Contacts of the helix formed by residues 284 - 314 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ALA* 3.4 31.0 - - + -
277A PHE* 4.0 16.2 - + + -
279A ARG* 3.4 48.0 - - + -
280A PRO 4.5 0.2 - - - -
281A ILE* 3.2 36.4 + - + +
282A ALA 4.2 0.2 - - - -
283A GLU* 1.3 77.0 - - - +
285A GLU* 1.3 57.5 + - - +
286A GLY 3.0 2.9 - - - +
287A VAL* 2.8 26.8 + - + +
288A SER* 2.9 10.0 + - - -
285D GLU* 3.4 27.4 - - + +
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Residues in contact with GLU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLU 3.3 4.8 + - - +
284A PHE* 1.3 70.9 - - - +
286A GLY* 1.3 57.9 + - - +
288A SER* 3.7 10.5 - - - -
289A PHE* 2.8 54.9 + - + +
373C GLU* 6.0 0.5 - - - +
377C LEU* 3.0 37.8 - - + +
284D PHE* 3.0 35.9 - - + +
285D GLU* 3.1 16.8 + - + +
286D GLY* 2.8 29.6 + - - +
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Residues in contact with GLY 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PHE* 5.0 0.2 - - - -
285A GLU* 1.3 74.2 - - - +
287A VAL* 1.3 58.4 + - - +
289A PHE* 4.5 2.5 - - - +
290A LYS* 3.2 33.3 + - - +
373B GLU* 5.1 3.8 - - - -
285D GLU* 2.7 26.7 + - - +
289D PHE* 3.7 25.8 - - - -
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ALA* 4.0 27.4 - - + -
281A ILE* 3.4 45.8 - - + +
282A ALA* 4.2 2.0 - - - -
284A PHE* 2.8 6.0 + - + +
286A GLY* 1.3 78.8 - - - +
288A SER* 1.3 66.1 + - - +
289A PHE 3.3 0.2 - - - -
290A LYS* 3.2 10.5 + - + +
291A LEU* 3.1 27.5 + - + +
343A ILE* 4.1 26.5 - - + +
373B GLU* 6.1 2.7 - - + -
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Residues in contact with SER 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ALA 2.5 26.8 + - - -
283A GLU* 4.3 3.3 + - - -
284A PHE 2.9 11.7 + - - -
285A GLU* 4.0 8.7 - - - -
287A VAL* 1.3 78.4 - - - +
289A PHE* 1.3 56.7 + - - +
291A LEU* 3.3 7.8 + - - +
292A ALA* 2.9 30.7 + - - +
376C LYS 4.9 0.2 - - - -
377C LEU* 4.0 16.0 - - - +
380C ALA* 3.7 24.0 - - - +
384C LEU* 4.6 3.3 - - - +
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Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLU* 2.8 48.1 + - + +
286A GLY* 4.5 3.6 - - - +
288A SER* 1.3 75.5 - - - +
290A LYS* 1.3 64.2 + - + +
292A ALA* 3.3 5.6 + - - +
293A GLU* 2.9 38.6 + - - +
373C GLU* 3.8 48.0 - - + -
376C LYS* 3.7 31.2 - - + -
377C LEU* 4.2 10.5 - - + -
286D GLY* 3.8 29.2 - - - -
290D LYS* 5.6 2.9 - - - -
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Residues in contact with LYS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLY 3.2 21.5 - - - +
287A VAL* 3.2 9.4 + - - +
289A PHE* 1.3 78.5 - - + +
291A LEU* 1.3 63.1 + - - +
293A GLU* 3.8 6.7 - - - +
294A ALA* 3.1 26.6 + - - +
339A GLU* 3.3 42.9 - - + +
342A GLN* 3.2 21.8 + - - +
343A ILE* 4.0 27.0 - - + +
373B GLU* 2.7 43.4 + - - +
289D PHE* 5.8 1.6 - - - -
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 3.8 23.9 - - + +
267A ALA* 4.1 12.6 - - + +
268A LEU* 3.9 25.6 - - + +
271A ALA* 4.2 11.7 - - + -
282A ALA* 5.0 0.4 - - + -
287A VAL* 3.1 26.6 + - + +
288A SER* 3.6 12.6 - - - +
290A LYS* 1.3 74.1 - - - +
292A ALA* 1.3 65.0 + - - +
294A ALA* 3.9 1.1 - - - +
295A ALA* 2.9 26.9 + - - +
343A ILE* 3.6 23.1 - - + -
380C ALA* 5.0 3.1 - - + -
383C LEU* 3.7 14.2 - - + +
384C LEU* 4.4 13.5 - - + -
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A SER 2.9 12.5 + - - +
289A PHE 3.7 3.4 - - - +
291A LEU* 1.3 77.8 - - - +
293A GLU* 1.3 61.7 + - - +
295A ALA* 3.3 1.7 + - - +
296A THR* 2.8 30.7 + - - -
327C LEU* 5.3 0.7 - - - -
376C LYS* 3.3 45.1 - - + +
379C ILE* 3.8 20.8 - - + +
380C ALA* 4.3 1.3 - - - +
383C LEU* 4.3 2.0 - - - +
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Residues in contact with GLU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PHE* 2.9 29.4 + - - +
290A LYS* 3.8 4.0 - - - +
292A ALA* 1.3 77.5 - - - +
294A ALA* 1.3 61.4 + - - +
296A THR* 3.3 5.6 + - - -
297A GLU* 3.0 38.6 + - - +
335A LYS* 5.2 10.2 + - - +
339A GLU* 4.6 10.8 - - - +
327C LEU* 5.3 4.9 - - + -
376C LYS* 2.6 41.8 + - - +
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 4.3 16.4 - - + -
290A LYS 3.1 16.2 + - - +
291A LEU 3.9 2.5 - - - +
293A GLU* 1.3 75.3 - - - +
295A ALA* 1.3 67.8 + - - +
297A GLU* 3.4 6.5 + - - +
298A LEU* 3.0 29.5 + - - +
332A ALA 6.0 0.2 - - - -
335A LYS* 6.4 0.9 - - - +
336A ALA* 3.8 31.0 - - + +
339A GLU* 5.7 3.8 - - + -
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 3.5 19.8 - - + +
291A LEU 2.9 17.9 + - - +
292A ALA* 3.7 2.9 - - - +
294A ALA* 1.3 76.1 - - - +
296A THR* 1.3 62.9 + - - +
298A LEU* 3.4 3.3 + - - +
299A GLU* 3.0 28.8 + - + +
324C GLN* 3.8 9.2 - - - +
379C ILE* 4.8 0.4 - - + -
383C LEU* 3.4 33.0 - - + -
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Residues in contact with THR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ALA 2.8 22.1 + - - -
293A GLU* 3.6 6.5 - - - -
295A ALA* 1.3 77.8 - - - +
297A GLU* 1.3 62.1 + - - +
299A GLU* 3.4 3.3 + - - +
300A ALA* 3.2 20.3 + - - +
304C LEU* 4.4 4.1 - - + +
324C GLN* 3.4 53.7 + - + +
327C LEU* 4.1 10.2 - - + +
328C PHE* 4.0 21.3 - - + -
379C ILE* 3.8 10.2 - - - +
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Residues in contact with GLU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLU* 3.0 30.2 + - - +
294A ALA* 4.0 5.6 - - - +
296A THR* 1.3 74.1 - - - +
298A LEU* 1.3 60.1 + - + +
300A ALA* 3.2 1.8 + - - -
301A ALA* 2.8 26.1 + - - +
328A PHE* 3.1 21.4 - - + -
332A ALA* 3.8 27.6 - - + +
335A LYS* 3.1 40.3 + - - -
328C PHE* 4.1 22.6 - - + -
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A VAL* 4.4 22.0 - - + +
260A GLY* 3.5 43.1 - - - +
261A GLN* 3.6 21.8 - - - +
264A LEU* 4.1 17.3 - - + -
294A ALA 3.0 22.4 + - - +
295A ALA* 3.8 3.6 - - - +
297A GLU* 1.3 74.0 - - + +
299A GLU* 1.3 66.7 + - - +
301A ALA* 3.1 7.1 + - + +
302A ARG* 2.9 27.9 + - - +
329A ALA 5.2 0.2 - - - +
332A ALA* 4.6 5.4 - - + +
333A ALA* 4.2 20.6 - - + +
336A ALA* 4.5 6.7 - - + -
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Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A GLN* 5.3 2.1 - - - +
295A ALA* 3.0 19.6 + - + +
296A THR 3.7 6.7 - - - +
298A LEU* 1.3 75.9 - - - +
300A ALA* 1.3 64.1 + - - +
302A ARG* 3.4 24.0 + - - +
303A LEU* 3.1 29.7 + - + +
304C LEU* 4.2 9.0 - - + -
307C LYS* 2.9 27.7 + - - +
320C LEU* 5.6 4.7 - - - +
324C GLN* 3.5 28.2 - - - +
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A THR 3.2 10.1 + - - +
297A GLU* 3.2 8.9 + - - +
298A LEU 3.2 0.4 - - - -
299A GLU* 1.3 81.6 - - - +
301A ALA* 1.3 62.3 + - - +
303A LEU* 3.2 6.6 + - - +
304A LEU* 2.9 27.4 + - - +
328A PHE* 3.8 15.9 - - + -
300C ALA* 3.8 20.8 - - + +
303C LEU* 5.1 0.2 - - - +
304C LEU* 4.0 23.1 - - + +
328C PHE* 4.9 2.5 - - + -
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A VAL* 3.9 13.3 - - + +
297A GLU 2.8 14.5 + - - +
298A LEU* 3.1 14.3 + - + +
300A ALA* 1.3 77.2 - - - +
302A ARG* 1.3 62.0 + - - +
304A LEU* 3.2 7.1 + - - +
305A TYR* 3.1 23.4 + - - +
325A ALA 5.1 0.3 - - - +
328A PHE* 3.7 13.2 - - + +
329A ALA* 3.7 31.4 - - - +
332A ALA* 4.8 2.9 - - + -
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Residues in contact with ARG 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE 5.6 1.6 - - - -
73A ARG* 4.3 17.7 - - - +
76A GLU* 3.0 33.4 + - - -
257A VAL* 3.5 15.2 - - + +
261A GLN* 2.9 32.5 + - - +
298A LEU* 2.9 10.7 + - - +
299A GLU* 3.7 35.2 + - - +
301A ALA* 1.3 72.9 - - - +
303A LEU* 1.3 68.1 + - + +
304A LEU 3.3 0.3 + - - -
305A TYR* 3.3 28.7 + - + +
306A LEU* 3.0 38.0 + - + +
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TRP* 3.9 12.1 - - + -
5A PHE* 3.6 32.3 - - + +
299A GLU* 3.1 16.0 + - - +
300A ALA* 3.5 7.0 - - - +
302A ARG* 1.3 76.9 - - + +
304A LEU* 1.3 62.4 + - - +
306A LEU* 3.4 9.1 + - + +
307A LYS* 3.0 25.3 + - - +
4C TRP* 5.4 1.1 - - + -
303C LEU* 3.7 46.6 - - + +
304C LEU* 3.7 28.3 - - + -
307C LYS* 4.2 18.2 - - + +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA 2.9 14.7 + - - +
301A ALA* 3.4 7.4 - - - +
302A ARG 3.2 0.2 - - - -
303A LEU* 1.3 77.4 - - - +
305A TYR* 1.3 62.4 - - - +
307A LYS* 3.4 8.4 + - + +
308A ALA* 3.1 21.7 + - - +
321A GLU* 4.5 2.6 - - - +
324A GLN* 4.0 18.4 - - + +
325A ALA* 3.7 13.8 - - - +
328A PHE* 3.5 44.9 - - + -
296C THR* 4.4 6.3 - - + +
299C GLU* 4.5 13.5 - - + +
300C ALA* 4.2 23.8 - - + +
303C LEU* 3.9 18.8 - - + -
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Residues in contact with TYR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA* 3.5 30.3 - - + -
73A ARG* 3.7 23.4 - - - +
76A GLU* 2.6 30.3 + - - +
250A ILE* 4.0 9.3 - - + +
253A ALA* 3.9 21.8 - - + -
254A ALA* 3.8 27.8 - - + -
257A VAL* 3.9 9.4 - - + -
301A ALA 3.1 8.1 + - - +
302A ARG* 3.3 33.4 + - + +
304A LEU* 1.3 76.7 - - - +
306A LEU* 1.3 86.9 + - + +
308A ALA* 3.2 4.0 + - - +
309A ALA* 2.9 25.1 + - + +
325A ALA* 3.7 8.7 - - + +
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TRP* 3.6 15.6 - - + -
5A PHE* 3.8 20.9 - - - +
69A ARG* 4.0 28.8 + - + +
73A ARG* 3.5 39.0 - - + +
302A ARG* 3.0 34.5 + - + +
303A LEU* 3.6 10.1 - - + +
305A TYR* 1.3 99.2 - - + +
307A LYS* 1.3 58.4 + - - +
309A ALA* 3.2 6.0 + - - +
310A GLU* 2.9 28.2 + - - +
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Residues in contact with LYS 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TRP* 3.6 4.6 - - + -
303A LEU 3.0 17.5 + - - +
304A LEU* 3.5 9.4 - - + +
306A LEU* 1.3 77.1 - - - +
308A ALA* 1.3 64.3 + - - +
310A GLU* 3.1 5.2 + - - +
311A LEU* 3.0 27.0 + - + +
321A GLU* 3.8 28.7 + - + +
324A GLN* 5.1 1.8 - - - +
5C PHE* 3.7 50.8 - - + -
299C GLU* 2.5 46.6 + - - +
303C LEU* 4.4 12.7 - - + +
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ILE* 3.7 15.5 - - + +
304A LEU 3.1 7.7 + - - +
305A TYR* 3.6 10.5 - - - +
307A LYS* 1.3 79.6 - - - +
309A ALA* 1.3 61.3 + - - +
311A LEU* 3.4 4.8 + - - +
312A LYS* 3.1 22.9 + - - +
318A PHE* 4.0 4.6 - - + -
321A GLU* 3.6 39.5 - - - +
322A ALA* 4.0 10.5 - - + +
325A ALA* 4.5 1.1 - - + -
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR* 3.9 13.1 - - + +
69A ARG* 3.7 31.4 - - - +
72A ALA* 5.0 1.8 - - + -
250A ILE* 4.0 15.0 - - + +
305A TYR 2.9 16.6 + - - +
306A LEU* 3.4 7.6 - - - +
308A ALA* 1.3 75.0 - - - +
310A GLU* 1.3 66.1 + - - +
312A LYS* 3.3 2.4 + - - +
313A ASP* 3.0 30.9 + - - +
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Residues in contact with GLU 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TRP* 2.5 37.2 + - + +
69A ARG* 3.9 18.1 + - - +
306A LEU 2.9 12.2 + - - +
307A LYS 3.3 9.2 - - - +
309A ALA* 1.3 78.4 - - - +
311A LEU* 1.3 62.6 + - - +
313A ASP* 3.4 12.2 + - - +
314A ALA* 3.1 23.0 + - - +
3C LEU* 3.6 28.3 - - + +
5C PHE* 3.7 13.2 - - + -
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LYS* 3.0 23.3 + - - +
308A ALA 3.7 6.7 - - - +
309A ALA 3.3 0.2 - - - -
310A GLU* 1.3 73.7 - - - +
312A LYS* 1.3 63.9 + - - +
314A ALA* 3.3 7.3 + - - +
316A ARG* 3.1 49.9 + - + +
317A PRO 3.7 13.0 - - - +
318A PHE* 3.8 7.6 - - + -
321A GLU* 3.3 46.9 - - + +
3C LEU* 3.6 24.7 - - + -
5C PHE* 3.9 11.2 - - + -
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Residues in contact with LYS 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.5 30.5 - - - +
68A THR* 3.6 25.5 + - + +
247A GLY* 4.4 15.5 + - - -
250A ILE* 4.1 4.3 - - + -
308A ALA 3.1 17.0 + - - +
309A ALA 3.3 4.7 + - - +
311A LEU* 1.3 77.4 - - - +
313A ASP* 1.3 59.1 + - - +
315A GLY* 3.1 18.9 + - - -
316A ARG 4.4 0.4 - - - -
318A PHE* 3.4 46.3 - - + -
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Residues in contact with ASP 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER* 3.6 13.8 - - - -
68A THR* 2.7 44.6 + - - -
69A ARG* 3.5 7.4 + - - +
309A ALA 3.0 21.8 + - - +
310A GLU* 3.9 11.3 - - - +
312A LYS* 1.3 76.6 - - - +
314A ALA* 1.3 59.8 + - - +
315A GLY 3.2 1.7 + - - -
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Residues in contact with ALA 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A GLU 3.1 17.4 + - - +
311A LEU* 3.6 7.2 - - - +
312A LYS 3.1 0.6 - - - -
313A ASP* 1.3 77.8 - - - +
315A GLY* 1.3 61.4 + - - +
316A ARG* 3.4 24.4 + - - +
3C LEU* 4.6 14.8 - - + -
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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