Contacts of the helix formed by residues 204 - 234 (chain B) in PDB entry 2RIB
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 VAL 204 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 5.0 4.0 - - - +
205B ALA* 1.3 65.1 + - + +
206B SER* 3.0 31.8 + - - +
207B LEU* 3.4 32.3 + - + +
208B ARG* 3.8 3.3 + - - +
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Residues in contact with ALA 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B VAL* 1.3 75.9 - - + +
206B SER* 1.3 64.4 + - - +
207B LEU 3.2 0.2 - - - -
208B ARG* 3.1 21.0 + - + +
209B GLN* 3.0 36.3 + - + +
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Residues in contact with SER 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B VAL* 3.0 20.3 - - - +
205B ALA* 1.3 78.5 - - - +
207B LEU* 1.3 64.4 + - - +
209B GLN* 3.3 18.1 + - - +
210B GLN* 3.1 37.3 + - - +
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Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 4.1 10.8 - - + -
204B VAL* 3.4 23.2 + - + +
205B ALA 3.2 0.2 - - - -
206B SER* 1.3 77.7 - - - +
208B ARG* 1.3 66.1 + - - +
210B GLN* 3.1 22.8 + - - +
211B VAL* 2.9 28.6 + - - +
207C LEU* 4.1 21.3 - - + -
208C ARG* 3.8 51.1 - - + +
211C VAL* 4.5 13.3 - - + +
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Residues in contact with ARG 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 3.9 27.2 - - + +
204B VAL 3.8 1.6 + - - +
205B ALA* 3.1 25.4 + - - +
207B LEU* 1.3 79.5 - - - +
209B GLN* 1.3 65.1 + - - +
211B VAL* 3.1 4.5 + - - +
212B GLU* 2.9 55.2 + - + +
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Residues in contact with GLN 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ALA* 3.0 24.5 + - + +
206B SER* 3.6 18.9 + - - +
208B ARG* 1.3 78.5 - - + +
210B GLN* 1.3 58.6 + - + +
212B GLU* 3.3 16.9 + - - +
213B ALA* 3.0 28.5 + - - +
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Residues in contact with GLN 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B SER* 3.1 29.3 + - - +
207B LEU* 3.1 22.5 + - - +
209B GLN* 1.3 75.0 - - + +
211B VAL* 1.3 61.6 + - - +
213B ALA* 3.3 7.6 + - - +
214B LEU* 2.9 34.2 + - - +
208C ARG* 6.1 1.4 - - - +
211C VAL* 4.1 11.2 - - + +
215C GLN* 2.7 39.3 + - - +
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 3.9 19.5 - - + -
210A GLN* 4.2 22.9 - - + +
211A VAL* 3.8 26.9 - - + +
214A LEU* 4.9 6.7 - - + -
207B LEU 2.9 19.7 + - - +
208B ARG 3.5 5.8 - - - +
210B GLN* 1.3 72.8 - - - +
212B GLU* 1.3 67.6 + - + +
214B LEU* 3.3 9.8 + - + +
215B GLN* 3.0 40.9 + - + +
211C VAL* 4.3 12.8 - - + -
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Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ARG* 2.9 52.7 + - + +
209B GLN* 3.6 21.9 + - - +
211B VAL* 1.3 77.2 - - + +
213B ALA* 1.3 62.2 + - - +
215B GLN* 3.4 20.0 + - - +
216B GLY* 3.3 17.0 + - - -
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Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B GLN 3.0 13.9 + - - +
210B GLN* 3.5 11.9 - - - +
211B VAL 3.2 0.2 - - - -
212B GLU* 1.3 75.7 - - - +
214B LEU* 1.3 66.3 + - - +
216B GLY* 3.1 4.2 + - - -
217B GLN* 3.1 30.8 + - + +
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Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 3.6 12.8 - - + -
210B GLN 2.9 18.8 + - - +
211B VAL* 3.3 11.2 + - + +
213B ALA* 1.3 76.0 - - + +
215B GLN* 1.3 57.5 + - - +
217B GLN* 3.3 17.9 + - - +
218B VAL* 2.9 35.4 + - + +
211C VAL* 4.0 23.8 - - + -
214C LEU* 3.6 28.7 - - + -
215C GLN* 3.9 26.5 - - + +
218C VAL* 3.8 26.2 - - + -
219C GLN* 5.0 1.1 - - - +
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Residues in contact with GLN 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLN* 3.1 30.2 + - - +
214A LEU* 3.7 28.3 - - + +
211B VAL* 3.0 23.7 + - - +
212B GLU* 3.6 21.0 + - - +
213B ALA 3.2 0.2 - - - -
214B LEU* 1.3 74.7 - - - +
216B GLY* 1.3 58.8 + - - +
218B VAL* 3.9 1.4 - - - +
219B GLN* 3.1 28.8 + - - +
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Residues in contact with GLY 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLU 3.3 6.8 + - - -
213B ALA* 3.1 7.9 + - - -
215B GLN* 1.3 78.2 - - - +
217B GLN* 1.3 63.8 + - - +
219B GLN* 3.5 8.3 + - - +
220B HIS* 3.2 21.1 + - - +
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Residues in contact with GLN 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ALA* 3.1 18.1 + - + +
214B LEU* 3.8 17.9 - - - +
216B GLY* 1.3 76.3 - - - +
218B VAL* 1.3 64.2 + - - +
220B HIS* 3.3 7.6 + - - +
221B LEU* 3.0 28.9 + - - +
218C VAL* 3.8 12.5 - - + +
219C GLN* 3.2 28.7 + - - +
222C GLN* 3.2 32.6 + - - +
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Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 3.9 24.9 - - + -
217A GLN* 4.9 5.6 - - + +
218A VAL* 3.6 31.2 - - + +
221A LEU* 4.9 5.8 - - + -
214B LEU 2.9 21.3 + - - +
215B GLN 3.9 3.6 - - - +
217B GLN* 1.3 74.3 - - - +
219B GLN* 1.3 60.1 + - - +
221B LEU* 3.3 9.8 + - + +
222B GLN* 2.9 57.7 + - + +
218C VAL* 4.1 15.5 - - + -
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Residues in contact with GLN 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B GLN 3.1 18.1 + - - +
216B GLY* 3.9 7.6 - - - +
217B GLN 3.3 0.2 - - - -
218B VAL* 1.3 77.3 - - - +
220B HIS* 1.3 62.7 + - - +
222B GLN* 3.4 14.3 + - + +
223B ALA* 3.0 25.4 + - + +
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Residues in contact with HIS 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B GLY 3.2 11.5 + - - +
217B GLN* 3.5 11.2 - - - +
218B VAL 3.2 0.2 - - - -
219B GLN* 1.3 79.4 - - - +
221B LEU* 1.3 70.1 + - + +
223B ALA* 3.3 5.2 + - - +
224B ALA* 2.9 42.4 + - + +
222C GLN* 5.7 5.2 - - + -
225C PHE* 5.8 2.2 - + - -
229C LYS* 5.7 4.8 + - - -
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 3.8 20.4 - - + -
217B GLN 3.0 19.0 + - - +
218B VAL* 3.7 9.9 - - + +
220B HIS* 1.3 86.1 - - + +
222B GLN* 1.3 58.1 + - - +
224B ALA* 3.8 2.5 - - - +
225B PHE* 2.7 34.6 + - - +
218C VAL* 4.4 12.8 - - + +
221C LEU* 4.1 23.6 - - + +
222C GLN* 4.0 37.5 - - + +
225C PHE* 4.1 29.9 - - + -
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Residues in contact with GLN 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLN* 3.6 41.9 + - - +
221A LEU* 4.3 18.9 - - + +
218B VAL* 2.9 36.5 + - + +
219B GLN* 3.8 15.3 - - + +
221B LEU* 1.3 76.4 - - - +
223B ALA* 1.3 57.6 + - - +
225B PHE* 3.8 4.6 - - - +
226B SER* 2.9 31.2 + - - -
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Residues in contact with ALA 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B GLN* 3.0 20.7 + - + +
220B HIS* 3.8 5.4 - - - +
222B GLN* 1.3 76.0 - - - +
224B ALA* 1.3 62.8 + - - +
226B SER* 3.3 7.6 + - - -
227B GLN* 3.3 20.8 + - - +
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Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B HIS* 2.9 34.1 + - + +
221B LEU* 3.8 2.5 - - - +
223B ALA* 1.3 75.9 - - - +
225B PHE* 1.3 62.7 + - - +
227B GLN* 3.3 10.3 + - - +
228B TYR* 3.1 31.3 + - + -
225C PHE* 3.5 25.4 - - + -
229C LYS* 5.5 1.3 - - + +
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Residues in contact with PHE 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 3.8 20.9 - - + -
224A ALA* 3.7 30.7 - - + -
225A PHE* 3.8 24.9 - + + -
228A TYR* 3.7 26.9 - + + -
221B LEU 2.7 24.1 + - - +
222B GLN 3.9 3.1 - - - +
224B ALA* 1.3 70.0 - - - +
226B SER* 1.3 65.8 + - - +
228B TYR* 3.2 3.4 + - + +
229B LYS* 2.9 60.4 + - + +
225C PHE* 3.8 28.9 - + + -
228C TYR* 5.0 6.5 - + - -
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Residues in contact with SER 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B GLN 2.9 19.3 + - - -
223B ALA* 3.5 8.5 - - - -
224B ALA 3.3 0.2 - - - -
225B PHE* 1.3 76.9 - - - +
227B GLN* 1.3 64.1 + - - +
229B LYS* 3.6 31.3 + - - +
230B LYS* 3.7 20.5 + - - +
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Residues in contact with GLN 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ALA 3.3 9.8 + - - +
224B ALA* 3.5 10.3 - - - +
225B PHE 3.1 0.2 - - - -
226B SER* 1.3 80.2 - - - +
228B TYR* 1.3 68.7 + - - +
230B LYS* 3.2 13.0 + - - +
231B VAL* 3.2 18.7 + - - +
242C GLU* 2.9 28.6 + - - +
244C ILE* 3.5 30.0 - - + +
355C PHE* 3.0 39.2 + - + +
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Residues in contact with TYR 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ALA* 3.1 27.9 + - + +
225B PHE* 3.2 4.9 + - + +
227B GLN* 1.3 80.2 - - - +
229B LYS* 1.3 61.0 + - - +
230B LYS 3.2 0.2 - - - -
231B VAL* 3.6 5.2 - - + +
232B GLU* 2.8 32.2 + - - +
225C PHE* 3.8 11.0 - + + -
228C TYR* 3.5 33.1 + + + +
229C LYS* 3.6 46.3 + - + +
232C GLU* 3.9 15.0 - - + -
233C LEU* 3.5 30.9 - - + +
239C SER* 4.6 4.3 - - - -
244C ILE* 3.4 30.2 - - + +
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Residues in contact with LYS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ALA* 5.6 1.7 - - + +
228A TYR* 3.5 44.4 - - + +
225B PHE* 2.9 47.7 + - + +
226B SER* 3.7 28.0 + - - +
227B GLN 3.2 0.6 - - - -
228B TYR* 1.3 76.3 - - - +
230B LYS* 1.3 63.8 + - + +
232B GLU* 3.8 1.0 - - - +
233B LEU* 3.2 31.5 + - - +
228C TYR* 5.0 0.2 - - - -
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Residues in contact with LYS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B SER* 3.8 20.4 - - - +
227B GLN* 3.2 9.3 + - - +
229B LYS* 1.3 76.6 - - + +
231B VAL* 1.3 65.0 + - - +
233B LEU* 3.4 5.6 + - - +
234B PHE* 3.3 22.9 + - - +
264C ALA* 3.9 14.4 - - - +
265C GLY* 3.6 29.4 + - - +
355C PHE* 3.8 21.8 - - + +
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLN* 3.2 14.5 + - + +
228B TYR* 3.6 9.9 - - + +
230B LYS* 1.3 76.5 - - - +
232B GLU* 1.3 60.9 + - - +
234B PHE* 3.3 7.4 + - - +
232C GLU* 3.5 24.0 - - + +
233C LEU* 4.8 4.9 - - + -
237C GLY* 6.1 0.2 - - - -
244C ILE* 3.8 35.9 - - + -
246C LYS* 2.9 39.6 + - + +
355C PHE* 3.6 34.5 - - + -
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Residues in contact with GLU 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A TYR* 2.6 42.9 - - + +
231A VAL* 3.2 18.3 - - + +
232A GLU* 3.0 24.0 + - - +
228B TYR 2.8 20.1 + - - +
229B LYS 3.8 4.7 - - - +
231B VAL* 1.3 74.8 - - - +
233B LEU* 1.3 61.2 + - + +
234B PHE 3.3 1.4 + - - +
236B ASN* 5.4 0.9 + - - +
237B GLY 5.2 0.7 + - - -
246B LYS* 5.3 10.2 + - - +
228C TYR* 2.6 35.2 + - - +
232C GLU* 3.4 24.2 - - - +
246C LYS* 3.6 9.0 + - - -
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A TYR* 3.6 25.4 - - + +
231A VAL* 4.2 11.9 - - + -
229B LYS 3.2 17.0 + - - +
230B LYS* 3.4 5.4 + - - +
231B VAL 3.3 0.2 - - - -
232B GLU* 1.3 77.7 - - - +
234B PHE* 1.3 58.5 + - - +
235B PRO* 3.5 1.2 - - - +
236B ASN 3.3 1.6 + - - -
237B GLY* 2.8 50.2 + - - +
238B GLN* 4.8 0.2 - - - -
239B SER* 3.6 38.1 - - - +
244B ILE* 3.8 26.0 - - + -
264C ALA* 6.1 0.4 - - - -
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Residues in contact with PHE 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LYS 3.3 15.1 + - - +
231B VAL 3.3 4.2 + - - +
232B GLU 3.2 2.0 - - - +
233B LEU* 1.3 77.1 - - - +
235B PRO* 1.3 75.1 - - + +
236B ASN 3.6 0.7 - - - -
246C LYS* 2.7 69.5 + - + -
248C ALA* 3.6 32.5 - - + -
260C LEU* 4.3 21.5 - - + -
264C ALA* 3.8 20.8 - - + +
351C VAL* 4.0 8.1 - - + -
353C CYS* 3.3 26.5 - - - -
355C PHE* 3.8 22.9 - + + -
----------------------------------------------------------
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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