Contacts of the helix formed by residues 221 - 246 (chain B) in PDB entry 1DKF
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 221 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLU* 4.6 13.5 - - - +
218B VAL* 5.0 3.8 - - + -
220B LEU* 1.3 73.1 - - - +
222B ILE* 1.3 51.8 + - - +
223B ASP* 3.2 12.3 + - - +
224B LEU* 2.7 43.4 + - + +
225B TRP* 2.7 31.7 + - - +
299B ASN* 2.8 30.5 + - + +
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Residues in contact with ILE 222 (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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220B LEU* 3.7 18.1 + - + +
221B ASP* 1.3 72.2 + - - +
223B ASP* 1.3 72.1 + - - +
225B TRP* 3.4 25.5 - - + +
226B ASP* 2.9 39.0 + - - +
402B ILE* 4.5 16.6 - - + -
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Residues in contact with ASP 223 (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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221B ASP* 3.0 9.2 + - - +
222B ILE* 1.3 90.5 - - + +
224B LEU* 1.3 64.4 + - - +
226B ASP* 3.5 19.8 + - - +
227B LYS* 3.6 27.6 + - - +
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Residues in contact with LEU 224 (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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210B THR* 5.7 8.7 - - - -
215B GLU* 6.6 0.2 - - + -
221B ASP* 2.7 41.3 + - + +
223B ASP* 1.3 69.6 - - - +
225B TRP* 1.3 67.0 + - - +
227B LYS* 3.0 18.1 + - + +
228B PHE* 3.0 23.8 + - - +
290B LEU* 5.5 2.7 - - + -
292B LEU* 4.1 30.5 - - + -
296B GLN* 3.5 39.9 - - + +
299B ASN* 4.1 5.2 - - + -
300B ALA* 3.9 8.5 - - + -
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Residues in contact with TRP 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 4.1 12.1 - - + -
221B ASP 2.7 12.3 + - - +
222B ILE* 3.4 26.2 - - + +
224B LEU* 1.3 77.3 - - - +
226B ASP* 1.3 72.1 + - - +
228B PHE* 3.8 22.7 - + - -
229B SER* 2.8 47.8 + - - -
300B ALA 3.0 35.6 + - - +
301B GLY* 4.1 5.6 - - - -
398B LEU* 3.7 30.1 - - + -
402B ILE* 3.7 32.0 - - + +
405B SER* 4.6 7.9 - - - +
406B MET* 4.0 17.7 - - + -
600B BMS 3.9 20.9 - + - -
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Residues in contact with ASP 226 (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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222B ILE* 2.9 28.3 + - - +
223B ASP* 3.7 18.7 - - - +
224B LEU 3.1 0.6 - - - -
225B TRP* 1.3 91.6 + - - +
227B LYS* 1.3 62.2 + - + +
229B SER* 3.9 4.3 - - - -
230B GLU* 3.2 25.3 + - - +
402B ILE* 6.0 0.3 - - - +
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Residues in contact with LYS 227 (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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208B TYR* 5.7 5.4 - - + +
210B THR 4.6 21.3 + - - +
223B ASP* 3.6 21.1 + - - +
224B LEU* 3.0 17.0 + - + +
226B ASP* 1.3 77.8 - - + +
228B PHE* 1.3 61.4 + - - +
230B GLU* 3.1 8.2 - - - +
231B LEU* 2.8 35.6 + - + +
290B LEU* 4.4 26.0 - - + -
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Residues in contact with PHE 228 (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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224B LEU 3.0 15.0 + - - +
225B TRP* 3.8 26.2 - + - +
227B LYS* 1.3 76.1 - - - +
229B SER* 1.3 59.4 + - - +
231B LEU* 3.4 7.6 + - - +
232B SER* 2.9 42.2 + - - -
286B PHE* 3.8 31.6 - + + -
290B LEU* 5.6 1.5 - - - +
292B LEU* 5.8 2.5 - - + -
297B MET* 4.8 1.8 - - + -
300B ALA* 3.4 34.1 - - + +
301B GLY* 4.5 4.7 - - - -
302B PHE* 3.9 21.1 - + - -
600B BMS 3.3 52.3 - + - -
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Residues in contact with SER 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B TRP* 2.8 47.2 + - - -
226B ASP* 3.9 5.6 - - - -
228B PHE* 1.3 74.4 - - - +
230B GLU* 1.3 61.1 + - - +
233B THR* 3.0 28.6 + - - -
405B SER* 5.8 0.5 - - - -
406B MET* 4.5 4.5 + - - +
600B BMS 3.1 35.1 - - - -
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Residues in contact with GLU 230 (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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226B ASP 3.2 12.6 + - - +
227B LYS* 3.1 12.6 - - - +
229B SER* 1.3 77.2 - - - +
231B LEU* 1.3 68.7 + - + +
233B THR* 2.9 19.9 + - - -
234B LYS* 3.1 47.1 + - - +
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Residues in contact with LEU 231 (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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227B LYS* 2.8 23.6 + - + +
228B PHE* 3.8 4.5 - - - +
230B GLU* 1.3 75.4 + - + +
232B SER* 1.3 56.9 + - - +
234B LYS* 3.3 21.1 + - + +
235B CYS* 2.9 23.9 + - - +
286B PHE* 3.6 30.3 - - + -
287B SER* 5.4 1.1 - - - -
288B ASP* 3.8 34.5 - - + +
290B LEU* 3.8 23.1 - - + -
600B BMS 3.6 33.1 + - + +
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Residues in contact with SER 232 (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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228B PHE* 2.9 23.9 + - - -
229B SER 3.7 1.3 - - - -
231B LEU* 1.3 73.4 - - - +
233B THR* 1.3 69.2 + - - +
235B CYS* 2.8 13.0 + - - +
236B ILE* 2.8 18.5 + - - +
269B LEU* 5.0 0.4 - - - -
600B BMS 3.1 74.1 + - - -
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Residues in contact with THR 233 (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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229B SER 3.0 12.9 + - - -
230B GLU* 2.9 12.2 + - - -
232B SER* 1.3 78.8 - - - +
234B LYS* 1.3 64.8 - - + +
236B ILE* 3.1 8.1 + - - +
237B ILE* 3.1 34.7 + - + +
407B PRO* 5.7 3.1 - - - +
409B LEU* 4.3 17.2 - - + +
600B BMS 3.3 21.3 - - - -
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Residues in contact with LYS 234 (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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230B GLU* 3.1 42.4 + - - +
231B LEU* 3.4 22.8 - - + +
232B SER 3.1 0.2 - - - -
233B THR* 1.3 82.1 - - + +
235B CYS* 1.3 56.9 + - - +
237B ILE* 3.1 18.0 + - + +
238B LYS* 2.9 32.4 + - + +
288B ASP* 6.4 1.1 - - - -
600B BMS 6.0 0.2 - - - +
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Residues in contact with CYS 235 (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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199B PHE* 4.4 2.7 - - - -
231B LEU 2.9 12.4 + - - +
232B SER 2.8 11.4 + - - +
234B LYS* 1.3 71.1 - - - +
236B ILE* 1.3 55.9 + - - +
238B LYS* 3.4 6.2 - - - +
239B THR* 2.7 38.7 + - - -
269B LEU* 4.0 11.4 - - + -
272B ARG* 3.7 32.1 - - - -
287B SER* 5.0 2.2 - - - -
600B BMS 3.5 41.7 - - + -
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Residues in contact with ILE 236 (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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232B SER 2.8 26.6 + - - +
233B THR* 3.4 7.2 - - - +
235B CYS* 1.3 72.7 - - - +
237B ILE* 1.3 68.0 + - - +
239B THR* 3.1 8.8 + - - -
240B VAL* 2.9 23.0 + - - +
265B CYS* 4.1 16.6 - - + -
269B LEU* 3.5 25.4 - - + -
409B LEU* 4.2 11.4 - - + -
410B ILE* 3.6 31.2 - - + -
413B MET* 4.0 12.8 - - + -
600B BMS 3.4 34.1 - - + +
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Residues in contact with ILE 237 (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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233B THR* 3.1 27.9 + - + +
234B LYS* 3.2 20.0 - - + +
236B ILE* 1.3 77.2 - - - +
238B LYS* 1.3 64.3 + - - +
240B VAL* 3.2 5.5 + - - +
241B GLU* 2.9 45.0 + - + +
409B LEU* 4.2 8.5 - - + -
413B MET* 3.6 34.2 - - + +
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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
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197B GLU 4.7 8.7 + - - -
198B THR* 3.4 44.5 - - - +
234B LYS* 2.9 19.7 + - + +
235B CYS* 3.4 11.0 - - - +
237B ILE* 1.3 78.9 - - - +
239B THR* 1.3 59.6 + - - +
241B GLU* 3.0 34.7 + - - +
242B PHE* 2.9 23.7 + - - +
272B ARG* 4.0 3.4 - - - +
287B SER* 6.5 0.9 - - - -
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Residues in contact with THR 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 CYS 2.7 25.2 + - - -
236B ILE* 3.1 8.9 + - - -
238B LYS* 1.3 73.1 - - - +
240B VAL* 1.3 57.0 + - - +
242B PHE* 3.1 15.0 + - + +
243B ALA* 2.9 26.6 + - + +
261B LEU* 4.7 8.3 - - + -
265B CYS* 4.6 14.6 - - - -
268B ILE* 3.7 41.8 - - + +
269B LEU* 3.5 17.0 - - + +
272B ARG* 3.9 9.5 + - - +
334B LEU* 6.3 0.4 - - + -
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Residues in contact with VAL 240 (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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236B ILE 2.9 17.4 + - - +
237B ILE 3.2 9.2 + - - +
239B THR* 1.3 77.7 - - - +
241B GLU* 1.3 62.7 + - + +
243B ALA* 3.3 3.5 + - - +
244B LYS* 3.1 30.2 + - + +
261B LEU* 3.5 27.8 - - + +
265B CYS* 5.4 0.9 - - - -
410B ILE* 4.3 14.6 - - + -
413B MET* 3.7 33.2 - - + -
414B LEU* 3.9 26.2 - - + -
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Residues in contact with GLU 241 (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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198B THR* 4.1 9.8 - - + +
237B ILE* 2.9 34.4 + - + +
238B LYS* 3.0 40.7 + - - +
240B VAL* 1.3 75.7 - - + +
242B PHE* 1.3 65.2 + - - +
244B LYS* 3.4 8.3 + - - +
245B GLN* 3.1 34.3 + - + +
413B MET* 5.9 0.9 - - - -
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Residues in contact with PHE 242 (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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191B VAL* 4.1 3.4 - - + -
194B ALA* 3.6 27.6 - - + -
195B HIS* 3.6 27.4 - - + -
198B THR* 3.4 21.5 - - - +
238B LYS 2.9 9.0 + - - +
239B THR* 3.1 18.4 + - + +
241B GLU* 1.3 77.5 - - - +
243B ALA* 1.3 60.3 + - + +
245B GLN* 2.8 28.2 + - - +
246B LEU* 3.2 35.4 + - + +
268B ILE* 5.8 3.4 - - + -
272B ARG* 3.8 13.5 - - - +
327B GLY* 3.4 24.7 - - - -
330B SER* 3.8 23.3 - - - -
331B ALA 4.2 2.9 - - - -
334B LEU* 5.1 3.1 - - + -
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Residues in contact with ALA 243 (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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239B THR 2.9 11.7 + - - +
240B VAL 3.6 8.1 - - - +
242B PHE* 1.3 76.7 - - + +
244B LYS* 1.3 58.6 + - - +
246B LEU* 2.9 29.0 + - - +
249B PHE* 3.1 37.9 - - + +
261B LEU* 3.9 11.0 - - + -
334B LEU* 3.6 24.7 - - + -
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Residues in contact with LYS 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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240B VAL* 3.1 22.5 + - + +
241B GLU* 3.6 13.0 - - - +
242B PHE 3.2 0.2 - - - -
243B ALA* 1.3 75.8 - - - +
245B GLN* 1.3 70.4 + - - +
246B LEU 3.4 5.0 + - - +
249B PHE* 4.0 9.6 - - + +
250B THR* 4.1 31.6 + - + +
257B GLN* 5.2 2.9 - - - +
413B MET* 4.3 7.1 + - - +
414B LEU* 3.5 42.5 + - + +
416B ASN* 4.1 9.1 + - - -
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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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190B LYS* 5.6 4.5 - - - +
194B ALA* 3.6 29.0 - - + +
197B GLU* 5.2 9.3 - - + +
198B THR* 5.4 3.1 - - + -
241B GLU* 3.1 29.0 + - + +
242B PHE* 2.8 13.2 + - - +
244B LYS* 1.3 87.1 + - - +
246B LEU* 1.3 62.3 + - - +
247B PRO* 3.4 8.3 - - - +
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Residues in contact with LEU 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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191B VAL* 4.2 18.6 - - + -
194B ALA* 4.7 3.6 - - + -
242B PHE* 3.5 44.6 - - + +
243B ALA* 2.9 16.3 + - - +
244B LYS 3.9 3.8 - - - +
245B GLN* 1.3 78.2 - - - +
247B PRO* 1.4 65.5 - - + +
248B GLY 3.2 0.7 + - - -
249B PHE* 2.9 30.3 + - + +
250B THR* 4.5 1.4 + - - -
331B ALA* 3.9 22.7 - - + -
334B LEU* 3.4 33.2 - - + -
335B ILE* 4.1 12.8 - - + -
355B LEU* 5.7 1.6 - - + -
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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