Contacts of the strand formed by residues 201 - 226 (chain N) in PDB entry 5D4C
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 GLY 201 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184N GLU* 3.5 8.4 - - - -
185N VAL* 2.7 40.8 + - - +
199N LEU 4.4 0.2 + - - -
200N ASP* 1.3 76.2 - - - +
202N VAL* 1.3 65.2 + - - -
395N VAL* 4.4 5.4 - - - +
396N VAL 3.2 9.4 - - - -
397N LYS* 4.3 4.7 - - - -
398N ALA 5.1 1.6 - - - -
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Residues in contact with VAL 202 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182N GLY* 4.1 15.3 - - - +
183N GLU 4.2 2.9 - - - -
184N GLU* 3.5 24.0 - - - +
201N GLY* 1.3 71.2 - - - -
203N ALA* 1.3 73.0 + - - +
204N LEU* 4.0 16.6 - - + +
394N LEU 3.4 2.4 - - - +
395N VAL* 4.4 0.9 - - - -
396N VAL* 2.6 40.1 + - + +
398N ALA* 3.4 29.8 - - + +
400N VAL* 3.9 24.5 - - + +
445N ARG* 5.3 2.9 - - - -
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Residues in contact with ALA 203 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179N VAL* 5.0 3.1 - - + -
180N LYS 4.6 9.6 - - - +
181N ASP* 5.1 0.9 - - - -
182N GLY* 3.0 26.0 + - - -
183N GLU 3.4 11.1 + - - +
185N VAL* 3.5 23.7 - - + +
191N LEU* 4.4 7.4 - - + -
201N GLY 3.7 2.0 + - - -
202N VAL* 1.3 72.3 - - - +
204N LEU* 1.3 66.6 + - - +
205N TYR* 6.3 0.7 - - + -
393N ILE* 4.0 18.2 - - + -
394N LEU 3.6 5.2 - - - -
395N VAL* 4.3 5.4 - - + +
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Residues in contact with LEU 204 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181N ASP* 3.7 4.3 - - - +
182N GLY* 4.5 5.4 - - - +
202N VAL* 4.0 16.2 - - + +
203N ALA* 1.3 84.3 - - - +
205N TYR* 1.3 66.4 + - - +
206N ARG* 5.3 2.7 - - - +
393N ILE* 3.3 7.2 - - - +
394N LEU* 2.9 49.6 + - + +
396N VAL* 4.4 16.4 - - + -
436N GLU* 5.7 0.7 - - - +
441N ARG* 3.6 42.2 - - - +
445N ARG* 4.1 31.9 - - - +
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Residues in contact with TYR 205 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176N ASP* 5.7 0.2 + - - -
177N ALA* 4.0 16.7 + - + +
179N VAL* 2.7 27.8 + - + -
180N LYS* 3.3 11.2 - - + +
181N ASP* 2.9 48.0 + - + +
203N ALA* 6.3 0.4 - - + -
204N LEU* 1.3 76.2 - - - +
206N ARG* 1.3 69.1 + - - +
207N PHE 3.5 7.3 + - - +
208N PRO* 5.9 3.4 - - + -
357N GLU* 5.1 1.6 - - - -
387N LEU* 3.3 37.9 - - + -
388N HIS* 4.6 7.6 - - - +
390N PRO* 3.8 32.1 - - + -
392N SER 4.0 0.9 - - - -
393N ILE* 4.3 13.7 - - + -
441N ARG* 3.5 14.6 + - - +
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Residues in contact with ARG 206 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168N THR* 4.7 4.0 + - + +
204N LEU* 4.7 3.2 - - - +
205N TYR* 1.3 76.7 + - - +
207N PHE* 1.3 90.5 + - + +
391N ALA* 2.9 24.8 + - - +
392N SER* 2.9 40.1 + - - +
394N LEU* 3.7 46.2 - - + +
441N ARG* 5.7 2.6 - - - +
98P GLU* 5.0 4.9 - - - +
101P GLU* 2.8 39.8 + - - -
102P LEU* 5.8 0.4 - - - +
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Residues in contact with PHE 207 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205N TYR* 3.5 6.5 + - - -
206N ARG* 1.3 116.0 - - + +
208N PRO* 1.3 75.2 - - + +
209N ARG* 6.0 0.7 - - + -
351N MET 5.9 3.1 - - - +
390N PRO* 3.0 20.4 - - - +
391N ALA* 3.0 16.9 + - + -
392N SER* 5.4 0.9 - - - -
97P GLU* 3.5 47.1 - - + -
98P GLU* 3.9 15.0 - - + -
101P GLU* 3.1 45.3 - - + -
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Residues in contact with PRO 208 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205N TYR* 5.9 4.3 - - + +
207N PHE* 1.3 90.4 - - + +
209N ARG* 1.3 62.4 + - - +
210N ARG 4.0 19.3 - - - +
211N VAL* 4.6 1.3 - - + -
347N VAL* 3.6 18.6 - - + +
353N VAL* 3.5 39.0 - - + +
387N LEU* 3.9 25.4 - - + -
388N HIS 4.4 4.3 - - - +
389N GLU 4.2 2.5 - - - +
390N PRO* 4.2 2.7 - - + -
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Residues in contact with ARG 209 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171N LEU 3.7 19.8 + - - -
172N PRO 4.7 2.4 + - - -
173N PRO* 4.0 27.1 - - - +
174N GLY 4.3 0.4 - - - +
207N PHE* 4.0 0.9 + - + -
208N PRO* 1.3 76.2 - - - +
210N ARG* 1.3 58.5 + - - +
346N ARG* 3.0 29.2 + - - +
347N VAL* 3.0 34.3 + - - +
349N PRO* 6.5 1.1 - - - -
389N GLU* 2.8 37.3 + - + +
390N PRO 3.7 17.8 + - - -
391N ALA* 3.7 25.5 + - + +
97P GLU* 5.0 6.9 + - - -
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Residues in contact with ARG 210 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176N ASP* 3.3 25.7 + - - +
208N PRO* 3.5 5.5 - - - +
209N ARG* 1.3 82.6 - - - +
211N VAL* 1.3 67.9 + - - +
212N ARG* 4.1 19.8 + - - +
344N ASP* 3.4 28.4 + - + +
345N TYR 3.3 17.5 - - - +
346N ARG* 4.2 10.6 - - - +
347N VAL* 4.6 0.2 - - - -
387N LEU* 4.2 0.5 - - - -
388N HIS* 3.0 73.9 + - - +
389N GLU* 3.8 27.5 + - - +
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Residues in contact with VAL 211 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208N PRO* 4.6 0.9 - - + -
210N ARG* 1.3 77.7 - - - +
212N ARG* 1.3 60.5 + - - +
213N VAL* 4.0 11.2 - - + -
343N LYS 3.4 4.7 - - - +
345N TYR* 2.9 46.7 + - + -
347N VAL* 3.7 21.1 - - + -
353N VAL* 3.9 21.3 - - + -
367N ILE* 3.7 25.6 - - + -
368N VAL* 4.2 9.0 - - + -
377N VAL* 5.9 0.2 - - + -
385N VAL* 3.8 17.7 - - + -
386N HIS 3.8 2.2 - - - -
387N LEU* 3.9 8.7 - - + -
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Residues in contact with ARG 212 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210N ARG* 4.0 15.4 - - - +
211N VAL* 1.3 70.7 - - - +
213N VAL* 1.3 61.5 + - - +
214N GLU* 3.6 18.2 + - - +
342N PRO* 3.4 37.3 - - + +
343N LYS 3.4 9.4 - - - +
344N ASP* 2.7 34.0 + - - +
386N HIS* 2.9 44.1 + - + +
388N HIS* 3.2 28.2 + - + +
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Residues in contact with VAL 213 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211N VAL* 4.0 10.1 - - + -
212N ARG* 1.3 75.2 - - - +
214N GLU* 1.3 64.7 + - - +
215N TYR* 3.4 33.9 - - + +
341N GLU 3.4 4.0 - - - +
342N PRO* 3.4 1.6 - - - +
343N LYS 2.9 33.2 + - - +
345N TYR* 3.6 29.4 - - + -
361N VAL* 4.8 4.9 - - + -
367N ILE* 3.8 24.5 - - + -
383N GLY 4.6 3.6 - - - -
384N VAL 3.6 18.6 - - - +
385N VAL* 4.7 5.8 - - + +
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Residues in contact with GLU 214 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212N ARG* 3.6 16.7 + - + +
213N VAL* 1.3 72.5 - - - +
215N TYR* 1.3 60.5 + - - +
216N VAL* 3.7 1.2 + - - +
316N GLN* 3.4 24.0 + - - +
340N THR* 3.6 19.0 - - + +
341N GLU 3.8 0.4 - - - -
342N PRO* 3.3 38.7 - - - +
383N GLY* 3.0 3.1 - - - -
384N VAL* 2.9 45.2 + - + +
386N HIS* 3.9 27.7 - - + +
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Residues in contact with TYR 215 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213N VAL* 3.4 40.3 - - + +
214N GLU* 1.3 71.3 - - - +
216N VAL* 1.3 65.0 + - - +
217N LYS* 3.4 15.0 + - + +
340N THR* 3.1 4.3 - - - -
341N GLU* 2.9 45.1 + - + +
343N LYS* 4.0 20.2 - - + -
345N TYR* 3.2 23.9 + - - -
367N ILE* 4.5 0.3 - - - +
379N ALA* 3.8 7.9 - - + -
380N GLU* 3.3 20.2 + - + -
381N ALA* 3.2 51.4 - - + -
382N GLU 3.4 7.4 - - - +
383N GLY* 4.0 0.2 - - - -
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Residues in contact with VAL 216 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214N GLU 4.6 0.7 - - - +
215N TYR* 1.3 70.4 - - - +
217N LYS* 1.3 65.6 + - - +
218N LYS* 3.8 33.4 + - + -
338N GLU* 5.8 1.1 - - + -
339N TRP 3.4 10.3 - - - +
340N THR* 3.9 14.4 - - + -
360N ARG* 4.8 12.1 - - - +
381N ALA* 5.6 3.5 - - - +
382N GLU* 3.1 36.7 + - - +
383N GLY* 4.2 14.1 - - - -
384N VAL* 5.2 5.2 - - + +
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Residues in contact with LYS 217 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215N TYR* 3.9 14.6 - - + +
216N VAL* 1.3 78.5 - - - +
218N LYS* 1.3 62.4 + - - +
219N GLU* 4.1 3.6 - - + -
262N LYS* 4.0 13.4 - - - +
338N GLU* 3.4 0.7 - - - -
339N TRP* 2.9 81.9 + - + +
341N GLU* 3.3 35.2 - - + -
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Residues in contact with LYS 218 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216N VAL* 3.8 24.2 + - + -
217N LYS* 1.3 76.3 - - - +
219N GLU* 1.3 69.1 + - - +
337N LEU 3.2 8.3 - - - +
338N GLU* 3.6 37.2 + - + +
382N GLU* 5.4 4.1 + - - -
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Residues in contact with GLU 219 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217N LYS* 5.1 2.9 - - + -
218N LYS* 1.3 81.6 - - - +
220N ARG* 1.3 65.6 + - - +
221N ALA* 4.2 0.4 - - - -
269N PHE* 4.7 8.3 - - + -
281N THR* 5.9 4.5 - - + +
336N PHE* 3.6 7.2 - - - +
337N LEU* 2.9 32.7 + - - +
339N TRP* 3.5 31.0 - - + -
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Residues in contact with ARG 220 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219N GLU* 1.3 82.5 + - - +
221N ALA* 1.3 62.4 + - - +
281N THR* 3.8 18.1 - - - +
323N GLU* 5.5 1.8 + - - -
332N TYR* 5.9 2.0 - - - -
334N THR* 3.3 40.4 + - + +
335N LEU 3.4 6.3 - - - +
336N PHE* 4.2 25.5 - - + -
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Residues in contact with ALA 221 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219N GLU 4.2 0.4 - - - -
220N ARG* 1.3 76.5 - - - +
222N GLY* 1.3 60.8 + - - +
269N PHE* 3.9 16.4 - - + -
281N THR* 3.7 20.4 - - + +
282N TYR 4.1 0.2 - - - -
283N PHE* 3.6 28.3 - - + +
334N THR* 4.8 1.3 - - - -
335N LEU* 2.9 39.5 + - - +
337N LEU* 4.1 4.4 - - + +
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Residues in contact with GLY 222 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221N ALA* 1.3 73.9 - - - +
223N LEU* 1.3 61.3 + - - +
281N THR 3.1 11.8 + - - -
282N TYR* 3.4 12.6 - - - +
283N PHE* 3.0 23.4 + - - +
332N TYR* 3.7 23.1 + - - -
333N LEU 3.1 10.3 - - - -
334N THR* 4.5 2.2 - - - -
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Residues in contact with LEU 223 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222N GLY* 1.3 75.4 - - - +
224N ARG* 1.3 68.5 + - - +
225N LEU* 3.8 24.7 - - + -
242N LEU* 3.7 30.5 - - + -
251N PHE* 3.7 16.6 - - + -
283N PHE* 3.6 19.3 - - + +
285N PRO* 4.0 17.0 - - + -
288N MET* 3.7 25.6 - - + -
311N LEU* 5.0 0.2 - - + -
331N VAL 3.9 0.7 - - - +
332N TYR* 3.7 6.8 - - - -
333N LEU* 2.8 39.2 + - + +
335N LEU* 4.8 10.3 - - + -
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Residues in contact with ARG 224 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223N LEU* 1.3 74.1 - - - +
225N LEU* 1.3 70.5 + - - +
249N TYR* 3.3 33.3 + - - +
251N PHE* 3.4 21.9 - - + -
252N ARG 6.0 0.9 - - - +
254N GLU* 2.5 44.2 + - - +
327N GLU* 3.0 35.9 + - - +
330N THR* 2.8 41.0 + - - -
331N VAL 3.5 7.6 - - - +
332N TYR* 3.8 25.0 - - + +
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Residues in contact with LEU 225 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223N LEU* 3.8 30.3 - - + -
224N ARG* 1.3 84.5 - - - +
226N PRO* 1.3 81.4 - - + +
229N ALA* 5.9 0.2 - - + -
230N TRP* 4.4 10.1 - - + +
242N LEU* 4.2 9.9 - - + -
243N ALA* 4.4 18.4 - - + -
245N LEU* 5.4 1.3 - - + -
249N TYR* 4.5 8.5 - - + -
288N MET* 5.9 2.0 - - + -
307N ALA* 5.6 1.6 - - + -
311N LEU* 4.5 19.7 - - + -
330N THR* 3.4 6.1 - - - -
331N VAL* 2.9 38.6 + - + +
333N LEU* 3.8 27.6 - - + -
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Residues in contact with PRO 226 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225N LEU* 1.3 91.5 - - + +
227N LEU* 1.3 64.5 + - - +
228N ALA* 3.3 2.9 - - + +
229N ALA* 4.1 14.6 - - + +
230N TRP* 3.4 20.8 + - - +
245N LEU* 3.7 22.4 - - + -
249N TYR* 3.6 40.8 - - + -
329N GLU 4.0 7.2 - - - +
330N THR* 4.4 5.6 - - + -
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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