Contacts of the helix formed by residues 557 - 580 (chain D) in PDB entry 5YD6
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 557 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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553D SER 2.9 19.8 + - - -
554D LYS* 3.5 8.3 - - - -
555D LEU 3.2 0.6 - - - -
556D LEU* 1.3 76.3 - - - +
558D LYS* 1.3 59.8 + - - +
559D LEU 3.2 0.4 - - - -
560D PRO* 3.3 18.0 - - - +
561D GLU* 3.6 20.2 + - - +
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Residues in contact with LYS 558 (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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449D LEU* 5.8 1.1 - - + -
489D PHE* 3.8 23.3 - - + -
492D ASN* 3.5 30.4 - - - +
493D LEU* 4.0 25.7 - - + +
496D MET* 3.6 28.0 - - - -
498D ILE* 5.5 0.2 - - + -
506D ILE* 5.3 7.0 - - + -
554D LYS 3.3 14.3 + - - +
555D LEU* 3.2 14.1 + - + +
556D LEU 3.0 1.4 - - - -
557D GLY* 1.3 76.7 - - - +
559D LEU* 1.3 60.6 + - - +
561D GLU* 2.7 35.0 + - - +
562D LEU* 2.9 28.9 + - - +
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Residues in contact with LEU 559 (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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445D GLU* 4.4 4.8 - - - +
506D ILE* 3.7 36.6 - - + +
509D LEU* 4.0 32.1 - - + +
510D ALA* 4.0 21.1 - - + +
556D LEU* 3.1 27.2 + - + +
558D LYS* 1.3 74.9 - - - +
560D PRO* 1.4 64.8 - - + +
562D LEU* 2.9 14.6 + - + +
563D ARG* 2.9 27.3 + - - +
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Residues in contact with PRO 560 (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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556D LEU 3.2 14.6 - - - +
557D GLY* 3.3 15.3 - - - +
559D LEU* 1.4 90.0 - - + +
561D GLU* 1.3 58.4 + - + +
563D ARG* 3.3 9.7 + - + +
564D THR* 3.1 26.5 + - - -
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Residues in contact with GLU 561 (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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489D PHE* 4.0 14.5 - - + -
492D ASN* 5.1 3.8 + - - +
557D GLY 3.6 14.3 + - - +
558D LYS* 2.7 46.0 + - - +
559D LEU 3.2 0.6 - - - -
560D PRO* 1.3 77.5 - - + +
562D LEU* 1.3 61.3 + - - +
564D THR* 3.5 8.7 + - - -
565D LEU* 3.1 25.5 + - - +
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Residues in contact with LEU 562 (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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445D GLU* 3.2 50.7 - - + +
448D VAL* 3.8 24.7 - - + -
449D LEU* 3.7 34.5 - - + +
489D PHE* 4.3 11.4 - - + -
510D ALA* 4.1 12.8 - - + -
558D LYS 2.9 15.3 + - - +
559D LEU* 3.2 16.2 - - + +
561D GLU* 1.3 74.8 - - - +
563D ARG* 1.3 58.1 + - - +
565D LEU* 3.2 6.7 + - - +
566D CYS* 2.9 28.4 + - - +
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Residues in contact with ARG 563 (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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445D GLU* 2.7 34.6 + - - -
510D ALA* 5.0 0.8 + - - +
513D THR* 4.0 16.4 + - - +
514D GLU 5.5 0.2 + - - -
515D ARG* 3.5 24.4 - - - +
559D LEU 2.9 11.3 + - - +
560D PRO* 3.3 13.9 + - + +
562D LEU* 1.3 74.8 - - - +
564D THR* 1.3 59.3 + - - +
566D CYS* 3.2 5.6 + - - +
567D THR* 3.0 29.9 + - - +
601D 8SU 2.9 50.3 + - - +
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Residues in contact with THR 564 (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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560D PRO 3.1 14.7 + - - -
561D GLU* 3.6 10.6 - - - -
562D LEU 3.3 0.2 - - - -
563D ARG* 1.3 74.4 - - - +
565D LEU* 1.3 61.0 + - + +
567D THR* 3.2 11.1 + - - -
568D GLN* 3.2 22.2 + - + +
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Residues in contact with LEU 565 (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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448D VAL* 3.6 26.2 - - + -
482D TRP* 2.8 36.9 + - - +
485D SER* 3.5 42.8 - - - +
486D ILE* 3.9 4.5 - - + +
489D PHE* 3.4 43.5 - - + -
561D GLU 3.1 13.5 + - - +
562D LEU* 3.2 9.2 + - - +
564D THR* 1.3 73.4 - - + +
566D CYS* 1.3 65.2 + - - +
568D GLN* 3.4 7.0 + - - +
569D GLY 3.2 5.0 + - - -
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Residues in contact with CYS 566 (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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444D LEU* 3.5 20.3 - - - +
445D GLU* 3.7 16.8 - - + +
448D VAL* 5.6 1.3 - - - +
482D TRP* 4.9 1.3 - - - -
562D LEU 2.9 12.9 + - - +
563D ARG 3.2 9.2 + - - +
565D LEU* 1.3 74.3 - - - +
567D THR* 1.3 55.1 + - - +
569D GLY* 3.0 3.5 + - - -
570D LEU* 2.8 32.1 + - - +
601D 8SU 1.6 73.8 - - + -
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Residues in contact with THR 567 (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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563D ARG* 3.0 16.9 + - - +
564D THR* 3.2 10.9 + - - -
566D CYS* 1.3 77.3 - - - +
568D GLN* 1.3 57.4 + - - +
570D LEU* 3.5 9.0 + - + +
571D GLN* 2.9 31.3 + - + +
601D 8SU 4.1 14.4 + - - +
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Residues in contact with GLN 568 (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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481D GLU* 3.0 28.5 + - - +
482D TRP* 3.6 25.9 - - + +
485D SER* 2.9 33.5 + - - -
564D THR* 3.2 11.3 + - + +
565D LEU* 3.5 14.9 - - - +
566D CYS 3.2 0.2 - - - -
567D THR* 1.3 79.0 - - - +
569D GLY* 1.3 58.8 + - - +
571D GLN* 3.4 24.4 + - - +
572D ARG* 3.4 18.2 + - - +
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Residues in contact with GLY 569 (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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444D LEU* 4.0 5.2 - - - -
482D TRP* 3.4 36.7 - - - -
565D LEU 3.2 6.9 + - - -
566D CYS 3.0 6.2 + - - -
568D GLN* 1.3 73.2 - - - +
570D LEU* 1.3 65.0 + - - +
571D GLN 3.1 1.3 - - - -
572D ARG* 3.1 6.8 + - - +
573D ILE* 3.1 25.4 + - - +
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Residues in contact with LEU 570 (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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444D LEU* 3.7 4.4 - - + +
566D CYS 2.8 18.8 + - - +
567D THR* 3.7 9.0 - - + +
569D GLY* 1.3 69.5 - - - +
571D GLN* 1.3 55.9 + - - +
573D ILE* 3.3 8.5 + - + +
574D PHE* 2.9 30.1 + - - +
592D PHE* 3.7 28.9 - - + -
595D THR* 5.1 4.0 - - + -
596D LEU* 4.3 17.9 - - + -
597D PRO* 5.5 3.8 - - + -
601D 8SU 3.4 68.2 - - + +
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Residues in contact with GLN 571 (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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567D THR* 2.9 19.3 + - + +
568D GLN* 3.4 27.7 + - - +
570D LEU* 1.3 74.1 - - - +
572D ARG* 1.3 58.8 + - - +
574D PHE* 3.5 11.4 + - + +
575D TYR* 3.0 28.6 + - + +
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Residues in contact with ARG 572 (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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403D ILE* 3.9 16.0 - - - +
406D PHE* 4.3 17.5 - - + -
477D ARG 3.0 22.4 + - - -
478D GLY* 2.9 26.3 + - - -
479D PHE 3.4 24.9 - - - +
480D GLY* 4.1 12.1 - - - +
482D TRP* 5.0 2.2 - - + -
568D GLN 3.4 9.4 + - - +
569D GLY* 3.1 12.4 + - - +
571D GLN* 1.3 75.7 - - - +
573D ILE* 1.3 64.6 + - - +
575D TYR* 3.4 23.3 + - - +
576D LEU* 3.1 48.6 + - + +
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Residues in contact with ILE 573 (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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406D PHE* 4.3 19.7 - - + -
407D TYR* 5.4 4.2 - - + -
410D LEU* 4.5 7.2 - - + -
444D LEU* 4.3 13.2 - - + -
569D GLY 3.1 20.2 + - - +
570D LEU* 3.5 10.5 - - - +
572D ARG* 1.3 72.3 - - - +
574D PHE* 1.3 65.5 + - - +
576D LEU* 3.3 8.8 + - - +
577D LYS* 3.1 26.6 + - + +
584D PRO* 5.5 4.7 - - + +
588D ILE* 4.2 19.3 - - + -
592D PHE* 3.7 27.4 - - + -
601D 8SU 3.8 34.5 - - + -
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Residues in contact with PHE 574 (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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570D LEU 2.9 16.4 + - - +
571D GLN* 3.6 12.3 - - + +
573D ILE* 1.3 76.3 - - - +
575D TYR* 1.3 67.8 + - + +
577D LYS* 3.3 6.4 + - + +
578D LEU* 3.0 58.5 + - + +
592D PHE* 3.9 28.3 - + + -
596D LEU* 6.1 2.5 - - + -
598D PHE* 6.4 2.0 - + - -
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Residues in contact with TYR 575 (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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571D GLN* 3.0 15.5 + - + +
572D ARG* 3.6 33.2 - - - +
573D ILE 3.3 0.2 - - - -
574D PHE* 1.3 83.6 - - + +
576D LEU* 1.3 62.1 + - + +
578D LEU* 3.8 6.2 - - + +
579D GLU* 2.9 61.2 + - + +
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Residues in contact with LEU 576 (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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403D ILE* 3.8 39.9 - - + -
406D PHE* 4.1 15.5 - - + -
407D TYR* 3.3 33.2 - - + +
572D ARG* 3.1 53.8 + - - +
573D ILE* 3.8 5.8 - - - +
574D PHE 3.3 0.2 - - - -
575D TYR* 1.3 79.1 - - + +
577D LYS* 1.3 57.7 + - - +
579D GLU* 3.3 25.4 - - - +
580D ASP* 3.1 22.7 + - - -
582D VAL 4.1 7.5 - - - +
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Residues in contact with LYS 577 (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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573D ILE* 3.1 17.7 + - + +
574D PHE* 3.6 5.8 - - + +
576D LEU* 1.3 74.1 - - - +
578D LEU* 1.3 65.9 + - - +
580D ASP* 3.3 21.4 + - - +
584D PRO* 4.1 23.0 - - + +
589D ASP* 2.7 38.4 + - - +
592D PHE* 4.3 20.9 - - + -
593D LEU* 4.2 28.4 - - - +
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Residues in contact with LEU 578 (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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574D PHE* 3.0 52.5 + - + +
575D TYR* 3.8 5.4 - - + +
577D LYS* 1.3 76.0 - - - +
579D GLU* 1.3 65.1 + - - +
580D ASP* 3.2 7.1 + - - +
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Residues in contact with GLU 579 (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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403D ILE* 4.8 6.9 - - - +
575D TYR* 2.9 53.4 + - + +
576D LEU* 3.3 29.3 - - - +
578D LEU* 1.3 72.3 - - - +
580D ASP* 1.3 61.7 + - - +
581D LEU* 3.2 46.0 + - + +
582D VAL* 3.9 10.7 + - - +
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Residues in contact with ASP 580 (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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576D LEU 3.1 13.5 + - - -
577D LYS* 3.4 17.8 - - - +
578D LEU 3.1 6.7 - - - +
579D GLU* 1.3 76.1 - - - +
581D LEU* 1.3 62.7 + - - +
582D VAL 3.7 0.7 - - - +
583D PRO* 3.6 26.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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