Contacts of the helix formed by residues 557 - 580 (chain B) in PDB entry 4JGV
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 GLY 557 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553B SER 2.9 17.4 + - - -
554B ARG* 3.8 5.4 - - - -
555B LEU 3.1 0.8 - - - -
556B LEU* 1.3 76.0 - - - +
558B LYS* 1.3 62.1 + - - +
559B LEU 3.3 0.2 - - - -
560B PRO* 3.2 22.6 - - - +
561B GLU* 4.1 7.0 - - - +
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Residues in contact with LYS 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B LEU* 6.4 0.7 - - + -
489B PHE* 3.9 25.3 - - + -
492B SER* 2.5 46.5 + - - -
493B LEU* 4.4 15.0 - - + +
496B LEU* 4.0 16.4 - - + -
506B LEU* 5.5 3.4 - - + -
554B ARG 3.9 13.5 - - - +
555B LEU* 2.9 15.6 + - - +
557B GLY* 1.3 78.0 - - - +
559B LEU* 1.3 66.3 - - + +
561B GLU* 2.6 51.2 + - - +
562B LEU* 3.3 7.4 + - - +
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Residues in contact with LEU 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B GLU* 5.6 0.2 - - - +
449B LEU* 5.2 3.8 - - + -
489B PHE* 6.5 0.4 - - + -
506B LEU* 3.7 37.0 - - + -
509B LEU* 4.8 13.7 - - + +
510B VAL* 3.8 28.5 - - + -
555B LEU 4.8 0.9 - - - +
556B LEU* 3.2 22.6 + - + +
558B LYS* 1.3 78.4 - - + +
560B PRO* 1.3 73.1 - - + +
562B LEU* 2.8 26.2 + - + +
563B ARG* 3.1 15.6 + - - +
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Residues in contact with PRO 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B LEU 3.5 8.1 - - - +
557B GLY* 3.2 18.4 - - - +
559B LEU* 1.3 95.0 - - + +
561B GLU* 1.3 61.9 + - + +
563B ARG* 3.3 18.6 + - + +
564B THR* 3.3 12.5 + - - -
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Residues in contact with GLU 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B PHE* 4.0 18.1 - - + -
492B SER* 4.8 2.6 + - - -
557B GLY 4.1 5.6 - - - +
558B LYS* 2.6 55.6 + - - +
560B PRO* 1.3 74.3 - - + +
562B LEU* 1.3 59.9 + - - +
563B ARG 3.3 0.2 - - - -
564B THR* 3.4 12.5 - - - +
565B LEU* 3.1 28.1 + - - +
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Residues in contact with LEU 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B GLU* 3.6 37.2 - - + +
448B ILE* 3.4 34.5 - - + +
449B LEU* 4.0 21.3 - - + +
489B PHE* 4.0 20.8 - - + -
510B VAL* 4.0 21.5 - - + -
558B LYS 3.3 7.8 + - - +
559B LEU* 2.8 21.4 + - + +
561B GLU* 1.3 75.2 - - - +
563B ARG* 1.3 62.5 + - - +
565B LEU* 3.2 5.5 + - + +
566B CYS* 3.0 21.1 + - - +
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Residues in contact with ARG 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B GLU* 3.4 30.0 + - - +
513B THR* 4.7 12.5 + - - +
514B ASP 4.8 4.6 + - - -
515B ARG* 3.2 28.0 - - - +
559B LEU 3.1 15.4 + - - +
560B PRO* 3.4 12.8 - - + +
561B GLU 3.3 0.2 - - - -
562B LEU* 1.3 77.0 - - - +
564B THR* 1.3 62.8 + - - +
566B CYS* 3.0 18.3 + - - +
567B THR* 3.0 15.3 + - - -
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Residues in contact with THR 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B PRO 3.3 12.6 + - - -
561B GLU* 3.4 14.0 + - - -
562B LEU 3.3 0.2 - - - -
563B ARG* 1.3 77.4 - - - +
565B LEU* 1.3 62.1 + - - +
567B THR* 3.1 22.8 + - - -
568B GLN* 3.3 18.3 + - + +
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Residues in contact with LEU 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B ILE* 3.7 26.0 - - + -
482B TRP* 2.8 39.2 + - + +
485B SER* 3.5 37.0 - - - +
486B ILE* 4.1 4.5 - - + +
489B PHE* 3.5 40.8 - - + -
561B GLU 3.1 10.2 + - - +
562B LEU* 3.5 10.5 - - + +
563B ARG 3.1 0.2 - - - -
564B THR* 1.3 77.9 - - - +
566B CYS* 1.3 64.7 + - - +
568B GLN* 3.4 14.3 + - - +
569B GLY 3.2 5.5 + - - -
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Residues in contact with CYS 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B SER 5.2 3.6 - - - -
444B LEU* 3.6 31.2 - - - +
445B GLU* 4.0 24.5 - - + -
448B ILE* 3.6 12.6 - - + +
562B LEU 3.0 12.0 + - - +
563B ARG* 3.2 15.3 - - - +
565B LEU* 1.3 73.5 - - - +
567B THR* 1.3 64.6 + - - +
569B GLY* 3.0 3.2 + - - +
570B LEU* 2.9 31.3 + - - +
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Residues in contact with THR 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A TYR* 4.0 17.9 - - + -
578A LEU* 4.0 23.2 - - + +
563B ARG 3.0 13.1 + - - -
564B THR* 3.1 15.8 + - - -
566B CYS* 1.3 75.0 - - - +
568B GLN* 1.3 65.4 + - + +
570B LEU* 2.9 14.3 + - - +
571B GLN* 2.8 39.8 + - - +
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Residues in contact with GLN 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B ASP* 4.6 5.0 - - - +
482B TRP* 3.3 29.4 + - + +
485B SER* 3.3 24.8 + - - -
564B THR* 3.6 21.0 + - + +
565B LEU* 3.4 23.2 - - - +
567B THR* 1.3 77.9 - - - +
569B GLY* 1.3 56.4 + - - +
571B GLN* 3.2 17.8 + - - +
572B ARG* 2.9 30.8 + - - +
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Residues in contact with GLY 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B LEU* 4.3 8.5 - - - -
482B TRP* 3.4 35.9 - - - +
565B LEU 3.2 4.9 + - - -
566B CYS 3.0 8.0 + - - -
568B GLN* 1.3 77.4 - - - +
570B LEU* 1.3 62.8 + - - +
572B ARG* 3.2 4.5 + - - +
573B ILE* 3.0 29.2 + - - +
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Residues in contact with LEU 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A PHE* 4.1 12.3 - - + -
578A LEU* 4.2 24.2 - - + -
444B LEU* 3.9 17.4 - - + +
566B CYS* 2.9 25.5 + - - +
567B THR* 3.4 13.2 - - - +
569B GLY* 1.3 75.6 - - - +
571B GLN* 1.3 57.9 + - - +
573B ILE* 3.2 3.3 + - + -
574B PHE* 2.9 26.3 + - - +
591B ILE* 6.1 1.3 - - + -
592B PHE* 3.3 35.9 - - + -
595B THR* 4.0 24.7 - - - +
596B LEU* 4.5 7.4 - - + -
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Residues in contact with GLN 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571A GLN* 4.3 11.3 + - - +
574A PHE* 3.8 21.3 - - + -
575A TYR* 3.4 42.3 - - - +
578A LEU* 4.6 0.7 - - + -
605A GOL 3.5 31.3 + - - +
567B THR* 2.8 29.9 + - + +
568B GLN* 3.2 19.4 + - - +
570B LEU* 1.3 76.7 - - - +
572B ARG* 1.3 58.1 + - - +
574B PHE* 3.4 5.6 - - - +
575B TYR* 3.0 26.9 + - - +
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Residues in contact with ARG 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B LYS* 4.5 6.1 - - - +
398B GLU* 3.8 12.1 + - - -
406B PHE* 4.1 20.4 - - + -
477B ARG 3.3 19.8 + - - -
478B GLY* 3.0 26.3 + - - -
479B PHE 3.3 21.5 - - - +
480B GLY* 3.8 12.7 - - - +
482B TRP* 4.6 6.1 - - + -
568B GLN 2.9 13.6 + - - +
569B GLY* 3.4 11.9 - - - +
571B GLN* 1.3 75.6 - - - +
573B ILE* 1.3 60.2 + - - +
575B TYR* 3.2 32.8 + - - +
576B LEU* 2.9 53.3 + - + +
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Residues in contact with ILE 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B PHE* 4.2 19.3 - - + -
407B TYR* 4.4 11.2 - - + +
410B LEU* 4.3 19.7 - - + -
444B LEU* 5.0 13.5 - - + -
482B TRP* 6.2 0.2 - - + -
569B GLY 3.0 17.3 + - - +
570B LEU* 3.7 7.9 - - + +
572B ARG* 1.3 73.2 - - - +
574B PHE* 1.3 57.0 + - - +
576B LEU* 3.2 7.0 + - - +
577B LYS* 2.7 46.8 + - + +
584B PRO* 5.1 3.4 - - + -
588B ILE* 4.5 13.7 - - + +
592B PHE* 3.6 32.5 - - + -
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Residues in contact with PHE 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570A LEU* 3.9 13.9 - - + -
571A GLN* 3.8 28.5 - - + -
574A PHE* 3.7 40.2 - + + -
592A PHE* 4.1 15.9 - + - -
596A LEU* 4.3 17.7 - - + -
598A PHE* 4.3 15.4 - + - -
570B LEU 2.9 13.8 + - - +
571B GLN 3.4 9.9 - - - +
573B ILE* 1.3 77.5 - - - +
575B TYR* 1.3 59.4 + - - +
577B LYS* 3.3 4.1 + - - +
578B LEU* 2.9 54.5 + - + +
592B PHE* 3.8 17.7 - + + -
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Residues in contact with TYR 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567A THR* 4.0 20.9 - - + -
571A GLN* 3.6 30.1 - - - +
397B LYS* 6.3 0.2 - - - -
398B GLU* 4.1 11.1 + - - -
571B GLN 3.0 11.6 + - - +
572B ARG* 3.4 36.8 - - - +
573B ILE 3.2 0.2 - - - -
574B PHE* 1.3 82.5 - - - +
576B LEU* 1.3 67.8 + - + +
578B LEU* 3.3 7.6 - - + +
579B GLU* 3.1 49.9 + - + +
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Residues in contact with LEU 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B GLU* 4.5 0.7 - - - +
403B VAL* 4.1 21.2 - - + +
406B PHE* 3.5 37.9 - - + -
407B TYR* 3.6 20.5 + - + +
478B GLY 4.2 4.7 - - - +
572B ARG* 2.9 53.4 + - + +
573B ILE* 3.8 2.0 - - - +
575B TYR* 1.3 82.4 - - + +
577B LYS* 1.3 56.3 + - - +
579B GLU* 3.4 22.8 - - - +
580B ASP* 2.7 32.6 + - - -
581B LEU 4.5 0.2 + - - -
582B VAL 4.8 3.6 - - - +
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Residues in contact with LYS 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A PRO* 5.2 1.2 - - - +
598A PHE* 3.7 48.4 - - + +
407B TYR* 4.2 1.8 - - - +
573B ILE* 2.7 25.6 + - + +
574B PHE* 3.5 6.5 - - - +
576B LEU* 1.3 76.1 - - - +
578B LEU* 1.3 66.9 + - - +
580B ASP* 3.7 13.2 + - - +
582B VAL 6.0 0.4 - - - -
584B PRO* 3.6 31.8 - - + +
589B ASP* 2.8 31.0 + - - +
592B PHE* 3.8 24.9 - - + -
593B MET* 3.2 22.2 - - - +
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Residues in contact with LEU 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A THR* 4.0 27.1 - - + -
570A LEU* 4.2 25.1 - - + -
571A GLN* 4.6 0.9 - - + -
595A THR 5.4 0.4 - - - +
596A LEU* 4.5 9.4 - - + -
597A PRO* 4.1 35.8 - - + +
598A PHE* 4.1 5.7 - - + -
574B PHE* 2.9 47.6 + - + +
575B TYR* 3.3 11.9 - - + +
577B LYS* 1.3 77.8 - - - +
579B GLU* 1.3 63.0 + - - +
580B ASP* 3.3 4.2 + - - +
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Residues in contact with GLU 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B GLU* 2.6 27.2 - - - +
403B VAL* 3.8 5.9 - - - +
575B TYR* 3.2 31.3 + - + +
576B LEU* 3.4 27.1 - - - +
578B LEU* 1.3 78.8 - - - +
580B ASP* 1.3 67.6 + - - +
581B LEU* 3.1 45.2 + - + +
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Residues in contact with ASP 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A PRO* 6.5 0.2 - - + -
576B LEU 2.7 21.8 + - - -
577B LYS* 3.7 14.1 - - - +
578B LEU 3.2 4.0 - - - +
579B GLU* 1.3 76.2 - - - +
581B LEU* 1.3 63.3 + - - +
582B VAL 3.3 4.2 - - - +
583B PRO* 3.7 27.9 - - - +
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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