Contacts of the helix formed by residues 557 - 580 (chain A) in PDB entry 5Y41
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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553A SER 2.8 15.9 + - - -
554A LYS* 3.5 8.3 - - - -
555A LEU 3.2 0.8 - - - -
556A LEU* 1.3 73.8 - - - +
558A LYS* 1.3 62.8 + - - +
559A LEU 3.2 0.2 - - - -
560A PRO* 3.3 18.5 - - - +
561A GLU* 3.6 19.4 - - - +
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Residues in contact with LYS 558 (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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449A LEU* 5.6 2.0 - - + -
489A PHE* 3.6 26.3 - - + -
492A ASN* 4.2 26.1 - - - +
493A LEU* 3.9 22.0 - - + +
496A MET* 3.7 28.8 - - - -
498A ILE* 5.3 1.6 - - + -
506A ILE* 5.5 5.4 - - + -
554A LYS* 3.3 18.0 + - - +
555A LEU* 3.2 15.3 + - - +
556A LEU 3.2 1.6 - - - -
557A GLY* 1.3 76.4 - - - +
559A LEU* 1.3 65.2 + - + +
561A GLU* 3.1 35.2 + - - +
562A LEU* 3.4 20.9 + - - +
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Residues in contact with LEU 559 (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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445A GLU* 4.3 5.0 - - - +
449A LEU* 5.1 0.2 - - + -
506A ILE* 3.8 22.9 - - + +
509A LEU* 4.0 28.5 - - + +
510A ALA* 3.6 33.0 - - + -
555A LEU 5.0 0.2 - - - +
556A LEU* 3.1 33.0 + - + +
558A LYS* 1.3 74.2 - - - +
560A PRO* 1.4 68.0 - - + +
562A LEU* 3.0 33.4 + - + +
563A ARG* 3.8 1.9 + - - +
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Residues in contact with PRO 560 (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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556A LEU 3.4 11.2 - - - +
557A GLY* 3.3 18.6 - - - +
559A LEU* 1.4 90.0 - - + +
561A GLU* 1.3 57.0 + - + +
563A ARG* 3.0 29.6 + - + +
564A THR* 4.0 3.6 + - - -
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Residues in contact with GLU 561 (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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489A PHE* 3.7 15.4 - - + -
492A ASN* 5.7 1.4 - - - +
557A GLY 3.6 16.2 - - - +
558A LYS* 3.1 46.7 + - - +
559A LEU 3.2 1.0 - - - -
560A PRO* 1.3 73.2 - - + +
562A LEU* 1.3 65.3 + - - +
563A ARG 3.3 0.5 + - - -
564A THR* 3.4 18.2 + - - -
565A LEU* 3.5 18.2 + - + +
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Residues in contact with LEU 562 (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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445A GLU* 3.6 43.0 - - + +
448A VAL* 4.2 9.2 - - + -
449A LEU* 3.8 30.3 - - + +
489A PHE* 3.8 29.2 - - + -
510A ALA* 4.2 9.0 - - + -
558A LYS 3.4 7.8 + - - +
559A LEU* 3.0 39.1 + - + +
561A GLU* 1.3 77.9 - - - +
563A ARG* 1.3 56.7 + - - +
565A LEU* 3.3 5.4 + - + +
566A CYS* 2.9 28.8 + - - +
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Residues in contact with ARG 563 (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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445A GLU* 3.8 15.3 - - - +
559A LEU 3.8 1.4 + - - +
560A PRO* 3.0 17.3 + - + +
562A LEU* 1.3 79.0 - - - +
564A THR* 1.3 56.8 + - - +
566A CYS* 3.1 4.7 + - - +
567A THR* 3.0 41.0 + - - +
601A RPG 3.9 59.7 + - + +
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Residues in contact with THR 564 (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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560A PRO 4.0 4.5 + - - -
561A GLU* 3.4 12.1 + - - -
562A LEU 3.4 0.2 - - - -
563A ARG* 1.3 76.7 - - - +
565A LEU* 1.3 59.7 + - + +
567A THR* 3.2 9.1 + - - -
568A GLN* 3.0 51.8 + - + +
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Residues in contact with LEU 565 (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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448A VAL* 3.8 23.1 - - + -
482A TRP* 2.8 33.1 + - - +
485A SER* 3.6 42.4 - - - +
486A ILE* 4.1 7.2 - - + +
489A PHE* 3.5 40.6 - - + -
561A GLU* 3.5 18.1 + - + +
562A LEU* 3.3 9.6 + - - +
563A ARG 3.3 0.6 - - - -
564A THR* 1.3 77.2 - - - +
566A CYS* 1.3 56.2 + - - +
568A GLN* 3.4 7.4 + - - +
569A GLY 3.1 10.7 + - - -
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Residues in contact with CYS 566 (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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444A LEU* 3.8 23.0 - - + +
445A GLU* 3.7 14.8 - - + +
448A VAL* 5.2 0.2 - - - +
482A TRP* 5.4 0.7 - - - -
562A LEU 2.9 13.6 + - - +
563A ARG 3.1 3.8 + - - +
565A LEU* 1.3 73.6 - - - +
567A THR* 1.3 57.4 + - - +
569A GLY* 3.0 4.2 + - - -
570A LEU* 2.9 26.3 + - - +
601A RPG 1.6 84.4 - - + -
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Residues in contact with THR 567 (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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563A ARG* 3.0 24.2 + - - +
564A THR* 3.6 11.1 - - - -
566A CYS* 1.3 77.1 - - - +
568A GLN* 1.3 58.2 + - + +
570A LEU* 3.3 9.9 + - + +
571A GLN* 2.9 27.9 + - + +
601A RPG 2.8 23.2 + - - +
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Residues in contact with GLN 568 (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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481A GLU* 5.4 0.7 - - - +
482A TRP* 3.5 24.9 - - + +
485A SER* 2.6 37.8 + - - -
564A THR* 3.0 42.1 + - + +
565A LEU* 3.8 5.9 - - - +
566A CYS 3.2 0.2 - - - -
567A THR* 1.3 76.7 - - - +
569A GLY* 1.3 61.5 + - - +
571A GLN* 3.5 20.5 + - - +
572A ARG* 3.2 20.8 + - - +
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Residues in contact with GLY 569 (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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444A LEU* 4.4 2.7 - - - -
482A TRP* 3.4 37.2 - - - -
565A LEU 3.1 7.5 + - - -
566A CYS 3.0 7.7 + - - -
568A GLN* 1.3 72.7 - - - +
570A LEU* 1.3 63.7 + - - +
572A ARG* 3.2 4.5 + - - +
573A ILE* 3.1 32.0 + - - +
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Residues in contact with LEU 570 (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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444A LEU* 4.1 17.4 - - + +
566A CYS 2.9 12.4 + - - +
567A THR* 3.5 11.4 - - + +
569A GLY* 1.3 75.1 - - - +
571A GLN* 1.3 56.4 + - - +
573A ILE* 3.3 3.9 + - + +
574A PHE* 2.8 30.5 + - - +
592A PHE* 3.4 35.2 - - + -
595A THR* 3.9 22.4 - - + -
596A LEU* 5.0 8.1 - - + -
601A RPG 3.7 50.9 - - + +
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Residues in contact with GLN 571 (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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481A GLU* 5.6 1.2 - - - +
567A THR* 2.9 17.6 + - + +
568A GLN* 3.5 19.7 - - - +
570A LEU* 1.3 75.2 - - - +
572A ARG* 1.3 58.9 + - - +
574A PHE* 3.4 12.1 + - + +
575A TYR* 2.9 29.9 + - + +
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Residues in contact with ARG 572 (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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403A ILE* 5.2 0.4 - - - +
406A PHE* 3.9 21.5 - - + -
476A VAL 4.6 0.2 + - - -
477A ARG 3.1 19.4 + - - -
478A GLY 2.8 24.6 + - - -
479A PHE 3.4 19.9 - - - +
480A GLY* 3.6 19.9 - - - +
482A TRP* 4.5 9.2 - - + -
568A GLN 3.2 13.4 + - - +
569A GLY 3.2 8.9 + - - +
571A GLN* 1.3 75.3 - - - +
573A ILE* 1.3 59.3 + - - +
575A TYR* 3.2 26.3 + - - +
576A LEU* 2.9 53.5 + - + +
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Residues in contact with ILE 573 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406A PHE* 4.3 18.6 - - + -
407A TYR* 5.2 3.4 - - + -
410A LEU* 4.1 17.3 - - + -
444A LEU* 4.7 7.6 - - + -
482A TRP* 6.0 0.2 - - + -
569A GLY 3.1 19.8 + - - +
570A LEU* 3.7 8.7 - - - +
572A ARG* 1.3 75.5 - - - +
574A PHE* 1.3 53.7 + - - +
576A LEU* 3.7 6.4 - - - +
577A LYS* 2.8 34.6 + - + +
584A PRO* 4.8 13.2 - - + -
588A ILE* 4.3 13.0 - - + -
592A PHE* 3.6 30.3 - - + -
601A RPG 3.9 28.0 - - + -
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Residues in contact with PHE 574 (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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570A LEU 2.8 17.7 + - - +
571A GLN* 3.4 13.7 - - + +
572A ARG 3.3 0.2 - - - -
573A ILE* 1.3 75.9 - - - +
575A TYR* 1.3 66.7 + + + +
577A LYS* 3.4 3.2 + - - +
578A LEU* 3.0 56.0 + - + +
592A PHE* 3.7 25.3 - + + -
596A LEU* 5.3 5.4 - - + -
598A PHE* 5.6 10.8 - + - -
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Residues in contact with TYR 575 (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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571A GLN* 2.9 19.8 + - + +
572A ARG* 3.5 35.4 - - - +
574A PHE* 1.3 82.5 - + + +
576A LEU* 1.3 57.2 + - + +
578A LEU* 3.2 9.8 + - + +
579A GLU* 2.7 65.7 + - + +
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Residues in contact with LEU 576 (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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403A ILE* 3.9 38.1 - - + -
406A PHE* 3.6 37.9 - - + -
407A TYR* 3.5 18.4 - - + +
478A GLY 4.0 2.2 - - - +
572A ARG* 2.9 55.6 + - - +
573A ILE* 3.8 3.8 - - - +
575A TYR* 1.3 75.5 - - + +
577A LYS* 1.3 57.9 + - - +
579A GLU* 3.3 13.1 + - - +
580A ASP* 2.9 26.3 + - - -
581A LEU 4.5 0.7 + - - -
582A VAL 4.4 5.9 - - - +
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Residues in contact with LYS 577 (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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407A TYR* 4.6 0.6 + - - -
573A ILE* 2.8 22.5 + - + +
574A PHE* 3.8 4.7 - - - +
576A LEU* 1.3 73.6 - - - +
578A LEU* 1.3 61.6 + - - +
580A ASP* 3.4 19.3 + - - +
583A PRO* 5.6 0.8 - - - +
584A PRO* 4.2 24.7 - - + +
589A ASP* 2.6 39.1 + - - +
592A PHE* 4.1 21.1 - - + -
593A LEU* 4.0 20.6 - - - +
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Residues in contact with LEU 578 (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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574A PHE* 3.0 54.9 + - + +
575A TYR* 3.6 7.6 - - + +
577A LYS* 1.3 73.7 - - - +
579A GLU* 1.3 66.8 + - - +
580A ASP* 3.4 5.5 + - - +
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Residues in contact with GLU 579 (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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398A ASP* 4.8 8.5 - - - +
403A ILE* 3.7 24.9 - - - +
575A TYR* 2.7 47.2 + - + +
576A LEU* 3.7 14.4 - - - +
578A LEU* 1.3 72.8 - - - +
580A ASP* 1.3 67.9 + - - +
581A LEU* 3.2 26.9 + - + +
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Residues in contact with ASP 580 (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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576A LEU 2.9 12.6 + - - -
577A LYS* 3.6 16.8 - - - +
578A LEU 3.2 5.3 - - - +
579A GLU* 1.3 79.8 - - - +
581A LEU* 1.3 64.3 + - - +
582A VAL 3.5 1.6 - - - +
583A PRO* 3.8 26.5 - - - +
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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