Contacts of the helix formed by residues 228 - 293 (chain C) in PDB entry 5KHU
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 TRP 228 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C THR* 3.8 28.9 - - - +
229C MET* 3.8 25.8 - - - +
----------------------------------------------------------
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Residues in contact with MET 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C TRP* 3.8 25.6 - - - +
230C LYS* 3.8 29.6 - - - +
----------------------------------------------------------
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Residues in contact with LYS 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C MET* 3.8 29.6 - - - +
231C GLU* 3.8 26.2 - - - +
----------------------------------------------------------
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Residues in contact with GLU 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C LYS* 3.8 28.7 - - - +
232C PHE* 3.8 26.7 - - - +
----------------------------------------------------------
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Residues in contact with PHE 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C GLU* 3.8 26.7 - - - +
233C PHE* 3.7 28.5 - - - +
----------------------------------------------------------
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Residues in contact with PHE 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C PHE* 3.7 29.4 - - - +
234C LEU* 3.8 27.4 - - - +
----------------------------------------------------------
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Residues in contact with LEU 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C PHE* 3.8 25.4 - - - +
235C ALA* 3.7 30.1 - - - +
237C ILE* 4.3 16.8 - - - +
----------------------------------------------------------
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Residues in contact with ALA 235 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C LEU* 3.7 29.2 - - - +
236C HIS* 3.8 26.5 - - - +
----------------------------------------------------------
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Residues in contact with HIS 236 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ALA* 3.8 29.8 - - - +
237C ILE* 3.8 24.0 - - - +
239C THR* 4.6 14.1 - - - +
----------------------------------------------------------
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Residues in contact with ILE 237 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C LEU* 4.3 18.8 - - - +
236C HIS* 3.8 30.1 - - - +
238C TYR* 3.8 26.0 - - - +
240C GLU* 4.3 18.8 - - - +
----------------------------------------------------------
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Residues in contact with TYR 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C ILE* 3.8 22.9 - - - +
239C THR* 3.7 29.2 - - - +
241C LEU* 4.6 11.9 - - - +
243C LEU* 4.5 21.1 - - - +
----------------------------------------------------------
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Residues in contact with THR 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C HIS* 4.6 17.0 - - - +
238C TYR* 3.7 29.2 - - - +
240C GLU* 3.8 25.6 - - - +
242C GLN* 4.7 13.9 - - - +
----------------------------------------------------------
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Residues in contact with GLU 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C ILE* 4.3 15.7 - - - +
239C THR* 3.8 25.4 - - - +
241C LEU* 3.8 28.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C TYR* 4.6 14.1 - - - +
240C GLU* 3.8 29.2 - - - +
242C GLN* 3.8 26.5 - - - +
----------------------------------------------------------
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Residues in contact with GLN 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C THR* 4.7 15.5 - - - +
241C LEU* 3.8 29.2 - - - +
243C LEU* 3.8 25.8 - - - +
----------------------------------------------------------
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Residues in contact with LEU 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C TYR* 4.5 14.4 - - - +
242C GLN* 3.8 22.7 - - - +
244C ILE* 3.7 30.7 - - - +
----------------------------------------------------------
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Residues in contact with ILE 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C LEU* 3.7 30.1 - - - +
245C GLU* 3.8 28.3 - - - +
247C ALA* 4.4 18.4 - - - +
----------------------------------------------------------
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Residues in contact with GLU 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ILE* 3.8 25.1 - - - +
246C GLU* 3.8 28.5 - - - +
----------------------------------------------------------
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Residues in contact with GLU 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C GLU* 3.8 28.5 - - - +
247C ALA* 3.8 25.8 - - - +
----------------------------------------------------------
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Residues in contact with ALA 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ILE* 4.4 17.3 - - - +
246C GLU* 3.8 26.2 - - - +
248C LEU* 3.8 29.6 - - - +
----------------------------------------------------------
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Residues in contact with LEU 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ALA* 3.8 24.9 - - - +
249C GLN* 3.8 29.8 - - - +
----------------------------------------------------------
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Residues in contact with GLN 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C LEU* 3.8 29.4 - - - +
250C LYS* 3.8 25.6 - - - +
----------------------------------------------------------
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Residues in contact with LYS 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C GLN* 3.8 29.4 - - - +
251C TYR* 3.8 26.2 - - - +
----------------------------------------------------------
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Residues in contact with TYR 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C LYS* 3.8 25.6 - - - +
252C GLN* 3.8 29.8 - - - +
254C LEU* 4.6 15.7 - - - +
----------------------------------------------------------
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Residues in contact with GLN 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C TYR* 3.8 29.6 - - - +
253C ASN* 3.8 25.4 - - - +
----------------------------------------------------------
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Residues in contact with ASN 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C GLN* 3.8 25.4 - - - +
254C LEU* 3.7 29.4 - - - +
256C ASP* 4.5 15.5 - - - +
----------------------------------------------------------
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Residues in contact with LEU 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C TYR* 4.6 15.9 - - - +
253C ASN* 3.7 29.8 - - - +
255C ILE* 3.8 27.8 - - - +
----------------------------------------------------------
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Residues in contact with ILE 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C LEU* 3.8 29.4 - - - +
256C ASP* 3.8 24.2 - - - +
259C PHE* 4.1 22.4 - - - +
260C SER* 4.4 14.8 - - - +
----------------------------------------------------------
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Residues in contact with ASP 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ASN* 4.5 18.8 - - - +
255C ILE* 3.8 25.1 - - - +
257C VAL* 3.8 29.4 - - - +
----------------------------------------------------------
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Residues in contact with VAL 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ASP* 3.8 29.4 - - - +
258C GLY* 3.8 25.8 - - - +
----------------------------------------------------------
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Residues in contact with GLY 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C VAL* 3.8 28.3 - - - +
259C PHE* 3.8 29.4 - - - +
----------------------------------------------------------
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Residues in contact with PHE 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C ILE* 4.1 13.7 - - - +
258C GLY* 3.8 29.4 - - - +
260C SER* 3.8 25.8 - - - +
----------------------------------------------------------
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Residues in contact with SER 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C ILE* 4.4 14.8 - - - +
259C PHE* 3.8 24.2 - - - +
261C LYS* 3.8 29.6 - - - +
----------------------------------------------------------
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Residues in contact with LYS 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C SER* 3.8 29.2 - - - +
262C SER* 3.8 27.6 - - - +
----------------------------------------------------------
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Residues in contact with SER 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C LYS* 3.8 28.3 - - - +
263C SER* 3.7 30.1 - - - +
----------------------------------------------------------
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Residues in contact with SER 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C SER* 3.7 29.6 - - - +
264C TYR* 3.8 25.1 - - - +
----------------------------------------------------------
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Residues in contact with TYR 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C SER* 3.8 27.8 - - - +
265C ILE* 3.8 30.3 - - - +
267C SER* 4.5 15.0 - - - +
----------------------------------------------------------
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Residues in contact with ILE 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C TYR* 3.8 25.8 - - - +
266C VAL* 3.7 28.9 - - - +
268C GLN* 4.6 14.8 - - - +
----------------------------------------------------------
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Residues in contact with VAL 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ILE* 3.7 29.2 - - - +
267C SER* 3.8 25.6 - - - +
269C ILE* 4.3 17.9 - - - +
----------------------------------------------------------
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Residues in contact with SER 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C TYR* 4.5 16.4 - - - +
266C VAL* 3.8 29.6 - - - +
268C GLN* 3.8 24.7 - - - +
----------------------------------------------------------
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Residues in contact with GLN 268 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ILE* 4.6 15.3 - - - +
267C SER* 3.8 29.2 - - - +
269C ILE* 3.8 25.6 - - - +
----------------------------------------------------------
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Residues in contact with ILE 269 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C VAL* 4.3 17.5 - - - +
268C GLN* 3.8 26.9 - - - +
270C ALA* 3.8 29.2 - - - +
272C ALA* 4.6 13.2 - - - +
----------------------------------------------------------
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Residues in contact with ALA 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C ILE* 3.8 29.4 - - - +
271C VAL* 3.8 26.0 - - - +
----------------------------------------------------------
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Residues in contact with VAL 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C ALA* 3.8 24.9 - - - +
272C ALA* 3.8 29.4 - - - +
274C HIS* 4.5 16.2 - - - +
----------------------------------------------------------
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Residues in contact with ALA 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C ILE* 4.6 15.9 - - - +
271C VAL* 3.8 26.2 - - - +
273C TYR* 3.8 29.4 - - - +
----------------------------------------------------------
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Residues in contact with TYR 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ALA* 3.8 29.8 - - - +
274C HIS* 3.8 24.5 - - - +
276C ILE* 4.3 20.0 - - - +
----------------------------------------------------------
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Residues in contact with HIS 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C VAL* 4.5 18.4 - - - +
273C TYR* 3.8 25.8 - - - +
275C ASN* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with ASN 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C HIS* 3.8 28.5 - - - +
276C ILE* 3.8 26.2 - - - +
----------------------------------------------------------
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Residues in contact with ILE 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C TYR* 4.3 18.6 - - - +
275C ASN* 3.8 28.3 - - - +
277C ARG* 3.8 24.9 - - - +
----------------------------------------------------------
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Residues in contact with ARG 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C ILE* 3.8 26.9 - - - +
278C ASP* 3.8 30.1 - - - +
----------------------------------------------------------
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Residues in contact with ASP 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ARG* 3.8 27.8 - - - +
279C ILE* 3.7 29.6 - - - +
----------------------------------------------------------
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Residues in contact with ILE 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C ASP* 3.7 28.0 - - - +
280C ASP* 3.7 29.6 - - - +
----------------------------------------------------------
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Residues in contact with ASP 280 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE* 3.7 29.6 - - - +
281C LYS* 3.8 28.5 - - - +
283C LEU* 4.3 18.4 - - - +
----------------------------------------------------------
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Residues in contact with LYS 281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ASP* 3.8 24.0 - - - +
282C ALA* 3.7 29.8 - - - +
----------------------------------------------------------
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Residues in contact with ALA 282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C LYS* 3.7 29.6 - - - +
283C LEU* 3.8 26.9 - - - +
----------------------------------------------------------
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Residues in contact with LEU 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ASP* 4.3 17.0 - - - +
282C ALA* 3.8 24.7 - - - +
284C SER* 3.8 29.8 - - - +
----------------------------------------------------------
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Residues in contact with SER 284 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C LEU* 3.8 28.5 - - - +
285C ILE* 3.7 29.8 - - - +
----------------------------------------------------------
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Residues in contact with ILE 285 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C SER* 3.7 29.6 - - - +
286C PHE* 3.8 25.8 - - - +
----------------------------------------------------------
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Residues in contact with PHE 286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ILE* 3.8 27.1 - - - +
287C ASN* 3.7 30.5 - - - +
289C LEU* 4.3 17.9 - - - +
----------------------------------------------------------
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Residues in contact with ASN 287 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C PHE* 3.7 30.1 - - - +
288C GLU* 3.8 26.0 - - - +
----------------------------------------------------------
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Residues in contact with GLU 288 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ASN* 3.8 29.6 - - - +
289C LEU* 3.8 25.8 - - - +
291C LYS* 4.2 17.3 - - - +
----------------------------------------------------------
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Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C PHE* 4.3 14.4 - - - +
288C GLU* 3.8 25.1 - - - +
290C ARG* 3.7 29.2 - - - +
292C GLN* 4.6 13.7 - - - +
----------------------------------------------------------
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Residues in contact with ARG 290 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C LEU* 3.7 29.4 - - - +
291C LYS* 3.8 25.4 - - - +
294C PRO* 4.7 17.9 - - - -
----------------------------------------------------------
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Residues in contact with LYS 291 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C GLU* 4.2 17.5 - - - +
290C ARG* 3.8 29.2 - - - +
292C GLN* 3.8 25.6 - - - +
----------------------------------------------------------
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Residues in contact with GLN 292 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C LEU* 4.6 16.8 - - - +
291C LYS* 3.8 29.6 - - - +
293C ASP* 3.8 26.2 - - - +
----------------------------------------------------------
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Residues in contact with ASP 293 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C GLN* 3.8 30.3 - - - +
294C PRO* 3.7 29.4 - - - -
----------------------------------------------------------
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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