Contacts of the helix formed by residues 196 - 231 (chain B) in PDB entry 2HL5
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 LEU 196 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ALA 4.5 7.0 - - - +
196A LEU* 4.2 20.4 - - + +
197A MET* 4.1 45.8 - - + +
200A VAL* 4.1 9.4 - - + +
194B ALA* 4.1 9.0 - - + +
195B GLU* 1.3 68.8 + - - +
197B MET* 1.3 64.1 + - - +
198B GLN 3.0 1.6 - - - +
199B GLN* 3.6 44.5 + - - +
200B VAL* 3.4 23.7 + - - +
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Residues in contact with MET 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 3.5 36.1 - - + -
194B ALA 4.4 4.7 - - - +
195B GLU* 2.8 41.4 - - - +
196B LEU* 1.3 74.8 - - - +
198B GLN* 1.3 66.0 + - - +
200B VAL* 3.2 17.3 + - - +
201B ASN* 3.2 13.2 + - - +
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Residues in contact with GLN 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLU* 2.6 46.2 + - + +
197B MET 1.3 82.0 - - - +
199B GLN* 1.3 64.0 + - + +
201B ASN* 3.3 12.3 + - - +
202B VAL* 3.3 20.9 + - + +
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Residues in contact with GLN 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A MET* 5.7 2.6 - - - +
200A VAL* 3.5 29.8 - - + +
204A LYS* 4.6 8.1 - - - +
195B GLU 5.0 0.8 - - - +
196B LEU* 3.6 38.7 + - - +
197B MET 3.2 0.2 - - - -
198B GLN* 1.3 80.2 - - + +
200B VAL* 1.3 62.2 + - - +
202B VAL* 3.5 5.4 + - - +
203B LEU* 3.0 33.9 + - + +
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Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 4.1 17.7 - - + +
199A GLN* 4.1 25.1 - - + +
200A VAL* 3.8 18.4 - - + +
203A LEU* 3.7 14.3 - - + +
196B LEU 3.4 13.9 + - - +
197B MET* 3.2 10.4 + - - +
199B GLN* 1.3 77.5 - - - +
201B ASN* 1.3 58.3 + - - +
203B LEU* 4.6 1.3 - - - -
204B LYS* 2.9 58.1 + - + +
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Residues in contact with ASN 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B MET 3.2 9.3 + - - +
198B GLN* 3.3 7.8 + - - +
200B VAL* 1.3 78.4 - - - +
202B VAL* 1.3 68.9 + - - +
204B LYS* 3.2 12.2 + - - +
205B LEU* 3.0 45.6 + - - +
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Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B GLN* 3.3 16.0 + - + +
199B GLN* 4.0 7.2 - - - +
201B ASN* 1.3 78.7 - - - +
203B LEU* 1.3 60.8 + - + +
205B LEU* 3.1 14.9 + - + +
206B THR* 2.9 37.2 + - - +
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A VAL* 3.7 35.4 - - + +
203A LEU* 3.8 17.7 - - + -
204A LYS* 4.0 25.1 - - + -
207A VAL* 4.1 24.2 - - + -
199B GLN* 3.0 25.7 + - + +
200B VAL 3.7 3.6 - - - +
202B VAL* 1.3 79.8 - - + +
204B LYS* 1.3 56.0 + - - +
206B THR* 3.1 8.6 + - - +
207B VAL* 2.9 34.9 + - - +
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Residues in contact with LYS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLN* 5.4 3.4 + - - -
203A LEU* 4.1 15.9 - - + +
200B VAL* 2.9 39.3 + - + +
201B ASN* 3.2 15.0 + - - +
203B LEU* 1.3 74.5 - - - +
205B LEU* 1.3 58.2 + - + +
207B VAL* 3.3 10.3 + - - +
208B GLU* 3.0 37.6 + - + +
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ASN* 3.0 46.2 + - - +
202B VAL* 3.1 12.3 + - + +
204B LYS* 1.3 73.2 - - + +
206B THR* 1.3 64.5 + - - +
208B GLU* 3.3 22.7 + - + +
209B ASP* 3.0 32.0 + - - +
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Residues in contact with THR 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A VAL* 4.1 17.5 - - + -
211A GLU* 5.4 2.0 - - - +
202B VAL* 2.9 23.9 + - - +
203B LEU* 3.1 12.2 + - + +
205B LEU* 1.3 73.6 - - - +
207B VAL* 1.3 61.1 + - - +
209B ASP* 3.3 8.3 + - + +
210B LEU* 2.9 49.3 + - + +
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Residues in contact with VAL 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 4.1 22.0 - - + -
206A THR* 4.1 17.9 - - + -
207A VAL* 3.6 20.2 - - + -
210A LEU* 3.8 19.2 - - + +
203B LEU 2.9 17.2 + - - +
204B LYS* 3.4 10.1 - - - +
206B THR* 1.3 75.6 - - - +
208B GLU* 1.3 58.9 + - + +
210B LEU* 3.2 2.6 + - - +
211B GLU* 2.9 50.9 + - - +
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Residues in contact with GLU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LYS* 3.0 24.1 + - + +
205B LEU* 3.3 27.8 + - + +
207B VAL* 1.3 76.7 - - + +
209B ASP* 1.3 64.7 + - - +
211B GLU* 3.4 12.5 + - - +
212B LYS* 3.1 46.5 + - - +
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Residues in contact with ASP 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 3.0 20.6 + - - +
206B THR* 3.7 11.2 - - + +
208B GLU* 1.3 77.4 - - - +
210B LEU* 1.3 59.3 + - + +
212B LYS* 3.3 17.7 + - - +
213B GLU* 2.9 31.1 + - - +
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A VAL* 3.8 19.5 - - + +
210A LEU* 3.8 19.0 - - + +
211A GLU* 3.8 34.5 - - + +
214A ARG* 3.6 34.2 - - + +
206B THR* 2.9 40.0 + - + +
207B VAL 3.8 3.4 - - - +
209B ASP* 1.3 74.5 - - + +
211B GLU* 1.3 61.2 - - - +
213B GLU* 3.6 9.5 - - - +
214B ARG* 2.8 32.6 + - - +
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Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A THR* 5.8 0.9 - - - +
210A LEU* 3.8 20.3 - - + +
207B VAL* 2.9 37.4 + - - +
208B GLU* 3.7 12.6 - - - +
210B LEU* 1.3 75.3 - - - +
212B LYS* 1.3 56.8 + - + +
214B ARG* 3.3 21.7 + - - +
215B ASP* 2.8 40.2 + - - +
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Residues in contact with LYS 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLU* 3.1 39.3 + - - +
209B ASP* 3.3 17.4 + - - +
211B GLU* 1.3 76.5 - - + +
213B GLU* 1.3 57.5 + - - +
215B ASP* 3.4 7.5 + - - +
216B PHE* 3.0 29.0 + - - +
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Residues in contact with GLU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ARG* 3.2 40.5 + - + +
209B ASP 2.9 17.2 + - - +
210B LEU* 3.6 11.5 - - - +
212B LYS* 1.3 73.5 - - - +
214B ARG* 1.3 65.9 + - - +
216B PHE* 3.3 8.9 + - + +
217B TYR* 3.1 61.9 + - + +
51C LEU* 3.7 15.3 - - - +
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Residues in contact with ARG 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 3.6 20.0 - - + +
213A GLU* 3.0 54.2 + - + +
214A ARG* 4.4 16.3 - - + +
217A TYR* 3.6 9.4 - - + -
210B LEU 2.8 21.1 + - - +
211B GLU* 3.5 25.3 + - - +
213B GLU* 1.3 72.6 - - - +
215B ASP* 1.3 81.7 + - - +
217B TYR* 3.4 4.5 + - - +
218B PHE* 2.9 30.0 + - - +
51D LEU* 3.6 30.6 - - - +
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Residues in contact with ASP 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B GLU* 2.8 22.9 + - - +
212B LYS* 3.6 7.2 - - - +
214B ARG* 1.3 105.6 + - - +
216B PHE* 1.3 56.2 + - - +
218B PHE* 3.8 5.1 - - - +
219B GLY* 2.9 27.5 + - - -
51D LEU* 3.8 11.8 - - - +
76D ARG* 5.0 13.1 + - - +
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Residues in contact with PHE 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ALA 3.6 14.1 - - - -
249A THR 4.2 2.2 - - - -
250A ASP* 4.1 25.6 - - + -
212B LYS 3.0 15.4 + - - +
213B GLU* 3.3 12.3 + - + +
215B ASP* 1.3 75.5 - - - +
217B TYR* 1.3 91.3 + + - +
219B GLY* 3.4 2.8 + - - -
220B LYS* 3.3 56.1 + - + +
54C THR* 3.7 28.7 - - + -
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Residues in contact with TYR 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ARG* 3.9 22.0 - - + -
217A TYR* 3.9 17.3 - - + -
218A PHE* 3.8 21.8 - + + +
221A LEU* 3.6 26.3 - - + +
213B GLU* 3.1 53.2 + - + +
214B ARG* 4.0 2.2 - - - +
216B PHE* 1.3 97.3 - + - +
218B PHE* 1.3 65.1 + - - +
220B LYS* 3.2 9.2 + - + +
221B LEU* 3.2 23.2 + - - +
49C MET* 5.0 4.7 - - + -
50C THR 4.1 4.0 + - - -
51C LEU* 3.4 31.1 + - + +
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Residues in contact with PHE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 3.9 21.4 - + + +
214B ARG 2.9 18.0 + - - +
215B ASP* 3.9 5.2 - - - +
217B TYR* 1.3 76.7 - - - +
219B GLY* 1.3 51.8 + - - +
221B LEU* 3.3 8.3 + - - +
222B ARG* 2.8 37.7 + - + +
46D TYR* 4.9 2.2 - - - -
49D MET* 3.6 36.3 - - + -
50D THR* 3.5 44.2 - - - -
51D LEU* 3.6 22.9 - - + -
76D ARG* 3.5 46.0 - - - +
78D TYR* 4.9 0.2 - + - -
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Residues in contact with GLY 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ASP 2.9 17.4 + - - -
216B PHE 3.4 2.7 + - - -
217B TYR 3.2 0.4 - - - -
218B PHE* 1.3 78.4 - - - +
220B LYS* 1.3 56.1 + - - +
222B ARG* 3.4 7.4 + - - +
223B ASN* 3.0 38.2 + - - -
76D ARG* 5.0 6.1 - - - -
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Residues in contact with LYS 220 (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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221A LEU* 3.8 26.9 - - + -
245A ILE* 2.8 43.5 + - + +
246A LEU* 3.3 17.8 + - - +
248A ALA* 2.8 29.3 + - - +
216B PHE* 3.3 47.1 + - + +
217B TYR* 3.2 7.7 + - + +
219B GLY* 1.3 72.6 - - - +
221B LEU* 1.3 60.4 + - - +
223B ASN* 3.1 2.9 + - - +
224B ILE* 2.9 36.0 + - + +
49C MET* 4.2 6.5 - - + -
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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
----------------------------------------------------------
217A TYR* 3.6 49.8 - - + +
220A LYS* 3.8 23.6 - - + -
221A LEU* 3.4 23.3 - - + -
224A ILE* 4.0 6.1 - - + -
217B TYR 3.2 9.3 + - - +
218B PHE* 3.5 8.3 - - - +
220B LYS* 1.3 76.5 - - - +
222B ARG* 1.3 58.8 + - - +
224B ILE* 3.3 3.9 + - - +
225B GLU* 2.8 30.1 + - - +
246B LEU* 3.7 23.8 - - + +
49D MET* 3.9 25.1 - - + -
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Residues in contact with ARG 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B PHE* 2.8 31.8 + - + +
219B GLY* 3.7 8.3 - - - +
220B LYS 3.2 0.2 - - - -
221B LEU* 1.3 72.6 - - - +
223B ASN* 1.3 60.6 + - - +
225B GLU* 3.0 28.3 + - - +
226B LEU* 3.0 62.5 + - + +
229B GLN* 4.3 0.4 - - - +
46D TYR* 3.3 44.9 + - - +
47D VAL 2.9 27.5 + - - +
48D GLY* 3.7 0.2 - - - -
49D MET* 4.8 3.7 - - - -
76D ARG* 4.6 11.2 - - - +
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Residues in contact with ASN 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ILE* 3.9 28.1 - - + +
219B GLY* 3.0 24.2 + - - +
220B LYS* 3.6 5.2 - - - +
222B ARG* 1.3 77.2 - - - +
224B ILE* 1.3 61.3 + - - +
226B LEU* 3.4 18.5 + - - +
227B ILE* 3.1 28.5 + - - +
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Residues in contact with ILE 224 (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 13.9 - - + -
224A ILE* 4.4 11.9 - - + -
242A ILE* 3.9 31.0 - - + -
245A ILE* 4.0 16.8 - - + -
246A LEU* 3.8 29.4 - - + -
220B LYS 2.9 21.6 + - - +
221B LEU* 3.7 4.5 - - - +
223B ASN* 1.3 71.9 - - - +
225B GLU* 1.3 67.0 + - - +
227B ILE* 3.2 9.6 + - - +
228B CYS* 3.0 22.5 + - - -
242B ILE* 3.8 29.4 - - + -
246B LEU* 4.6 3.1 - - + -
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Residues in contact with GLU 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU 2.8 18.8 + - - +
222B ARG* 3.0 30.8 + - - +
224B ILE* 1.3 73.9 - - - +
226B LEU* 1.3 56.8 + - - +
228B CYS* 3.3 4.4 + - + +
229B GLN* 3.0 41.0 + - + +
243B VAL* 6.5 0.2 - - + -
246B LEU* 3.7 19.5 - - + +
247B TYR* 2.5 37.6 + - - +
48D GLY* 2.9 23.2 - - - -
49D MET* 3.0 27.8 + - - +
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ARG* 3.0 56.2 + - + +
223B ASN* 3.5 23.1 - - - +
224B ILE 3.2 0.2 - - - -
225B GLU* 1.3 73.4 - - - +
227B ILE* 1.3 65.1 + - + +
229B GLN* 3.3 22.6 + - - +
230B GLU* 3.0 39.4 + - - +
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Residues in contact with ILE 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A VAL* 3.7 30.3 - - + +
241A ARG* 3.7 60.3 - - + +
242A ILE* 3.9 17.7 - - + -
245A ILE* 4.0 15.9 - - + -
223B ASN 3.1 15.8 + - - +
224B ILE* 3.2 7.4 + - - +
226B LEU* 1.3 75.6 - - + +
228B CYS* 1.3 62.1 + - - +
230B GLU* 3.2 8.9 + - - +
231B ASN* 2.9 34.3 + - - +
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Residues in contact with CYS 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 4.5 2.7 - - - -
224B ILE* 3.0 19.0 + - - +
225B GLU* 3.5 10.5 - - + +
227B ILE* 1.3 76.2 - - - +
229B GLN* 1.3 62.7 + - + +
231B ASN 3.3 3.6 + - - -
232B GLU* 3.3 22.7 + - - +
239B LEU* 4.2 33.2 - - + +
242B ILE* 3.9 28.3 - - - -
243B VAL* 3.8 27.9 - - + +
246B LEU* 4.7 1.8 - - - -
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Residues in contact with GLN 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ARG* 4.3 0.2 - - - +
225B GLU* 3.0 37.0 + - + +
226B LEU* 3.3 27.3 + - - +
228B CYS* 1.3 75.7 - - + +
230B GLU* 1.3 63.1 + - + +
231B ASN 3.2 0.9 + - - -
232B GLU* 3.2 37.7 - - - +
247B TYR* 4.4 4.7 + - - +
29D VAL* 6.2 0.3 - - - +
47D VAL* 3.1 42.5 + - - +
56D LYS* 5.4 1.2 - - - +
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ARG* 3.3 34.6 + - - +
226B LEU* 3.0 30.1 + - - +
227B ILE* 3.5 10.4 - - - +
229B GLN* 1.3 76.3 - - + +
231B ASN* 1.3 66.5 + - - +
232B GLU 3.6 1.0 + - - -
233B GLY 5.2 0.9 + - - -
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Residues in contact with ASN 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A VAL* 3.6 27.9 - - - +
241A ARG* 4.4 9.3 - - - +
227B ILE* 2.9 30.9 + - - +
228B CYS 3.5 4.3 - - - -
229B GLN 3.1 0.4 - - - -
230B GLU* 1.3 90.4 - - - +
232B GLU* 1.3 62.4 + - - +
233B GLY 3.2 3.4 - - - +
234B GLU* 3.3 39.0 + - - +
235B ASN 4.4 0.7 + - - -
236B ASP 5.2 0.3 + - - -
239B LEU* 3.7 23.9 - - + +
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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