Contacts of the helix formed by residues 210 - 234 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 3.8 23.6 - - + -
208A VAL* 2.8 19.4 + - + +
209A ASP* 1.3 71.6 - - - +
211A LYS* 1.3 59.2 + - - +
212A ILE 3.4 2.9 - - - -
213A HIS* 3.4 29.3 + - + +
214A ASP* 3.0 33.0 + - - +
260A VAL* 4.0 4.3 - - + -
243D ASN* 3.7 4.0 - - - -
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Residues in contact with LYS 211 (chain A).
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* 2.7 36.3 + - - +
210A ALA* 1.3 71.3 - - - +
212A ILE* 1.3 61.1 + - - +
214A ASP* 3.5 7.1 + - - +
215A ARG* 3.0 34.6 + - + +
223D THR* 3.6 28.9 - - + +
226D GLU* 3.8 21.5 - - + -
227D ASP* 3.0 42.4 + - - +
230D LYS* 4.0 7.5 - - - +
240D VAL* 5.7 0.2 - - - +
243D ASN* 2.9 12.7 + - - +
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ALA 3.4 0.4 - - - -
211A LYS* 1.3 73.6 - - - +
213A HIS* 1.3 67.6 + - - +
215A ARG* 3.3 1.7 + - - -
216A PHE* 2.9 55.6 + - + +
255A LEU* 6.1 0.4 - - + -
219D GLY 4.2 1.6 - - - +
220D ILE* 3.9 19.5 - - + +
223D THR* 3.7 29.8 - - + +
243D ASN* 4.3 7.2 + - - +
246D TRP* 3.8 28.5 - - + +
247D ALA* 3.9 34.3 - - + +
250D GLN* 4.3 5.2 - - + -
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Residues in contact with HIS 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 3.7 24.0 - - + -
4A PHE* 4.8 1.7 - + - -
203A TYR* 5.4 0.4 - - - -
210A ALA* 3.5 23.6 - - + +
212A ILE* 1.3 77.2 - - - +
214A ASP* 1.3 59.9 + - - +
216A PHE* 3.4 5.4 + - - +
217A ALA* 2.9 31.2 + - - +
255A LEU 3.8 14.9 + - - -
256A ILE* 3.4 32.0 - - - +
258A ALA* 2.8 30.4 + - - +
260A VAL* 3.7 11.0 - - + -
246D TRP* 3.5 31.5 + + - -
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Residues in contact with ASP 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2A LYS* 4.3 4.5 + - - -
203A TYR* 3.4 10.6 - - - -
208A VAL 4.1 11.2 - - - +
210A ALA* 3.0 22.0 + - - +
211A LYS* 3.7 7.7 - - - +
213A HIS* 1.3 79.1 - - - +
215A ARG* 1.3 57.4 + - - +
217A ALA* 3.4 1.2 + - - +
218A GLU* 2.8 37.9 + - - +
303A LYS* 3.0 29.9 + - - -
306A GLN* 3.1 32.7 + - - +
310A ARG* 4.8 3.4 - - - +
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Residues in contact with ARG 215 (chain A).
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* 3.0 22.1 + - + +
212A ILE 3.9 3.1 - - - +
214A ASP* 1.3 77.1 - - + +
216A PHE* 1.3 60.4 + - + +
218A GLU* 3.8 7.0 + - - +
219A GLY* 2.9 26.0 + - - -
310A ARG* 3.3 53.2 - - - +
215D ARG* 4.7 5.0 - - - +
219D GLY* 3.6 38.4 - - - +
222D LEU* 3.7 41.1 - - - +
223D THR* 4.0 3.9 + - - +
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Residues in contact with PHE 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ILE* 2.9 44.5 + - + +
213A HIS* 3.8 4.3 - - - +
215A ARG* 1.3 78.6 - - + +
217A ALA* 1.3 64.9 + - - +
219A GLY 3.2 1.0 + - - -
220A ILE* 3.0 24.4 + - - +
255A LEU* 3.9 28.3 - - + -
256A ILE* 3.8 11.7 - - + -
216D PHE* 3.4 80.0 - + + -
219D GLY* 5.0 0.2 - - - -
220D ILE* 4.1 18.8 - - + -
250D GLN* 4.0 17.9 - - + -
255D LEU* 4.6 0.9 - - + -
256D ILE* 5.1 2.2 - - + -
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Residues in contact with ALA 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A THR* 3.3 26.3 - - + +
203A TYR* 3.6 34.1 - - + -
213A HIS 2.9 18.6 + - - +
214A ASP 3.7 3.1 - - - +
216A PHE* 1.3 76.1 - - - +
218A GLU* 1.3 63.1 + - - +
220A ILE* 3.2 6.0 + - - -
221A LEU* 3.0 20.6 + - - +
256A ILE* 4.3 10.4 - - + +
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Residues in contact with GLU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TYR* 2.6 35.3 + - + +
214A ASP 2.8 24.1 + - - +
215A ARG* 3.8 14.1 + - - +
217A ALA* 1.3 73.2 - - - +
219A GLY* 1.3 55.3 - - - +
221A LEU* 3.3 3.1 + - - +
222A LEU* 2.8 42.1 + - + +
306A GLN* 2.8 24.4 + - - -
310A ARG* 2.9 45.2 + - + +
311A VAL* 4.2 13.4 - - + +
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Residues in contact with GLY 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ARG 2.9 16.7 + - - -
216A PHE* 3.2 4.5 + - - -
217A ALA 3.1 0.6 - - - -
218A GLU* 1.3 73.5 - - - +
220A ILE* 1.3 63.7 + - - +
222A LEU* 3.9 1.7 - - - +
223A THR* 2.8 30.9 + - - -
212D ILE* 4.4 2.7 - - - -
215D ARG* 3.6 32.8 - - - +
216D PHE* 5.0 1.3 - - - -
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Residues in contact with ILE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A THR* 3.3 19.5 - - - +
216A PHE 3.0 15.2 + - - +
217A ALA* 3.2 5.4 + - - +
219A GLY* 1.3 74.7 - - - +
221A LEU* 1.3 57.6 + - - +
223A THR* 3.2 2.9 + - - -
224A LEU* 2.9 45.4 + - + +
247A ALA* 4.0 18.8 - - + +
250A GLN* 3.7 34.1 - - + +
251A ALA* 4.0 7.0 - - + +
256A ILE* 4.2 18.4 - - + -
212D ILE* 3.8 20.2 - - + -
216D PHE* 4.1 10.7 - - + -
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PHE* 3.6 56.0 - - + +
199A THR* 3.7 14.1 - - + +
200A VAL* 4.0 3.8 - - + -
203A TYR* 4.0 23.3 - - + -
217A ALA 3.0 19.2 + - - +
218A GLU 3.3 6.5 + - - +
220A ILE* 1.3 75.7 - - - +
222A LEU* 1.3 63.1 + - - +
224A LEU* 3.2 5.0 + - - +
225A ILE* 3.0 30.3 + - - +
307A TYR* 3.9 14.1 - - + -
311A VAL* 3.9 29.2 - - + -
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A GLU* 2.8 29.5 + - + +
219A GLY* 3.9 3.8 - - - +
221A LEU* 1.3 76.4 - - - +
223A THR* 1.3 61.2 + - - +
225A ILE* 3.4 7.5 + - + +
226A GLU* 3.0 41.0 + - + +
310A ARG 3.9 21.3 - - - +
311A VAL* 3.5 28.3 - - - +
215D ARG* 3.6 39.7 - - - +
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Residues in contact with THR 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A GLY 2.8 22.5 + - - -
220A ILE 3.2 4.2 + - - -
222A LEU* 1.3 74.3 - - - +
224A LEU* 1.3 60.4 + - + +
226A GLU* 3.3 9.0 + - - +
227A ASP* 2.9 29.9 + - + +
243A ASN* 4.2 20.6 - - + +
244A VAL* 6.4 0.2 - - + -
247A ALA* 4.6 2.2 - - + -
211D LYS* 3.6 40.4 + - + +
212D ILE* 3.7 23.4 - - + +
215D ARG* 4.1 3.8 - - - +
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Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A VAL* 4.0 24.9 - - + +
195A ALA* 3.8 18.2 - - + -
196A PHE* 3.5 44.2 - - + +
220A ILE* 2.9 31.1 + - + +
221A LEU* 3.7 4.7 - - - +
223A THR* 1.3 75.9 - - - +
225A ILE* 1.3 58.3 + - - +
227A ASP* 5.5 0.2 - - - -
228A GLY* 2.8 32.0 + - - +
229A PRO* 3.5 2.1 - - - +
244A VAL* 4.6 20.6 - - + +
247A ALA* 3.8 21.8 - - + -
333A PHE* 3.6 5.7 - - - -
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Residues in contact with ILE 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A PHE* 3.8 17.7 - - + -
221A LEU 3.0 18.8 + - - +
222A LEU* 3.8 7.9 - - + +
223A THR 3.3 0.2 - - - -
224A LEU* 1.3 78.4 - - - +
226A GLU* 1.3 63.6 + - + +
229A PRO* 3.2 19.4 - - - +
311A VAL* 3.4 39.3 - - + +
312A TRP* 3.5 40.8 - - + -
333A PHE* 3.7 15.5 - - + -
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Residues in contact with GLU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LEU* 3.0 31.1 + - - +
223A THR* 3.8 5.8 + - - +
225A ILE* 1.3 81.6 - - + +
227A ASP* 1.3 69.7 + - - +
229A PRO* 3.8 5.5 - - - +
230A LYS* 3.7 23.7 - - - +
211D LYS* 3.4 29.9 - - - +
215D ARG* 3.2 29.2 + - - -
310D ARG* 5.4 3.9 + - - -
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Residues in contact with ASP 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A THR* 2.9 16.0 + - + +
226A GLU* 1.3 72.0 - - - +
228A GLY* 1.3 65.8 + - - +
229A PRO 3.4 0.9 - - - -
230A LYS* 3.0 23.5 + - - -
231A ALA* 2.9 21.3 + - - +
240A VAL* 3.3 29.4 - - + +
243A ASN* 2.8 36.2 + - + +
244A VAL* 4.0 11.8 - - + +
211D LYS* 2.8 29.8 + - - -
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Residues in contact with GLY 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A VAL* 4.8 0.2 - - - +
192A VAL* 3.8 27.7 - - - +
223A THR 4.1 0.4 + - - -
224A LEU* 2.8 22.6 + - - -
227A ASP* 1.3 70.4 - - - +
229A PRO* 1.3 67.7 - - - +
231A ALA* 3.1 17.0 + - - +
232A LEU* 3.6 9.4 + - - +
244A VAL* 4.1 7.1 - - - +
337A LEU* 4.1 6.3 - - - +
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Residues in contact with PRO 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LEU 3.5 3.1 - - - +
225A ILE 3.2 25.4 - - - +
226A GLU 3.8 4.5 - - - +
227A ASP 3.7 0.9 - - - -
228A GLY* 1.3 89.0 - - - +
230A LYS* 1.3 60.7 + - + +
232A LEU* 3.2 18.7 + - + +
233A LYS* 3.2 33.9 + - - +
333A PHE* 3.9 19.3 - - + -
336A GLN* 6.6 0.2 - - + -
337A LEU* 3.9 13.9 - - + -
55C LYS* 5.0 0.6 - - - +
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Residues in contact with LYS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLU* 3.7 16.7 + - - +
227A ASP* 3.0 33.9 + - - +
229A PRO* 1.3 77.1 - - + +
231A ALA* 1.3 56.7 + - - +
233A LYS* 4.3 11.4 - - + +
234A GLU* 2.7 57.4 + - - +
240A VAL* 3.7 21.6 - - + +
211D LYS* 3.8 13.5 - - - +
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A VAL* 3.8 22.2 - - + +
227A ASP 2.9 11.5 + - - +
228A GLY 3.1 11.6 + - - +
230A LYS* 1.3 76.6 - - - +
232A LEU* 1.3 59.7 + - - +
234A GLU 4.1 1.6 - - - -
235A PRO* 3.4 22.5 - - - +
240A VAL* 3.5 10.3 - - + +
241A ARG* 3.8 28.0 + - - +
244A VAL* 4.3 12.1 - - + -
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A PRO* 3.6 41.9 - - + +
188A VAL* 3.8 20.2 - - + -
189A ALA* 4.3 3.4 - - + +
228A GLY 3.6 6.9 + - - +
229A PRO* 3.2 10.3 + - + +
230A LYS 3.1 0.6 - - - -
231A ALA* 1.3 79.1 - - - +
233A LYS* 1.3 58.1 + - - +
234A GLU 3.7 0.3 + - - -
235A PRO* 4.1 4.7 - - - +
336A GLN 4.8 0.4 - - - +
337A LEU* 3.6 47.8 - - + +
23C ARG* 5.2 1.6 + - - -
55C LYS* 3.5 32.2 - - + +
56C GLY* 3.2 19.2 - - - -
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Residues in contact with LYS 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PRO* 3.2 31.9 + - - +
230A LYS* 4.0 10.5 - - + +
232A LEU* 1.3 76.3 - - - +
234A GLU* 1.3 68.9 + - + +
235A PRO* 3.6 3.1 - - - +
52C ASP* 5.9 0.4 + - - -
55C LYS* 3.7 33.1 - - + +
56C GLY* 3.5 20.5 + - - +
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Residues in contact with GLU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LYS* 2.7 46.2 + - + +
231A ALA* 4.0 4.3 - - - +
233A LYS* 1.3 83.5 - - + +
235A PRO* 1.3 67.1 - - - +
236A GLU 3.2 2.5 - - - -
237A ASN* 3.0 46.6 + - + +
240A VAL* 4.9 0.3 - - - +
241A ARG* 4.4 2.4 - - - -
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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