Contacts of the helix formed by residues 455 - 477 (chain A) in PDB entry 6QVC
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 ASN 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A VAL* 5.0 8.0 - - - +
437A ALA* 5.6 4.0 - - - +
453A ARG 4.1 2.0 + - - -
454A VAL* 1.3 78.5 - - - +
456A VAL* 1.3 76.3 + - - +
457A VAL* 3.2 25.0 + - + +
458A ILE* 3.0 41.3 + - + +
459A ILE* 3.5 2.3 + - - +
504A MET* 5.1 11.9 - - - -
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Residues in contact with VAL 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A TRP* 4.6 21.8 - - + +
434A VAL* 4.2 22.0 - - + -
437A ALA* 4.8 13.9 - - + -
449A TRP* 3.3 27.8 - - + +
450A ILE* 4.7 9.4 - - + -
451A HIS 5.2 1.3 - - - +
454A VAL 4.4 6.5 - - - +
455A ASN* 1.3 83.4 + - - +
457A VAL* 1.3 63.3 + - - +
458A ILE 3.2 0.4 - - - -
459A ILE* 3.2 14.9 - - + +
460A ILE* 3.0 38.8 + - + +
500A GLU* 5.3 2.5 - - + +
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Residues in contact with VAL 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A VAL* 6.1 3.8 - - + -
455A ASN* 3.4 29.2 - - - +
456A VAL* 1.3 82.7 - - - +
458A ILE* 1.3 66.8 + - + +
460A ILE* 3.4 8.8 + - - +
461A PHE* 2.9 29.6 + - + +
497A LEU* 3.8 21.1 - - + +
500A GLU* 6.0 4.9 - - + -
501A ILE* 3.8 22.0 - - + -
504A MET* 5.9 6.5 - - + -
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Residues in contact with ILE 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A VAL* 3.9 21.1 - - + -
455A ASN* 3.0 28.9 + - + +
457A VAL* 1.3 86.9 - - + +
459A ILE* 1.3 56.5 + - - +
461A PHE* 3.3 8.2 + - + +
462A LEU* 2.9 51.2 + - + +
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Residues in contact with ILE 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A GLN 5.5 0.2 - - - +
413A PHE* 4.0 30.8 - - + +
414A MET* 5.2 3.0 - - - +
415A ALA* 5.6 3.8 - - + +
448A VAL 4.8 2.7 - - - +
449A TRP* 3.4 56.8 - - + +
450A ILE 4.3 1.1 - - - +
451A HIS* 4.7 11.4 - - + +
454A VAL* 3.9 20.2 - - + +
455A ASN 3.7 13.0 - - - +
456A VAL* 3.2 16.8 - - + +
458A ILE* 1.3 77.0 - - - +
460A ILE* 1.3 60.6 + - - +
462A LEU* 3.9 2.7 - - + +
463A PHE* 2.9 29.8 + - - +
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Residues in contact with ILE 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LEU* 6.2 1.8 - - + -
433A TRP* 4.4 23.1 - - + -
449A TRP* 3.7 24.9 - - + -
456A VAL* 3.0 27.4 + - + +
457A VAL* 3.8 6.5 - - - +
459A ILE* 1.3 77.5 - - - +
461A PHE* 1.3 55.8 + - - +
463A PHE* 3.4 8.0 + - + +
464A PHE* 2.9 28.6 + - + +
493A ALA* 3.9 15.9 - - + +
496A ARG* 4.9 9.0 - - + +
497A LEU* 3.8 33.2 - - + +
500A GLU* 4.6 18.8 - - + -
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Residues in contact with PHE 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A VAL* 2.9 18.0 + - + +
458A ILE* 3.5 10.3 - - + +
460A ILE* 1.3 78.6 - - - +
462A LEU* 1.3 69.7 + - + +
464A PHE* 3.3 14.1 + + - +
465A VAL* 3.0 44.2 + - + +
497A LEU* 4.5 22.6 - - + +
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Residues in contact with LEU 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A MET* 6.5 0.7 - - + -
413A PHE* 4.2 29.8 - - + +
414A MET* 4.1 4.3 - - - -
454A VAL* 6.4 0.4 - - + -
458A ILE* 2.9 35.1 + - + +
459A ILE* 4.0 4.0 - - + +
461A PHE* 1.3 84.3 - - + +
463A PHE* 1.3 60.4 - - - +
465A VAL* 3.4 13.6 - - + +
466A MET* 2.9 35.5 + - - +
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Residues in contact with PHE 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A MET* 3.6 41.8 - - + +
415A ALA 5.0 6.1 - - - -
418A LEU* 5.2 8.7 - - + -
423A ALA* 5.3 10.8 - - + -
427A LEU* 5.0 8.1 - - + -
449A TRP* 4.2 25.4 - + + -
459A ILE 2.9 18.6 + - - +
460A ILE* 3.5 7.4 - - + +
462A LEU* 1.3 76.7 - - - +
464A PHE* 1.3 58.6 + - - +
467A LYS* 2.9 66.6 + - + +
489A VAL* 4.4 19.5 - - + -
490A LEU* 6.0 0.7 - - + -
493A ALA* 4.1 24.0 - - + -
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Residues in contact with PHE 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A LEU* 3.7 31.9 - - + -
460A ILE* 2.9 18.9 + - + +
461A PHE* 3.6 16.2 - + - +
463A PHE* 1.3 81.9 - - - +
465A VAL* 1.3 65.6 + - + +
468A PHE* 2.9 38.6 + + + +
490A LEU* 3.3 51.1 - - + +
493A ALA* 3.8 15.7 - - + -
494A PHE* 4.0 28.9 - + + -
497A LEU* 5.6 5.2 - - + -
532A LEU* 5.1 1.3 - - + -
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Residues in contact with VAL 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A PHE* 3.0 36.1 + - + +
462A LEU* 3.4 21.3 - - + +
464A PHE* 1.3 84.6 - - + +
466A MET* 1.3 61.9 + - + +
468A PHE* 3.2 13.6 + - + +
469A TRP* 3.0 36.0 + - + +
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Residues in contact with MET 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ILE* 5.6 0.7 - - + -
404A PHE* 3.5 46.2 - - + +
414A MET* 3.7 18.6 - - + -
462A LEU 2.9 19.4 + - - +
465A VAL* 1.3 78.2 - - + +
467A LYS* 1.3 64.7 + - - +
469A TRP* 3.2 36.2 + - + +
470A MET* 3.0 59.0 + - + +
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Residues in contact with LYS 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A GLY 5.2 1.8 + - - -
228A PRO* 3.6 40.2 - - - +
414A MET* 3.9 5.2 - - + -
418A LEU 5.7 2.6 + - - -
420A PRO* 4.9 11.7 - - - +
463A PHE* 2.9 54.9 + - + +
464A PHE* 4.9 0.2 - - - -
466A MET* 1.3 74.8 - - - +
468A PHE* 1.3 57.4 + - - +
470A MET* 3.7 20.5 - - + +
471A SER* 3.0 33.9 + - - -
486A PRO* 6.2 1.3 - - - -
489A VAL* 4.8 12.3 - - + -
490A LEU* 3.7 18.9 - - + +
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Residues in contact with PHE 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A LEU* 4.5 20.6 - - + -
364A VAL* 5.1 4.5 - - + -
365A PHE* 3.5 44.9 - + + -
368A LEU* 4.4 20.0 - - + -
464A PHE* 2.9 33.2 + + + +
465A VAL* 3.3 16.4 - - + +
466A MET 3.1 0.2 - - - -
467A LYS* 1.3 77.0 - - - +
469A TRP* 1.3 68.9 + - + +
471A SER* 3.3 15.8 + - - -
472A ILE* 3.7 9.8 - - + +
490A LEU* 3.6 25.1 - - + +
532A LEU* 6.2 3.1 - - + -
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Residues in contact with TRP 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A VAL* 6.4 2.2 - - + -
401A ILE* 5.1 9.2 - - + -
404A PHE* 4.3 20.0 - + - -
465A VAL* 3.0 38.0 + - + +
466A MET* 3.2 39.9 - - + +
468A PHE* 1.3 83.5 - + + +
470A MET* 1.3 68.7 + - + +
471A SER 3.4 0.2 - - - -
472A ILE* 3.3 26.6 - - + +
473A VAL* 3.6 13.9 - - + +
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Residues in contact with MET 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A PRO* 5.3 7.0 - - + -
401A ILE* 3.7 50.3 - - + +
404A PHE* 5.3 2.0 - - - +
405A THR* 4.7 7.6 - - + +
414A MET* 4.1 5.2 - - + -
466A MET* 3.0 66.6 + - + +
467A LYS* 3.7 27.1 - - + +
468A PHE 3.2 0.4 - - - -
469A TRP* 1.3 83.4 - - + +
471A SER* 1.3 60.9 + - - +
472A ILE 3.4 0.2 - - - -
473A VAL* 3.3 8.0 + - - +
474A ALA* 2.9 27.4 + - - +
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Residues in contact with SER 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A PRO* 4.8 5.8 - - - -
365A PHE* 3.6 18.9 - - - -
467A LYS* 3.0 14.0 + - - -
468A PHE 3.3 11.6 + - - -
469A TRP 3.4 0.2 - - - -
470A MET* 1.3 75.2 - - - +
472A ILE* 1.3 62.5 + - - +
474A ALA* 3.1 9.5 + - - +
475A THR* 2.9 30.0 + - - +
486A PRO* 4.0 30.8 - - - +
490A LEU* 3.9 8.4 - - - +
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Residues in contact with ILE 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A PHE* 3.5 45.3 - - + +
368A LEU* 5.0 13.2 - - + +
369A HIS* 4.6 22.4 + - - +
372A VAL* 5.4 9.4 - - + -
468A PHE* 3.7 11.2 - - + +
469A TRP* 3.3 29.8 - - + +
471A SER* 1.3 75.8 + - - +
473A VAL* 1.3 68.2 - - + +
475A THR* 3.3 9.2 - - + +
476A THR* 2.2 39.4 + - - +
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Residues in contact with VAL 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A VAL* 5.9 5.8 - - + -
393A TYR* 5.1 4.5 + - - +
397A VAL* 4.0 31.4 - - + -
401A ILE* 5.3 11.9 - - + -
469A TRP* 3.6 27.6 - - + +
470A MET* 3.3 9.3 + - - +
471A SER 3.2 0.2 - - - -
472A ILE* 1.3 86.8 - - + +
474A ALA* 1.3 61.8 + - - +
476A THR* 3.2 21.8 + - - +
477A MET* 3.4 12.0 + - + +
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Residues in contact with ALA 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ILE* 4.2 14.7 - - + +
228A PRO* 3.3 30.1 - - + +
229A VAL* 5.7 3.8 - - + +
401A ILE* 5.4 4.2 - - + +
470A MET 2.9 13.5 + - - +
471A SER* 3.1 13.2 + - - +
473A VAL* 1.3 77.6 - - - +
475A THR* 1.3 61.2 + - - +
477A MET* 3.3 31.7 - - - +
479A ILE* 4.0 6.8 - - - +
481A CYS* 5.2 0.2 - - - +
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Residues in contact with THR 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A PHE* 5.5 5.2 - - + -
369A HIS* 4.0 25.4 - - + +
471A SER 2.9 16.4 + - - +
472A ILE* 3.3 21.8 - - + +
474A ALA* 1.3 73.3 - - - +
476A THR* 1.3 63.4 + - - +
477A MET 3.5 2.5 - - - +
481A CYS* 2.9 44.6 + - - +
482A GLY 5.0 5.8 + - - -
483A GLY* 5.8 2.0 - - - -
486A PRO* 6.4 1.6 - - - -
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Residues in contact with THR 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A HIS* 5.0 1.6 + - - -
372A VAL* 3.5 30.6 - - + +
373A MET* 4.5 14.9 - - - +
376A VAL* 3.9 25.9 - - + +
393A TYR* 3.3 23.2 - - + +
472A ILE 2.2 29.2 + - - -
473A VAL* 3.2 13.6 + - - -
475A THR* 1.3 79.3 - - - +
477A MET* 1.3 66.4 + - - +
478A PRO* 3.8 1.0 - - - +
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Residues in contact with MET 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ILE* 4.6 11.7 - - - -
227A ILE* 5.4 9.4 - - + -
393A TYR* 3.8 13.5 - - + -
394A PRO* 4.0 23.3 - - + -
397A VAL* 4.2 16.8 - - + -
398A THR* 4.2 20.0 - - - +
401A ILE* 6.1 2.9 - - + -
473A VAL* 3.4 22.7 + - + +
474A ALA* 3.3 24.0 - - - +
475A THR 3.9 2.3 - - - +
476A THR* 1.3 82.5 - - - +
478A PRO* 1.4 63.3 - - + +
479A ILE* 2.6 43.1 + - + +
481A CYS* 5.1 0.2 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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