Contacts of the helix formed by residues 690 - 714 (chain D) in PDB entry 6NYY
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 SER 690 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687C LYS* 3.8 6.7 - - - +
691C GLU* 4.7 3.4 - - - -
694C ALA* 3.3 30.1 + - - -
695C ARG* 3.8 9.4 - - - -
698C ASP* 2.7 16.5 + - - +
687D LYS* 5.0 1.7 - - - +
689D TYR* 1.3 94.0 - - - +
691D GLU* 1.3 63.1 + - - +
692D ALA* 3.4 4.1 + - - +
693D THR* 2.8 32.2 + - - -
694D ALA* 3.5 5.9 + - - +
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Residues in contact with GLU 691 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691C GLU* 4.3 30.7 + - + +
687D LYS* 5.5 4.9 - - - +
690D SER* 1.3 73.6 - - - +
692D ALA* 1.3 55.5 + - - +
693D THR 3.1 1.8 - - - -
694D ALA* 3.1 7.3 + - - +
695D ARG* 2.7 34.8 + - + +
686E GLU* 5.2 5.2 - - - +
690E SER* 3.3 14.4 - - - -
691E GLU* 2.5 47.2 + - + +
692E ALA 4.2 1.1 + - - +
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Residues in contact with ALA 692 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695C ARG* 3.7 37.4 - - + +
699C ASP* 6.1 0.2 - - - +
690D SER* 3.4 2.7 + - - +
691D GLU* 1.3 78.3 - - - +
693D THR* 1.3 57.7 + - - +
695D ARG* 3.9 13.5 - - - +
696D LEU* 3.3 21.1 + - - +
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Residues in contact with THR 693 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698C ASP* 3.3 21.6 + - - +
699C ASP* 5.5 0.7 + - - -
702C ARG* 3.6 23.8 + - - +
670D VAL* 5.1 6.1 - - + -
675D PHE* 5.0 7.0 - - + -
689D TYR* 3.7 27.1 - - + -
690D SER* 2.8 18.0 + - - -
692D ALA* 1.3 77.9 - - - +
694D ALA* 1.3 60.6 + - - +
695D ARG 3.2 0.2 - - - -
696D LEU* 2.9 7.6 + - + +
697D ILE* 2.8 42.9 + - + +
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Residues in contact with ALA 694 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687D LYS* 5.1 10.8 - - + -
689D TYR* 3.7 23.7 - - + +
690D SER 3.5 9.7 + - - +
691D GLU* 3.1 16.0 + - - +
693D THR* 1.3 75.2 - - - +
695D ARG* 1.3 63.3 + - - +
697D ILE* 4.0 4.4 - - - +
698D ASP* 3.3 22.5 + - - +
690E SER* 3.3 27.9 - - - +
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Residues in contact with ARG 695 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691D GLU* 2.7 20.1 + - + +
692D ALA* 4.0 11.9 - - - +
693D THR 3.2 0.2 - - - -
694D ALA* 1.3 72.1 - - - +
696D LEU* 1.3 62.7 + - - +
698D ASP* 3.8 1.1 + - - +
699D ASP* 3.0 42.9 + - - +
690E SER* 3.8 10.0 - - - +
692E ALA* 3.7 32.3 - - + +
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Residues in contact with LEU 696 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702C ARG* 3.9 28.3 - - - +
669D LYS* 3.6 40.4 - - + +
670D VAL* 4.2 11.9 - - + -
692D ALA 3.3 14.3 + - - +
693D THR* 2.9 10.1 + - + +
695D ARG* 1.3 79.6 - - - +
697D ILE* 1.3 61.8 + - - +
699D ASP* 3.8 7.9 + - + +
700D GLU* 3.3 27.3 + - + +
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Residues in contact with ILE 697 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658D TYR* 4.0 21.3 - - + -
661D ILE* 4.3 9.1 - - + +
662D VAL* 3.7 31.9 - - + -
670D VAL* 4.1 25.1 - - + -
675D PHE* 5.4 2.7 - - + -
689D TYR* 3.5 42.2 - - + +
693D THR* 2.8 27.6 + - + +
694D ALA* 3.5 4.9 + - - +
696D LEU* 1.3 73.6 - - - +
698D ASP* 1.3 60.5 + - - +
700D GLU* 2.9 19.1 + - - +
701D VAL* 3.0 13.4 + - + +
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Residues in contact with ASP 698 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658D TYR* 2.6 37.8 + - - -
694D ALA* 3.3 10.4 + - - +
695D ARG 4.5 2.0 - - - +
697D ILE* 1.3 74.5 - - - +
699D ASP* 1.3 65.1 + - - +
701D VAL* 4.0 6.7 - - - +
702D ARG* 3.4 30.8 + - - +
673E ILE* 5.1 1.4 - - - +
675E PHE* 5.1 1.1 - - - -
688E PRO 5.1 0.2 - - - +
689E TYR* 3.5 6.3 - - - -
690E SER* 2.8 38.0 + - - +
693E THR* 3.4 20.5 + - + +
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Residues in contact with ASP 699 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695D ARG* 3.0 34.8 + - - +
696D LEU* 3.9 10.6 - - + +
697D ILE 3.2 0.6 - - - -
698D ASP* 1.3 77.8 - - - +
700D GLU* 1.3 59.4 + - + +
702D ARG* 2.5 40.4 + - - +
703D ILE* 3.0 37.4 + - + +
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Residues in contact with GLU 700 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661D ILE* 3.7 7.6 - - + +
667D ASN* 3.4 36.3 + - - +
669D LYS* 3.3 37.8 + - + +
670D VAL* 4.6 1.8 - - + -
696D LEU* 3.3 18.4 + - + +
697D ILE* 2.9 9.9 + - - +
699D ASP* 1.3 76.6 - - + +
701D VAL* 1.3 59.6 + - - +
703D ILE* 3.5 28.4 + - - +
704D LEU* 3.0 27.7 + - - +
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Residues in contact with VAL 701 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654D THR* 5.1 3.1 - - + +
657D ALA* 3.8 22.0 - - + +
658D TYR* 3.6 37.2 - - + +
661D ILE* 3.8 17.9 - - + -
697D ILE* 3.0 16.4 + - + +
698D ASP* 4.2 7.2 - - - +
700D GLU* 1.3 77.0 - - - +
702D ARG* 1.3 57.5 + - - +
704D LEU* 3.1 4.0 + - - +
705D ILE* 2.9 43.6 + - + +
673E ILE* 4.1 15.9 - - + -
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Residues in contact with ARG 702 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698D ASP* 3.4 17.9 + - - +
699D ASP* 2.5 39.5 + - - +
701D VAL* 1.3 79.3 - - - +
703D ILE* 1.3 61.1 + - + +
705D ILE* 5.1 1.8 - - - -
706D ASN* 2.9 39.0 + - - +
669E LYS 3.7 13.3 + - - -
670E VAL* 3.3 30.5 + - - +
671E GLY* 5.0 1.3 - - - -
673E ILE* 3.7 15.2 - - + +
692E ALA* 5.8 2.4 + - - +
693E THR* 3.7 27.9 + - - +
696E LEU* 4.2 23.4 - - - +
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Residues in contact with ILE 703 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669D LYS* 5.9 2.2 - - - +
699D ASP* 3.0 22.0 + - + +
700D GLU* 3.7 33.0 - - - +
701D VAL 3.3 0.2 - - - -
702D ARG* 1.3 76.6 - - + +
704D LEU* 1.3 62.0 + - - +
706D ASN* 4.0 2.3 - - - +
707D ASP* 3.0 43.9 + - - +
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Residues in contact with LEU 704 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618D LYS* 6.1 4.9 - - - -
622D LEU* 5.3 9.0 - - + +
625D MET* 4.3 13.0 - - + -
657D ALA* 3.7 34.1 - - + +
660D GLN* 3.5 27.4 - - + +
661D ILE* 4.4 10.5 - - + -
700D GLU 3.0 18.0 + - - +
701D VAL 3.1 5.1 + - - +
703D ILE* 1.3 76.0 - - - +
705D ILE* 1.3 61.1 + - + +
707D ASP* 3.2 7.5 + - + +
708D ALA* 3.0 24.9 + - - +
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Residues in contact with ILE 705 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625D MET* 4.2 6.7 - - + -
629D LEU* 4.0 8.5 - - + -
653D VAL* 3.7 39.9 - - + +
654D THR* 4.5 5.8 - - - -
657D ALA* 4.3 5.6 - - + -
701D VAL* 2.9 25.6 + - + +
702D ARG* 4.7 2.2 - - - +
704D LEU* 1.3 75.9 - - - +
706D ASN* 1.3 53.4 + - - +
708D ALA* 2.9 8.3 + - - -
709D TYR* 2.6 34.0 + - - +
672E GLN* 3.7 31.6 - - + +
673E ILE* 3.7 28.0 - - + -
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Residues in contact with ASN 706 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702D ARG* 2.9 31.1 + - - +
703D ILE* 4.6 1.8 - - - +
705D ILE* 1.3 77.0 - - - +
707D ASP* 1.3 61.0 + - - +
709D TYR* 3.9 14.2 - - - +
710D LYS* 3.3 38.5 + - - +
668E GLU 5.5 2.5 + - - +
671E GLY* 4.5 13.3 - - - -
672E GLN* 4.1 25.5 + - - +
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Residues in contact with ASP 707 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622D LEU* 5.1 3.7 - - + +
703D ILE* 3.0 33.5 + - - +
704D LEU* 3.2 7.8 + - + +
705D ILE 3.1 0.6 - - - -
706D ASN* 1.3 79.9 - - - +
708D ALA* 1.3 61.5 + - - +
709D TYR 3.3 0.4 - - - -
710D LYS* 4.1 10.9 + - - +
711D ARG* 3.3 24.4 + - - +
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Residues in contact with ALA 708 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622D LEU* 3.9 19.2 - - + +
625D MET* 4.0 18.8 - - + -
626D CYS* 3.7 15.0 - - - +
629D LEU* 3.8 16.7 - - + +
704D LEU 3.0 11.9 + - - +
705D ILE 2.9 8.3 + - - +
707D ASP* 1.3 75.0 - - - +
709D TYR* 1.3 62.2 + - - +
711D ARG 3.7 0.3 + - - -
712D THR* 2.9 28.1 + - - -
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Residues in contact with TYR 709 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629D LEU* 3.9 16.8 - - + +
632D ARG* 4.5 17.5 - - + +
633D VAL* 3.8 21.2 - - + +
636D GLU* 3.9 29.6 + - - +
642D ILE* 5.6 0.3 - - - +
705D ILE 2.6 19.7 + - - +
706D ASN* 4.0 18.2 - - - +
707D ASP 3.3 0.4 - - - -
708D ALA* 1.3 71.8 - - - +
710D LYS* 1.3 67.3 + - + +
712D THR* 3.2 5.7 + - - -
713D VAL* 3.0 49.1 + - + +
672E GLN* 4.3 34.1 + - + -
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Residues in contact with LYS 710 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706D ASN* 3.3 26.2 + - + +
707D ASP* 4.5 10.3 + - - +
708D ALA 3.5 0.2 - - - -
709D TYR* 1.3 83.3 - - + +
711D ARG* 1.3 56.6 + - - +
713D VAL* 3.9 7.0 - - - +
714D ALA* 3.2 27.0 + - - +
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Residues in contact with ARG 711 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585D LEU* 3.5 22.6 - - - +
622D LEU* 3.8 24.3 - - - +
623D ASP* 2.9 30.3 + - - -
626D CYS* 3.1 28.6 - - - +
707D ASP 3.3 17.3 + - - +
708D ALA 4.0 5.2 - - - +
709D TYR 3.2 0.8 - - - -
710D LYS* 1.3 78.9 - - - +
712D THR* 1.3 58.0 + - - +
714D ALA* 3.8 5.8 + - - +
715D LEU* 3.4 21.1 + - - +
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Residues in contact with THR 712 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581D ALA* 4.7 5.6 - - + -
626D CYS* 3.2 38.5 + - - +
629D LEU* 4.6 2.9 - - - +
630D GLY* 3.7 22.0 - - - +
633D VAL* 3.8 18.5 - - + +
708D ALA 2.9 16.8 + - - -
709D TYR* 3.2 5.6 + - - -
711D ARG* 1.3 76.3 - - - +
713D VAL* 1.3 58.5 + - - +
714D ALA 3.2 1.1 - - - -
715D LEU* 2.9 8.0 + - + +
716D LEU* 2.9 35.2 + - + -
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Residues in contact with VAL 713 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633D VAL* 3.7 23.6 - - + -
636D GLU* 5.0 7.6 - - - +
637D ILE* 5.0 4.5 - - + -
709D TYR* 3.0 47.4 + - + +
710D LYS* 4.2 6.7 - - - +
712D THR* 1.3 74.4 - - - +
714D ALA* 1.3 60.1 + - - +
715D LEU 3.3 0.7 + - - -
716D LEU 4.2 0.2 - - - -
717D THR* 2.9 37.7 + - + +
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Residues in contact with ALA 714 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710D LYS 3.2 19.6 + - - +
711D ARG* 4.0 6.7 - - - +
713D VAL* 1.3 76.1 - - - +
715D LEU* 1.3 59.0 + - - +
717D THR* 3.9 11.6 + - - -
718D GLU* 4.0 16.3 - - - +
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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