Contacts of the helix formed by residues 284 - 314 (chain B) in PDB entry 2CX9
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 PHE 284 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ALA* 3.5 26.2 - - + -
277B PHE* 3.9 26.5 - + + -
279B ARG* 3.3 46.9 - - + -
280B PRO 4.8 0.2 - - - -
281B ILE* 3.6 28.5 - - + +
282B ALA 3.2 1.9 - - - +
283B GLU* 1.3 79.8 - - - +
285B GLU* 1.3 60.0 + - - +
286B GLY 4.2 0.7 - - - +
287B VAL* 2.9 25.8 + - + +
288B SER* 2.9 11.4 + - - -
285C GLU* 3.3 26.2 - - + +
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B GLU 4.7 5.4 - - - +
284B PHE* 1.3 69.4 - - - +
286B GLY* 1.3 59.2 + - - +
288B SER* 3.7 10.3 - - - -
289B PHE* 2.8 57.0 + - + +
284C PHE* 3.3 29.2 - - + +
285C GLU* 3.2 21.4 + - + +
286C GLY* 2.7 33.3 + - - +
377D LEU* 3.4 33.6 - - + +
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Residues in contact with GLY 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLU* 4.7 4.7 - - - +
285B GLU* 1.3 72.5 - - - +
287B VAL* 1.3 60.4 + - - +
289B PHE* 4.8 2.0 - - - +
290B LYS* 3.3 33.0 + - - +
285C GLU* 2.7 27.0 + - - +
289C PHE* 3.7 26.9 - - - -
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLU* 6.0 3.6 - - + -
271B ALA* 4.0 27.6 - - + -
281B ILE* 3.1 43.3 - - + +
282B ALA* 4.4 1.3 - - - -
284B PHE* 2.9 8.3 + - + +
286B GLY* 1.3 81.1 - - - +
288B SER* 1.3 66.6 + - - +
289B PHE 3.2 1.6 - - - -
290B LYS* 3.1 9.1 + - + +
291B LEU* 3.1 29.1 + - + +
343B ILE* 4.2 23.1 - - + -
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Residues in contact with SER 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ALA* 2.4 27.7 + - - -
283B GLU 4.6 1.1 - - - -
284B PHE 2.9 10.7 + - - -
285B GLU* 4.1 8.3 - - - -
287B VAL* 1.3 77.6 - - - +
289B PHE* 1.3 64.4 + - - +
291B LEU* 3.4 7.4 + - - +
292B ALA* 3.0 24.1 + - - +
377D LEU* 4.3 14.1 - - - +
380D ALA* 3.7 28.0 - - - +
384D LEU* 4.7 4.7 - - - +
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Residues in contact with PHE 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLU* 2.8 43.2 + - + +
286B GLY* 4.8 3.1 - - - +
288B SER* 1.3 77.8 - - - +
290B LYS* 1.3 64.6 + - + +
292B ALA* 3.2 3.3 + - - +
293B GLU* 3.0 36.3 + - - +
286C GLY* 3.5 33.7 - - - -
290C LYS* 5.9 1.8 - - - -
373D GLU* 3.8 44.4 - - + -
376D LYS* 3.9 33.4 - - + -
377D LEU* 4.0 15.0 - - + -
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Residues in contact with LYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ARG* 5.6 1.6 - - - +
373A GLU* 3.4 34.5 + - - -
376A LYS* 5.8 3.2 - - - +
286B GLY 3.3 23.1 - - - +
287B VAL* 3.1 7.3 + - - +
289B PHE* 1.3 78.4 - - + +
291B LEU* 1.3 62.3 + - - +
293B GLU* 3.6 11.7 + - - +
294B ALA* 3.1 26.0 + - - +
339B GLU* 2.6 44.0 + - + +
342B GLN* 4.3 6.5 - - - +
343B ILE* 4.1 30.1 - - + +
289C PHE* 6.0 0.6 - - - -
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 3.8 25.3 - - + +
267B ALA* 4.0 3.1 - - + -
268B LEU* 3.7 42.6 - - + +
271B ALA* 4.3 11.7 - - + -
282B ALA* 5.0 2.5 - - + -
287B VAL* 3.1 27.9 + - + +
288B SER* 3.7 13.5 - - - +
290B LYS* 1.3 78.0 - - - +
292B ALA* 1.3 61.6 + - - +
294B ALA* 4.7 0.2 - - - -
295B ALA* 3.1 26.2 + - - +
343B ILE* 3.7 22.9 - - + -
380D ALA* 5.3 3.8 - - + -
383D LEU* 3.6 6.6 - - + +
384D LEU* 4.6 9.9 - - + -
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B SER 3.0 14.3 + - - +
289B PHE 3.7 3.6 - - - +
291B LEU* 1.3 77.4 - - - +
293B GLU* 1.3 58.6 + - - +
295B ALA* 3.4 2.4 + - - +
296B THR* 2.8 33.5 + - - -
327D LEU* 5.3 0.9 - - - -
376D LYS* 3.4 41.7 - - + +
379D ILE* 3.8 22.3 - - + +
380D ALA* 4.3 1.3 - - - +
383D LEU* 4.3 1.5 - - - +
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Residues in contact with GLU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PHE* 3.0 27.5 + - - +
290B LYS* 4.0 11.8 - - - +
292B ALA* 1.3 76.1 - - - +
294B ALA* 1.3 57.4 - - - +
296B THR* 3.5 5.2 + - - -
297B GLU* 3.0 38.1 + - + +
335B LYS* 4.3 27.1 + - - +
339B GLU* 6.2 0.3 - - - +
327D LEU* 5.2 4.9 - - + -
376D LYS* 2.5 42.2 + - + +
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 4.2 14.8 - - + -
290B LYS 3.1 16.3 + - - +
291B LEU 3.9 2.9 - - - +
293B GLU* 1.3 77.3 - - - +
295B ALA* 1.3 65.2 + - - +
297B GLU* 3.4 6.8 + - - +
298B LEU* 3.0 31.3 + - - +
332B ALA 6.0 0.4 - - - -
335B LYS* 5.8 2.4 - - - +
336B ALA* 3.9 30.5 - - + +
339B GLU* 5.9 2.9 - - + -
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 3.6 19.6 - - + +
291B LEU 3.1 8.7 + - - +
292B ALA 3.8 2.9 - - - +
294B ALA* 1.3 76.8 - - - +
296B THR* 1.3 57.9 + - - +
298B LEU* 3.3 3.6 + - - +
299B GLU* 3.0 34.7 + - + +
324D GLN* 3.9 9.0 - - - +
379D ILE* 4.8 0.4 - - + -
383D LEU* 3.4 41.5 - - + -
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Residues in contact with THR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA 2.8 22.1 + - - -
293B GLU* 3.7 6.1 - - - -
295B ALA* 1.3 77.9 - - - +
297B GLU* 1.3 62.4 + - - +
299B GLU* 3.5 2.6 + - - +
300B ALA* 3.1 21.3 + - - +
304D LEU* 4.3 3.9 - - + +
324D GLN* 3.5 54.7 + - + +
327D LEU* 4.2 9.7 - - + +
328D PHE* 3.9 21.3 - - + -
379D ILE* 3.7 10.2 - - - +
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Residues in contact with GLU 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B GLU* 3.0 19.1 + - - +
294B ALA* 4.0 5.7 - - - +
296B THR* 1.3 76.9 - - - +
298B LEU* 1.3 58.3 + - - +
300B ALA* 3.2 1.9 + - - -
301B ALA* 2.8 26.1 + - - +
328B PHE* 3.2 23.9 - - + -
332B ALA* 3.8 30.2 - - + +
335B LYS* 3.8 35.8 + - - +
328D PHE* 4.5 19.2 - - + -
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B VAL* 4.3 22.8 - - + +
260B GLY* 3.6 41.1 - - - +
261B GLN* 3.8 20.6 - - - +
264B LEU* 4.1 17.9 - - + -
294B ALA 3.0 22.6 + - - +
295B ALA* 3.8 4.0 - - - +
297B GLU* 1.3 76.7 - - + +
299B GLU* 1.3 66.0 + - + +
301B ALA* 3.2 6.0 + - + +
302B ARG* 3.0 27.3 + - - +
329B ALA 5.3 0.2 - - - +
332B ALA* 4.7 4.5 - - + +
333B ALA* 4.2 20.9 - - + +
336B ALA* 4.3 7.9 - - + -
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B GLN* 5.9 1.1 - - - +
295B ALA* 3.0 23.4 + - + +
296B THR 3.8 4.7 - - - +
298B LEU* 1.3 75.9 - - + +
300B ALA* 1.3 63.2 + - - +
302B ARG* 3.5 22.8 + - - +
303B LEU* 3.2 29.8 + - + +
304D LEU* 4.3 8.5 - - + -
307D LYS* 2.9 28.0 + - - +
320D LEU* 5.0 8.7 - - - +
321D GLU* 5.6 0.7 - - - +
324D GLN* 3.7 26.4 + - - +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B THR 3.1 12.8 + - - +
297B GLU* 3.5 7.9 - - - +
299B GLU* 1.3 77.7 - - - +
301B ALA* 1.3 64.2 + - - +
303B LEU* 3.3 6.2 + - - +
304B LEU* 3.0 27.7 + - - +
328B PHE* 3.8 16.6 - - + -
300D ALA* 3.9 19.4 - - + +
304D LEU* 4.0 24.4 - - + +
328D PHE* 4.8 2.7 - - + -
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B VAL* 3.8 13.6 - - + +
297B GLU 2.8 16.8 + - - +
298B LEU* 3.2 10.1 + - + +
300B ALA* 1.3 78.3 - - - +
302B ARG* 1.3 60.8 + - - +
304B LEU* 3.2 7.9 + - - +
305B TYR* 3.1 22.5 + - - +
325B ALA 5.0 0.5 - - - +
328B PHE* 3.7 13.6 - - + +
329B ALA* 3.7 32.4 - - - +
332B ALA* 4.9 2.7 - - + -
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Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE 5.5 2.2 - - - -
73B ARG* 4.2 16.3 - - - +
76B GLU* 2.8 35.7 + - - +
257B VAL* 3.4 15.0 - - + +
261B GLN* 3.0 31.5 + - - +
298B LEU 3.0 18.0 + - - +
299B GLU* 3.7 27.6 + - - +
301B ALA* 1.3 74.1 - - - +
303B LEU* 1.3 69.0 + - + +
304B LEU 3.2 0.3 + - - -
305B TYR* 3.2 25.8 + - + -
306B LEU* 2.9 40.4 + - + +
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Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TRP* 3.9 12.3 - - + -
5B PHE* 3.7 31.4 - - + +
299B GLU* 3.2 11.2 + - - +
300B ALA* 3.3 7.4 + - - +
302B ARG* 1.3 78.8 - - + +
304B LEU* 1.3 57.4 + - - +
306B LEU* 3.4 10.7 + - + +
307B LYS* 3.0 30.5 + - - +
4D TRP* 5.6 1.3 - - + -
303D LEU* 3.9 40.2 - - + +
304D LEU* 3.7 29.6 - - + -
307D LYS* 4.1 19.7 - - + +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ALA 3.0 15.6 + - - +
301B ALA* 3.3 7.6 - - - +
302B ARG 3.1 0.2 - - - -
303B LEU* 1.3 76.6 - - - +
305B TYR* 1.3 61.8 - - - +
307B LYS* 3.4 9.1 + - + +
308B ALA* 3.1 18.7 + - - +
321B GLU* 4.7 1.4 - - - +
324B GLN* 4.1 16.2 - - + +
325B ALA* 3.7 19.3 - - + +
328B PHE* 3.5 44.2 - - + -
296D THR* 4.4 6.7 - - + +
299D GLU* 4.5 9.6 - - + -
300D ALA* 4.1 23.8 - - + +
303D LEU* 3.6 22.9 - - + -
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Residues in contact with TYR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA* 3.4 30.3 - - + -
73B ARG* 3.6 24.2 - - - +
76B GLU* 2.7 30.0 + - - +
250B ILE* 3.9 11.5 - - + +
253B ALA* 3.8 23.1 - - + -
254B ALA* 3.8 28.3 - - + -
257B VAL* 3.9 12.6 - - + -
301B ALA 3.1 8.4 + - - +
302B ARG* 3.2 33.8 + - + +
304B LEU* 1.3 74.1 - - - +
306B LEU* 1.3 87.3 + - + +
308B ALA* 3.4 2.3 + - - +
309B ALA* 2.9 25.0 + - + +
325B ALA* 3.7 7.8 - - + +
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TRP* 3.5 18.7 - - + -
5B PHE* 4.0 15.7 - - - +
69B ARG* 3.8 28.8 - - + +
73B ARG* 3.7 37.7 - - + +
302B ARG* 2.9 38.3 + - + +
303B LEU* 3.6 12.1 - - + +
305B TYR* 1.3 98.1 - - + +
307B LYS* 1.3 56.7 + - - +
309B ALA* 3.3 5.6 + - - +
310B GLU* 3.0 28.4 + - - +
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Residues in contact with LYS 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TRP* 3.6 4.4 - - + -
303B LEU 3.0 17.5 + - - +
304B LEU* 3.5 8.9 - - + +
305B TYR 3.2 0.2 - - - -
306B LEU* 1.3 73.4 - - - +
308B ALA* 1.3 66.0 + - - +
310B GLU* 3.1 4.2 + - - +
311B LEU* 3.0 26.4 + - + +
321B GLU* 3.9 27.5 + - + +
324B GLN* 4.8 2.6 - - - +
5D PHE* 3.7 51.1 - - + -
299D GLU* 3.2 35.8 + - - +
303D LEU* 4.2 21.0 - - + +
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ILE* 3.8 14.6 - - + +
304B LEU 3.1 10.9 + - - +
305B TYR* 3.9 5.6 - - - +
307B LYS* 1.3 78.2 - - - +
309B ALA* 1.3 58.0 + - - +
311B LEU* 3.3 4.6 + - - +
312B LYS* 3.0 28.4 + - - +
318B PHE* 4.0 4.5 - - + -
321B GLU* 3.8 41.3 - - + +
322B ALA* 3.8 12.3 - - + +
325B ALA* 4.6 1.1 - - + -
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR* 3.9 13.2 - - + +
69B ARG* 3.7 29.8 - - - +
72B ALA* 5.1 2.2 - - + -
250B ILE* 3.9 15.2 - - + +
305B TYR 2.9 17.7 + - - +
306B LEU* 3.5 7.0 - - - +
308B ALA* 1.3 79.3 - - - +
310B GLU* 1.3 56.3 + - - +
312B LYS* 3.3 2.8 + - - +
313B ASP* 2.9 35.2 + - - +
----------------------------------------------------------
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Residues in contact with GLU 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TRP* 2.7 31.0 + - + +
69B ARG* 3.7 19.4 + - - +
306B LEU 3.0 11.7 + - - +
307B LYS* 3.4 8.5 - - - +
309B ALA* 1.3 75.8 - - - +
311B LEU* 1.3 65.5 + - - +
313B ASP* 3.3 14.4 + - - +
314B ALA* 3.0 23.7 + - - +
3D LEU* 3.8 26.7 - - + +
5D PHE* 3.7 18.6 - - + -
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LYS* 3.0 25.3 + - - +
308B ALA* 3.3 7.4 + - - +
310B GLU* 1.3 75.0 - - - +
312B LYS* 1.3 62.3 + - - +
314B ALA* 3.1 7.7 + - - -
316B ARG* 2.9 67.2 + - + +
317B PRO 4.0 7.9 - - - +
318B PHE* 3.8 8.5 - - + -
321B GLU* 3.3 46.0 - - + +
3D LEU* 3.8 8.1 - - + -
5D PHE* 3.9 12.3 - - + -
6D GLU* 4.5 2.5 - - - +
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Residues in contact with LYS 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 4.1 17.8 - - - +
68B THR* 3.1 33.0 + - + +
247B GLY* 4.4 13.5 - - - -
250B ILE* 4.1 4.5 - - + -
308B ALA 3.0 13.2 + - - +
309B ALA 3.5 8.3 - - - +
311B LEU* 1.3 76.7 - - - +
313B ASP* 1.3 57.2 + - - +
315B GLY* 2.9 20.1 + - - -
316B ARG 4.5 0.7 - - - -
318B PHE* 3.5 48.1 - - + -
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Residues in contact with ASP 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B SER* 3.9 13.7 - - - -
68B THR* 3.0 40.1 + - - -
69B ARG* 3.4 12.1 + - - +
309B ALA 2.9 23.2 + - - +
310B GLU* 3.6 15.5 - - - +
312B LYS* 1.3 76.7 + - - +
314B ALA* 1.3 58.6 + - - +
315B GLY 3.3 1.6 + - - -
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Residues in contact with ALA 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B GLU 3.0 15.9 + - - +
311B LEU 3.6 5.6 - - - +
312B LYS 3.1 0.4 - - - -
313B ASP* 1.3 75.7 - - - +
315B GLY* 1.3 64.7 + - - +
316B ARG* 3.3 13.2 + - + +
3D LEU* 4.3 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