Contacts of the helix formed by residues 389 - 411 (chain B) in PDB entry 3MY0
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 CYS 389 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B LEU* 5.6 0.7 - - - -
386B ARG* 3.0 53.2 + - - +
387B THR 3.4 0.8 + - - -
388B ASP* 1.3 80.3 - - - +
390B PHE* 1.3 68.2 + - - +
391B GLU* 3.8 19.1 - - - -
392B SER* 3.4 18.8 - - - -
393B TYR* 3.5 12.3 - - - -
395B TRP* 5.4 2.0 - - - -
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Residues in contact with PHE 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ALA* 3.4 46.0 - - + -
326B ILE 3.8 4.0 - - - -
327B ALA* 3.8 19.3 - - + -
353B VAL* 3.4 30.5 - - + -
355B HIS* 3.6 39.7 - - + +
362B LEU* 4.1 18.6 - - + +
388B ASP 4.2 0.6 - - - -
389B CYS* 1.3 71.5 - - - +
391B GLU* 1.3 69.1 + - + +
393B TYR* 3.0 20.5 + - - +
394B LYS* 3.4 36.0 + - + -
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Residues in contact with GLU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B CYS* 3.4 11.4 - - - -
390B PHE* 1.3 79.7 - - + +
392B SER* 1.3 63.9 + - - +
394B LYS* 3.1 34.4 + - - +
395B TRP* 3.1 60.2 + - + -
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Residues in contact with SER 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B GLU* 4.8 2.0 - - - +
385B ILE* 3.9 17.5 - - - -
386B ARG* 2.8 44.0 + - - +
389B CYS* 3.4 12.8 + - - -
390B PHE 3.1 0.2 + - - -
391B GLU* 1.3 77.1 - - - +
393B TYR* 1.3 63.3 + - - +
395B TRP* 3.0 30.8 + - - +
396B THR* 3.2 17.3 + - - +
476B PRO* 5.6 0.6 - - - +
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Residues in contact with TYR 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ALA* 3.8 19.6 - - + +
329B ARG* 3.6 41.2 + - + +
353B VAL* 3.9 21.8 - - + -
362B LEU* 4.7 13.0 - - + +
385B ILE* 4.1 20.2 - - + -
386B ARG 4.8 0.2 - - - -
387B THR* 2.9 50.0 + - + +
389B CYS 3.5 23.8 - - - -
390B PHE* 3.0 13.6 + + - +
392B SER* 1.3 75.7 - - - +
394B LYS* 1.3 61.3 + - - +
396B THR* 2.7 24.7 + - + -
397B ASP* 3.2 11.8 + - - +
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Residues in contact with LYS 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B HIS* 3.5 53.3 + - + +
327B ALA* 4.1 2.6 - - + +
390B PHE* 3.4 36.5 + - + +
391B GLU* 3.1 37.4 + - - +
393B TYR* 1.3 77.0 - - - +
395B TRP* 1.3 68.6 + - + +
397B ASP* 3.1 14.6 + - - +
398B ILE* 3.1 17.3 + - + +
481B THR* 6.3 1.6 - - - +
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Residues in contact with TRP 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B GLU* 4.4 0.7 - - - +
386B ARG* 5.3 8.3 - - - -
389B CYS* 5.4 1.3 - - - -
391B GLU* 3.1 51.2 + - + -
392B SER* 3.0 30.3 + - - +
394B LYS* 1.3 81.2 - - + +
396B THR* 1.3 54.1 + - - +
398B ILE* 3.5 12.0 + - + +
399B TRP 3.2 15.1 + - - -
476B PRO* 3.1 47.6 + - + +
477B SER* 3.6 35.2 + - - +
479B ARG* 2.7 37.6 + - + +
480B LEU 5.2 1.3 - - - -
481B THR* 5.6 7.3 - - + +
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Residues in contact with THR 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ARG* 4.8 10.9 - - - +
375B TYR 4.9 1.4 - - - +
377B ALA* 4.2 14.7 - - + +
379B GLU* 3.6 15.3 - - - +
380B VAL* 3.7 27.8 - - + -
385B ILE* 3.9 13.5 - - + -
392B SER 3.2 13.9 + - - +
393B TYR* 2.7 21.5 + - + +
395B TRP* 1.3 74.3 - - - +
397B ASP* 1.3 67.9 + - - +
398B ILE 3.2 0.2 - - - -
399B TRP* 3.6 3.8 - - - +
400B ALA* 3.3 22.0 + - - +
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Residues in contact with ASP 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LEU* 3.8 13.0 - - + +
314B HIS* 2.8 28.8 + - + +
327B ALA* 3.5 1.6 - - - -
328B HIS* 2.7 33.2 + - - +
329B ARG* 2.9 29.3 + - - -
331B PHE* 4.4 8.3 + - + +
393B TYR 3.2 8.7 + - - +
394B LYS 3.1 10.2 + - - +
396B THR* 1.3 82.1 + - - +
398B ILE* 1.3 57.3 + - - +
400B ALA* 3.3 8.5 + - - +
401B PHE* 2.9 27.8 + - - +
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Residues in contact with ILE 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LEU* 4.3 7.9 - - + -
314B HIS* 4.2 13.2 - - + +
394B LYS* 3.1 16.7 + - + +
395B TRP* 3.6 14.6 - - + +
396B THR 3.2 0.2 - - - -
397B ASP* 1.3 72.8 - - - +
399B TRP* 1.3 67.4 + - - +
401B PHE* 2.9 14.5 + - - +
402B GLY 3.0 11.1 + - - -
471B CYS* 3.4 32.6 - - - +
479B ARG* 4.0 9.2 - - + -
480B LEU 3.3 29.2 - - - +
481B THR* 3.9 2.7 - - - -
482B ALA* 3.6 27.4 - - - +
485B ILE* 4.3 5.8 - - + -
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Residues in contact with TRP 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ARG 5.4 0.2 + - - -
375B TYR 3.3 18.7 + - - -
376B MET 3.6 11.1 + - - -
377B ALA* 3.7 12.3 - - + -
378B PRO* 3.5 38.1 - - + -
395B TRP 3.2 3.6 + - - -
396B THR 3.6 8.3 - - - +
398B ILE* 1.3 75.5 - - - +
400B ALA* 1.3 67.2 + - - +
402B GLY* 2.9 15.1 + - - -
403B LEU* 3.2 29.0 + - + +
425B PHE* 4.5 16.3 - + - -
442B VAL* 3.9 17.3 - - + -
446B GLN* 6.0 1.3 - - - -
447B GLN 4.8 0.9 - - - -
448B THR* 4.0 20.0 - - + -
471B CYS 3.4 13.6 + - - -
472B TRP* 3.5 50.9 + + + -
473B TYR 4.9 0.7 - - - -
474B PRO 5.5 0.2 - - - -
479B ARG* 3.8 24.0 - - - +
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Residues in contact with ALA 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B PHE* 3.1 33.4 - - + +
375B TYR* 4.1 18.0 - - + +
396B THR 3.3 10.4 + - - +
397B ASP* 3.4 9.9 - - - +
398B ILE 3.3 0.6 - - - -
399B TRP* 1.3 86.0 - - - +
401B PHE* 1.3 60.8 + - - +
403B LEU* 3.3 9.2 + - - +
404B VAL* 3.1 25.5 + - - +
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Residues in contact with PHE 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ALA 4.0 8.5 - - - -
306B ALA* 4.0 15.5 - - + -
307B ALA* 3.8 41.3 - - + -
310B LEU* 3.8 18.6 - - + -
331B PHE* 3.7 26.2 - + + -
397B ASP 2.9 14.2 + - - +
398B ILE* 2.9 13.6 + - - +
400B ALA* 1.3 72.5 - - - +
402B GLY* 1.3 67.9 + - - +
404B VAL* 2.9 8.1 + - + +
405B LEU* 2.9 49.1 + - + -
467B MET* 5.0 0.2 - - + -
471B CYS* 4.2 2.9 - - - -
485B ILE* 3.7 33.7 - - + -
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Residues in contact with GLY 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ILE 3.0 6.9 + - - -
399B TRP 2.9 4.8 + - - -
401B PHE* 1.3 77.7 - - - +
403B LEU* 1.3 59.5 + - - +
405B LEU* 3.3 9.4 + - - +
406B TRP 3.1 18.2 + - - -
468B MET* 3.8 4.2 - - - +
471B CYS* 3.6 18.1 - - - -
472B TRP* 3.2 30.7 - - - -
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Residues in contact with LEU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ARG 4.1 11.7 - - - +
375B TYR* 4.2 14.6 - - + -
399B TRP* 3.2 37.1 + - + +
400B ALA 3.5 7.9 - - - +
401B PHE 3.1 0.6 - - - -
402B GLY* 1.3 76.3 - - - +
404B VAL* 1.3 63.1 + - - +
406B TRP* 3.4 5.4 - - - +
407B GLU* 3.2 26.8 + - - +
424B PRO* 4.0 17.0 - - + +
425B PHE* 3.8 20.9 - - + -
449B PRO* 3.6 34.3 - - + -
472B TRP* 3.5 19.1 - - + +
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Residues in contact with VAL 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU* 3.8 25.5 - - + +
306B ALA* 5.6 4.3 - - + -
331B PHE* 3.7 26.2 - - + -
332B LYS* 3.8 6.1 - - - -
333B SER* 3.7 27.4 - - - +
336B VAL* 5.4 1.3 - - + -
375B TYR* 4.1 1.6 - - + -
400B ALA 3.1 13.8 + - - +
401B PHE* 2.9 13.1 + - + +
403B LEU* 1.3 75.2 - - - +
405B LEU* 1.3 65.3 + - + +
407B GLU* 3.3 15.2 + - - +
408B ILE* 3.2 26.7 + - + +
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Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ALA* 3.8 29.6 - - + -
401B PHE* 2.9 41.6 + - + +
402B GLY* 3.3 8.5 + - - +
404B VAL* 1.3 74.3 - - + +
406B TRP* 1.3 53.6 + - - +
408B ILE* 3.0 12.1 + - + +
409B ALA* 2.7 34.8 + - - +
464B LEU* 3.9 15.6 - - + +
467B MET* 3.1 43.1 - - + +
468B MET* 3.6 25.0 - - + +
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Residues in contact with TRP 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B GLY 3.1 10.0 + - - +
403B LEU* 3.4 10.1 - - - +
405B LEU* 1.3 79.2 - - - +
407B GLU* 1.3 75.6 + - + +
409B ALA* 3.4 2.5 - - + +
410B ARG* 2.8 60.4 + - + +
422B ARG 3.3 22.4 - - - -
423B PRO 3.6 11.9 - - - -
424B PRO* 3.7 13.7 - - + -
425B PHE 5.1 0.2 - - - -
426B TYR* 3.6 35.7 - + - -
449B PRO* 3.6 29.8 - - + +
450B THR 3.5 25.4 + - - -
451B ILE* 4.8 4.3 - - - -
452B PRO* 4.6 7.5 - - + +
468B MET* 3.8 14.9 - - - -
472B TRP* 4.2 15.9 - + + -
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Residues in contact with GLU 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU* 6.2 0.2 - - + -
289B LEU* 3.2 23.7 - - + +
333B SER* 2.5 32.2 + - - -
375B TYR* 2.4 34.4 + - - -
403B LEU 3.2 12.6 + - - +
404B VAL* 3.4 10.6 - - - +
406B TRP* 1.3 87.2 - - + +
408B ILE* 1.3 62.1 + - - +
410B ARG* 3.9 3.8 + - - +
411B ARG* 3.7 13.2 + - - +
421B TYR* 2.7 31.4 + - + +
422B ARG 5.1 0.7 - - - -
424B PRO* 3.5 22.6 - - + +
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Residues in contact with ILE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU* 4.2 27.8 - - + -
289B LEU* 3.9 12.8 - - + -
294B LEU* 3.6 20.6 - - + +
299B ALA* 3.7 24.9 - - + +
302B LEU* 4.4 8.5 - - + +
303B ALA* 4.1 29.8 - - + +
404B VAL* 3.2 18.1 + - + +
405B LEU* 3.0 15.5 + - + +
407B GLU* 1.3 74.3 - - - +
409B ALA* 1.3 65.5 + - - +
411B ARG* 3.1 12.8 + - - +
412B THR* 2.8 16.3 + - - -
464B LEU* 4.7 5.8 - - + -
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Residues in contact with ALA 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B LEU 2.7 11.0 + - - +
406B TRP* 3.4 6.5 - - + +
408B ILE* 1.3 73.4 - - - +
410B ARG* 1.3 62.1 + - - +
412B THR* 3.0 28.9 + - - +
452B PRO* 6.1 1.8 - - + -
454B ARG* 4.2 4.9 + - - -
455B LEU* 4.6 24.0 - - + +
461B LEU* 5.0 4.3 - - + -
464B LEU* 5.0 5.2 - - + -
468B MET* 3.1 36.6 - - + -
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Residues in contact with ARG 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B TRP* 2.8 48.5 + - + +
407B GLU* 4.0 7.2 - - - +
409B ALA* 1.3 72.4 - - - +
411B ARG* 1.3 58.3 + - + +
412B THR 3.2 2.6 + - - -
419B GLU* 3.6 60.5 + - + +
420B ASP* 2.9 25.4 + - - +
421B TYR* 4.9 2.0 - - + +
422B ARG* 3.4 40.1 - - - +
426B TYR* 3.5 28.6 + - - -
452B PRO* 5.7 8.5 - - - -
454B ARG* 3.7 8.8 + - - +
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Residues in contact with ARG 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU* 2.6 39.2 + - + +
290B GLN 3.1 22.6 + - - -
291B ARG 4.2 5.3 + - - -
292B GLN 3.5 19.1 + - - +
293B THR* 3.5 19.5 - - - +
294B LEU* 3.0 25.3 + - + -
407B GLU 3.7 10.7 + - - +
408B ILE 3.1 11.5 + - - +
409B ALA 3.1 1.2 - - - -
410B ARG* 1.3 78.1 - - + +
412B THR* 1.3 58.8 + - - +
418B VAL* 3.4 24.5 + - - +
419B GLU 3.0 25.7 + - - -
420B ASP* 4.1 6.4 + - - +
421B TYR* 3.7 28.4 - - - +
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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