Contacts of the helix formed by residues 554 - 577 (chain B) in PDB entry 5OC9
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 VAL 554 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ASN* 3.3 44.5 + - + +
401B ILE* 3.6 34.7 - - + +
402B LEU* 4.3 24.9 - - + +
405B LEU* 5.8 2.2 - - + -
552B ILE 3.7 1.0 + - - -
553B GLY* 1.3 68.3 - - - -
555B TRP* 1.3 64.0 + - - +
556B GLN 3.2 1.6 - - - -
557B LEU* 3.2 20.0 + - + +
558B ALA* 3.2 18.9 + - - +
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Residues in contact with TRP 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B ILE* 3.8 28.4 - - + +
405B LEU* 3.6 36.8 - - + -
494B THR* 5.2 1.0 + - - -
495B PHE* 3.5 35.8 - + - +
498B TYR* 3.5 43.2 - + + -
499B LEU* 3.7 17.7 - - - -
502B PHE* 3.7 17.7 - + + -
552B ILE* 3.3 36.8 - - + +
553B GLY 3.1 0.4 - - - -
554B VAL* 1.3 75.5 - - - +
556B GLN* 1.4 58.4 + - - +
558B ALA* 3.4 11.6 - - + +
559B PHE* 2.9 54.2 + + + -
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Residues in contact with GLN 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LEU* 3.1 36.6 + - - +
261B TRP* 3.2 27.6 + - - -
262B LYS* 3.5 30.1 - - + +
552B ILE* 3.5 16.7 - - + +
553B GLY 3.5 12.6 + - - +
555B TRP* 1.4 76.6 - - - +
557B LEU* 1.4 55.6 + - - +
559B PHE* 3.6 3.5 + - - +
560B GLU* 3.0 55.4 + - - +
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Residues in contact with LEU 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A PHE* 5.0 12.6 - - + -
611A PHE* 5.2 15.9 - - + -
402B LEU* 4.3 5.8 - - + -
553B GLY 4.7 0.4 + - - -
554B VAL* 3.2 28.7 + - + +
556B GLN* 1.4 74.7 - - - +
558B ALA* 1.3 56.9 + - - +
560B GLU* 3.4 1.8 + - - +
561B THR* 2.8 42.0 + - - +
710B 79M 3.5 36.5 + - - +
712B 79M 3.8 32.3 - - + -
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Residues in contact with ALA 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B LEU* 6.3 0.2 - - + -
405B LEU* 3.4 33.2 - - + -
502B PHE* 3.3 20.8 - - + -
554B VAL 3.2 9.4 + - - +
555B TRP* 3.3 16.4 + - + +
557B LEU* 1.3 78.3 - - - +
559B PHE* 1.4 55.7 + - - +
561B THR* 3.4 4.9 + - - -
562B MET 3.1 21.5 + - - -
712B 79M 3.9 16.9 - - + +
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Residues in contact with PHE 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B PHE* 3.6 36.3 - + - -
218B PHE* 4.2 6.7 - + - -
258B LEU* 3.4 30.7 - - + +
498B TYR* 4.5 4.7 - + - -
501B LEU* 3.8 5.4 - - + -
502B PHE* 3.6 43.1 - + + -
505B PHE* 3.2 49.0 - + + -
552B ILE* 5.1 2.2 - - + -
555B TRP* 2.9 43.7 + + + +
556B GLN* 4.0 4.3 - - - +
558B ALA* 1.4 73.3 - - - +
560B GLU* 1.4 59.6 + - - +
562B MET* 3.4 5.6 + - - -
563B SER 3.1 21.0 + - - -
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Residues in contact with GLU 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LEU* 3.8 17.0 - - + +
259B GLU* 3.5 10.4 - - - +
262B LYS* 3.3 24.6 + - - -
556B GLN* 3.0 42.3 + - - +
557B LEU* 3.8 3.5 - - - +
558B ALA 3.4 0.2 - - - -
559B PHE* 1.4 71.5 - - - +
561B THR* 1.3 59.3 + - - +
563B SER* 2.7 21.9 + - - -
564B VAL* 3.1 11.6 + - - +
610B ALA* 5.4 0.3 - - - +
709B 79M 3.3 23.6 + - - +
710B 79M 2.9 38.2 + - - +
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Residues in contact with THR 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B LEU* 2.8 24.5 + - - +
558B ALA 3.6 5.4 - - - -
560B GLU* 1.3 72.5 - - - +
562B MET* 1.4 60.1 + - - +
564B VAL* 3.1 3.8 + - - +
565B ILE* 2.9 42.2 + - + +
710B 79M 3.8 35.8 + - + -
712B 79M 3.7 39.2 - - + +
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Residues in contact with MET 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B PHE* 3.7 27.8 - - + -
413B PHE* 4.3 5.8 - - + -
502B PHE* 3.5 34.5 - - + +
505B PHE* 3.7 22.7 - - + -
506B GLY* 3.7 26.9 - - - -
509B SER* 3.9 4.0 + - - +
510B LEU* 3.6 31.7 - - - +
558B ALA 3.1 12.4 + - - +
559B PHE 3.4 10.1 - - - +
561B THR* 1.4 76.3 - - - +
563B SER* 1.4 56.2 + - - +
565B ILE* 3.4 7.9 + - - +
566B SER* 3.0 27.2 + - - -
712B 79M 4.3 2.6 - - + +
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Residues in contact with SER 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B SER* 3.7 16.8 - - - -
258B LEU* 4.0 8.0 - - - +
505B PHE* 4.1 4.9 - - - -
509B SER* 5.0 0.2 - - - -
559B PHE 3.1 12.0 + - - -
560B GLU* 2.7 23.4 + - - -
562B MET* 1.4 73.0 - - - +
564B VAL* 1.4 60.8 + - - +
566B SER* 2.7 23.8 + - - -
567B VAL* 3.6 2.1 - - - +
606B LYS* 3.3 30.5 + - - -
709B 79M 3.5 19.3 + - - -
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Residues in contact with VAL 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B GLU 3.1 15.9 + - - +
561B THR 3.1 8.4 + - - +
563B SER* 1.4 76.1 - - - +
565B ILE* 1.4 64.4 + - + +
566B SER 3.2 0.2 - - - -
567B VAL* 3.2 24.1 + - - +
568B VAL* 3.9 6.4 + - - +
603B LEU* 4.0 9.8 - - + +
606B LYS* 4.7 2.2 - - + -
709B 79M 3.4 71.3 - - + +
710B 79M 3.7 28.5 - - + +
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Residues in contact with ILE 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B PHE* 4.2 13.2 - - + -
417B PHE* 3.8 23.8 - - + -
510B LEU* 4.2 9.4 - - + -
561B THR* 2.9 29.6 + - + +
562B MET* 3.8 7.6 - - - +
564B VAL* 1.4 77.5 - - + +
566B SER* 1.4 54.0 + - - +
568B VAL* 3.1 15.3 + - + +
569B THR* 2.8 41.0 + - - +
709B 79M 4.5 18.4 - - + -
710B 79M 6.1 0.4 - - + -
712B 79M 3.8 28.3 - - + -
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Residues in contact with SER 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ASN* 5.2 0.2 + - - -
251B LEU* 3.6 11.0 - - - +
254B SER* 4.2 6.4 + - - -
509B SER* 3.4 33.7 - - - -
510B LEU* 3.7 9.4 - - - -
562B MET 3.0 14.8 + - - -
563B SER* 2.7 26.2 + - - -
565B ILE* 1.4 75.1 - - - +
567B VAL* 1.4 55.9 + - - +
568B VAL 3.4 0.2 - - - -
569B THR* 3.9 4.3 - - - -
570B ASN* 2.8 38.0 + - - +
606B LYS* 4.7 0.2 + - - -
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Residues in contact with VAL 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU* 3.7 17.2 - - + +
563B SER 3.6 13.5 - - - +
564B VAL 3.5 14.4 - - - +
565B ILE 3.2 0.6 - - - -
566B SER* 1.4 72.9 - - - +
568B VAL* 1.3 66.3 + - + +
570B ASN* 4.3 0.7 - - - +
571B CYS* 3.1 31.4 + - - +
599B GLU* 3.8 27.4 - - + +
602B LEU* 3.8 22.4 - - + -
603B LEU* 3.9 16.8 - - + -
606B LYS* 3.7 26.5 - - + -
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Residues in contact with VAL 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A HIS* 4.6 7.9 - - + +
564B VAL 3.9 10.8 - - - +
565B ILE* 3.4 13.2 - - + +
567B VAL* 1.3 76.8 - - + +
569B THR* 1.4 55.2 + - - +
571B CYS* 3.9 1.7 - - - +
572B ALA* 3.0 33.2 + - + +
599B GLU* 3.4 29.2 - - + +
603B LEU* 5.2 3.4 - - + -
709B 79M 4.2 28.5 - - + -
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Residues in contact with THR 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B PHE* 4.2 5.9 - - + -
421B PHE* 3.7 26.2 - - + -
510B LEU* 3.5 42.1 - - + +
511B PHE* 3.9 18.8 - - + -
565B ILE* 2.8 22.7 + - - +
566B SER 3.9 4.5 - - - -
568B VAL* 1.4 75.8 - - - +
570B ASN* 1.4 56.6 + - - +
572B ALA* 3.2 3.9 + - - +
573B LEU* 3.0 36.3 + - + +
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Residues in contact with ASN 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ALA* 3.8 19.9 - - + +
250B ASN* 3.8 12.2 + - - +
251B LEU* 4.0 16.8 - - + +
509B SER 3.0 24.2 + - - -
510B LEU 3.8 11.3 + - - +
513B CYS* 3.5 26.5 + - - +
566B SER 2.8 28.6 + - - +
567B VAL 4.3 1.6 - - - +
569B THR* 1.4 73.2 - - - +
571B CYS* 1.4 62.0 + - - +
573B LEU* 4.1 6.2 - - - +
574B ILE* 3.2 32.2 + - - +
708B 79M 5.2 1.8 - - + -
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Residues in contact with CYS 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LEU* 5.4 0.7 - - - -
567B VAL* 3.1 24.7 + - - +
568B VAL 3.9 2.9 - - - +
569B THR 3.3 0.2 - - - -
570B ASN* 1.4 74.3 - - - +
572B ALA* 1.3 59.4 + - - +
574B ILE* 4.0 1.4 - - - +
575B GLY 3.0 21.7 + - - -
595B VAL* 3.4 26.9 - - + +
598B VAL* 4.4 0.7 - - - -
599B GLU* 3.8 28.5 - - + -
602B LEU* 3.8 29.2 - - - -
708B 79M 4.0 23.5 - - + +
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Residues in contact with ALA 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B PHE* 3.6 22.4 - - + -
568B VAL* 3.0 20.5 + - + +
569B THR* 3.6 4.5 - - - +
571B CYS* 1.3 74.5 - - - +
573B LEU* 1.4 53.3 + - - +
575B GLY* 3.2 2.4 + - - -
576B MET* 2.8 42.7 + - + +
595B VAL* 4.8 5.4 - - - -
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Residues in contact with LEU 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ALA* 4.6 6.1 - - + -
421B PHE* 3.8 20.2 - - + -
426B MET* 3.9 25.0 - - + +
510B LEU 3.9 12.3 - - - +
511B PHE* 4.1 7.0 - - + -
513B CYS* 5.1 13.5 - - + -
514B VAL* 3.8 32.8 - - + -
569B THR* 3.0 39.1 + - + +
570B ASN* 4.1 5.6 - - - +
572B ALA* 1.4 74.9 - - - +
574B ILE* 1.4 61.5 + - - +
576B MET* 3.6 7.3 + - - +
577B SER* 3.3 19.8 + - - -
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Residues in contact with ILE 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B TYR* 3.8 24.7 - - + +
243B TYR* 4.0 28.0 - - + +
244B VAL* 4.3 2.5 - - + -
247B ALA* 3.7 29.2 - - + -
513B CYS* 4.7 7.6 - - + -
570B ASN 3.2 20.8 + - - +
571B CYS 4.2 2.0 - - - +
573B LEU* 1.4 73.6 - - + +
575B GLY* 1.3 65.3 + - - +
577B SER* 2.7 28.8 + - - +
580B VAL* 3.2 9.5 - - + +
708B 79M 3.8 40.6 - - + -
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Residues in contact with GLY 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B CYS 3.0 16.5 + - - -
572B ALA* 3.2 4.5 + - - -
574B ILE* 1.3 76.0 - - - +
576B MET* 1.3 56.3 + - - +
577B SER 4.2 0.7 - - - +
580B VAL* 4.3 9.2 - - - +
581B ASN* 3.0 17.7 + - - -
591B LEU* 3.9 17.5 - - - +
595B VAL* 3.9 22.2 - - - -
708B 79M 4.8 0.8 - - - +
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Residues in contact with MET 576 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ALA 4.0 9.0 - - - +
421B PHE* 3.6 54.3 - - + +
424B LYS* 3.8 31.0 - - + +
426B MET* 4.6 10.8 - - + -
572B ALA* 2.8 20.6 + - + +
573B LEU* 3.7 9.0 - - - +
574B ILE 3.2 0.2 - - - -
575B GLY* 1.3 74.3 - - - +
577B SER* 1.4 65.2 + - - +
578B PRO* 3.6 3.3 - - - +
581B ASN* 3.0 11.8 + - - +
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Residues in contact with SER 577 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B TYR* 5.3 1.6 - - - +
243B TYR* 5.8 9.4 - - - -
573B LEU 3.3 10.2 + - - -
574B ILE* 2.7 22.9 + - - +
576B MET* 1.4 75.7 - - - +
578B PRO* 1.4 74.1 - - - +
579B GLN* 3.2 8.0 + - - +
580B VAL* 3.2 17.5 + - - +
581B ASN* 3.0 21.7 + - - -
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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
------------------------------------------------------------
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