Contacts of the helix formed by residues 307 - 337 (chain D) in PDB entry 2VIG
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 LEU 307 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLN* 3.8 14.6 - - - +
501C FAD 3.5 56.1 - - + +
299D ALA* 5.1 11.4 - - + +
300D PHE* 5.4 4.3 - - + -
303D PRO 4.6 2.7 - - - +
304D LEU* 2.9 33.7 + - + +
306D LYS* 1.3 79.1 - - + +
308D GLN* 1.3 65.6 + - - +
309D VAL 3.3 0.2 - - - -
310D ILE* 3.2 13.7 + - + +
311D GLN* 3.0 23.7 + - - +
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Residues in contact with GLN 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 3.8 15.4 - - - +
308A GLN* 3.1 23.8 + - + +
309A VAL* 3.2 37.1 + - + +
400B LEU* 3.8 27.6 - - + +
501B FAD 2.9 31.3 + - - -
306D LYS 3.6 3.8 + - - -
307D LEU* 1.3 68.9 - - - +
309D VAL* 1.3 60.0 + - - +
311D GLN* 3.1 13.6 + - - +
312D PHE* 2.9 33.7 + - + -
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Residues in contact with VAL 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLN* 3.1 27.6 + - + +
309A VAL* 4.5 5.6 - - + +
312A PHE* 3.2 56.1 - - + -
396C GLU* 4.0 8.3 - - + -
501C FAD 4.2 12.6 - - + +
308D GLN* 1.3 78.8 - - - +
310D ILE* 1.3 59.4 + - + +
312D PHE* 3.2 8.8 + - - +
313D LYS* 3.0 46.9 + - + +
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Residues in contact with ILE 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C FAD 3.8 33.4 - - - +
294D ALA* 4.1 23.3 - - + -
304D LEU* 3.4 32.1 - - + +
305D THR* 4.5 1.8 - - - +
307D LEU* 3.2 20.4 + - + +
309D VAL* 1.3 73.9 - - + +
311D GLN* 1.3 64.4 + - - +
313D LYS* 3.3 17.5 + - + +
314D LEU* 3.1 32.7 + - + +
366D ILE* 4.2 26.0 - - + -
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Residues in contact with GLN 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LEU* 3.4 24.0 - - + +
403B ALA* 3.3 31.6 - - + +
407B LEU* 4.6 9.9 - - + +
305D THR* 2.8 31.2 + - - +
306D LYS* 3.9 15.8 + - - +
307D LEU 3.0 12.9 + - - +
308D GLN* 3.1 13.4 + - - +
310D ILE* 1.3 77.7 - - - +
312D PHE* 1.3 60.0 + - + +
314D LEU* 3.4 7.6 + - + +
315D ALA* 3.0 23.6 + - - +
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Residues in contact with PHE 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A VAL* 3.3 45.1 - - + -
396B GLU* 3.4 37.9 - - + -
399B ARG* 3.6 34.0 - - + -
400B LEU* 3.5 30.7 - - + -
501B FAD 4.8 3.6 - + - -
308D GLN* 2.9 17.5 + - + +
309D VAL* 3.5 10.5 - - - +
311D GLN* 1.3 77.9 - - - +
313D LYS* 1.3 64.1 + - - +
315D ALA* 3.4 4.8 + - - +
316D ASP* 3.1 32.8 + - - +
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Residues in contact with LYS 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PHE* 5.5 2.4 - - - -
396C GLU* 2.7 43.9 + - - +
501C FAD 4.9 0.7 - - - -
309D VAL* 3.0 27.1 + - + +
310D ILE* 3.3 18.1 + - + +
312D PHE* 1.3 74.0 - - - +
314D LEU* 1.3 57.9 + - - +
316D ASP* 3.3 8.7 + - - +
317D MET* 2.9 37.0 + - - +
362D GLN* 3.0 34.2 + - - +
365D GLN* 4.4 5.3 - - + +
366D ILE* 3.9 30.3 - - + -
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Residues in contact with LEU 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ALA* 5.5 2.0 - - + -
406B LEU* 3.6 15.3 - - + +
407B LEU* 4.2 27.1 - - + -
287D LEU* 3.8 11.8 - - + +
290D ALA* 4.2 7.9 - - + -
291D VAL* 3.6 26.7 - - + +
294D ALA* 4.9 3.4 - - + -
305D THR* 4.3 10.3 - - + -
310D ILE* 3.1 30.7 + - + +
311D GLN* 3.8 7.2 - - - +
313D LYS* 1.3 77.2 - - - +
315D ALA* 1.3 59.5 + - - +
317D MET* 3.4 6.4 + - - +
318D ALA* 3.0 29.5 + - - +
366D ILE* 3.8 22.2 - - + -
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Residues in contact with ALA 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ARG* 3.4 37.9 - - + +
402B ILE* 3.7 28.5 - - + +
403B ALA* 3.9 5.3 - - - +
406B LEU* 4.7 0.6 - - - +
311D GLN 3.0 15.5 + - - +
312D PHE 3.9 3.8 - - - +
313D LYS 3.4 0.2 - - - -
314D LEU* 1.3 75.2 - - - +
316D ASP* 1.3 59.8 + - - +
318D ALA* 3.4 2.5 + - - +
319D LEU* 2.9 30.4 + - - +
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Residues in contact with ASP 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU* 5.0 2.9 - - - +
399B ARG* 2.9 41.3 + - - +
312D PHE* 3.1 17.7 + - - +
313D LYS* 3.6 9.3 - - - +
315D ALA* 1.3 76.8 - - - +
317D MET* 1.3 62.7 + - + +
319D LEU* 3.4 8.0 + - - +
320D ALA* 3.0 26.7 + - - +
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Residues in contact with MET 317 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D LEU* 3.7 24.7 - - + -
290D ALA* 4.0 21.3 - - + -
313D LYS 2.9 28.5 + - - +
314D LEU* 3.6 9.2 - - - +
316D ASP* 1.3 78.4 - - + +
318D ALA* 1.3 61.7 + - - +
320D ALA* 3.5 0.8 + - - -
321D LEU* 3.1 19.4 + - - +
358D ALA 5.2 0.4 - - - +
359D ILE* 3.4 62.5 - - + +
362D GLN* 3.8 23.3 - - + -
363D ALA* 4.1 4.9 - - - +
366D ILE* 3.9 12.8 - - - -
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Residues in contact with ALA 318 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B MET* 3.8 15.5 - - + -
402B ILE* 4.7 2.5 - - + -
406B LEU* 3.8 28.7 - - + -
287D LEU* 4.1 11.4 - - + +
314D LEU 3.0 16.8 + - - +
315D ALA* 3.7 5.6 - - - +
316D ASP 3.4 0.2 - - - -
317D MET* 1.3 72.5 - - - +
319D LEU* 1.3 61.1 + - - +
321D LEU* 3.5 1.9 + - - +
322D GLU* 3.0 40.7 + - - +
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Residues in contact with LEU 319 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 3.5 30.5 - - + -
347B MET* 3.7 32.5 - - + +
350B LEU* 3.8 35.4 - - + -
351B ALA* 4.4 11.7 - - + +
354B GLU* 5.8 1.8 - - - +
399B ARG* 5.7 1.8 - - - +
402B ILE* 5.0 2.5 - - + -
315D ALA 2.9 17.8 + - - +
316D ASP* 3.7 9.6 - - - +
317D MET 3.3 0.2 - - - -
318D ALA* 1.3 73.7 - - - +
320D ALA* 1.3 66.3 + - - +
322D GLU* 4.0 0.5 - - - +
323D SER* 3.0 29.1 + - - -
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Residues in contact with ALA 320 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D ASP 3.0 18.1 + - - +
317D MET* 3.9 4.3 - - - +
319D LEU* 1.3 75.1 - - - +
321D LEU* 1.3 58.3 - - - +
323D SER* 3.8 4.9 - - - -
324D ALA* 3.0 29.5 + - - +
355D ALA* 4.1 21.3 - - + +
358D ALA* 6.1 2.2 - - + -
359D ILE* 4.4 5.6 - - + -
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Residues in contact with LEU 321 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D LEU* 3.7 29.8 - - + +
283D ALA* 3.9 13.9 - - + +
284D GLN* 3.4 42.8 - - - +
287D LEU* 3.9 19.3 - - + -
317D MET 3.1 16.0 + - - +
318D ALA 3.8 4.0 - - - +
319D LEU 3.2 0.2 - - - -
320D ALA* 1.3 76.2 - - - +
322D GLU* 1.3 63.2 + - + +
324D ALA* 3.3 3.8 + - - +
325D ARG* 2.9 45.9 + - - +
355D ALA* 5.0 1.3 - - + -
359D ILE* 3.9 8.0 - - + +
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Residues in contact with GLU 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 4.6 1.8 - - + -
330B ARG* 3.0 36.2 + - - +
343B LYS* 3.0 30.0 + - - +
347B MET* 3.4 20.3 - - - +
406B LEU* 4.8 5.4 - - - +
318D ALA* 3.0 21.4 + - - +
319D LEU 4.2 1.6 - - - +
321D LEU* 1.3 75.7 - - + +
323D SER* 1.3 66.1 + - - +
325D ARG* 3.2 11.0 + - - +
326D LEU* 3.1 28.7 + - - +
504D EDO 3.5 19.5 + - - +
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Residues in contact with SER 323 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B SER* 3.2 32.0 + - - -
326B LEU* 5.6 0.2 - - - +
327B LEU* 4.2 25.2 - - - +
319D LEU* 3.0 22.1 + - - -
320D ALA* 3.8 6.5 - - - -
322D GLU* 1.3 77.5 - - - +
324D ALA* 1.3 60.9 + - - -
325D ARG 3.3 0.2 + - - -
326D LEU* 3.4 3.7 + - - +
327D LEU* 3.3 24.3 + - - +
351D ALA* 6.0 0.3 - - - +
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Residues in contact with ALA 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D LEU* 3.7 9.2 - - + -
320D ALA 3.0 20.0 + - - +
321D LEU* 3.3 6.5 + - - +
323D SER* 1.3 76.1 - - - +
325D ARG* 1.3 58.0 + - - +
327D LEU* 3.5 4.5 + - - +
328D THR* 3.1 30.8 + - - -
348D ALA* 4.9 1.0 - - - -
351D ALA* 4.1 16.1 - - + +
352D ALA* 3.7 33.9 - - - +
355D ALA* 4.7 2.5 - - + -
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Residues in contact with ARG 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D GLU* 2.9 37.8 + - - +
280D LEU* 3.6 13.0 - - + +
284D GLN* 3.0 24.8 + - - +
321D LEU* 2.9 37.5 + - - +
322D GLU* 3.2 23.4 + - - +
324D ALA* 1.3 74.5 - - - +
326D LEU* 1.3 60.4 + - - +
328D THR* 3.2 1.2 + - - -
329D TRP* 2.8 65.7 + - + +
504D EDO 3.0 31.1 + - - +
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Residues in contact with LEU 326 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B SER 5.9 0.2 - - - +
326B LEU* 3.7 45.7 - - + +
327B LEU* 3.8 26.7 - - + +
330B ARG* 4.2 20.9 - - + +
322D GLU 3.1 16.0 + - - +
323D SER* 3.8 4.5 - - - +
325D ARG* 1.3 73.7 - - - +
327D LEU* 1.3 58.3 + - - +
329D TRP* 3.7 11.0 - - + +
330D ARG* 2.8 31.9 + - - +
504D EDO 3.4 26.7 - - - -
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Residues in contact with LEU 327 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 3.5 20.6 - - + -
323B SER* 4.2 27.8 - - - +
326B LEU* 3.8 17.4 - - + +
323D SER 3.3 12.1 + - - +
324D ALA* 3.6 7.2 - - - +
326D LEU* 1.3 76.9 - - - +
328D THR* 1.3 58.4 + - - +
330D ARG* 3.5 30.6 + - - +
331D ALA* 3.1 23.7 + - - +
344D GLU 4.2 3.0 - - - +
347D MET* 3.8 11.9 - - + +
348D ALA* 3.7 17.6 - - + +
351D ALA* 3.4 31.0 - - + -
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Residues in contact with THR 328 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ALA* 4.2 10.5 - - + -
273D ILE* 4.1 14.4 - - + +
276D ALA* 3.5 21.2 - - + +
277D SER* 3.5 24.2 - - - +
280D LEU* 3.8 19.7 - - + +
324D ALA 3.1 15.5 + - - -
325D ARG 3.5 8.1 - - - -
326D LEU 3.2 0.2 - - - -
327D LEU* 1.3 76.6 - - - +
329D TRP* 1.3 58.5 + - + +
331D ALA* 3.3 5.0 + - - +
332D ALA* 3.0 25.5 + - - +
348D ALA* 3.6 11.6 + - - +
352D ALA* 4.6 0.3 - - - +
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Residues in contact with TRP 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D LEU* 3.9 33.9 - - + -
42D LEU* 5.8 3.4 - - + -
96D LEU* 3.8 20.6 - - + -
99D ALA* 4.6 9.7 - - + +
100D ILE* 4.0 28.8 - - + +
103D GLU* 4.8 6.4 + - - -
280D LEU* 5.3 1.4 - - - +
325D ARG* 2.8 49.1 + - + +
326D LEU* 3.9 11.9 - - + +
328D THR* 1.3 83.8 - - + +
330D ARG* 1.3 60.2 + - - +
332D ALA* 3.8 4.9 - - - +
333D MET* 2.9 47.3 + - + +
504D EDO 4.0 21.5 - - - -
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Residues in contact with ARG 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B GLU* 2.8 36.5 + - - +
326B LEU* 4.0 29.7 - - + +
326D LEU 2.8 22.0 + - - +
327D LEU* 3.6 21.7 + - - +
329D TRP* 1.3 71.7 - - - +
331D ALA* 1.3 62.2 + - - +
333D MET* 3.3 16.2 + - + +
334D LEU* 2.9 38.5 + - + +
343D LYS* 4.8 1.2 - - - +
344D GLU* 3.5 31.1 + - - +
347D MET* 3.3 23.6 - - - +
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Residues in contact with ALA 331 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D ILE* 3.8 15.8 - - + +
327D LEU 3.1 14.8 + - - +
328D THR 3.6 7.4 - - - +
330D ARG* 1.3 76.9 - - - +
332D ALA* 1.3 57.1 - - - +
334D LEU* 3.3 4.4 + - - +
335D LYS* 3.1 28.6 + - - +
341D PHE* 3.9 4.5 - - - +
344D GLU* 3.8 13.4 - - - +
345D ALA* 3.8 32.1 - - + +
348D ALA* 4.6 2.5 - - + -
----------------------------------------------------------
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Residues in contact with ALA 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D TYR* 3.5 31.4 - - + +
96D LEU* 3.8 9.2 - - + +
99D ALA* 4.6 3.8 - - + -
273D ILE* 4.2 17.2 - - + +
328D THR 3.0 16.7 + - - +
329D TRP* 3.8 7.9 - - - +
331D ALA* 1.3 74.0 - - - +
333D MET* 1.3 61.5 + - - +
335D LYS* 3.4 2.1 + - - +
336D ASP* 2.9 35.6 + - - +
----------------------------------------------------------
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Residues in contact with MET 333 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU* 4.4 29.4 - - + -
326D LEU 5.4 0.2 - - - +
329D TRP* 2.9 41.6 + - + +
330D ARG* 3.7 11.2 - - + +
332D ALA* 1.3 75.0 - - - +
334D LEU* 1.3 65.1 + - + +
336D ASP* 3.4 6.4 + - - +
337D ASN* 2.8 37.8 + - - +
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Residues in contact with LEU 334 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D ARG* 2.9 30.0 + - + +
331D ALA 3.7 4.7 - - - +
333D MET* 1.3 75.3 - - + +
335D LYS* 1.3 64.8 + - - +
337D ASN* 3.3 6.5 + - + +
339D LYS* 2.9 53.9 + - + +
340D PRO 3.7 14.1 - - - +
341D PHE* 3.8 3.4 - - + -
344D GLU* 3.5 46.9 - - + +
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Residues in contact with LYS 335 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ASP* 3.8 11.1 + - - -
95D TYR* 3.1 53.3 - - + -
270D MET* 2.9 33.9 - - + -
273D ILE* 4.5 2.7 - - + -
331D ALA 3.1 15.9 + - - +
332D ALA* 3.7 4.7 - - - +
334D LEU* 1.3 76.9 - - - +
336D ASP* 1.3 64.9 + - - +
338D LYS* 3.1 15.9 + - - +
339D LYS 4.3 0.4 - - - -
341D PHE* 3.7 42.2 - - + -
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Residues in contact with ASP 336 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ASP* 4.9 1.7 - - - +
94D ASP* 3.4 22.5 - - + +
95D TYR* 2.7 30.0 + - - +
96D LEU* 3.1 27.0 + - - +
332D ALA 2.9 22.6 + - - +
333D MET* 3.7 8.3 - - - +
334D LEU 3.3 0.2 - - - -
335D LYS* 1.3 80.1 - - - +
337D ASN* 1.3 62.2 + - - +
338D LYS* 3.2 8.9 + - - +
----------------------------------------------------------
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Residues in contact with ASN 337 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D MET* 2.8 34.2 + - - +
334D LEU* 3.3 3.1 + - - +
335D LYS 3.3 0.8 - - - -
336D ASP* 1.3 79.0 - - - +
338D LYS* 1.3 70.3 + - - +
339D LYS* 3.2 29.0 + - + +
----------------------------------------------------------
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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