Contacts of the helix formed by residues 712 - 737 (chain A) in PDB entry 5FFV
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 THR 712 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A ASN* 3.5 10.4 - - + +
709A ALA* 2.8 34.9 + - + +
710A LYS 3.2 0.8 - - - -
711A ASP* 1.3 93.0 - - - +
713A ILE* 1.3 64.5 + - - +
714A PHE* 3.7 10.2 + - + -
715A TYR* 3.2 14.7 + - - +
716A ARG* 3.1 25.8 + - - +
802A EDO 3.5 20.4 - - - +
14C ALY 6.2 0.4 - - - +
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Residues in contact with ILE 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A ILE* 4.7 8.3 - - + -
712A THR* 1.3 73.3 - - - +
714A PHE* 1.3 61.2 + - + +
716A ARG* 4.4 17.2 - - + +
717A ALA* 2.7 39.9 + - + +
802A EDO 3.3 30.8 + - - +
17C ARG* 3.9 44.4 - - + +
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Residues in contact with PHE 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A ILE* 3.8 25.8 - - + -
653A PHE* 4.1 0.7 - - - -
704A CYS* 3.2 16.5 - - - -
708A ASN* 3.7 33.0 - - - +
712A THR* 3.1 6.7 - - + +
713A ILE* 1.3 80.1 - - + +
715A TYR* 1.3 62.2 + - - +
717A ALA* 3.3 5.0 + - - +
718A ALA 3.0 17.8 + - - -
802A EDO 4.0 17.9 - - - -
14C ALY 3.7 36.6 - - + -
15C ALA 3.7 25.6 - - - -
17C ARG* 4.0 31.0 - - + -
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Residues in contact with TYR 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A CYS* 4.1 5.8 - - - -
705A LEU* 3.4 43.2 - - + +
708A ASN* 3.4 21.7 - - + +
709A ALA 3.2 17.5 - - - +
710A LYS* 3.6 41.1 - - + +
712A THR* 3.2 7.6 + - - +
714A PHE* 1.3 79.0 - - - +
716A ARG* 1.3 66.8 + - + +
718A ALA* 3.1 5.2 + - - +
719A VAL* 3.1 37.9 + - + +
705B LEU* 4.3 11.4 + - - +
706B LYS* 6.5 0.4 - - - -
710B LYS* 4.5 0.9 - - - -
715B TYR* 2.8 33.5 + - - -
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Residues in contact with ARG 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A LYS 3.9 10.0 + - - +
711A ASP* 3.5 33.1 + - - +
712A THR 3.1 16.6 + - - +
713A ILE* 4.0 15.0 - - + +
715A TYR* 1.3 80.2 - - + +
717A ALA* 1.3 62.4 + - - +
719A VAL* 3.4 7.7 + - - +
720A ARG* 3.1 22.3 + - - +
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Residues in contact with ALA 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A ILE* 3.6 27.1 - - + -
653A PHE* 4.0 10.9 - - + -
713A ILE* 2.7 29.1 + - + +
714A PHE 3.7 3.6 - - - +
716A ARG* 1.3 74.1 - - - +
718A ALA* 1.3 56.9 + - - +
720A ARG* 3.4 8.6 + - - +
721A LEU* 2.9 28.2 + - - +
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Residues in contact with ALA 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A PHE* 3.7 12.3 - - + -
701A VAL* 3.8 17.1 - - + +
704A CYS* 3.7 32.5 - - + -
705A LEU* 3.7 14.1 - - + -
714A PHE 3.0 5.5 + - - -
715A TYR 3.1 8.5 + - - +
717A ALA* 1.3 73.9 - - - +
719A VAL* 1.3 65.7 + - - +
721A LEU* 3.3 4.1 + - - +
722A ARG* 2.9 24.8 + - - +
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Residues in contact with VAL 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A VAL* 5.4 0.4 - - - -
705A LEU* 3.9 13.0 - - + -
715A TYR* 3.1 37.4 + - + +
716A ARG* 3.6 9.4 - - - +
718A ALA* 1.3 76.6 - - - +
720A ARG* 1.3 62.6 + - - +
722A ARG* 3.4 7.6 + - - +
723A GLU* 3.1 47.7 + - + +
702B SER* 6.5 0.9 - - - -
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Residues in contact with ARG 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A LYS 5.7 0.6 + - - +
649A THR* 4.7 17.6 + - - +
716A ARG 3.1 14.5 + - - +
717A ALA* 3.6 11.9 - - - +
719A VAL* 1.3 78.2 - - - +
721A LEU* 1.3 56.4 + - - +
723A GLU* 3.1 14.5 + - - +
724A GLN* 2.8 66.3 + - + +
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Residues in contact with LEU 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A LEU 4.2 7.0 - - - +
647A LYS* 4.0 37.0 - - + +
648A ASP* 4.0 12.1 - - + +
653A PHE* 3.7 31.0 - - + -
675A PHE* 4.2 8.1 - - + -
697A PHE* 3.6 23.0 - - + -
700A ILE* 4.1 14.8 - - + -
701A VAL* 4.1 7.6 - - + -
717A ALA 2.9 17.2 + - - +
718A ALA* 3.3 5.8 + - - +
720A ARG* 1.3 75.3 - - - +
722A ARG* 1.3 58.5 + - - +
724A GLN* 4.8 4.3 - - - -
725A GLY* 2.7 30.0 + - - -
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Residues in contact with ARG 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A PHE* 4.3 8.5 - - + -
698A ASN* 4.2 19.3 + - - +
701A VAL* 4.0 24.5 - - + +
718A ALA 2.9 12.6 + - - +
719A VAL* 3.6 11.2 - - - +
720A ARG 3.3 0.2 - - - -
721A LEU* 1.3 78.0 - - - +
723A GLU* 1.3 65.3 + - + +
725A GLY* 3.9 0.5 - - - -
726A GLY* 3.2 20.3 + - - -
698B ASN* 3.4 33.5 + - - +
722B ARG* 3.4 60.5 - - - +
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Residues in contact with GLU 723 (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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719A VAL* 3.1 32.5 + - + +
720A ARG* 3.5 15.7 - - - +
722A ARG* 1.3 82.9 - - + +
724A GLN* 1.3 63.7 + - + +
726A GLY* 3.5 8.7 + - - -
727A ALA* 4.6 2.1 + - - +
702B SER* 5.8 3.5 - - - -
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Residues in contact with GLN 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A LYS* 3.6 53.4 - - + +
649A THR* 5.4 2.7 + - - +
720A ARG* 2.8 63.4 + - + +
721A LEU* 4.1 1.9 - - - +
723A GLU* 1.3 76.5 - - + +
725A GLY* 1.3 64.6 + - - +
726A GLY 3.4 0.5 + - - -
727A ALA* 4.0 7.6 + - - +
728A VAL* 3.8 14.7 + - - +
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Residues in contact with GLY 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A LEU* 3.9 22.0 - - - -
647A LYS* 4.7 3.3 - - - +
697A PHE* 4.1 5.4 - - - -
721A LEU* 2.7 22.7 + - - -
722A ARG 3.3 1.5 + - - -
724A GLN* 1.3 72.5 - - - +
726A GLY* 1.3 64.2 + - - +
727A ALA 3.4 0.2 - - - -
728A VAL* 3.1 5.9 + - - +
729A LEU* 2.9 31.9 + - - +
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Residues in contact with GLY 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A ARG 3.2 14.1 + - - -
723A GLU 3.5 5.0 + - - -
724A GLN 3.2 2.2 - - - -
725A GLY* 1.3 77.0 - - - +
727A ALA* 1.3 56.4 + - - +
729A LEU* 3.3 7.9 + - - +
730A ARG* 2.9 44.9 + - - +
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Residues in contact with ALA 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A GLU 4.6 2.2 + - - +
724A GLN 4.0 6.9 + - - +
725A GLY 3.4 0.4 - - - -
726A GLY* 1.3 75.9 - - - +
728A VAL* 1.3 64.3 + - + +
730A ARG* 3.6 19.9 - - - +
731A GLN* 3.0 26.9 + - - +
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Residues in contact with VAL 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A THR* 4.0 7.6 - - + -
643A GLN* 3.7 41.1 - - + +
644A LEU* 3.7 25.4 - - + -
647A LYS* 3.8 21.1 - - - +
724A GLN 3.8 15.7 - - - +
725A GLY* 3.1 8.5 + - - +
727A ALA* 1.3 77.0 - - + +
729A LEU* 1.3 58.5 + - - +
731A GLN* 3.9 5.2 + - - +
732A ALA* 3.0 28.1 + - - +
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Residues in contact with LEU 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A THR* 4.6 1.6 - - + -
644A LEU* 4.1 25.6 - - + -
690A PHE* 3.8 25.4 - - + -
693A PHE* 4.2 10.1 - - + -
694A GLU* 3.4 36.7 - - + +
697A PHE* 3.5 33.0 - - + -
698A ASN* 4.8 2.5 - - - +
725A GLY 2.9 20.6 + - - +
726A GLY* 3.8 5.8 - - - +
728A VAL* 1.3 73.0 - - - +
730A ARG* 1.3 61.6 + - - +
732A ALA* 4.5 0.2 - - - -
733A ARG* 3.0 31.7 + - - +
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Residues in contact with ARG 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A GLY* 2.9 30.9 + - - +
727A ALA* 3.6 29.8 - - - +
728A VAL 3.3 0.2 - - - -
729A LEU* 1.3 78.3 - - - +
731A GLN* 1.3 61.0 + - - +
733A ARG* 3.8 5.3 - - - +
734A ARG* 3.3 48.9 + - - +
691B ASP* 3.4 34.3 + - - -
694B GLU* 3.1 26.5 + - - -
698B ASN* 5.8 0.6 + - - -
733B ARG* 3.6 16.2 - - - +
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Residues in contact with GLN 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A LEU* 5.6 2.4 - - - +
639A LYS* 5.8 4.6 - - - +
643A GLN* 4.9 12.7 + - - +
727A ALA 3.0 17.0 + - - +
728A VAL* 3.9 4.8 + - - +
730A ARG* 1.3 76.9 - - - +
732A ALA* 1.3 73.1 + - - +
734A ARG* 3.2 17.5 + - - +
735A GLN* 3.1 46.7 + - - +
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Residues in contact with ALA 732 (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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636A LEU* 3.8 6.8 - - + +
640A THR* 3.3 35.7 - - + +
643A GLN* 5.3 1.8 - - - +
690A PHE* 3.7 13.5 - - + -
728A VAL 3.0 19.8 + - - +
731A GLN* 1.3 85.6 - - - +
733A ARG* 1.3 62.6 + - - +
735A GLN* 3.2 8.1 + - - +
736A ALA* 2.9 22.2 + - - +
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Residues in contact with ARG 733 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A PHE* 3.6 40.3 - - + +
691A ASP* 2.8 31.9 + - - +
694A GLU* 2.8 30.9 + - - -
729A LEU 3.0 18.1 + - - +
730A ARG* 3.8 6.3 - - - +
732A ALA* 1.3 77.0 - - - +
734A ARG* 1.3 58.3 + - + +
736A ALA* 3.2 1.4 + - - +
737A GLU* 2.9 64.1 + - + +
801A EDO 3.2 16.4 + - - -
730B ARG* 3.3 13.5 - - - +
733B ARG* 5.4 12.8 - - - +
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Residues in contact with ARG 734 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730A ARG* 3.3 38.4 + - - +
731A GLN* 3.2 14.7 + - - +
733A ARG* 1.3 80.5 - - + +
735A GLN* 1.3 65.6 + - - +
737A GLU* 3.3 6.7 + - - +
738A LYS* 3.1 30.9 + - - +
691B ASP* 4.1 7.1 + - - -
733B ARG* 3.4 15.5 - - - +
737B GLU* 3.0 40.4 + - - +
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Residues in contact with GLN 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A LEU* 4.1 19.9 - - + +
731A GLN* 3.1 40.4 + - - +
732A ALA 3.2 7.4 + - - +
734A ARG* 1.3 77.8 - - - +
736A ALA* 1.3 62.2 + - - +
738A LYS* 2.8 54.9 + - - +
739A MET* 3.7 13.0 + - + +
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Residues in contact with ALA 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A PHE* 4.2 14.8 - - + -
636A LEU* 3.6 17.6 - - + +
690A PHE* 4.1 22.4 - - + -
732A ALA 2.9 12.9 + - - +
733A ARG* 3.6 7.6 - - - +
735A GLN* 1.3 75.5 - - - +
737A GLU* 1.3 62.1 + - + +
738A LYS 3.2 0.2 - - - -
739A MET* 3.1 30.7 + - - +
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Residues in contact with GLU 737 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A PHE* 5.6 2.1 - - + +
733A ARG* 2.9 60.0 + - + +
734A ARG* 3.6 6.9 - - - +
735A GLN 3.2 0.2 - - - -
736A ALA* 1.3 79.8 - - + +
738A LYS* 1.3 59.2 + - - +
739A MET 3.5 1.7 - - - -
801A EDO 3.1 20.4 + - - -
734B ARG* 4.6 16.2 - - - +
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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
------------------------------------------------------------
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