Contacts of the helix formed by residues 231 - 266 (chain B) in PDB entry 1ZV0
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 ASN 231 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B ILE 4.3 9.5 + - - -
230B LYS* 1.3 79.2 - - - +
232B LYS* 1.3 73.1 + - - +
233B PRO 3.7 0.4 - - - -
234B ARG* 3.3 34.1 + - - +
235B ASN* 3.4 23.2 + - - +
308B LYS* 6.5 0.2 - - + -
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Residues in contact with LYS 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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130B ILE* 5.5 0.2 - - - +
132B HIS* 4.7 20.4 - - + -
222B LEU* 2.9 37.2 + - + +
223B LYS* 4.6 7.0 - - + +
224B LYS* 4.6 4.8 - - - +
225B ALA* 4.9 3.4 + - - +
228B ILE* 3.8 30.0 - - + +
229B GLN* 3.7 33.3 - - + +
230B LYS 3.4 1.0 - - - +
231B ASN* 1.3 84.7 + - - +
233B PRO* 1.4 64.9 - - + +
234B ARG 3.1 0.6 + - - -
235B ASN* 3.6 3.9 + - - +
236B ASP* 2.9 33.0 + - + +
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Residues in contact with PRO 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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223B LYS* 6.1 2.5 - - - -
229B GLN* 3.8 21.8 - - + +
230B LYS 3.6 17.5 - - - +
232B LYS* 1.4 91.5 - - + +
234B ARG* 1.3 57.3 + - - +
236B ASP* 4.1 9.9 - - + +
237B ASP* 3.0 34.0 - - - +
307B LYS* 3.3 17.6 - - - -
326B SER* 4.2 17.7 - - - +
327B HIS* 4.4 12.6 - - + -
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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
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230B LYS* 3.6 16.8 + - - +
231B ASN* 3.4 21.1 - - - +
232B LYS 3.1 0.6 + - - -
233B PRO* 1.3 78.4 - - - +
235B ASN* 1.3 61.1 + - - +
237B ASP* 3.1 4.2 + - - +
238B ILE* 2.9 30.0 + - - +
307B LYS* 4.0 21.6 + - + -
308B LYS* 4.1 39.0 + - + +
311B ARG* 5.0 6.5 - - - +
312B TYR* 4.9 11.7 + - - -
326B SER* 3.2 35.4 + - - +
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Residues in contact with ASN 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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61B THR* 5.5 0.3 - - - +
130B ILE* 5.1 1.8 - - + -
231B ASN* 3.4 34.1 + - - +
232B LYS* 4.3 3.5 - - - +
234B ARG* 1.3 74.8 - - - +
236B ASP* 1.3 58.8 + - - +
238B ILE* 3.8 11.4 - - - +
239B PHE* 3.0 51.0 + - + -
308B LYS* 3.0 35.8 + - - +
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Residues in contact with ASP 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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130B ILE* 3.2 28.7 - - + +
219B TRP* 3.6 14.9 - - - +
223B LYS* 3.0 39.4 + - - +
232B LYS* 2.9 27.7 + - + +
233B PRO* 4.1 4.8 - - + +
235B ASN* 1.3 71.3 - - - +
237B ASP* 1.3 61.3 + - - +
239B PHE* 4.4 4.5 - - - +
240B LYS* 3.0 43.2 + - - +
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Residues in contact with ASP 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 PRO* 3.0 27.0 + - - +
234B ARG 3.1 4.9 + - - +
236B ASP* 1.3 85.5 - - - +
238B ILE* 1.3 65.2 + - - +
239B PHE 3.2 1.1 - - - -
240B LYS* 3.2 32.3 + - - +
241B ILE* 3.2 16.5 + - - +
306B GLY* 3.9 6.4 + - - +
307B LYS* 3.1 39.1 + - - +
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Residues in contact with ILE 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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63B ALA* 6.0 6.7 - - + -
234B ARG 2.9 14.4 + - - +
235B ASN* 3.7 21.1 - - - +
237B ASP* 1.3 71.6 - - - +
239B PHE* 1.3 78.6 + - + +
241B ILE* 3.2 25.6 - - + +
242B ILE* 2.9 27.5 + - + +
302B TYR* 4.5 11.9 - - + +
306B GLY* 3.8 14.1 - - - +
308B LYS* 4.7 14.6 - - + +
309B PHE* 4.2 32.1 - - + +
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Residues in contact with PHE 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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126B ARG* 3.2 66.6 - - + -
129B ALA* 4.6 7.4 - - + -
130B ILE* 4.0 27.6 - - + -
218B ILE* 3.8 25.5 - - + +
219B TRP* 5.7 8.3 - - + -
235B ASN* 3.0 35.8 + - + +
236B ASP* 4.8 4.5 - - - +
237B ASP 3.2 0.8 - - - -
238B ILE* 1.3 87.8 - - + +
240B LYS* 1.3 64.6 + - - +
241B ILE 3.1 1.1 - - - -
242B ILE* 3.3 9.6 + - + +
243B MET* 3.0 25.9 + - - +
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Residues in contact with LYS 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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219B TRP* 3.5 46.9 - - + +
223B LYS* 5.1 0.2 - - - +
236B ASP* 3.0 42.9 + - - +
237B ASP* 3.2 26.7 + - - +
239B PHE* 1.3 75.5 - - - +
241B ILE* 1.3 57.6 + - + +
243B MET* 3.9 11.4 - - - +
244B ALA* 3.3 23.9 + - - +
305B LEU* 5.0 3.7 - - + +
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Residues in contact with ILE 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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237B ASP 3.2 17.3 - - - +
238B ILE* 3.2 29.3 + - + +
239B PHE 3.1 0.6 - - - -
240B LYS* 1.3 74.4 - - + +
242B ILE* 1.3 62.5 + - + +
243B MET 3.0 4.6 + - - -
244B ALA* 3.0 4.5 + - - +
245B ILE* 2.9 35.1 + - + +
301B PHE* 3.1 27.4 - - + +
302B TYR* 3.5 19.7 - - + +
305B LEU* 3.2 56.3 - - + +
306B GLY 3.5 2.0 - - - +
309B PHE* 6.0 0.4 - - + -
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Residues in contact with ILE 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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67B LEU* 6.0 3.8 - - + -
119B LEU* 4.6 13.2 - - + -
122B LEU* 4.6 32.3 - - + -
126B ARG* 3.9 26.5 - - + -
218B ILE* 6.1 0.9 - - + -
238B ILE 2.9 13.1 + - - +
239B PHE* 3.3 18.1 + - + +
241B ILE* 1.3 76.2 - - + +
243B MET* 1.3 58.8 + - - +
245B ILE* 3.9 22.7 - - + +
246B VAL* 3.4 22.8 + - + +
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Residues in contact with MET 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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215B TYR* 3.5 42.0 - - + +
218B ILE* 5.6 7.4 - - + -
219B TRP* 5.7 12.3 - - + -
239B PHE 3.0 16.7 + - - +
240B LYS* 3.9 10.8 - - - +
241B ILE 3.0 0.2 - - - -
242B ILE* 1.3 77.1 - - + +
244B ALA* 1.3 66.8 + - - +
245B ILE 3.2 1.6 - - - -
246B VAL* 3.1 16.5 + - - +
247B LEU* 3.1 36.6 + - + +
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Residues in contact with ALA 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 LYS 3.3 12.8 + - - +
241B ILE* 3.0 9.4 + - - +
243B MET* 1.3 84.1 - - - +
245B ILE* 1.3 56.5 + - - +
247B LEU* 3.5 11.5 + - + +
248B PHE* 3.1 29.1 + - - +
301B PHE* 3.9 28.9 - - + -
305B LEU* 5.1 4.5 - - + -
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Residues in contact with ILE 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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8A PBF 4.3 27.4 - - + -
119B LEU* 5.8 1.8 - - + -
241B ILE* 2.9 21.5 + - + +
242B ILE* 3.9 28.0 - - + +
243B MET 3.2 0.2 - - - -
244B ALA* 1.3 77.2 - - - +
246B VAL* 1.3 59.3 + - + +
248B PHE* 3.8 4.9 + - - +
249B PHE* 3.0 26.6 + - + +
297B LEU* 4.8 6.4 - - + +
298B ASN* 4.1 27.6 - - - +
301B PHE* 3.3 38.8 - - + +
302B TYR* 4.4 6.1 - - + +
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Residues in contact with VAL 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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119B LEU* 5.2 8.3 - - + -
211B ILE* 4.5 20.6 - - + +
212B LEU* 4.1 26.2 - - + -
215B TYR* 4.5 21.1 - - + -
242B ILE* 3.4 24.0 + - + +
243B MET* 3.1 10.1 + - - +
245B ILE* 1.3 77.5 - - + +
247B LEU* 1.3 66.2 + - - +
249B PHE* 3.5 8.6 + - + +
250B PHE* 3.2 31.6 + - + +
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Residues in contact with LEU 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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215B TYR* 3.5 27.4 - - + +
243B MET* 3.1 37.7 + - + +
244B ALA* 3.8 11.9 - - + +
246B VAL* 1.3 77.9 - - + +
248B PHE* 1.3 56.0 + - - +
250B PHE* 3.3 3.5 + - - +
251B PHE* 2.9 59.0 + - + -
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Residues in contact with PHE 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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244B ALA 3.1 16.8 + - - +
245B ILE* 4.1 4.5 - - - +
247B LEU* 1.3 73.4 - - - +
249B PHE* 1.3 63.8 + - - +
251B PHE* 3.4 18.7 + + + +
252B SER* 3.0 32.2 + - - -
293B PHE* 4.0 26.2 - + - -
297B LEU* 3.8 25.8 - - + -
301B PHE* 3.8 31.6 - + + -
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Residues in contact with PHE 249 (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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8A PBF 3.3 70.7 - + + +
116B VAL* 5.2 1.3 - - + -
119B LEU* 3.7 29.8 - - + -
208B PHE* 3.5 37.5 - + - -
211B ILE* 5.5 2.5 - - + -
245B ILE* 3.0 20.7 + - + +
246B VAL* 3.7 11.2 - - + +
247B LEU 3.4 0.2 - - - -
248B PHE* 1.3 74.9 - - - +
250B PHE* 1.3 71.1 + + - +
252B SER* 3.3 0.6 + - - -
253B TRP* 2.9 35.2 + + + +
297B LEU* 3.9 9.9 - - + +
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Residues in contact with PHE 250 (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 PHE* 3.8 40.8 - + - -
211B ILE* 4.9 4.0 - - + -
212B LEU* 3.7 47.3 - - + -
246B VAL* 3.2 24.9 + - + +
247B LEU* 4.0 4.0 - - - +
249B PHE* 1.3 94.2 - + - +
251B PHE* 1.3 64.8 + - + +
252B SER 3.0 0.3 + - - -
253B TRP* 5.1 0.7 - - - +
254B ILE* 2.7 67.6 + - + +
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Residues in contact with PHE 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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247B LEU* 2.9 56.6 + - + +
248B PHE* 3.8 22.0 - + + +
250B PHE* 1.3 72.2 - - + +
252B SER* 1.3 56.9 + - - +
254B ILE* 4.9 2.7 - - + -
255B PRO* 3.2 25.8 - - - +
290B ILE* 6.0 2.3 - - - +
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Residues in contact with SER 252 (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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248B PHE* 3.0 23.9 + - - -
249B PHE* 3.6 1.1 - - - -
250B PHE 3.0 0.8 + - - -
251B PHE* 1.3 78.8 - - - +
253B TRP* 1.3 80.0 + - - +
255B PRO* 3.9 4.9 - - - +
290B ILE* 5.4 3.6 - - - +
291B ALA* 2.9 33.5 + - - +
293B PHE* 3.3 35.0 - - - -
297B LEU* 4.4 2.3 - - - +
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Residues in contact with TRP 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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7A PRO* 3.8 29.8 - - + +
8A PBF 3.5 51.6 + + + +
208B PHE* 6.0 1.3 - - + -
249B PHE* 2.9 30.5 + + + +
250B PHE* 5.4 0.4 - - + -
252B SER* 1.3 81.0 - - - +
254B ILE* 1.3 56.5 + - - +
255B PRO 3.5 0.7 - - - -
256B HIS* 3.6 38.4 - + - -
257B GLN* 2.7 42.5 + - + +
291B ALA* 3.0 21.2 + - - -
292B TYR* 3.5 24.7 - + - -
293B PHE 3.4 20.1 + - - -
294B ASN* 4.1 5.1 - - + +
297B LEU* 5.6 1.2 - - + +
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Residues in contact with ILE 254 (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 PHE* 5.6 4.5 - - + -
250B PHE* 2.7 65.1 + - + +
251B PHE* 4.7 3.1 - - + +
253B TRP* 1.3 71.4 - - - +
255B PRO* 1.4 63.3 - - + +
257B GLN* 4.9 12.6 - - + -
258B ILE* 2.8 60.4 + - + +
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Residues in contact with PRO 255 (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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251B PHE* 3.2 26.9 - - - +
252B SER 3.9 3.6 - - - +
253B TRP 3.6 2.2 - - - -
254B ILE* 1.4 99.0 - - + +
256B HIS* 1.3 60.2 + - - +
258B ILE* 4.1 6.0 - - + +
259B PHE 3.2 15.9 + - - -
287B THR* 3.3 34.3 - - + +
290B ILE* 5.0 9.0 - - + -
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Residues in contact with HIS 256 (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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5A ILE* 4.4 11.5 - - + +
7A PRO* 3.5 26.6 - - + +
253B TRP* 3.4 29.5 + + + +
254B ILE 3.4 0.2 - - - -
255B PRO* 1.3 76.9 - - - +
257B GLN* 1.3 60.4 + - - +
259B PHE* 3.0 4.9 + - - +
260B THR* 2.7 46.2 + - + -
287B THR* 3.7 11.5 + - - +
288B ILE* 3.7 40.0 + - + +
291B ALA* 3.1 34.3 - - + +
292B TYR* 4.9 4.2 + + - -
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Residues in contact with GLN 257 (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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6A HIS* 3.0 42.3 + - - -
7A PRO* 3.8 17.9 + - - +
204B PHE* 3.3 40.3 - - + -
208B PHE* 5.6 0.7 - - + -
253B TRP* 2.7 27.9 + - + +
254B ILE* 4.2 12.6 - - + +
256B HIS* 1.3 74.5 - - + +
258B ILE* 1.3 54.7 + - - +
260B THR* 3.4 11.0 - - - +
261B PHE* 2.8 35.4 + - + +
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Residues in contact with ILE 258 (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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254B ILE* 2.8 58.3 + - + +
255B PRO* 4.1 5.6 - - + +
257B GLN* 1.3 72.2 - - - +
259B PHE* 1.3 61.0 + - + +
261B PHE* 3.2 6.4 + - - +
262B LEU* 2.9 31.0 + - + +
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Residues in contact with PHE 259 (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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255B PRO 3.2 6.2 + - - +
256B HIS* 3.0 4.1 + - - +
258B ILE* 1.3 78.1 - - + +
260B THR* 1.3 61.4 + - - +
262B LEU* 3.3 28.5 + - + +
263B ASP* 3.1 47.0 + - - +
279B ILE* 5.7 3.4 - - + -
283B ALA* 3.7 24.2 - - + -
284B MET* 3.4 39.0 - - + -
287B THR* 3.0 41.9 - - + +
288B ILE* 5.1 0.9 - - + -
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Residues in contact with THR 260 (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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4A TYR* 4.7 8.8 - - - +
5A ILE* 2.9 32.1 + - - +
6A HIS* 4.4 4.9 - - + -
256B HIS* 2.7 29.7 + - + -
257B GLN* 3.4 37.0 - - - +
259B PHE* 1.3 73.3 - - - +
261B PHE* 1.3 62.4 + - - +
263B ASP* 3.5 7.3 + - - +
264B VAL* 3.4 24.1 + - + +
284B MET* 4.8 5.6 - - - +
288B ILE* 4.8 9.3 - - - +
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Residues in contact with PHE 261 (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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6A HIS* 4.1 22.0 - + - -
200B ASN* 6.1 1.1 - - - -
205B LEU* 5.8 8.3 - - + -
257B GLN* 2.8 28.5 + - + +
258B ILE* 3.7 5.8 - - - +
260B THR* 1.3 70.4 - - - +
262B LEU* 1.3 67.7 + - - +
264B VAL* 3.3 24.9 + - + +
265B LEU* 3.4 21.1 - - + +
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Residues in contact with LEU 262 (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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258B ILE* 2.9 19.6 + - + +
259B PHE* 3.5 43.5 - - + +
261B PHE* 1.3 75.4 - - - +
263B ASP* 1.3 65.1 + - - +
264B VAL 3.2 1.0 + - - -
265B LEU* 3.2 34.7 + - + +
266B ILE* 3.9 12.3 + - + +
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Residues in contact with ASP 263 (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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2A ARG* 2.9 52.9 + - - +
4A TYR* 5.3 5.4 - - + -
259B PHE* 3.1 28.6 + - - +
260B THR* 3.6 11.0 - - - +
261B PHE 3.4 0.2 - - - -
262B LEU* 1.3 75.2 - - - +
264B VAL* 1.3 62.0 + - + +
266B ILE* 3.2 9.7 + - - -
279B ILE* 3.2 27.4 - - - +
284B MET* 3.1 36.8 - - + +
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Residues in contact with VAL 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ASP* 4.7 1.0 - - - +
2A ARG* 4.1 11.8 - - + +
4A TYR* 5.9 3.8 - - + -
6A HIS* 5.3 2.0 - - + -
184B TYR* 3.5 57.7 - - + +
260B THR* 3.4 16.8 + - + +
261B PHE* 3.3 22.8 + - + +
262B LEU 3.2 1.8 + - - -
263B ASP* 1.3 76.4 - - + +
265B LEU* 1.3 63.4 + - - +
266B ILE 3.3 1.9 + - - -
267B GLN* 3.2 21.9 - - + +
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Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B PHE* 3.4 24.2 - - + +
262B LEU* 3.2 36.6 - - + +
263B ASP 3.4 0.2 + - - -
264B VAL* 1.3 78.7 - - + +
266B ILE* 1.3 68.8 + - + +
267B GLN* 3.2 17.7 + - - +
270B ILE* 3.9 12.1 - - - +
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Residues in contact with ILE 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ARG* 2.9 39.6 + - - +
262B LEU* 3.9 18.1 + - + +
263B ASP* 3.2 5.3 + - - +
265B LEU* 1.3 84.3 - - + +
267B GLN* 1.3 61.4 + - - +
270B ILE* 5.5 0.4 - - - -
272B ARG* 3.5 28.7 - - - +
277B ALA* 3.7 21.9 - - + +
279B ILE* 5.8 0.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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