Contacts of the helix formed by residues 564 - 585 (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 GLN 564 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562D VAL* 5.8 4.6 + - - +
563D LEU* 1.3 76.3 - - - +
565D PRO* 1.3 75.4 - - + +
566D GLU* 3.2 4.5 - - + +
567D GLU* 2.8 52.2 + - + +
568D LYS* 2.8 14.2 + - - +
480E ILE* 6.0 0.4 - - - +
612E GLU* 4.6 14.8 + - - +
753E LYS* 3.6 25.4 + - - +
758E GLU 5.0 0.7 - - - +
759E PHE* 3.4 26.2 + - - +
760E VAL* 5.4 0.6 - - - +
761E GLU* 5.3 2.1 + - - +
762E GLY 5.0 6.4 + - - +
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Residues in contact with PRO 565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564D GLN* 1.3 96.1 - - + +
566D GLU* 1.3 64.1 + - + +
568D LYS* 4.2 9.2 - - + +
569D LYS* 3.6 20.6 + - - +
753E LYS* 5.8 0.9 - - - +
761E GLU* 4.3 9.4 - - + +
762E GLY* 4.1 24.9 - - - +
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Residues in contact with GLU 566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564D GLN* 3.2 5.1 - - + +
565D PRO* 1.3 82.4 - - + +
567D GLU* 1.3 61.1 + - + +
569D LYS* 4.1 25.4 + - - +
570D THR* 2.9 21.7 + - - -
639D PHE* 5.6 2.3 - - - -
641D ARG* 5.3 6.2 + - - -
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Residues in contact with GLU 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563D LEU* 3.4 26.0 - - + +
564D GLN* 2.8 40.1 + - + +
566D GLU* 1.3 79.2 - - + +
568D LYS* 1.3 59.7 + - - +
569D LYS 3.2 1.3 - - - -
570D THR* 3.0 8.2 + - - -
571D VAL* 2.9 32.8 + - - +
603D LEU* 6.1 0.9 - - + -
612E GLU 3.5 6.9 - - - +
613E GLN* 3.3 37.3 - - + +
614E TYR* 4.3 9.0 - - - +
615E LEU* 5.0 13.0 - - + -
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Residues in contact with LYS 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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562D VAL* 5.2 3.9 - - - +
563D LEU* 3.8 44.6 + - + +
564D GLN 2.8 16.2 + - - +
565D PRO* 4.7 7.2 - - + +
567D GLU* 1.3 72.1 - - - +
569D LYS* 1.3 56.9 + - - +
571D VAL* 4.2 6.6 - - - +
572D ALA* 3.0 32.2 + - - +
596D ILE* 4.8 22.7 - - + +
731D LEU* 3.4 18.8 - - + +
734D GLU* 5.5 6.3 + - - +
762E GLY* 4.2 17.6 + - - +
763E THR* 4.3 13.5 - - - +
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Residues in contact with LYS 569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565D PRO 3.6 17.9 + - - +
566D GLU* 4.2 27.8 + - - +
567D GLU 3.2 1.0 - - - -
568D LYS* 1.3 76.9 - - - +
570D THR* 1.3 60.6 + - - +
572D ALA* 4.4 0.5 - - - +
573D TYR* 3.3 50.8 + - + -
639D PHE* 4.0 17.6 - - + -
731D LEU* 4.2 21.6 - - + +
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Residues in contact with THR 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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566D GLU 2.9 17.4 + - - -
567D GLU* 3.0 9.2 + - - -
569D LYS* 1.3 77.4 - - - +
571D VAL* 1.3 59.9 + - - +
573D TYR* 3.4 3.3 + - - +
574D HIS* 3.0 26.7 + - - +
635D GLU* 3.5 21.7 - - + +
639D PHE* 3.2 28.5 - - + -
641D ARG* 5.8 0.5 + - - -
643D THR* 4.0 13.2 - - + -
615E LEU* 3.7 21.5 - - + -
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Residues in contact with VAL 571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563D LEU* 4.0 10.3 - - + -
567D GLU 2.9 19.1 + - - +
568D LYS* 4.2 5.8 - - - +
570D THR* 1.3 76.7 - - - +
572D ALA* 1.3 57.3 + - - +
574D HIS* 3.2 6.1 + - - +
575D GLN* 2.9 32.8 + - + +
596D ILE* 4.3 13.0 - - + +
603D LEU* 3.8 25.4 - - + +
604D GLY* 3.7 31.9 - - - +
615E LEU* 3.8 20.2 - - + -
6J ALA* 4.7 6.7 - - + -
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Residues in contact with ALA 572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568D LYS 3.0 19.7 + - - +
569D LYS 4.4 2.9 - - - +
571D VAL* 1.3 77.5 - - - +
573D TYR* 1.3 57.8 + - + +
576D ALA* 3.0 30.3 + - - +
596D ILE* 3.8 19.7 - - + +
727D ALA* 3.3 22.9 - - + +
730D LEU* 3.8 5.8 - - + +
731D LEU* 3.8 19.5 - - + -
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Residues in contact with TYR 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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569D LYS* 3.3 38.0 + - + +
570D THR* 3.4 5.9 + - - +
571D VAL 3.3 0.2 - - - -
572D ALA* 1.3 75.5 - - + +
574D HIS* 1.3 63.5 + - - +
576D ALA* 4.2 1.5 - - - -
577D GLY 3.4 5.5 + - - -
634D SER* 2.8 27.9 + - - +
635D GLU* 4.8 10.3 - - + -
638D PHE* 3.5 45.3 - + + -
639D PHE* 3.4 31.6 - + + -
723D VAL* 5.0 0.7 - - + -
724D GLU* 4.5 21.8 + - + +
727D ALA* 3.5 25.4 - - + -
728D LEU* 4.9 11.5 - - + +
731D LEU* 6.1 3.1 - - + -
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Residues in contact with HIS 574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570D THR 3.0 16.7 + - - +
571D VAL* 3.2 8.9 + - - +
573D TYR* 1.3 78.7 - - - +
575D GLN* 1.3 65.4 + - - +
577D GLY 3.2 9.7 + - - -
578D HIS* 3.2 19.0 + + - -
631D GLY* 3.0 43.4 + - - -
632D ARG 3.9 2.2 - - - -
635D GLU* 4.0 16.5 - - - +
645D GLY 4.6 1.3 + - - -
646D ALA* 4.0 19.1 - - + -
649D ASP* 2.8 12.7 + - - -
803D ZN 2.3 32.8 - - - -
5J ALA 3.6 1.8 + - - -
6J ALA* 3.5 23.1 - - + +
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Residues in contact with GLN 575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571D VAL* 2.9 19.2 + - + +
572D ALA 4.2 2.2 - - - +
574D HIS* 1.3 83.2 - - - +
576D ALA* 1.3 61.5 + - - +
578D HIS* 3.2 10.7 + - - +
579D ALA* 3.0 25.6 + - - +
594D VAL* 3.8 19.9 - - + +
595D SER 3.7 12.1 - - - +
596D ILE* 4.2 9.4 - - + -
604D GLY* 3.4 22.0 - - - +
605D TYR 3.6 27.5 - - - +
606D ALA* 3.8 11.1 + - - +
730D LEU* 4.4 0.9 - - + -
803D ZN 4.3 0.6 - - - -
4J ALA 4.0 1.0 - - - +
5J ALA* 3.5 9.9 - - - +
6J ALA* 3.4 21.6 - - - +
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Residues in contact with ALA 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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572D ALA 3.0 19.2 + - - +
573D TYR 4.2 1.6 - - - +
574D HIS 3.3 0.2 - - - -
575D GLN* 1.3 75.6 - - - +
577D GLY* 1.3 58.5 + - - +
579D ALA* 4.1 8.1 - - - -
580D VAL* 2.9 33.1 + - - +
723D VAL* 3.7 32.9 - - + +
726D VAL* 4.0 15.3 - - + -
727D ALA* 3.8 9.4 - - + -
730D LEU* 4.2 1.2 - - + +
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Residues in contact with GLY 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 TYR 3.4 5.5 + - - -
574D HIS 3.2 7.1 + - - -
575D GLN 3.2 1.0 - - - -
576D ALA* 1.3 79.3 - - - +
578D HIS* 1.3 60.2 + - - +
581D ALA* 3.3 28.1 + - - +
630D GLY* 3.4 27.9 - - - +
634D SER* 3.8 12.3 - - - -
716D LEU* 4.1 6.5 - - - +
723D VAL* 4.8 1.1 - - - -
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Residues in contact with HIS 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 HIS* 3.2 30.1 + + - -
575D GLN* 3.2 20.5 + - - +
577D GLY* 1.3 75.5 - - - +
579D ALA* 1.3 62.9 + - - +
582D GLY* 3.3 14.9 + - - -
594D VAL* 5.7 0.4 - - + -
606D ALA* 4.8 5.8 - - + -
608D TYR* 2.8 27.0 + - + +
627D MET* 3.3 19.6 + - - +
628D THR* 3.3 29.5 - - + -
631D GLY* 3.8 5.3 + - - -
649D ASP* 3.0 10.5 + - - -
803D ZN 2.2 35.5 - - - -
4J ALA* 3.8 18.4 - - + +
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Residues in contact with ALA 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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575D GLN 3.0 16.0 + - - +
576D ALA* 3.8 8.7 - - - +
577D GLY 3.3 0.2 - - - -
578D HIS* 1.3 75.8 - - - +
580D VAL* 1.3 60.0 + - - +
582D GLY* 3.4 2.1 + - - -
583D TRP* 2.9 28.7 + - - +
591D LEU* 3.8 14.9 - - - +
594D VAL* 3.8 16.8 - - + +
726D VAL* 4.3 9.4 - - + -
741D MET* 3.8 23.7 - - + +
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Residues in contact with VAL 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 ALA 2.9 18.7 + - - +
579D ALA* 1.3 72.8 - - - +
581D ALA* 1.3 64.8 + - - +
583D TRP* 3.1 13.8 + - - -
584D TYR* 3.1 40.2 + - + +
716D LEU* 4.1 7.6 - - + -
719D LYS* 4.3 8.5 - - + -
722D ASP* 3.8 5.8 - - + +
723D VAL* 3.8 34.5 - - + -
726D VAL* 3.8 29.2 - - + -
745D LEU* 4.7 5.6 - - + -
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Residues in contact with ALA 581 (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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577D GLY 3.3 19.7 + - - +
580D VAL* 1.3 78.2 - - - +
582D GLY* 1.3 61.6 + - - +
584D TYR 4.2 0.2 - - - -
585D LEU* 3.3 33.6 + - + +
626D CYS 4.1 18.6 - - - +
627D MET* 4.5 5.8 - - - -
630D GLY* 4.6 5.6 - - - -
712D THR* 4.7 0.9 - - + -
715D LEU* 3.9 24.7 - - + -
716D LEU* 4.2 9.9 - - + +
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Residues in contact with GLY 582 (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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578D HIS 3.3 18.9 + - - -
579D ALA 3.6 1.6 - - - -
581D ALA* 1.3 78.5 - - - +
583D TRP* 1.3 59.7 + - - +
585D LEU 4.2 0.4 - - - +
588D ALA* 3.9 12.3 - - - +
589D ASP 4.0 3.6 - - - +
591D LEU* 5.6 5.3 - - - +
608D TYR* 4.9 6.5 - - - -
627D MET* 3.8 18.0 - - - +
748D ARG* 3.5 23.9 + - - -
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Residues in contact with TRP 583 (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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579D ALA 2.9 16.5 + - - +
580D VAL* 3.1 10.7 + - - +
582D GLY* 1.3 78.8 - - - +
584D TYR* 1.3 89.7 + + + +
585D LEU 3.5 0.4 - - - +
591D LEU* 5.3 12.6 - - + -
738D LYS* 4.6 20.4 - - + -
741D MET* 4.0 37.7 - - + -
742D VAL* 3.9 23.6 - - + -
745D LEU* 3.7 26.1 + - + +
746D GLY 3.3 22.4 - - - -
748D ARG* 3.2 66.7 + - + +
749D PRO* 4.2 5.7 - - + +
750D PHE* 4.5 0.5 - - - -
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Residues in contact with TYR 584 (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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580D VAL* 3.1 45.3 + - + +
581D ALA 4.8 0.7 - - - +
583D TRP* 1.3 99.1 - + + +
585D LEU* 1.3 62.9 + - - +
715D LEU* 4.6 19.7 - - + +
719D LYS* 3.6 35.2 + - + -
722D ASP* 3.1 25.0 + - + -
745D LEU* 3.8 26.8 + - + +
749D PRO* 4.5 18.4 - - + -
750D PHE* 3.3 20.2 - - - -
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Residues in contact with LEU 585 (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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581D ALA 3.3 22.2 + - - +
582D GLY 4.2 0.3 - - - +
583D TRP 3.5 0.2 - - - -
584D TYR* 1.3 81.6 - - - +
586D GLU* 1.3 60.1 + - - +
588D ALA* 4.0 11.7 + - + -
623D ASP* 3.6 33.4 - - + +
626D CYS* 3.7 22.0 - - + +
627D MET* 4.0 7.6 - - + +
711D ARG* 3.5 31.2 - - - +
715D LEU* 4.1 21.5 - - + -
748D ARG* 2.9 26.0 + - - -
750D PHE* 3.7 3.3 - - - -
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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
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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) + - + + + + + -
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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