Contacts of the helix formed by residues 230 - 256 (chain B) in PDB entry 3FZM
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 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B SER* 3.5 18.6 - - - -
154B GLN* 3.9 15.9 - - + -
155B GLU* 3.2 53.6 - - + +
158B GLU* 4.0 17.5 - - + -
226B LEU* 4.5 3.6 - - + -
227B PRO* 2.8 50.0 + - + +
229B ASN* 1.3 83.8 - - - +
231B LYS* 1.3 62.2 + - - +
232B ASP 3.2 3.2 + - - -
233B SER* 3.3 13.8 + - - -
234B ARG* 3.0 24.1 + - - +
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Residues in contact with LYS 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLU* 3.8 0.6 + - - -
228B GLU 4.5 4.9 - - - +
229B ASN 2.7 13.7 + - - +
230B PHE* 1.3 72.0 - - - +
232B ASP* 1.3 61.8 + - - +
234B ARG* 3.6 17.7 + - - +
235B LEU* 3.1 28.9 + - - +
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Residues in contact with ASP 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ASN* 4.0 18.7 + - - -
155B GLU* 3.4 14.3 + - - +
159B LEU* 3.9 16.6 - - + +
230B PHE 3.2 0.6 - - - -
231B LYS* 1.3 79.5 - - - +
233B SER* 1.3 64.1 + - - +
235B LEU* 3.5 8.9 + - - +
236B LYS* 3.1 25.3 + - - +
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Residues in contact with SER 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLU* 2.9 32.2 + - - +
158B GLU* 3.4 18.9 - - - +
159B LEU* 3.7 14.8 + - - +
162B LEU* 3.4 8.9 - - - +
226B LEU* 3.5 21.8 - - - -
230B PHE* 3.5 11.4 - - - -
232B ASP* 1.3 74.4 - - - +
234B ARG* 1.3 57.2 + - - +
236B LYS 3.4 0.3 + - - -
237B ARG* 2.8 31.7 + - - +
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Residues in contact with ARG 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ASP* 4.3 2.9 - - - +
294A TYR* 5.3 10.0 + - - +
226B LEU* 3.7 29.4 - - + +
227B PRO 3.3 22.2 - - - -
228B GLU* 2.8 47.2 + - - +
230B PHE 3.0 17.1 + - - +
231B LYS* 3.9 15.4 - - - +
233B SER* 1.3 75.9 - - - +
235B LEU* 1.3 58.0 + - - +
237B ARG* 3.9 11.9 - - - +
238B LYS* 3.1 27.9 + - - +
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Residues in contact with LEU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LYS 3.1 18.8 + - - +
232B ASP* 3.5 10.7 + - - +
233B SER 3.3 0.2 - - - -
234B ARG* 1.3 78.3 - - - +
236B LYS* 1.3 57.5 + - - +
238B LYS* 3.6 6.4 + - + +
239B GLY* 3.0 23.9 + - - -
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Residues in contact with LYS 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LEU* 3.7 35.0 - - + +
162B LEU* 3.6 29.8 - - + +
163B LYS* 4.3 13.0 - - - +
166B GLU* 3.1 39.8 + - + +
232B ASP 3.1 16.5 + - - +
233B SER 3.9 2.5 - - - +
235B LEU* 1.3 76.2 - - - +
237B ARG* 1.3 58.3 + - - +
239B GLY* 4.1 1.1 - - - +
240B LEU* 3.1 28.3 + - + +
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Residues in contact with ARG 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLU* 3.0 39.9 + - - +
285A ASP* 3.2 21.9 + - - +
294A TYR* 3.2 28.2 + - - -
162B LEU* 3.8 16.8 - - + +
221B ILE* 3.6 32.2 + - + +
224B LEU* 3.3 23.1 + - - +
226B LEU* 3.6 35.7 + - + +
233B SER 2.8 17.9 + - - +
234B ARG* 3.9 12.1 - - - +
236B LYS* 1.3 76.2 - - - +
238B LYS* 1.3 58.5 + - - +
240B LEU* 3.5 2.0 + - - +
241B VAL* 3.0 28.8 + - + +
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Residues in contact with LYS 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ASP* 3.5 22.4 + - + +
286A SER* 4.2 13.9 - - - -
290A GLY* 4.3 9.7 + - - -
292A ASP* 3.2 34.9 + - - +
234B ARG 3.1 19.5 + - - +
235B LEU* 4.0 7.0 - - + +
236B LYS 3.3 0.2 - - - -
237B ARG* 1.3 74.6 - - - +
239B GLY* 1.3 65.8 + - - +
241B VAL* 3.6 1.5 + - + +
242B LYS* 3.0 54.7 + - + +
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Residues in contact with GLY 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B LEU 3.0 16.7 + - - -
236B LYS* 4.1 1.6 - - - -
238B LYS* 1.3 77.0 - - - +
240B LEU* 1.3 56.2 + - - +
242B LYS* 3.7 6.3 - - - +
243B LYS* 2.8 31.7 + - - +
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Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU* 4.0 13.9 - - + +
165B LEU* 3.9 30.5 - - + +
166B GLU* 3.7 32.1 - - + +
169B VAL* 3.7 32.5 - - + -
221B ILE* 3.9 18.2 - - + -
236B LYS 3.1 19.2 + - - +
237B ARG* 3.9 4.9 - - - +
239B GLY* 1.3 75.1 - - - +
241B VAL* 1.3 61.7 + - - +
243B LYS* 3.2 13.5 + - + +
244B VAL* 2.9 28.6 + - + +
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ARG* 3.7 12.3 - - - +
285A ASP* 3.5 37.7 - - + +
286A SER* 3.7 15.9 - - - -
218B LEU* 4.2 14.4 - - + -
221B ILE* 3.7 31.0 - - + -
222B ASP* 5.2 0.2 - - - +
237B ARG 3.0 22.0 + - - +
238B LYS 4.0 3.4 - - - +
240B LEU* 1.3 75.0 - - - +
242B LYS* 1.3 59.2 + - - +
244B VAL* 3.4 2.3 + - - +
245B GLN* 3.0 40.5 + - - +
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Residues in contact with LYS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A SER* 4.7 10.1 - - - +
238B LYS* 3.0 53.4 + - + +
239B GLY* 3.7 6.1 - - - +
241B VAL* 1.3 75.5 - - - +
243B LYS* 1.3 60.3 + - - +
245B GLN* 3.6 9.8 + - - +
246B ALA* 3.2 22.5 + - - +
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Residues in contact with LYS 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B VAL* 4.4 11.6 - - + +
170B GLU* 5.2 14.7 + - + +
239B GLY 2.8 18.7 + - - +
240B LEU* 3.6 13.5 - - + +
242B LYS* 1.3 73.8 - - - +
244B VAL* 1.3 67.5 + - - +
246B ALA* 3.1 8.8 + - - +
247B PHE* 3.0 53.7 + - + -
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B VAL* 3.6 35.0 - - + -
214B PHE* 3.6 32.1 - - + +
217B ILE* 4.1 10.5 - - + -
218B LEU* 3.8 28.3 - - + -
221B ILE* 5.2 0.2 - - + -
240B LEU* 2.9 24.8 + - + +
241B VAL 3.7 3.8 - - - +
243B LYS* 1.3 71.6 - - - +
245B GLN* 1.3 52.6 + - - +
247B PHE* 3.1 12.0 + - - +
248B LEU* 2.8 37.6 + - + +
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Residues in contact with GLN 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ARG* 3.0 17.6 - - - +
286A SER* 2.6 47.6 + - - -
287A LEU 4.7 3.0 + - - -
218B LEU* 4.5 13.5 - - + +
241B VAL* 3.0 25.3 + - + +
242B LYS* 3.7 10.3 - - - +
243B LYS 3.2 0.2 - - - -
244B VAL* 1.3 76.4 - - - +
246B ALA* 1.3 55.8 + - - +
248B LEU* 3.4 11.9 + - + +
249B ALA* 3.0 26.2 + - - +
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Residues in contact with ALA 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B LYS 3.2 12.6 + - - +
243B LYS* 3.1 11.4 + - - +
245B GLN* 1.3 72.4 - - - +
247B PHE* 1.3 60.9 + - + +
249B ALA* 3.5 7.6 + - - +
250B GLU* 3.1 36.9 + - + +
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Residues in contact with PHE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B VAL* 3.9 9.4 - - + -
173B ALA* 3.7 26.2 - - + -
176B LEU* 3.6 11.2 - - + +
214B PHE* 3.5 35.9 - + + -
243B LYS* 3.0 58.1 + - + -
244B VAL* 3.3 6.5 - - - +
246B ALA* 1.3 74.3 - - + +
248B LEU* 1.3 59.2 + - - +
250B GLU* 3.1 32.3 + - - +
251B CYS* 2.9 32.0 + - - -
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ARG* 3.9 26.1 + - - +
211B ILE* 3.8 45.8 - - + +
214B PHE* 3.9 13.4 - - + -
215B MET* 4.2 11.2 - - + -
218B LEU* 3.9 27.6 - - + -
244B VAL* 2.8 23.9 + - + +
245B GLN* 3.5 16.4 - - + +
246B ALA 3.3 0.2 - - - -
247B PHE* 1.3 72.5 - - - +
249B ALA* 1.3 59.3 + - - +
251B CYS* 3.1 7.8 + - - +
252B ASP* 3.1 29.5 + - - +
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ARG* 5.0 0.4 - - - +
245B GLN 3.0 14.5 + - - +
246B ALA* 3.7 12.1 - - - +
247B PHE 3.3 0.2 - - - -
248B LEU* 1.3 73.5 - - - +
250B GLU* 1.3 62.3 + - + +
252B ASP* 3.4 11.0 + - - +
253B THR* 3.2 26.3 + - - -
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Residues in contact with GLU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 3.9 17.7 - - + +
180B ASN* 5.7 1.9 + - - -
246B ALA* 3.1 25.6 + - - +
247B PHE* 3.2 40.2 - - - +
249B ALA* 1.3 76.6 - - + +
251B CYS* 1.3 58.1 + - - +
253B THR* 3.5 9.9 + - - -
254B VAL* 3.2 25.0 + - - +
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Residues in contact with CYS 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B LEU* 4.1 12.8 - - - -
207B VAL* 3.4 16.2 - - + +
210B THR* 3.8 29.6 - - - -
211B ILE* 3.4 31.2 - - + -
214B PHE* 4.1 11.9 - - - -
247B PHE 2.9 19.2 + - - -
248B LEU* 3.1 6.5 + - - +
250B GLU* 1.3 73.1 - - - +
252B ASP* 1.3 65.1 + - - +
254B VAL* 3.3 7.3 + - - +
255B GLU* 3.2 20.1 + - - +
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Residues in contact with ASP 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ARG* 2.7 46.4 + - - -
211B ILE* 3.9 2.8 - - - +
248B LEU 3.1 12.8 + - - +
249B ALA* 3.7 10.3 - - - +
250B GLU 3.3 0.4 - - - -
251B CYS* 1.3 73.4 - - - +
253B THR* 1.3 66.3 + - - +
255B GLU* 3.9 11.9 - - - +
256B GLN* 2.6 43.6 + - - +
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Residues in contact with THR 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B ALA 3.2 13.3 + - - -
250B GLU* 3.6 12.5 - - - -
251B CYS 3.3 0.4 - - - -
252B ASP* 1.3 76.5 - - - +
254B VAL* 1.3 59.0 + - + +
256B GLN* 3.0 22.7 - - - +
257B ASN* 3.6 11.0 - - - +
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Residues in contact with VAL 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 4.5 11.0 - - + -
179B LEU* 5.4 7.0 - - + +
180B ASN* 3.8 21.3 - - - +
183B LEU* 3.8 26.4 - - + +
203B LEU* 6.0 1.3 - - + -
207B VAL* 3.6 25.1 - - + -
250B GLU 3.2 18.8 - - - +
251B CYS* 3.3 9.2 + - - +
252B ASP 3.2 0.6 - - - -
253B THR* 1.3 77.3 - - + +
255B GLU* 1.3 62.0 + - - +
257B ASN* 3.2 18.5 - - - +
258B ILE* 3.6 16.5 - - + +
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Residues in contact with GLU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ARG* 4.9 1.0 + - - -
204B ASP* 3.4 17.9 - - - +
207B VAL* 3.8 12.5 - - + +
208B LYS* 3.1 37.2 + - - +
211B ILE* 3.7 24.0 - - - +
251B CYS 3.2 10.3 + - - +
252B ASP* 3.9 7.8 - - - +
254B VAL* 1.3 78.9 - - - +
256B GLN* 1.3 81.6 + - - +
258B ILE* 3.0 28.8 - - - +
259B CYS 5.2 0.2 - - - +
260B GLN* 4.1 3.6 + - - +
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Residues in contact with GLN 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ASP* 2.6 46.2 + - - +
253B THR* 3.0 10.1 - - - +
255B GLU* 1.3 92.5 + - - +
257B ASN* 1.3 66.5 + - - +
260B GLN* 3.4 17.0 - - - +
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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