Contacts of the strand formed by residues 547 - 571 (chain A) in PDB entry 5C58
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 547 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525A LEU* 3.6 11.9 - - - -
543A LEU 3.3 12.0 + - - -
544A THR 3.9 6.6 + - - +
545A GLY 5.2 0.9 - - - -
546A CYS* 1.3 78.3 + - - +
548A THR* 1.3 69.8 + - - +
666A LEU* 5.6 0.9 - - - -
62B ASN* 2.7 42.4 + - - +
63B GLN* 4.1 5.9 + - - -
64B VAL* 3.7 13.3 - - - +
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Residues in contact with THR 548 (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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523A PRO* 4.0 0.7 - - - +
524A ASP* 2.7 39.9 + - - +
526A ALA* 2.7 30.4 + - + +
527A LYS* 4.4 13.3 - - - +
546A CYS 4.6 0.2 - - - -
547A SER* 1.3 82.3 + - - +
549A THR* 1.3 76.2 + - + +
550A THR* 3.5 4.7 + - - +
63B GLN* 3.2 11.3 + - - +
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Residues in contact with THR 549 (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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521A SER* 4.4 12.6 - - - -
522A TYR 3.9 8.0 + - - -
548A THR* 1.3 82.7 - - + +
550A THR* 1.3 64.5 + - - +
551A ARG* 3.9 3.1 + - - +
63B GLN* 3.1 23.4 - - - +
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Residues in contact with THR 550 (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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520A LEU 3.8 1.0 - - - +
521A SER* 3.3 7.2 - - - -
522A TYR* 3.0 68.4 + - + +
524A ASP* 2.9 32.5 + - - +
526A ALA* 4.7 6.4 - - - +
531A ARG* 5.3 2.5 - - - +
548A THR* 3.5 4.5 + - - +
549A THR* 1.3 73.7 - - - +
551A ARG* 1.3 69.1 + - - +
552A GLU* 5.0 2.0 - - + -
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Residues in contact with ARG 551 (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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518A THR 4.8 0.6 - - - -
519A GLY* 3.2 21.2 - - - +
520A LEU* 3.3 12.8 - - - +
521A SER* 3.2 23.6 + - - +
549A THR* 3.9 3.8 + - - +
550A THR* 1.3 78.9 - - - +
552A GLU* 1.3 83.2 + - - +
553A ASP* 2.5 38.3 + - - +
599A ASN* 5.5 3.8 - - - +
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Residues in contact with GLU 552 (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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519A GLY* 3.5 3.1 - - - -
520A LEU* 3.2 24.6 + - + +
522A TYR* 3.5 28.6 + - + +
550A THR* 4.1 2.1 - - + -
551A ARG* 1.3 87.7 + - - +
553A ASP* 1.3 64.6 + - - +
554A TRP* 3.2 48.5 + - + +
664A PRO* 5.7 2.6 - - - +
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Residues in contact with ASP 553 (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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518A THR 3.9 2.6 - - - +
519A GLY* 4.4 0.9 - - - -
551A ARG* 2.5 45.7 + - - +
552A GLU* 1.3 78.3 - - - +
554A TRP* 1.3 70.7 + - - +
555A ASP 4.2 0.9 + - - -
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Residues in contact with TRP 554 (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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517A GLN* 3.5 7.4 - - - +
518A THR* 2.7 57.0 + - + +
519A GLY* 4.3 6.7 - - - -
520A LEU* 5.1 6.4 - - + +
552A GLU* 3.2 50.4 + - + +
553A ASP* 1.3 78.1 - - - +
555A ASP* 1.3 61.2 + - - +
556A VAL* 3.7 4.6 + - + -
610A PRO* 5.1 3.8 - - + +
612A PRO* 3.9 28.6 - - + +
613A PHE* 3.5 38.1 - + - -
721A LEU* 5.1 15.2 - - + +
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Residues in contact with ASP 555 (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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516A GLY 4.1 2.0 - - - +
517A GLN* 3.4 29.7 + - + +
553A ASP 4.2 1.2 + - - -
554A TRP* 1.3 72.7 - - - +
556A VAL* 1.3 66.4 + - - +
557A ASP* 3.4 9.7 + - - +
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Residues in contact with VAL 556 (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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514A LEU* 3.8 16.6 - - + +
515A ARG* 3.3 5.7 - - - +
516A GLY 2.8 36.6 + - - +
518A THR* 4.5 5.8 - - + -
554A TRP* 4.5 4.3 - - + -
555A ASP* 1.3 72.9 - - - +
557A ASP* 1.3 62.7 + - - +
558A ARG* 4.0 23.8 - - + +
596A THR* 4.3 10.1 - - + -
597A LEU* 3.6 23.8 - - + -
612A PRO* 3.6 33.0 - - + +
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Residues in contact with ASP 557 (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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513A ARG* 3.5 27.9 + - - +
514A LEU 3.6 2.7 - - - -
515A ARG* 3.4 22.2 - - + +
555A ASP* 3.4 11.1 + - - +
556A VAL* 1.3 75.5 - - - +
558A ARG* 1.3 59.2 + - - +
559A ASP* 4.9 4.1 - - - +
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Residues in contact with ARG 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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512A TYR* 2.7 26.3 + - - +
513A ARG* 3.2 2.9 - - - +
514A LEU* 2.8 60.0 + - + +
556A VAL* 4.0 17.6 - - + +
557A ASP* 1.3 75.1 - - - +
559A ASP* 1.3 64.3 + - - +
560A GLN* 3.8 15.1 - - - +
591A PRO* 4.0 6.0 - - - +
596A THR* 4.8 4.3 - - - -
612A PRO 2.9 27.0 + - - -
613A PHE* 4.5 4.9 - - - +
614A LEU 2.9 27.3 + - - +
615A GLN* 4.8 1.4 - - - +
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Residues in contact with ASP 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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511A ARG* 2.6 38.4 + - - +
512A TYR* 3.1 19.5 - - - +
513A ARG* 3.8 22.5 + - + -
557A ASP* 4.9 4.2 - - - +
558A ARG* 1.3 78.5 - - - +
560A GLN* 1.3 67.1 + - - +
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Residues in contact with GLN 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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511A ARG* 3.5 10.8 - - - +
512A TYR* 3.3 52.2 + - + -
558A ARG* 3.8 12.4 - - - +
559A ASP* 1.3 79.0 - - - +
561A GLY* 1.3 61.3 + - - +
588A TRP* 3.2 24.6 - - + -
616A PRO* 3.5 30.5 - - - +
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Residues in contact with GLY 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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509A TYR* 3.7 21.3 + - - -
510A ASP 3.1 13.5 - - - -
511A ARG* 4.2 1.6 - - - +
560A GLN* 1.3 79.2 - - - +
562A LYS* 1.3 70.6 + - - +
588A TRP* 4.3 4.6 - - - -
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Residues in contact with LYS 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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508A ARG 3.7 0.7 - - - +
509A TYR* 3.9 4.3 - - - -
510A ASP* 3.1 29.7 + - - +
561A GLY* 1.3 78.6 - - - +
563A LEU* 1.3 76.7 + - - +
564A SER* 3.6 7.1 + - - +
588A TRP* 3.4 53.3 - - + +
618A ARG* 4.4 31.9 - - + +
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Residues in contact with LEU 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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507A LEU* 3.9 40.6 - - + -
508A ARG 3.3 24.5 - - - +
509A TYR* 3.9 20.2 - - + +
562A LYS* 1.3 86.4 - - - +
564A SER* 1.3 63.6 + - - +
565A PRO* 4.1 6.5 - - + +
586A LYS* 5.6 1.7 - - - +
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Residues in contact with SER 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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507A LEU* 3.3 5.1 - - - -
508A ARG* 2.8 57.3 + - - +
510A ASP* 4.6 0.2 + - - -
562A LYS* 3.6 9.5 + - - +
563A LEU* 1.3 80.1 + - - +
565A PRO* 1.3 65.2 - - - +
566A THR* 4.4 3.2 + - - -
586A LYS* 3.2 26.3 + - - +
587A SER* 4.5 0.4 - - - -
588A TRP* 4.0 18.4 - - - +
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Residues in contact with PRO 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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506A GLY 3.6 5.8 - - - +
507A LEU* 4.3 6.3 - - + -
563A LEU* 4.1 6.3 - - + +
564A SER* 1.3 83.9 - - - +
566A THR* 1.3 66.5 + - - +
567A LEU* 5.8 5.2 - - + -
584A TYR* 5.1 7.9 - - + -
585A GLY* 3.3 2.2 - - - -
586A LYS* 3.0 71.1 + - + +
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Residues in contact with THR 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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212A THR* 5.0 8.1 - - - +
213A THR* 4.4 6.1 + - - -
214A GLY* 4.0 29.5 + - - +
504A GLU* 5.5 4.5 - - + -
505A GLY* 3.3 4.5 - - - -
506A GLY* 2.7 42.4 + - - +
508A ARG* 5.3 1.4 + - - -
564A SER 4.4 3.8 + - - -
565A PRO* 1.3 80.1 + - - +
567A LEU* 1.3 73.1 + - - +
568A ALA* 6.1 0.9 - - + -
583A THR* 6.5 0.4 - - - -
584A TYR 3.5 9.0 - - - +
585A GLY* 4.2 4.8 - - - -
586A LYS 4.9 2.9 + - - -
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Residues in contact with LEU 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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504A GLU 3.6 5.6 - - - +
505A GLY* 3.7 16.8 - - - -
565A PRO* 5.8 4.7 - - + -
566A THR* 1.3 88.0 - - - +
568A ALA* 1.3 62.0 + - - +
569A VAL* 5.7 4.5 - - + -
582A THR 4.8 0.2 - - - -
583A THR* 3.3 4.7 - - - -
584A TYR* 2.7 56.5 + - + +
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Residues in contact with ALA 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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120A PRO* 4.8 13.0 - - + +
121A ARG* 6.1 1.8 - - + -
502A THR* 4.0 1.9 - - - +
503A LEU* 3.7 3.6 - - - +
504A GLU* 2.8 59.8 + - + +
566A THR* 6.1 1.8 - - + -
567A LEU* 1.3 77.7 - - - +
569A VAL* 1.3 67.4 + - - +
582A THR 3.6 4.7 - - - -
583A THR* 3.9 15.9 - - + -
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Residues in contact with VAL 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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120A PRO* 5.4 0.4 - - - -
501A LEU* 5.5 2.2 - - + -
502A THR* 3.8 7.4 - - - +
503A LEU* 3.9 19.5 - - + -
567A LEU* 5.7 3.6 - - + -
568A ALA* 1.3 81.4 - - - +
570A ALA* 1.3 67.0 + - - +
571A VAL* 5.0 9.2 - - + -
581A TYR* 3.1 3.3 - - - +
582A THR* 2.8 47.8 + - - +
583A THR* 5.0 0.2 - - - +
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Residues in contact with ALA 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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120A PRO* 4.0 9.6 - - + -
500A TRP 3.9 0.6 - - - +
501A LEU* 3.7 0.2 - - - -
502A THR* 2.9 48.2 + - - +
569A VAL* 1.3 78.5 - - - +
571A VAL* 1.3 68.9 + - - +
579A GLU* 3.4 21.8 - - - +
580A LEU 3.2 11.9 - - - +
581A TYR* 3.6 12.8 - - + -
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Residues in contact with VAL 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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500A TRP* 3.2 19.3 - - + +
501A LEU* 3.6 24.7 - - + -
569A VAL* 5.0 8.5 - - + -
570A ALA* 1.3 83.2 - - - +
572A ARG* 1.3 69.1 + - - +
573A PRO* 3.8 3.6 - - + +
579A GLU* 3.4 4.2 - - - -
580A LEU* 2.9 48.1 + - + +
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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