Contacts of the helix formed by residues 604 - 629 (chain B) in PDB entry 5J3V
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 TYR 604 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B ILE* 3.9 19.5 + - + +
563B GLN* 5.0 5.4 - - - +
566B MET* 3.6 52.7 - - + +
567B PRO* 5.2 3.3 - - + +
570B ILE* 4.4 23.6 - - + -
600B GLY 4.2 9.6 - - - -
601B PHE* 2.8 21.5 + - + +
603B PRO* 1.3 96.1 - - + +
605B CYS* 1.3 60.8 + - - +
606B GLU 3.6 1.6 - - - -
607B PRO* 3.9 9.0 - - - +
608B VAL* 3.2 27.4 + - - +
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Residues in contact with CYS 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B PHE* 3.0 21.0 + - + +
602B LEU* 3.2 31.5 + - - -
603B PRO 3.6 0.2 - - - -
604B TYR* 1.3 77.7 - - - +
606B GLU* 1.3 72.4 + - - +
608B VAL* 3.3 2.1 + - - +
609B TYR* 2.7 38.7 + - - +
651B LEU* 4.2 2.9 - - + +
655B LEU* 3.6 28.0 - - + -
658B ASN 6.0 1.1 - - - -
662B LEU* 4.1 15.0 - - + -
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Residues in contact with GLU 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B LEU 4.6 0.8 + - - +
605B CYS* 1.3 87.9 - - - +
607B PRO* 1.3 69.8 - - + +
609B TYR* 3.8 1.4 - - - +
610B GLN* 3.1 25.1 + - + +
662B LEU* 3.8 27.9 - - + +
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Residues in contact with PRO 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B TRP* 4.2 9.1 + - - +
603B PRO 4.9 4.7 - - - +
604B TYR* 3.9 15.9 - - - +
605B CYS 3.7 1.1 - - - -
606B GLU* 1.3 96.4 - - + +
608B VAL* 1.3 63.5 + - + +
610B GLN* 3.5 4.6 + - + +
611B ARG* 3.3 23.6 + - - +
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Residues in contact with VAL 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B ILE* 5.1 9.6 - - + -
573B TRP* 3.6 31.6 - - + +
590B LEU* 4.8 4.3 - - + -
601B PHE* 3.9 19.7 - - + -
604B TYR 3.2 21.3 - - - +
605B CYS 3.3 3.7 + - - +
606B GLU 3.3 0.4 - - - -
607B PRO* 1.3 79.8 - - + +
609B TYR* 1.3 63.5 + - - +
611B ARG 3.5 0.2 + - - -
612B CYS* 3.2 23.4 + - - -
647B LEU* 3.7 34.8 - - + -
651B LEU* 4.1 12.6 - - + -
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Residues in contact with TYR 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B CYS 2.7 21.3 + - - +
606B GLU 3.8 3.4 - - - +
608B VAL* 1.3 75.0 - - - +
610B GLN* 1.3 73.7 + - + +
612B CYS* 3.3 4.9 + - - +
613B VAL* 3.3 28.2 + - + +
648B LEU* 3.6 17.5 - - + -
651B LEU* 4.0 16.2 - - + -
659B ILE* 4.4 15.5 - - + -
662B LEU* 3.0 60.1 + - + -
663B VAL* 3.3 7.0 - - + -
666B SER* 2.3 38.6 + - - -
668B ILE* 3.1 30.9 - - + +
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Residues in contact with GLN 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B GLU* 3.1 17.7 + - + +
607B PRO* 4.0 5.2 - - + +
609B TYR* 1.3 91.3 - - + +
611B ARG* 1.3 62.6 + - - +
613B VAL* 3.4 9.5 + - - +
614B ASN* 3.1 57.9 + - - +
666B SER* 5.3 6.5 - - - -
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Residues in contact with ARG 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B TRP* 2.8 75.0 + - + +
576B LEU 2.8 23.0 + - - -
577B LYS* 3.3 14.1 + - - +
578B ASP* 2.9 36.1 + - - +
583B LEU* 3.6 21.5 - - - +
587B LEU* 6.1 0.7 - - - -
607B PRO 3.3 7.7 + - - +
609B TYR 3.3 0.2 - - - -
610B GLN* 1.3 79.5 - - - +
612B CYS* 1.3 57.9 + - - +
614B ASN* 3.3 10.8 + - + +
615B LEU* 2.9 35.2 + - + +
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Residues in contact with CYS 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B TRP* 4.6 2.0 - - - -
587B LEU* 4.6 6.7 - - - -
608B VAL* 3.2 18.5 + - - -
609B TYR 3.6 7.9 - - - +
610B GLN 3.2 0.8 - - - -
611B ARG* 1.3 76.5 - - - +
613B VAL* 1.3 65.0 + - - +
615B LEU* 3.2 5.3 + - - +
616B VAL* 3.1 29.3 + - - +
644B ALA* 3.6 17.6 - - - +
647B LEU* 3.5 42.8 - - - -
648B LEU* 3.7 22.7 - - + -
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Residues in contact with VAL 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B TYR* 3.3 32.5 + - + +
610B GLN* 3.7 11.7 - - - +
611B ARG 3.4 0.2 - - - -
612B CYS* 1.3 75.8 - - - +
614B ASN* 1.3 60.5 + - - +
616B VAL* 3.4 5.5 + - - +
617B GLN* 3.0 30.4 + - - +
648B LEU* 4.2 6.7 - - + -
666B SER* 4.7 6.1 - - - +
667B ASN* 4.1 14.4 - - - +
668B ILE* 3.9 32.5 - - + -
671B LEU* 3.6 22.8 - - + +
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Residues in contact with ASN 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B ASP* 5.0 7.2 - - - +
610B GLN* 3.1 43.2 + - - +
611B ARG* 3.6 11.2 - - + +
613B VAL* 1.3 78.0 - - - +
615B LEU* 1.3 59.8 + - - +
617B GLN* 3.7 11.0 + - - +
618B LYS* 2.9 44.1 + - + +
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Residues in contact with LEU 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B TRP* 6.2 0.2 - - + -
578B ASP* 3.6 46.9 - - + +
583B LEU* 4.5 12.1 - - + -
587B LEU* 4.1 20.4 - - + -
611B ARG* 2.9 26.8 + - + +
612B CYS* 3.2 9.4 + - - +
614B ASN* 1.3 76.2 - - - +
616B VAL* 1.3 59.9 + - - +
618B LYS* 4.2 6.6 - - - +
619B THR* 2.7 34.6 + - - -
640B PHE* 4.4 20.9 - - + +
644B ALA* 3.9 20.2 - - + -
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Residues in contact with VAL 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B CYS 3.1 16.6 + - - +
613B VAL* 3.7 7.9 - - - +
615B LEU* 1.3 76.2 - - - +
617B GLN* 1.3 63.4 + - - +
619B THR* 3.8 1.4 - - - -
620B LEU* 3.1 31.0 + - + +
641B MET* 4.2 13.0 - - + +
644B ALA* 3.9 15.9 - - + -
645B LEU* 3.7 27.8 - - + +
648B LEU* 4.8 3.1 - - + -
668B ILE* 6.4 0.7 - - + -
671B LEU* 4.2 14.1 - - + -
675B CYS* 3.7 30.1 - - - -
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Residues in contact with GLN 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B VAL* 3.0 19.7 + - - +
614B ASN* 3.7 12.7 + - - +
615B LEU 3.3 0.2 - - - -
616B VAL* 1.3 78.1 - - - +
618B LYS* 1.3 59.0 + - + +
620B LEU* 3.5 3.2 + - - +
621B ALA* 3.0 29.8 + - + +
667B ASN* 3.9 17.7 + - - +
671B LEU* 3.8 32.9 - - + +
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Residues in contact with LYS 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B ASP* 3.3 41.4 + - - +
579B GLU* 5.5 4.8 - - - +
614B ASN* 2.9 27.1 + - + +
615B LEU* 4.2 6.3 - - - +
617B GLN* 1.3 75.2 - - + +
619B THR* 1.3 60.1 + - - +
621B ALA* 3.7 5.8 - - - +
622B GLN* 2.8 33.1 + - - +
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Residues in contact with THR 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B LEU* 2.7 23.6 + - - +
616B VAL 3.8 3.4 - - - -
618B LYS* 1.3 78.5 - - - +
620B LEU* 1.3 61.7 + - - +
622B GLN* 3.5 0.6 + - - -
623B ALA* 3.1 22.6 + - + +
636B PRO* 3.6 25.1 - - + +
637B ASP 4.2 11.2 + - - +
638B LYS* 4.2 4.3 - - + -
640B PHE* 3.9 17.5 - - - +
641B MET* 3.7 36.1 + - + -
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Residues in contact with LEU 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616B VAL* 3.1 23.5 + - + +
617B GLN 3.8 4.0 - - - +
619B THR* 1.3 75.8 - - - +
621B ALA* 1.3 62.6 + - - +
623B ALA* 3.2 9.9 + - + +
624B MET* 3.1 28.9 + - + +
641B MET* 3.6 24.5 - - + -
671B LEU* 3.8 40.4 - - + +
674B GLN* 3.8 35.4 - - + +
675B CYS* 4.0 10.8 - - - -
678B ASP* 4.7 8.7 - - - +
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Residues in contact with ALA 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617B GLN* 3.0 19.8 + - + +
618B LYS* 3.7 7.6 - - - +
620B LEU* 1.3 76.5 - - - +
622B GLN* 1.3 62.9 + - - +
624B MET* 3.2 16.5 + - - +
625B LEU* 3.1 29.0 + - + +
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Residues in contact with GLN 622 (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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618B LYS 2.8 17.7 + - - +
619B THR* 4.6 0.2 - - - -
621B ALA* 1.3 76.5 - - - +
623B ALA* 1.3 61.8 + - - +
625B LEU* 3.5 16.1 + - - +
626B ASN* 3.2 20.4 + - - +
633B TYR* 3.9 13.4 - - - +
634B GLU* 2.6 42.0 + - - +
635B ALA 4.8 0.2 - - - -
636B PRO* 3.6 24.2 - - + +
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Residues in contact with ALA 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B THR* 3.1 14.5 + - + +
620B LEU* 3.4 15.3 - - + +
621B ALA 3.2 0.4 - - - -
622B GLN* 1.3 77.6 - - - +
624B MET* 1.3 57.4 + - + +
626B ASN* 3.5 4.1 + - - +
627B ASN* 3.0 27.0 + - - +
636B PRO* 3.6 18.4 - - + +
638B LYS* 4.9 14.4 - - - -
641B MET* 6.4 0.9 - - + -
678B ASP* 5.9 1.1 - - - +
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Residues in contact with MET 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B LEU* 3.1 16.8 + - - +
621B ALA* 3.4 15.7 - - - +
623B ALA* 1.3 75.4 - - + +
625B LEU* 1.3 65.8 + - + +
627B ASN* 3.1 8.6 + - - +
628B ALA* 3.1 22.9 + - - +
674B GLN* 4.9 12.3 - - - +
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Residues in contact with LEU 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B ALA* 3.1 14.9 + - + +
622B GLN* 3.8 21.1 - - - +
623B ALA 3.4 0.2 - - - -
624B MET* 1.3 80.2 - - + +
626B ASN* 1.3 57.1 + - - +
628B ALA* 3.6 5.9 + - + +
629B GLN 3.1 22.3 + - - -
633B TYR* 3.3 58.9 - - + +
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Residues in contact with ASN 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622B GLN 3.2 13.8 + - - +
623B ALA* 3.6 10.8 - - - +
624B MET 3.2 0.4 - - - -
625B LEU* 1.3 73.0 - - - +
627B ASN* 1.3 67.3 + - - +
628B ALA 3.0 3.4 + - - -
629B GLN 4.3 0.4 - - - -
630B PRO* 3.1 38.4 + - - +
633B TYR* 3.3 20.2 + - - +
634B GLU* 4.2 3.8 - - - +
635B ALA* 3.1 40.8 - - - +
636B PRO* 4.7 0.9 - - + -
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Residues in contact with ASN 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B ALA 3.0 17.5 + - - +
624B MET* 3.1 8.7 + - - +
626B ASN* 1.3 78.6 + - - +
628B ALA* 1.3 59.8 + - - +
630B PRO* 4.8 4.2 - - - +
679B LYS* 4.4 18.0 - - - +
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Residues in contact with ALA 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B MET 3.1 13.0 + - - +
625B LEU* 3.9 7.9 - - + +
626B ASN 3.0 0.8 - - - -
627B ASN* 1.3 79.9 - - - +
629B GLN* 1.3 69.1 + - + +
630B PRO* 3.6 7.1 - - - +
633B TYR* 6.0 0.7 - - + -
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Residues in contact with GLN 629 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B LEU 3.1 5.4 + - - +
626B ASN 3.4 3.1 - - - -
628B ALA* 1.3 89.2 - - + +
630B PRO* 1.3 59.4 - - - +
631B ASP* 3.0 11.3 + - + +
632B GLN* 2.9 30.8 - - + +
633B TYR* 3.0 45.4 + - + +
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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