Contacts of the helix formed by residues 401 - 424 (chain B) in PDB entry 5NC5
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 ALA 401 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B GLY 3.2 10.7 + - - +
398B MET* 3.2 11.8 + - - +
399B VAL 3.1 0.4 - - - -
400B LEU* 1.3 75.3 - - - +
402B ILE* 1.3 65.7 + - - +
403B GLY 3.2 2.9 - - - -
404B LEU* 3.2 15.3 + - + +
405B LEU* 3.1 25.9 + - + +
474B ILE* 4.4 17.0 - - + +
477B ALA* 4.1 25.8 - - + -
478B MET* 5.7 1.1 - - + +
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Residues in contact with ILE 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B THR* 3.7 25.8 - - + +
344B LEU* 3.5 38.1 - - + -
347B ALA* 4.1 20.6 - - + -
398B MET 3.4 6.1 + - - +
399B VAL* 3.2 27.6 + - + +
401B ALA* 1.3 77.8 - - - +
403B GLY* 1.3 59.4 + - - +
405B LEU* 3.1 11.2 + - + +
406B VAL* 2.8 40.3 + - + +
982B PHE* 4.3 14.8 - - + -
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Residues in contact with GLY 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LEU 4.5 0.8 + - - -
401B ALA 3.2 0.8 - - - -
402B ILE* 1.3 79.2 - - - +
404B LEU* 1.3 55.6 + - - +
406B VAL* 4.0 5.2 - - - +
407B ASP* 3.0 31.9 + - - +
937B LEU* 4.1 15.6 - - - +
978B THR* 4.6 1.1 - - - +
982B PHE* 3.5 36.4 - - - -
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Residues in contact with LEU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LEU 4.8 4.0 - - - +
401B ALA* 3.2 16.7 + - + +
403B GLY* 1.3 77.3 - - - +
405B LEU* 1.4 64.3 + - + +
407B ASP* 3.9 1.8 - - - -
408B ASP* 3.4 12.5 + - - +
449B LEU* 4.4 20.4 - - + -
453B PHE* 4.5 22.0 - - + -
474B ILE* 4.7 8.5 - - + -
478B MET* 4.4 20.2 - - + -
481B SER* 4.8 0.7 - - - -
933B THR* 4.1 18.8 - - + +
936B GLY* 4.6 2.9 - - - -
937B LEU* 3.9 29.2 - - + +
940B LYS* 3.2 28.8 + - + +
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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
----------------------------------------------------------
372B VAL* 4.2 18.9 - - + +
375B VAL* 3.9 20.6 - - + -
376B LEU* 4.1 28.3 - - + -
398B MET* 5.5 1.6 - - - +
401B ALA* 3.1 20.1 + - + +
402B ILE* 3.6 11.2 - - + +
404B LEU* 1.4 75.4 - - + +
406B VAL* 1.3 69.2 + - + +
408B ASP* 3.4 10.2 + - - +
409B ALA* 3.4 11.6 + - - +
477B ALA* 3.8 39.9 - - + +
478B MET* 4.5 2.9 - - - +
481B SER* 3.8 18.4 + - - +
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Residues in contact with VAL 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B ALA* 5.0 8.7 - - + +
348B ILE* 6.5 0.2 - - + -
351B VAL* 3.7 33.2 - - + -
372B VAL* 4.3 20.6 - - + -
402B ILE* 2.8 31.8 + - + +
403B GLY* 4.0 5.6 - - - +
405B LEU* 1.3 75.5 - - + +
407B ASP* 1.3 66.3 + - - +
409B ALA* 3.0 7.3 + - - +
410B ILE* 3.0 34.8 + - + +
978B THR* 4.8 8.1 - - + +
981B ALA* 4.6 9.2 - - + -
982B PHE* 5.5 3.1 - - + +
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Residues in contact with ASP 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B GLY 3.0 20.3 + - - +
404B LEU 4.1 4.0 - - - +
406B VAL* 1.3 77.8 - - - +
408B ASP* 1.3 62.2 + - - +
410B ILE* 3.9 1.1 - - - +
411B VAL* 2.9 45.6 + - - +
937B LEU* 3.7 16.8 - - + +
940B LYS* 3.3 33.4 - - - +
941B ASN* 4.0 9.5 - - - +
944B LEU* 5.1 1.0 - - - +
974B PRO 4.7 1.4 - - - +
978B THR* 2.8 39.4 + - + +
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Residues in contact with ASP 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B LEU 3.4 3.9 + - - +
405B LEU 3.4 3.7 + - - +
406B VAL 3.3 1.0 - - - -
407B ASP* 1.3 79.8 - - - +
409B ALA* 1.3 62.9 + - - +
411B VAL* 4.1 3.2 - - - +
412B VAL* 3.5 24.9 + - - +
442B LEU* 3.6 17.3 - - - +
445B ILE* 5.6 0.3 - - - +
478B MET* 4.7 3.1 - - - +
481B SER* 2.6 38.9 + - - +
482B VAL* 3.9 16.9 - - - +
485B ALA* 4.4 16.9 - - + +
940B LYS* 2.8 34.9 + - - -
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Residues in contact with ALA 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B VAL* 6.0 0.2 - - + -
368B PRO* 3.7 34.1 - - + -
371B ALA* 4.5 9.6 - - + -
372B VAL* 4.5 10.3 - - + -
405B LEU 3.4 7.3 + - - +
406B VAL 3.0 9.4 + - - +
408B ASP* 1.3 76.8 - - - +
410B ILE* 1.3 65.7 + - - +
412B VAL* 4.1 1.2 - - - +
413B VAL* 3.3 28.8 + - + +
489B THR* 4.8 11.1 - - + +
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Residues in contact with ILE 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B VAL* 4.5 16.8 - - + -
354B VAL* 5.2 4.0 - - + -
355B MET* 4.4 23.2 - - + +
368B PRO* 5.4 0.2 - - + -
406B VAL* 3.0 30.8 + - + +
407B ASP 3.9 2.2 - - - +
409B ALA* 1.3 75.3 - - + +
411B VAL* 1.3 60.5 + - + +
414B GLU* 2.9 31.4 + - - +
974B PRO* 4.1 14.1 - - + +
977B MET* 4.1 28.5 - - + +
978B THR* 3.7 40.8 - - - +
981B ALA* 5.0 1.3 - - + -
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Residues in contact with VAL 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B ASP* 2.9 43.5 + - - +
408B ASP* 4.1 4.3 - - - +
410B ILE* 1.3 77.8 - - + +
412B VAL* 1.3 63.6 + - + +
414B GLU* 4.9 1.3 - - - -
415B ASN* 3.3 24.4 + - - +
438B ILE* 3.8 19.7 - - + -
442B LEU* 4.5 13.0 - - + -
940B LYS* 5.8 0.7 - - - -
941B ASN* 6.0 0.4 - - - +
944B LEU* 4.1 22.9 - - + -
971B ARG* 4.0 25.6 + - - +
974B PRO* 4.9 7.4 - - + -
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Residues in contact with VAL 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ASP 3.5 16.8 + - - +
409B ALA 4.1 2.2 - - - +
410B ILE 3.4 0.8 - - - -
411B VAL* 1.3 78.0 - - + +
413B VAL* 1.3 63.0 + - - +
415B ASN* 3.6 0.9 + - - +
416B VAL* 3.4 23.9 + - - +
435B MET* 3.4 36.1 - - + +
438B ILE* 4.1 9.6 - - + -
442B LEU* 4.3 12.3 - - + -
485B ALA* 4.1 17.7 - - + +
489B THR* 3.6 31.9 - - - +
490B PRO* 4.5 0.7 - - + -
493B CYS* 4.3 10.8 - - - -
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Residues in contact with VAL 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B MET* 3.2 30.5 - - + -
359B LEU* 4.1 4.9 - - + -
364B ALA* 4.1 19.5 - - + +
367B ILE* 3.4 37.9 - - + -
368B PRO* 4.7 2.0 - - + -
409B ALA 3.3 16.3 + - - +
412B VAL* 1.3 74.2 - - + +
414B GLU* 1.4 65.3 + - - +
416B VAL* 3.2 4.3 + - - +
417B GLU* 3.1 23.4 + - + +
489B THR* 5.3 0.4 - - + -
493B CYS* 3.6 19.5 - - - -
497B LEU* 4.7 3.3 - - + +
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Residues in contact with GLU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B MET* 5.2 0.6 - - + +
359B LEU* 5.0 3.6 - - + -
410B ILE 2.9 18.6 + - - +
411B VAL 4.4 0.7 - - - +
413B VAL* 1.4 78.9 - - - +
415B ASN* 1.3 64.0 + - - +
417B GLU* 3.3 7.3 + - - +
418B ARG* 2.8 32.7 + - - +
970B MET 3.8 6.6 - - - +
971B ARG* 3.5 14.4 + - - -
973B ARG* 2.9 32.8 + - - +
974B PRO* 3.1 36.0 - - + +
977B MET* 3.3 33.9 - - + -
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Residues in contact with ASN 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B VAL 3.3 17.9 + - - +
412B VAL 3.9 1.3 - - - +
413B VAL 3.2 0.6 - - - -
414B GLU* 1.3 87.0 + - - +
416B VAL* 1.3 60.2 + - - +
418B ARG* 2.7 24.9 + - - +
419B VAL* 3.0 31.1 + - - +
434B SER* 2.6 35.1 + - - +
437B GLN* 2.7 25.3 + - - +
438B ILE* 4.5 9.1 - - + +
948B PHE* 3.6 4.9 - - - -
971B ARG* 3.1 20.3 + - - +
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Residues in contact with VAL 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B VAL 3.4 11.8 + - - +
413B VAL 3.2 8.4 + - - +
415B ASN* 1.3 77.4 - - - +
417B GLU* 1.3 63.1 + - - +
419B VAL* 3.3 3.5 + - - +
420B MET* 3.0 31.1 + - + +
427B PRO* 4.5 2.0 - - + +
430B ALA* 4.4 6.3 - - + -
431B THR* 3.6 43.7 - - + +
434B SER* 3.5 24.9 - - - +
435B MET* 4.7 1.8 - - + -
493B CYS* 4.3 6.1 - - - -
497B LEU* 3.8 22.0 - - + -
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Residues in contact with GLU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU* 3.8 39.6 - - + +
361B ASN* 3.3 26.2 + - - -
364B ALA* 4.1 2.8 - - + +
413B VAL* 3.1 21.2 + - + +
414B GLU 3.6 7.6 - - - +
416B VAL* 1.3 78.1 - - - +
418B ARG* 1.3 60.5 + - - +
420B MET* 2.8 35.8 + - - +
421B ALA* 3.1 23.6 + - - +
497B LEU* 4.1 12.9 - - + +
498B LYS 4.4 1.4 - - - +
500B ILE* 3.6 23.4 - - + +
973B ARG* 4.3 4.3 - - - +
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Residues in contact with ARG 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B GLU* 2.8 24.6 + - - +
415B ASN* 2.7 32.7 + - - +
417B GLU* 1.3 70.1 - - - +
419B VAL* 1.3 80.6 + - - +
421B ALA* 3.3 4.8 + - - -
422B GLU* 3.0 60.8 + - + +
437B GLN* 3.0 25.5 + - - +
948B PHE* 3.6 10.9 - - - -
969B ARG* 5.5 0.2 - - - +
970B MET* 3.7 49.9 - - - +
971B ARG* 4.2 4.8 - - - +
973B ARG* 3.7 15.4 - - - +
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Residues in contact with VAL 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B ASN* 3.0 36.6 + - - +
416B VAL 3.7 4.0 - - - +
418B ARG* 1.3 92.7 - - - +
420B MET* 1.3 62.9 + - - +
422B GLU* 4.7 2.5 - - - -
423B GLU* 3.1 35.1 + - + +
425B LEU* 4.7 3.0 + - + -
430B ALA* 4.2 22.2 - - + +
433B LYS* 3.9 24.2 - - + -
434B SER* 4.1 9.2 - - - -
437B GLN* 4.2 11.9 - - - +
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Residues in contact with MET 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B VAL* 3.0 19.8 + - + +
417B GLU* 2.8 37.9 - - - +
418B ARG 3.2 0.2 - - - -
419B VAL* 1.3 74.9 - - - +
421B ALA* 1.3 61.1 + - - +
424B GLY 2.9 24.3 + - - +
425B LEU 3.6 13.5 - - - +
427B PRO* 3.7 32.5 - - - -
430B ALA* 3.5 18.4 - - + -
497B LEU* 4.4 10.8 - - + -
498B LYS 3.2 25.4 - - - +
499B PRO* 3.9 7.2 - - - -
500B ILE* 3.1 26.0 - - + +
502B LYS* 4.4 0.3 - - - -
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Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B GLU 3.1 16.7 + - - +
418B ARG* 3.9 5.2 - - - +
420B MET* 1.3 77.9 - - - +
422B GLU* 1.3 58.9 + - + +
423B GLU 3.6 0.2 + - - -
500B ILE* 3.6 19.4 - - + +
501B ALA 4.4 0.4 - - - -
503B GLY* 2.8 33.1 + - - -
504B ASP 3.3 21.8 - - - +
505B HIS* 4.0 15.4 + - + -
973B ARG* 6.3 0.2 - - - +
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Residues in contact with GLU 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ARG* 3.0 54.5 + - + +
419B VAL* 4.2 1.3 - - - +
421B ALA* 1.3 78.1 - - + +
423B GLU* 1.3 71.0 + - + +
502B LYS* 3.4 17.8 + - - -
503B GLY* 5.0 0.4 - - - +
505B HIS* 4.0 20.8 + - + +
969B ARG* 2.9 42.3 + - - -
970B MET* 4.5 1.9 - - - +
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Residues in contact with GLU 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B VAL* 3.1 21.3 + - + +
421B ALA 3.4 0.4 - - - -
422B GLU* 1.3 89.5 - - + +
424B GLY* 1.3 62.2 + - - +
425B LEU* 3.4 18.9 + - + +
433B LYS* 2.9 38.8 + - - +
437B GLN* 5.5 2.9 + - - -
502B LYS* 3.6 21.7 + - - +
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Residues in contact with GLY 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B MET 2.9 16.2 + - - -
423B GLU* 1.3 77.5 - - - +
425B LEU* 1.3 65.0 + - - +
426B PRO* 3.6 4.7 - - - +
499B PRO* 6.1 0.9 - - - +
500B ILE 3.8 11.7 - - - +
501B ALA* 5.2 0.2 - - - -
502B LYS* 3.8 17.8 - - - +
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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