Contacts of the helix formed by residues 609 - 632 (chain A) in PDB entry 6V3O
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 609 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A GLY* 2.8 23.6 + - - -
608A ALA* 1.3 77.2 - - - +
610A ARG* 1.3 65.0 + - - -
611A LEU 3.5 2.2 - - - -
612A SER* 4.3 0.9 - - - -
613A ALA* 3.2 20.1 + - - +
724A ALA* 5.6 1.6 - - - -
728A TYR* 3.4 29.3 - - - -
789A PRO 5.2 0.2 - - - -
792A LEU 4.3 3.8 - - - -
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Residues in contact with ARG 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A TYR* 4.5 14.1 + - - +
602A SER* 4.5 11.3 - - - +
605A GLY* 4.2 12.2 + - - -
609A GLY* 1.3 72.5 - - - -
611A LEU* 1.3 59.5 + - - +
613A ALA* 3.3 3.5 + - - +
614A ALA* 2.9 31.5 + - + +
642A GLY 2.5 27.2 + - - -
643A GLY* 4.7 2.0 - - - -
644A THR* 4.7 3.0 - - - +
778A ILE* 5.7 0.6 - - - +
789A PRO 4.2 7.4 + - - +
790A VAL* 3.1 36.3 - - - +
792A LEU 4.5 5.1 + - - -
794A VAL* 5.2 4.3 - - + -
825A THR* 5.9 5.2 - - + -
828A LEU* 3.3 32.0 - - - +
829A LEU* 4.8 9.4 - - + -
970A GLY* 3.2 35.3 + - - -
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Residues in contact with LEU 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A GLY 3.5 0.2 - - - -
610A ARG* 1.3 78.6 - - - +
612A SER* 1.3 63.8 + - - +
614A ALA* 3.2 6.3 + - + +
615A TRP* 3.1 21.5 + - - +
717A MET* 4.2 22.0 - - + -
720A MET* 3.8 36.3 - - + +
721A ALA* 5.3 1.8 - - - +
724A ALA* 4.4 11.1 - - + +
794A VAL* 3.7 28.4 - - + +
797A ALA* 3.9 17.9 - - + -
798A PHE* 4.8 5.6 - - + -
821A PHE* 5.9 0.2 - - + -
822A PHE* 5.1 9.2 - - + -
825A THR* 4.4 21.3 - - + -
826A LEU* 5.6 2.5 - - + -
829A LEU* 6.1 2.5 - - + -
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Residues in contact with SER 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A LEU* 4.6 6.7 - - - +
608A ALA* 3.3 17.4 + - - -
609A GLY 3.8 0.8 + - - -
610A ARG 3.4 0.4 - - - -
611A LEU* 1.3 76.3 - - - +
613A ALA* 1.3 58.2 + - - +
615A TRP* 3.3 1.8 + - - +
616A GLN* 2.9 32.7 + - - +
721A ALA* 3.1 29.5 + - - +
724A ALA* 3.6 6.1 - - - +
725A THR* 2.8 33.5 + - - -
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Residues in contact with ALA 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A LEU* 4.0 12.9 - - + +
571A LEU* 4.9 2.4 - - - +
601A TYR* 4.8 3.6 - - - +
604A SER* 3.7 16.2 - - - +
605A GLY* 3.6 25.1 - - - +
609A GLY 3.2 18.1 + - - +
610A ARG* 3.6 5.2 - - - +
612A SER* 1.3 79.3 - - - +
614A ALA* 1.3 56.8 + - - +
616A GLN* 3.5 1.2 + - - +
617A LEU* 2.9 31.4 + - - +
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Residues in contact with ALA 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A TYR* 6.2 3.8 - - + -
610A ARG* 2.9 21.0 + - + +
611A LEU* 3.6 5.8 - - + +
612A SER 3.2 0.4 - - - -
613A ALA* 1.3 75.7 - - - +
615A TRP* 1.3 61.4 + - - +
617A LEU* 3.5 9.4 + - - +
618A TYR 3.2 17.3 + - - -
821A PHE* 3.6 21.9 - - + -
825A THR* 4.1 25.8 - - + +
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Residues in contact with TRP 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A LEU 3.1 12.3 + - - +
612A SER* 4.0 4.0 - - - +
614A ALA* 1.3 74.8 - - - +
616A GLN* 1.3 67.1 + - - +
617A LEU 3.2 0.4 - - - -
618A TYR* 3.4 23.8 + + + -
619A ARG* 3.2 43.3 + - + +
714A ARG* 3.9 39.7 - - + -
717A MET* 3.5 50.3 - - + +
718A ASP* 2.8 26.5 + - - -
721A ALA* 4.3 10.8 - - + -
819A TRP* 3.6 27.8 - + - -
821A PHE* 4.0 16.8 - + - -
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Residues in contact with GLN 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A LEU* 4.3 19.7 - - + +
571A LEU* 3.7 24.0 + - + -
572A GLN* 3.1 39.2 + - - +
612A SER 2.9 17.4 + - - +
613A ALA 4.0 2.7 - - - +
615A TRP* 1.3 79.0 - - - +
617A LEU* 1.3 56.6 + - - +
619A ARG* 3.3 30.0 + - - +
620A ALA* 2.8 27.8 + - - +
623A GLU* 5.5 1.4 + - - -
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Residues in contact with LEU 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A LEU* 4.5 16.3 - - + +
599A VAL* 3.7 37.5 - - + -
600A GLY 5.7 4.5 - - - +
601A TYR* 3.3 47.6 - - + +
613A ALA 2.9 18.8 + - - +
614A ALA* 3.6 9.0 - - - +
615A TRP 3.2 0.2 - - - -
616A GLN* 1.3 73.8 - - - +
618A TYR* 1.3 66.8 + - - +
620A ALA* 3.1 4.8 + - + +
621A GLN* 2.9 44.9 + - + +
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Residues in contact with TYR 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A ALA 3.2 10.5 + - - +
615A TRP* 3.8 30.5 - + + +
616A GLN 3.4 0.2 - - - -
617A LEU* 1.3 78.4 - - - +
619A ARG* 1.3 63.7 + - - +
621A GLN* 3.6 10.6 + - - +
622A GLU* 3.1 47.7 + - - +
658A SER 4.2 5.8 - - - -
659A GLN 4.5 0.4 + - - -
660A PRO* 3.7 39.8 - - + +
661A PRO* 3.9 9.2 - - - +
706A PRO* 5.6 2.0 - - + +
707A VAL 4.8 1.9 + - - -
709A PRO* 3.6 32.9 - - + +
714A ARG* 4.7 0.9 - - - -
819A TRP* 4.5 4.1 + + - -
821A PHE* 3.9 38.4 - + + -
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Residues in contact with ARG 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A TRP* 3.2 55.9 + - + +
616A GLN* 3.8 25.3 + - - +
617A LEU 3.2 0.4 - - - -
618A TYR* 1.3 75.9 - - - +
620A ALA* 1.3 60.4 + - - +
622A GLU* 3.3 15.3 - - - +
623A GLU* 2.9 59.1 + - - +
714A ARG* 4.7 4.7 - - - +
718A ASP* 4.5 7.2 + - - -
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Residues in contact with ALA 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A LEU* 3.8 42.6 - - + +
574A ALA* 5.1 1.8 - - + -
575A PRO* 4.8 6.7 - - - -
599A VAL* 6.1 0.9 - - + -
616A GLN* 2.8 21.2 + - - +
617A LEU* 3.1 5.1 + - + +
619A ARG* 1.3 73.4 - - - +
621A GLN* 1.3 60.2 + - - +
623A GLU* 3.4 2.6 + - - +
624A MET* 2.9 43.4 + - - +
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Residues in contact with GLN 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A VAL* 5.0 3.5 - - + +
601A TYR* 4.7 0.2 + - - -
617A LEU* 2.9 44.4 + - + +
618A TYR* 3.8 8.3 - - - +
620A ALA* 1.3 77.7 - - + +
622A GLU* 1.3 64.0 + - - +
624A MET* 3.8 7.6 - - - +
625A ALA* 2.9 26.3 + - - +
635A LEU* 5.3 0.7 - - - +
637A LEU* 3.5 29.2 - - + +
639A HIS* 3.5 13.3 - - - -
659A GLN* 3.0 24.3 + - - +
660A PRO* 3.3 28.6 - - + +
663A THR* 4.1 12.7 - - + +
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Residues in contact with GLU 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A TYR* 3.1 36.5 + - + +
619A ARG* 3.3 16.7 - - - +
621A GLN* 1.3 78.7 - - - +
623A GLU* 1.3 66.1 + - + +
625A ALA* 3.4 2.8 + - - +
626A GLN* 3.0 40.3 + - + +
660A PRO* 4.5 12.6 - - + +
661A PRO* 5.6 3.4 - - + +
663A THR* 5.5 0.2 - - - -
709A PRO* 4.8 1.7 - - - +
714A ARG* 2.7 41.0 + - - -
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Residues in contact with GLU 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A GLN 4.7 4.5 - - - +
575A PRO* 3.3 30.5 - - + +
616A GLN* 5.9 1.1 + - - -
619A ARG* 2.9 56.3 + - - +
620A ALA* 4.9 1.0 - - - -
622A GLU* 1.3 75.8 - - + +
624A MET* 1.3 66.2 + - - +
626A GLN* 3.1 10.5 + - + +
627A VAL* 3.0 25.9 + - + +
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Residues in contact with MET 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A PHE* 3.9 9.0 - - + -
571A LEU* 6.2 0.4 - - - -
574A ALA* 4.3 9.4 - - + -
575A PRO* 4.1 22.7 - - + -
578A VAL* 3.3 32.4 - - + +
597A VAL* 3.4 42.0 - - + -
599A VAL* 5.6 5.6 - - - -
620A ALA* 2.9 27.1 + - - +
621A GLN* 3.8 5.6 - - - +
623A GLU* 1.3 75.6 - - - +
625A ALA* 1.3 57.7 + - - +
627A VAL* 3.3 9.0 + - - +
628A ALA* 2.9 29.3 + - - +
635A LEU* 3.8 14.6 - - + +
637A LEU* 4.8 9.9 - - - -
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Residues in contact with ALA 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A GLN 2.9 17.0 + - - +
622A GLU* 3.6 6.3 - - - +
624A MET* 1.3 78.7 - - - +
626A GLN* 1.3 63.5 + - - +
628A ALA* 3.2 4.4 + - - +
629A LYS* 2.8 31.6 + - - +
635A LEU* 4.1 12.0 - - + +
661A PRO 5.2 1.6 - - - +
662A ASP* 3.8 24.5 - - + +
663A THR* 4.9 8.1 - - + +
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Residues in contact with GLN 626 (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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622A GLU* 3.0 37.8 + - + +
623A GLU* 3.1 9.8 + - - +
625A ALA* 1.3 82.2 - - - +
627A VAL* 1.3 64.0 + - + +
629A LYS* 3.5 13.5 + - - +
630A ARG* 3.1 32.8 + - - +
661A PRO 5.1 6.9 + - - -
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Residues in contact with VAL 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A PRO* 4.0 22.4 - - + +
578A VAL* 4.3 6.3 - - + -
579A GLU* 3.5 42.8 - - + +
582A PHE* 4.1 7.6 - - + -
623A GLU* 3.0 16.9 + - + +
624A MET* 3.6 9.2 - - - +
626A GLN* 1.3 76.5 - - + +
628A ALA* 1.3 63.5 + - - +
630A ARG* 3.1 31.5 + - - +
631A TYR* 3.2 21.4 + - + -
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Residues in contact with ALA 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A VAL* 5.7 0.2 - - + -
582A PHE* 3.9 21.8 - - + -
624A MET 2.9 16.8 + - - +
625A ALA* 3.2 5.1 + - - +
627A VAL* 1.3 77.3 - - - +
629A LYS* 1.3 61.5 + - - +
631A TYR 3.3 1.4 + - - -
632A GLY 3.0 4.7 + - - -
633A VAL 2.9 43.0 + - - +
635A LEU* 3.8 24.2 - - + -
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Residues in contact with LYS 629 (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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625A ALA 2.8 20.1 + - - +
626A GLN* 3.9 15.3 - - - +
628A ALA* 1.3 72.2 - - - +
630A ARG* 1.3 64.1 + - + +
632A GLY* 3.2 11.9 + - - -
633A VAL 4.4 2.2 + - - -
662A ASP* 4.4 18.7 + - + +
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Residues in contact with ARG 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A GLU* 2.6 39.1 + - - -
626A GLN* 3.1 17.1 + - - +
627A VAL* 3.1 30.1 + - - +
629A LYS* 1.3 78.9 - - + +
631A TYR* 1.3 74.7 + - + +
632A GLY 3.6 0.2 + - - -
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Residues in contact with TYR 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A GLU* 3.2 41.2 + - + -
582A PHE* 3.7 48.7 - + + -
583A SER* 2.8 31.3 + - - -
588A MET* 3.6 20.7 - - + +
627A VAL* 3.2 21.9 + - + +
628A ALA 3.3 0.6 + - - +
629A LYS 3.3 0.2 - - - -
630A ARG* 1.3 90.9 + - + +
632A GLY* 1.3 63.0 + - - +
633A VAL* 3.4 4.5 - - + -
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Residues in contact with GLY 632 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A MET* 5.6 0.7 - - - +
593A GLY* 4.2 11.1 - - - +
628A ALA 3.0 4.5 + - - -
629A LYS* 3.2 11.6 + - - -
630A ARG 3.3 1.2 + - - -
631A TYR* 1.3 79.3 - - - +
633A VAL* 1.3 60.4 + - - +
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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