Contacts of the helix formed by residues 577 - 600 (chain A) in PDB entry 6DBV
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 ARG 577 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A LEU* 5.7 1.2 - - - +
545A VAL* 3.1 30.0 - - - +
546A SER* 2.3 43.2 + - - -
547A THR 5.1 0.2 - - - -
548A SER* 2.5 29.6 + - - -
551A VAL* 4.2 18.5 - - + +
552A GLY 4.8 5.5 + - - +
554A ILE* 4.6 4.9 - - + +
575A ARG* 3.7 6.7 - - - +
576A PHE* 1.3 75.4 - - - +
578A TYR* 1.3 66.4 + - - +
579A ASP* 3.1 27.7 + - - +
580A VAL* 2.8 27.5 + - + +
581A ALA 3.1 9.2 + - - -
700A GLU* 3.9 7.2 - - - +
169B THR* 5.0 0.9 + - - +
170B GLN* 3.1 31.8 - - - +
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Residues in contact with TYR 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A PHE 3.6 2.6 + - - -
577A ARG* 1.3 69.6 - - - +
579A ASP* 1.3 58.3 + - - +
581A ALA* 3.0 6.1 + - - +
582A LEU* 2.9 47.7 + - + +
615A VAL* 5.5 0.5 - - - +
617A GLU* 3.5 26.2 + - - +
642A PHE* 4.5 5.2 - + - -
644A PHE* 4.2 11.8 - + - +
677A LEU* 3.3 44.6 - - + -
697A VAL* 4.2 18.2 - - + -
700A GLU* 2.7 34.3 + - + +
701A ARG* 4.7 10.1 - - + +
704A MET* 5.1 6.1 - - + -
724A PHE* 3.0 42.3 - + - -
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Residues in contact with ASP 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A PHE* 3.6 24.0 - - - -
538A TRP* 3.6 27.5 + - + -
542A LEU* 4.5 5.5 - - + +
545A VAL* 5.3 3.1 - - - +
577A ARG* 3.2 38.9 + - - +
578A TYR* 1.3 77.2 - - - +
580A VAL* 1.3 76.0 + - - +
582A LEU* 3.2 5.7 + - - +
583A VAL* 2.9 35.1 + - - +
700A GLU* 5.0 3.5 - - + +
704A MET* 3.8 18.8 - - + +
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Residues in contact with VAL 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A PRO* 3.8 9.6 - - + -
532A GLY* 3.1 38.8 - - - +
536A PHE* 4.4 11.2 - - + -
549A TRP* 3.9 17.0 - - - +
551A VAL* 4.0 6.5 - - + +
552A GLY* 5.3 0.7 - - - -
576A PHE* 5.6 0.9 - - + -
577A ARG* 2.8 27.7 + - + +
579A ASP* 1.3 97.5 + - - +
581A ALA* 1.3 57.4 + - - +
583A VAL* 3.1 12.8 - - + +
584A SER* 2.9 29.1 + - - -
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Residues in contact with ALA 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A PRO* 5.2 2.7 - - - -
576A PHE* 4.1 23.0 - - + +
577A ARG 3.1 8.6 + - - +
578A TYR 3.0 10.7 + - - +
580A VAL* 1.3 77.6 - - - +
582A LEU* 1.3 63.8 + - - +
584A SER* 3.2 7.7 + - - -
585A ALA* 2.9 22.2 + - - +
644A PHE* 4.2 10.5 - - + -
677A LEU* 3.9 23.6 - - + -
1014A TRP* 3.9 9.6 - - + -
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Residues in contact with LEU 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A TRP* 6.2 0.2 - - + -
578A TYR* 2.9 45.9 + - + +
579A ASP* 3.6 8.3 - - - +
581A ALA* 1.3 75.4 - - - +
583A VAL* 1.3 61.3 + - + +
585A ALA* 3.1 7.2 + - + +
586A LEU* 2.9 29.5 + - - +
615A VAL* 5.0 6.7 - - + -
644A PHE* 3.4 33.2 - - + -
646A ILE* 5.2 2.8 - - + +
704A MET* 4.1 14.4 - - - -
709A LEU* 5.7 1.8 - - + -
722A PHE* 4.0 34.5 - - + -
724A PHE* 4.0 13.0 - - + -
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Residues in contact with VAL 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A GLY 6.1 0.4 - - - +
534A HIS* 4.8 10.1 - - + +
536A PHE* 3.9 30.3 - - + -
538A TRP* 4.9 1.3 - - + -
579A ASP 2.9 20.7 + - - +
580A VAL* 3.1 24.9 - - + +
582A LEU* 1.3 73.2 - - + +
584A SER* 1.3 66.4 + - - +
586A LEU* 4.4 5.2 - - - +
587A LYS* 2.9 28.6 + - - +
709A LEU* 3.8 19.5 - - + -
711A ILE* 3.7 33.0 - - + +
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Residues in contact with SER 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A LEU 3.4 16.5 + - - -
530A LEU 3.8 4.4 + - - -
531A PRO* 4.3 14.4 - - - -
532A GLY 5.4 0.9 - - - -
534A HIS* 4.9 9.8 + - - -
580A VAL 2.9 18.3 + - - -
581A ALA* 3.4 6.5 - - - -
583A VAL* 1.3 79.7 - - - +
585A ALA* 1.3 55.5 + - - +
587A LYS* 3.8 2.9 - - - +
588A ASP* 2.9 32.7 + - - +
1014A TRP* 3.1 24.1 - - - -
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Residues in contact with ALA 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A ALA 2.9 13.2 + - - +
582A LEU* 3.4 11.2 - - - +
584A SER* 1.3 77.0 - - - +
586A LEU* 1.3 56.6 + - - +
588A ASP* 3.2 6.8 - - - +
589A LEU* 3.0 32.4 + - - +
644A PHE* 4.7 5.4 - - + -
646A ILE* 3.5 17.3 - - + -
675A ARG* 3.1 30.3 - - - +
1014A TRP* 4.1 7.1 - - + -
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Residues in contact with LEU 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A LEU 2.9 14.5 + - - +
583A VAL* 4.1 5.2 - - - +
585A ALA* 1.3 73.4 - - - +
587A LYS* 1.3 63.5 + - - +
588A ASP 3.0 4.0 - - - -
589A LEU* 3.0 9.2 + - + +
590A GLU* 2.9 19.2 + - - -
593A ILE* 5.2 7.2 - - + +
613A VAL* 4.3 15.5 - - + -
646A ILE* 4.5 6.5 - - + +
649A ILE* 5.4 5.6 - - + -
709A LEU* 5.4 4.0 - - + -
711A ILE* 5.0 10.1 - - + -
713A VAL* 4.7 13.9 - - + -
720A PHE* 3.4 59.0 - - + -
722A PHE* 4.4 15.9 - - + -
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Residues in contact with LYS 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A HIS* 2.6 73.1 + - + +
583A VAL 2.9 22.6 + - - +
584A SER 4.1 0.4 - - - +
586A LEU* 1.3 75.4 - - - +
588A ASP* 1.3 58.5 + - - +
590A GLU* 3.2 28.8 - - + +
711A ILE* 4.2 14.8 - - + +
712A SER* 3.6 33.4 - - - +
713A VAL* 5.7 1.6 - - + -
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Residues in contact with ASP 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A LEU* 4.1 12.1 - - - +
584A SER* 2.9 21.9 + - - +
585A ALA* 3.2 9.9 - - - +
587A LYS* 1.3 75.8 - - - +
589A LEU* 1.3 72.8 + - - +
590A GLU* 3.0 8.9 + - - +
591A GLU* 4.1 7.8 + - - +
592A ASP* 5.5 0.3 - - - +
675A ARG* 4.6 2.4 + - - -
1014A TRP* 5.8 1.7 - - + -
1018A SER* 2.4 35.3 + - - -
1019A LYS* 3.6 12.1 + - - +
1020A TYR* 3.9 18.2 + - - +
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Residues in contact with LEU 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A ALA 3.0 20.2 + - - +
586A LEU* 3.0 6.5 + - + +
588A ASP* 1.3 90.0 - - - +
590A GLU* 1.3 65.0 + - - +
591A GLU 3.1 1.6 - - - -
592A ASP* 2.7 26.8 + - + +
593A ILE* 2.9 23.3 + - + -
646A ILE* 4.2 23.3 - - + -
649A ILE* 5.9 0.7 - - + -
663A PHE* 3.5 33.4 - - + -
675A ARG* 3.9 11.4 - - - +
1019A LYS* 3.6 27.8 - - + +
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Residues in contact with GLU 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A LEU 2.9 7.2 + - - +
587A LYS* 3.2 28.0 - - + +
588A ASP 3.0 1.4 - - - +
589A LEU* 1.3 74.7 - - - +
591A GLU* 1.3 67.0 + - - +
593A ILE* 3.0 10.7 - - - +
594A MET* 3.0 30.2 + - - +
712A SER 5.3 0.4 - - - +
713A VAL* 3.1 25.6 - - + -
714A GLY* 2.3 38.2 + - - -
715A GLY 4.3 1.0 + - - -
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Residues in contact with GLU 591 (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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588A ASP 4.1 5.4 + - - +
589A LEU 3.0 1.5 + - - -
590A GLU* 1.3 84.4 + - - +
592A ASP* 1.3 73.1 + - - +
594A MET* 3.3 2.6 + - - +
595A GLU* 2.9 34.0 + - + +
1020A TYR* 6.5 2.0 - - + -
1023A LYS* 5.7 4.7 + - - +
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Residues in contact with ASP 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A LEU* 2.7 24.6 + - + +
591A GLU* 1.3 90.4 - - - +
593A ILE* 1.3 55.7 + - + +
595A GLU* 2.7 29.3 - - - +
596A GLY* 2.9 12.0 + - - -
663A PHE* 5.3 21.2 - - + +
1019A LYS* 4.4 24.8 - - - +
1023A LYS* 4.5 19.8 + - - +
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Residues in contact with ILE 593 (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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586A LEU* 5.2 7.2 - - + +
589A LEU* 2.9 25.8 + - + +
590A GLU* 3.0 26.5 - - - +
592A ASP* 1.3 78.4 - - + +
594A MET* 1.3 78.3 + - + +
596A GLY* 3.4 0.7 + - - -
597A LEU* 2.9 30.1 + - + +
611A PHE* 5.7 3.4 - - + -
649A ILE* 3.6 38.8 - - + -
662A ILE* 4.0 11.7 - - + +
663A PHE* 5.1 5.8 - - + -
713A VAL* 3.9 23.6 - - + -
718A ARG* 4.4 8.5 - - - +
720A PHE* 5.4 7.6 - - + -
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Residues in contact with MET 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A GLU* 3.0 41.4 + - - +
591A GLU* 3.8 3.6 - - - +
593A ILE* 1.3 82.5 - - + +
595A GLU* 1.3 59.1 + - - +
597A LEU* 3.4 7.6 + - + +
598A ARG* 2.9 42.5 + - + +
604A ASP* 4.5 18.6 - - + -
714A GLY* 3.8 11.9 - - - +
718A ARG* 3.0 46.0 - - - +
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Residues in contact with GLU 595 (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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591A GLU* 2.9 25.5 + - + +
592A ASP* 2.7 27.2 - - - +
594A MET* 1.3 76.5 - - - +
596A GLY* 1.3 63.5 + - - +
598A ARG* 3.3 12.6 + - - +
599A GLU* 2.9 32.7 + - + +
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Residues in contact with GLY 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A ASP 2.9 8.1 + - - -
593A ILE 3.8 1.1 - - - -
595A GLU* 1.3 92.0 + - - +
597A LEU* 1.3 54.6 + - - +
599A GLU* 3.0 10.5 + - - +
600A ARG* 2.7 35.9 + - - +
662A ILE* 4.2 20.3 - - - +
663A PHE* 6.2 0.9 - - - -
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Residues in contact with LEU 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A ILE* 2.9 18.3 + - + +
594A MET* 3.6 10.1 - - + +
596A GLY* 1.3 74.2 - - - +
598A ARG* 1.3 63.4 + - - +
600A ARG* 3.5 5.4 + - - +
601A ALA 3.3 14.4 + - - -
602A LEU* 3.4 24.8 + - + +
603A ASP 3.1 27.8 - - - +
604A ASP* 3.3 18.2 - - - +
607A CYS 5.4 1.3 - - - +
608A THR* 5.1 1.6 - - + -
611A PHE* 4.2 17.9 - - + -
662A ILE* 3.9 12.3 - - + +
718A ARG* 3.2 37.0 - - - +
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Residues in contact with ARG 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A MET* 2.9 31.6 + - + +
595A GLU* 3.5 11.4 - - - +
597A LEU* 1.3 75.3 - - - +
599A GLU* 1.3 61.8 + - - +
601A ALA* 3.1 14.9 + - - +
602A LEU 5.2 0.2 - - - -
604A ASP* 4.0 27.5 + - - +
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Residues in contact with GLU 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A GLU* 2.9 22.8 + - + +
596A GLY* 3.0 13.6 + - - +
598A ARG* 1.3 74.9 - - - +
600A ARG* 1.3 79.9 + - - +
601A ALA* 3.0 12.4 + - - +
662A ILE 5.7 0.9 - - - +
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Residues in contact with ARG 600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A GLY 2.7 19.1 + - - +
597A LEU* 4.0 6.3 - - - +
599A GLU* 1.3 86.8 + - - +
601A ALA* 1.3 62.6 + - - +
602A LEU* 3.0 19.4 + - + +
651A ILE* 6.4 0.2 - - + -
660A ILE* 3.4 41.7 - - + +
661A THR* 4.2 20.4 + - - +
662A ILE* 5.6 6.1 + - + -
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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