 3.0 14.9 + - - -
403F MG 2.1 28.6 - - - -
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Residues in contact with ASP 244 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193F TYR* 2.7 27.6 + - - -
200F LYS* 4.9 2.6 + - - -
240F GLN* 2.9 37.3 + - - +
241F ILE 3.1 8.3 + - - +
243F ASP* 1.3 75.6 - - - +
245F TYR* 1.3 66.4 + - - +
247F ASP* 3.4 15.1 - - - +
248F LEU 3.9 0.2 + - - -
261F ASP* 4.0 14.3 - - - +
267F CYS 4.5 0.2 - - - +
268F SER* 3.5 14.4 - - - -
269F TRP* 2.9 28.5 + - + +
270F LEU* 3.5 16.3 - - - +
401F JD5 4.7 1.2 + - - -
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Residues in contact with TYR 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F ILE 3.0 15.7 + - - +
242F GLN 3.7 2.7 - - - +
244F ASP* 1.3 77.1 - - - +
246F LEU* 1.3 80.0 + - + +
248F LEU 3.3 2.4 + - - -
249F PHE* 2.9 68.8 + + + +
269F TRP* 5.2 1.1 - - + -
270F LEU* 4.0 17.7 - - + +
311F PRO* 3.9 31.3 + - + +
314F PHE* 3.7 53.2 - + + -
315F LEU* 5.0 7.4 - - + +
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Residues in contact with LEU 246 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242F GLN* 2.9 43.4 + - + +
243F ASP* 3.9 7.9 - - - +
245F TYR* 1.3 91.1 - - + +
247F ASP* 1.3 64.8 + - - +
248F LEU 3.1 2.9 - - - -
250F GLY* 3.0 39.1 + - - +
255F THR* 4.2 14.3 + - + +
257F LYS* 5.6 2.2 - - - +
351F ARG 4.9 0.9 - - - +
352F ARG* 3.9 39.5 - - + +
353F LYS 4.1 13.9 - - - +
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Residues in contact with ASP 247 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243F ASP* 2.9 14.5 + - - +
244F ASP 3.4 9.6 - - - +
245F TYR 3.2 0.6 - - - -
246F LEU* 1.3 76.5 - - - +
248F LEU* 1.3 61.2 + - + +
250F GLY 5.6 0.3 - - - +
257F LYS* 4.3 14.4 + - - +
258F ILE 4.8 0.2 - - - +
259F GLY* 3.2 40.8 + - - -
260F THR* 3.1 7.0 + - - -
261F ASP* 2.9 57.7 + - + +
403F MG 4.0 9.5 - - - -
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Residues in contact with LEU 248 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F ASP 3.9 0.6 + - - +
245F TYR 3.3 2.4 + - - -
247F ASP* 1.3 83.4 - - + +
249F PHE* 1.3 74.0 + - + +
250F GLY 3.6 5.2 - - - +
262F ILE* 3.6 26.0 - - + -
270F LEU* 3.9 14.1 - - + -
298F VAL* 5.1 6.5 - - + -
302F LYS* 3.5 48.9 + - + +
305F TYR* 3.3 39.0 - - + -
----------------------------------------------------------
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Residues in contact with PHE 249 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245F TYR* 2.9 56.1 + + + +
246F LEU* 4.6 0.4 - - - -
248F LEU* 1.3 98.6 - - + +
250F GLY* 1.3 65.5 + - - +
251F ASP 3.9 0.2 + - - -
270F LEU* 4.0 17.7 - - + -
302F LYS* 4.0 19.3 - - + +
305F TYR* 4.1 13.9 - - + -
306F GLU* 3.7 37.0 - - + -
311F PRO* 4.1 22.0 - - + -
----------------------------------------------------------
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Residues in contact with GLY 250 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246F LEU* 3.0 43.1 + - - +
247F ASP 5.6 0.2 - - - +
248F LEU 4.4 4.5 - - - +
249F PHE* 1.3 84.5 - - - +
251F ASP* 1.3 62.8 + - - -
252F PRO* 3.6 8.1 - - - +
255F THR* 4.2 5.4 - - - -
352F ARG 5.3 0.4 - - - -
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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