Contacts of the helix formed by residues 210 - 234 (chain D) in PDB entry 1OJ7
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 ALA 210 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ASN* 3.8 3.8 - - - -
1D LEU* 4.1 11.2 - - + -
208D VAL* 2.8 17.8 + - + +
209D ASP* 1.3 71.2 - - - +
211D LYS* 1.3 59.3 + - - +
212D ILE 3.4 2.7 - - - -
213D HIS* 3.6 30.1 - - + +
214D ASP* 3.0 32.9 + - - +
260D VAL* 3.9 17.5 - - + -
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Residues in contact with LYS 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A THR* 3.6 24.7 - - + +
226A GLU* 3.4 28.5 - - - +
227A ASP* 2.8 42.2 + - - +
230A LYS* 3.8 13.2 - - - +
240A VAL* 5.5 0.2 - - - +
243A ASN* 3.0 11.8 + - - +
209D ASP* 2.9 33.8 + - - +
210D ALA* 1.3 71.8 - - - +
212D ILE* 1.3 61.1 + - - +
214D ASP* 3.7 7.1 - - - +
215D ARG* 2.9 34.8 + - + +
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Residues in contact with ILE 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A GLY 4.1 2.0 - - - +
220A ILE* 3.8 23.3 - - + +
223A THR* 3.7 19.7 - - + +
243A ASN* 4.2 9.5 + - - +
246A TRP* 3.8 27.1 - - + +
247A ALA* 3.7 41.5 - - + +
250A GLN* 4.2 4.9 - - + -
210D ALA 3.4 0.6 - - - -
211D LYS* 1.3 73.0 - - - +
213D HIS* 1.3 62.6 + - - +
215D ARG* 3.3 2.4 + - - -
216D PHE* 2.9 60.8 + - + -
255D LEU* 6.1 0.2 - - + -
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Residues in contact with HIS 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TRP* 3.4 33.5 + + - -
1D LEU* 3.8 20.2 - - + -
4D PHE* 4.9 1.6 - + - -
203D TYR* 5.5 0.4 - - - -
210D ALA* 3.4 23.4 + - + +
211D LYS 3.4 0.2 - - - -
212D ILE* 1.3 77.3 - - - +
214D ASP* 1.3 59.4 + - - +
216D PHE* 3.8 5.0 - - - +
217D ALA* 2.9 32.0 + - - +
255D LEU 3.8 9.6 + - - -
256D ILE* 3.3 36.7 - - - +
258D ALA* 2.8 31.7 + - - +
260D VAL* 3.7 12.3 - - + -
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Residues in contact with ASP 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2D LYS* 4.3 5.4 + - - -
203D TYR* 3.5 10.7 - - - -
208D VAL 4.2 10.9 - - - +
210D ALA* 3.0 22.6 + - - +
211D LYS* 3.7 7.5 - - - +
212D ILE 3.3 0.2 - - - -
213D HIS* 1.3 79.3 - - - +
215D ARG* 1.3 58.4 + - - +
217D ALA* 3.3 1.2 + - - +
218D GLU* 2.8 38.2 + - - +
303D LYS* 3.0 27.7 + - - -
306D GLN* 3.1 33.7 + - - +
310D ARG* 4.7 3.8 - - - +
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Residues in contact with ARG 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ARG* 4.7 5.4 - - - +
216A PHE* 5.1 0.2 - - - -
219A GLY* 3.6 37.9 - - - +
222A LEU* 3.6 32.4 - - - +
223A THR* 4.1 3.5 + - - +
226A GLU* 3.2 27.1 + - - -
211D LYS* 2.9 22.3 + - + +
212D ILE* 3.9 3.4 - - - +
214D ASP* 1.3 76.5 - - - +
216D PHE* 1.3 60.3 + - + +
218D GLU* 3.7 13.2 + - - +
219D GLY* 2.8 26.0 + - - -
310D ARG* 3.4 47.8 - - - +
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Residues in contact with PHE 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PHE* 3.4 80.1 - + + -
220A ILE* 4.1 12.3 - - + -
250A GLN* 4.0 33.0 - - + -
255A LEU* 4.8 0.7 - - + -
256A ILE* 5.2 2.0 - - + -
212D ILE* 2.9 44.1 + - + +
213D HIS* 3.8 1.8 - - - +
215D ARG* 1.3 78.9 - - + +
217D ALA* 1.3 65.0 + - - +
219D GLY 3.2 0.7 + - - -
220D ILE* 3.0 24.1 + - - +
255D LEU* 3.9 18.6 - - + -
256D ILE* 3.8 13.5 - - + -
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Residues in contact with ALA 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D THR* 3.3 25.8 - - + +
203D TYR* 3.8 26.9 - - + -
213D HIS 2.9 17.7 + - - +
214D ASP 3.7 3.4 - - - +
216D PHE* 1.3 78.0 - - - +
218D GLU* 1.3 61.7 + - - +
220D ILE* 3.2 2.2 + - - -
221D LEU* 3.1 28.1 + - - +
256D ILE* 4.4 13.8 - - + +
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Residues in contact with GLU 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D TYR* 2.6 36.4 + - + +
214D ASP 2.8 24.9 + - - +
215D ARG* 3.7 13.9 + - - +
217D ALA* 1.3 72.4 - - - +
219D GLY* 1.3 57.5 + - - +
221D LEU* 3.4 2.5 + - - +
222D LEU* 2.9 43.1 + - + +
306D GLN* 2.7 23.7 + - - -
310D ARG* 2.9 44.8 + - + +
311D VAL* 4.2 14.1 - - + -
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Residues in contact with GLY 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ILE* 4.5 3.1 - - - -
215A ARG* 3.6 32.2 - - - +
216A PHE* 5.0 1.6 - - - -
215D ARG 2.8 16.3 + - - -
216D PHE* 3.2 5.4 + - - -
217D ALA 3.2 0.4 - - - -
218D GLU* 1.3 74.5 - - - +
220D ILE* 1.3 59.2 + - - +
222D LEU* 3.5 2.1 + - - +
223D THR* 2.8 33.8 + - - -
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Residues in contact with ILE 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ILE* 3.9 19.5 - - + -
216A PHE* 4.1 11.0 - - + -
199D THR* 3.3 18.6 - - - +
216D PHE 3.0 18.1 + - - +
217D ALA* 3.2 6.0 + - - +
219D GLY* 1.3 74.8 - - - +
221D LEU* 1.3 57.4 + - - +
223D THR* 3.3 2.8 + - - -
224D LEU* 2.9 45.7 + - + +
247D ALA* 4.0 18.8 - - + +
250D GLN* 3.6 35.9 - - + +
251D ALA* 4.0 7.0 - - + -
256D ILE* 4.1 18.2 - - + -
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Residues in contact with LEU 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D PHE* 3.5 51.9 - - + +
199D THR* 3.7 13.2 - - + +
200D VAL* 3.9 18.8 - - + -
203D TYR* 4.0 18.2 - - + -
217D ALA 3.1 18.0 + - - +
218D GLU 3.7 4.0 - - - +
220D ILE* 1.3 76.7 - - - +
222D LEU* 1.3 61.5 + - - +
224D LEU* 3.2 4.8 + - + +
225D ILE* 3.0 30.2 + - - +
307D TYR* 4.0 8.5 - - + -
311D VAL* 4.0 29.2 - - + -
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Residues in contact with LEU 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ARG* 3.7 46.4 - - - +
218D GLU* 2.9 30.4 + - + +
219D GLY* 3.9 4.0 - - - +
221D LEU* 1.3 75.1 - - - +
223D THR* 1.3 58.4 + - - +
225D ILE* 3.4 8.2 + - + +
226D GLU* 3.1 28.6 + - - +
310D ARG 3.8 20.2 - - - +
311D VAL* 3.5 29.4 - - - +
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Residues in contact with THR 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A LYS* 3.6 43.0 + - + +
212A ILE* 3.7 23.1 - - + +
215A ARG* 4.0 4.7 + - - +
219D GLY 2.8 21.0 + - - -
220D ILE 3.5 4.7 - - - -
222D LEU* 1.3 75.2 - - - +
224D LEU* 1.3 60.3 + - + +
226D GLU* 3.8 3.7 - - - +
227D ASP* 2.9 30.2 + - + +
243D ASN* 4.2 21.1 - - + +
244D VAL* 5.7 0.4 - - - +
247D ALA* 4.7 2.9 - - + -
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Residues in contact with LEU 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D VAL* 4.0 24.2 - - + +
195D ALA* 3.8 14.1 - - + -
196D PHE* 3.5 43.5 - - + +
220D ILE* 2.9 38.0 + - + +
221D LEU* 3.2 4.2 + - - +
223D THR* 1.3 74.1 - - - +
225D ILE* 1.3 62.9 + - - +
228D GLY* 2.8 30.3 + - - +
244D VAL* 4.6 20.0 - - + +
247D ALA* 3.9 20.6 - - + -
333D PHE* 3.5 8.6 - - - -
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Residues in contact with ILE 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D PHE* 3.9 16.4 - - + -
221D LEU 3.0 19.0 + - - +
222D LEU* 3.7 7.9 - - + +
224D LEU* 1.3 78.1 - - - +
226D GLU* 1.3 58.6 + - - +
229D PRO* 3.1 23.7 - - - +
311D VAL* 3.4 39.9 - - + +
312D TRP* 3.5 41.1 - - + -
333D PHE* 3.7 14.3 - - + -
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Residues in contact with GLU 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A LYS* 3.8 15.9 - - + -
222D LEU 3.1 17.9 + - - +
223D THR* 3.9 4.0 - - - +
225D ILE* 1.3 80.7 - - - +
227D ASP* 1.3 66.2 + - - +
229D PRO* 3.7 6.2 - - - +
230D LYS* 3.1 48.3 + - - +
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Residues in contact with ASP 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ASP* 4.4 0.2 - - - +
211A LYS* 3.0 20.9 + - + -
223D THR 2.9 16.4 + - - +
226D GLU* 1.3 72.5 - - - +
228D GLY* 1.3 60.1 + - - +
229D PRO 3.5 0.9 - - - -
230D LYS* 2.8 32.5 + - - -
231D ALA* 3.0 25.8 + - - +
240D VAL* 3.4 34.8 - - + +
243D ASN* 2.8 35.7 + - + +
244D VAL* 3.9 7.7 - - + +
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Residues in contact with GLY 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D VAL* 4.8 0.2 - - - +
192D VAL* 3.9 25.8 - - - +
223D THR 4.1 0.2 + - - -
224D LEU* 2.8 18.6 + - - -
227D ASP* 1.3 76.9 - - - +
229D PRO* 1.3 66.1 - - - +
231D ALA* 3.2 17.0 + - - +
232D LEU* 3.7 6.6 + - - +
244D VAL* 4.2 6.3 - - - +
337D LEU* 3.9 10.3 - - - +
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Residues in contact with PRO 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D LEU 3.6 3.1 - - - +
225D ILE 3.1 25.1 - - - +
226D GLU 3.7 4.0 - - - +
227D ASP 3.7 0.7 - - - -
228D GLY* 1.3 91.2 - - - +
230D LYS* 1.3 62.9 + - + +
232D LEU* 3.3 17.1 + - + +
233D LYS* 3.3 37.1 + - - +
333D PHE* 3.9 19.5 - - + -
336D GLN 6.1 1.3 - - - +
337D LEU* 3.8 12.5 - - + -
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Residues in contact with LYS 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LYS* 4.0 9.3 - - - +
226D GLU* 3.1 39.1 + - - +
227D ASP* 2.8 34.6 + - - +
228D GLY 3.3 1.0 - - - -
229D PRO* 1.3 75.2 - - + +
231D ALA* 1.3 57.6 + - - +
233D LYS* 4.4 11.2 - - + +
234D GLU* 2.7 51.6 + - - +
240D VAL* 3.8 23.2 - - + +
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Residues in contact with ALA 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D VAL* 3.7 23.7 - - + +
227D ASP 3.0 12.5 + - - +
228D GLY* 3.2 12.2 + - - +
230D LYS* 1.3 76.3 - - - +
232D LEU* 1.3 61.7 + - - +
234D GLU 4.4 0.4 - - - -
235D PRO* 3.4 23.4 - - - +
240D VAL* 3.5 10.3 - - + +
241D ARG* 3.8 26.8 + - - +
244D VAL* 4.4 10.8 - - + -
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Residues in contact with LEU 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D PRO* 3.5 41.5 - - + +
188D VAL* 3.7 20.2 - - + -
189D ALA* 4.3 3.1 - - + +
228D GLY 4.1 6.5 - - - +
229D PRO* 3.3 9.3 + - + +
230D LYS 3.2 0.4 - - - -
231D ALA* 1.3 80.7 - - - +
233D LYS* 1.3 63.4 + - + +
234D GLU 3.7 0.2 + - - -
235D PRO* 3.7 12.3 - - - +
336D GLN 4.7 3.6 - - - +
337D LEU* 3.4 49.4 - - + +
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Residues in contact with LYS 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D PRO* 3.3 35.7 + - - +
230D LYS* 4.0 9.2 - - + +
232D LEU* 1.3 78.7 - - + +
234D GLU* 1.3 68.2 + - + +
235D PRO* 3.6 6.1 - - - +
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Residues in contact with GLU 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D LYS* 2.7 41.6 + - + +
231D ALA* 4.1 1.0 - - - +
233D LYS* 1.3 82.6 - - + +
235D PRO* 1.3 67.6 - - - +
236D GLU* 3.2 3.1 - - - -
237D ASN* 3.1 47.1 + - + +
240D VAL* 4.8 0.6 - - - +
241D ARG* 4.4 4.7 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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