Contacts of the helix formed by residues 564 - 585 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562A VAL* 5.6 4.3 - - + -
563A LEU* 1.3 72.0 - - - +
565A PRO* 1.3 61.4 - - + +
566A GLU* 4.3 10.4 - - + +
567A GLU* 2.8 35.2 + - + +
568A LYS* 2.7 32.1 + - - +
611B LYS* 4.3 23.3 - - - +
612B GLU 4.7 9.6 + - - +
613B GLN* 4.1 11.0 - - - +
753B LYS* 4.7 22.2 - - - +
762B GLY* 6.0 0.4 - - - -
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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
----------------------------------------------------------
563A LEU 3.4 6.9 - - - +
564A GLN* 1.3 84.2 - - + +
566A GLU* 1.3 59.6 + - - +
567A GLU 3.3 0.2 - - - -
568A LYS* 4.0 11.4 - - + +
569A LYS* 3.3 28.2 + - - +
753B LYS* 6.0 2.9 - - - +
762B GLY* 4.4 26.7 - - - +
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Residues in contact with GLU 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A GLN* 3.1 8.9 - - + +
565A PRO* 1.3 81.9 - - - +
567A GLU* 1.3 63.9 + - + +
569A LYS* 4.1 9.4 + - - +
570A THR* 3.1 21.3 + - - -
639A PHE* 4.6 7.6 - - - -
641A ARG* 2.8 36.3 + - - +
620B GLN* 6.4 0.4 - - - +
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Residues in contact with GLU 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A GLN* 2.8 26.0 + - + +
566A GLU* 1.3 83.2 - - + +
568A LYS* 1.3 62.4 + - - +
569A LYS 3.2 1.6 - - - -
570A THR* 3.3 7.9 + - - +
571A VAL* 3.2 28.3 + - + +
613B GLN* 2.9 35.0 - - - +
614B TYR* 3.3 23.1 + - + +
615B LEU* 3.1 36.6 + - + +
620B GLN* 4.8 2.4 + - - +
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Residues in contact with LYS 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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563A LEU* 4.3 37.8 - - + +
564A GLN 2.7 19.9 + - - +
565A PRO* 4.3 7.9 - - + -
567A GLU* 1.3 69.5 - - - +
569A LYS* 1.3 60.5 + - - +
571A VAL* 3.7 6.3 + - + +
572A ALA* 3.1 26.0 + - - +
596A ILE* 4.3 21.6 - - + +
598A PRO* 5.7 2.7 - - - +
603A LEU* 5.6 4.0 - - + -
731A LEU* 3.9 17.0 + - + +
734A GLU* 2.5 36.8 + - - -
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Residues in contact with LYS 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A PRO* 3.3 21.5 + - - +
566A GLU* 4.1 11.1 + - - +
567A GLU 3.2 0.4 - - - -
568A LYS* 1.3 78.4 - - - +
570A THR* 1.3 56.8 + - - +
572A ALA* 3.3 7.8 + - + +
573A TYR* 2.9 47.7 + - + +
639A PHE* 3.8 25.8 - - + -
728A LEU* 6.5 0.2 - - - -
731A LEU* 4.2 24.8 - - + +
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Residues in contact with THR 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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566A GLU 3.1 15.6 + - - -
567A GLU* 3.3 10.8 + - - +
568A LYS 3.3 0.6 - - - -
569A LYS* 1.3 75.5 - - - +
571A VAL* 1.3 60.3 + - - +
573A TYR* 3.3 2.3 + - - +
574A HIS* 2.9 27.0 + - - +
635A GLU* 3.8 22.0 - - - +
639A PHE* 3.5 27.7 - - + -
641A ARG* 5.2 2.6 + - - -
643A THR* 4.0 16.8 - - + -
615B LEU* 3.8 20.2 - - + -
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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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567A GLU* 3.2 17.3 + - + +
568A LYS* 3.7 4.9 + - + +
570A THR* 1.3 72.7 - - - +
572A ALA* 1.3 64.2 + - - +
574A HIS* 4.2 8.1 - - + -
575A GLN* 3.2 33.7 + - + +
596A ILE* 3.7 22.2 - - + +
603A LEU* 4.3 41.5 - - + +
604A GLY* 5.7 0.4 - - - -
614B TYR* 6.5 0.2 - - + -
615B LEU* 3.8 22.7 - - + -
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Residues in contact with ALA 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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568A LYS 3.1 16.3 + - - +
569A LYS* 3.4 8.5 - - - +
570A THR 3.2 0.4 - - - -
571A VAL* 1.3 78.7 - - - +
573A TYR* 1.3 65.9 + - + +
576A ALA* 3.3 25.1 + - - +
596A ILE* 3.7 21.2 - - + +
727A ALA* 4.0 7.6 - - + +
730A LEU* 3.8 7.9 - - + +
731A LEU* 3.8 24.7 - - + +
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Residues in contact with TYR 573 (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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569A LYS* 2.9 31.7 + - + +
570A THR 3.3 4.2 + - - +
572A ALA* 1.3 77.0 - - + +
574A HIS* 1.3 63.1 + - - +
576A ALA* 3.9 3.0 - - - +
577A GLY 3.2 10.9 + - - -
634A SER* 2.8 33.0 + - - +
635A GLU* 5.1 2.0 - - + -
638A PHE* 3.4 36.1 - + + -
639A PHE* 3.4 36.8 - + + -
724A GLU* 3.1 33.7 + - - -
727A ALA* 3.5 26.9 - - + -
728A LEU* 4.5 11.7 - - + +
731A LEU* 5.8 2.0 - - + -
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Residues in contact with HIS 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A THR 2.9 11.9 + - - +
571A VAL* 3.9 10.1 - - + +
572A ALA 3.2 0.2 - - - -
573A TYR* 1.3 77.7 - - - +
575A GLN* 1.3 73.4 + - - +
576A ALA 3.3 0.5 + - - -
577A GLY 3.3 8.1 + - - -
578A HIS* 3.0 29.3 + + - -
631A GLY* 3.3 28.0 - - - -
632A ARG 3.9 3.6 - - - -
635A GLU* 3.2 26.8 + - - +
645A GLY* 4.3 9.3 + - - -
646A ALA* 4.2 18.2 - - + -
649A ASP* 2.7 13.5 + - - -
801A ZN 2.2 34.1 - - - -
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Residues in contact with GLN 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 VAL* 3.2 25.6 + - + +
574A HIS* 1.3 83.0 - - + +
576A ALA* 1.3 59.2 + - - +
578A HIS* 3.9 10.4 + - - +
579A ALA* 3.5 18.4 + - - +
594A VAL* 3.8 25.7 - - + +
595A SER 4.7 0.4 - - - +
596A ILE* 4.0 13.5 - - + -
604A GLY 5.7 1.7 - - - -
605A TYR* 3.4 15.3 - - - +
606A ALA* 3.3 29.4 - - - +
608A TYR* 5.1 0.9 + - - -
730A LEU* 4.0 8.1 - - + -
801A ZN 3.8 23.2 - - - -
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Residues in contact with ALA 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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572A ALA 3.3 18.6 + - - +
573A TYR* 4.2 2.9 - - - +
574A HIS 3.2 0.4 - - - -
575A GLN* 1.3 76.7 - - - +
577A GLY* 1.3 58.9 + - - +
578A HIS 3.2 1.6 - - - -
579A ALA* 3.6 6.6 - - - +
580A VAL* 2.9 33.8 + - - +
723A VAL* 4.4 8.7 - - + +
726A VAL* 4.3 9.6 - - + -
727A ALA* 3.7 31.2 - - + +
730A LEU* 4.6 4.7 - - + -
736A LEU* 5.8 0.2 - - - -
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Residues in contact with GLY 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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573A TYR 3.2 11.1 + - - -
574A HIS 3.3 2.4 + - - -
576A ALA* 1.3 73.9 - - - +
578A HIS* 1.3 63.0 + - - +
580A VAL* 5.1 1.1 - - - -
581A ALA* 3.3 27.4 + - - +
630A GLY 3.6 24.5 - - - +
634A SER* 3.8 15.6 + - - -
716A LEU* 4.3 5.1 - - - +
723A VAL* 4.5 4.9 - - - -
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Residues in contact with HIS 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 HIS* 3.0 27.1 + + - -
575A GLN* 3.9 13.3 + - - +
576A ALA 3.2 0.4 - - - -
577A GLY* 1.3 78.8 - - - +
579A ALA* 1.3 57.6 + - - +
582A GLY* 3.0 25.1 + - - -
608A TYR* 3.3 23.2 + + - +
627A MET* 3.2 41.3 - - - +
628A THR* 2.9 22.1 + - + -
631A GLY* 3.5 14.1 - - - -
649A ASP* 3.1 15.5 + - - -
801A ZN 2.8 29.3 - - - -
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Residues in contact with ALA 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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575A GLN 3.5 13.0 + - - +
576A ALA* 3.2 12.0 + - - +
578A HIS* 1.3 77.3 - - - +
580A VAL* 1.3 65.3 + - - +
582A GLY* 3.4 7.2 + - - -
583A TRP* 3.3 18.9 + - - +
591A LEU* 3.7 29.9 - - + +
594A VAL* 4.6 9.4 - - + -
608A TYR* 4.9 3.8 - - - -
726A VAL* 4.4 7.9 - - + -
736A LEU* 5.1 2.2 - - + -
741A MET* 4.1 10.4 - - + +
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Residues in contact with VAL 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 ALA 2.9 19.5 + - - +
579A ALA* 1.3 75.9 - - - +
581A ALA* 1.3 59.0 + - - +
583A TRP* 3.1 23.9 + - - +
584A TYR* 3.3 33.5 + - + -
716A LEU* 4.2 7.0 - - + -
719A LYS* 4.6 2.5 - - + +
722A ASP* 3.7 28.7 - - + +
723A VAL* 3.7 30.1 - - + -
726A VAL* 3.8 20.2 - - + -
741A MET* 4.9 1.3 - - - -
745A LEU* 4.4 4.9 - - + -
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Residues in contact with ALA 581 (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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577A GLY 3.3 19.9 + - - +
578A HIS 4.6 0.7 - - - +
580A VAL* 1.3 79.3 - - - +
582A GLY* 1.3 55.4 + - - +
583A TRP 3.2 2.6 + - - -
584A TYR 4.3 0.4 - - - -
585A LEU* 3.3 31.9 + - + +
626A CYS 4.4 16.6 - - - +
627A MET* 4.5 5.4 - - - +
630A GLY* 4.6 2.2 - - - -
712A THR* 4.7 2.0 - - + -
715A LEU* 4.0 17.3 - - + -
716A LEU* 3.9 21.7 - - + +
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Residues in contact with GLY 582 (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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578A HIS 3.0 19.7 + - - -
579A ALA 3.6 4.0 - - - +
580A VAL 3.2 0.6 - - - -
581A ALA* 1.3 76.2 - - - +
583A TRP* 1.3 60.8 + - - +
584A TYR 3.9 0.2 - - - -
585A LEU 4.9 1.6 - - - -
588A ALA* 4.2 11.7 - - - -
589A ASP 3.4 20.7 - - - +
590A PRO* 4.3 6.2 - - - +
591A LEU* 5.0 2.7 + - - +
608A TYR* 5.9 2.1 - - - -
627A MET* 3.7 16.1 - - - +
748A ARG* 4.5 5.7 + - - -
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Residues in contact with TRP 583 (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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579A ALA 3.3 10.8 - - - +
580A VAL* 3.1 13.6 + - - +
582A GLY* 1.3 79.0 - - - +
584A TYR* 1.3 90.6 + + - +
585A LEU 3.6 0.7 - - - -
590A PRO* 5.5 4.0 - - + -
591A LEU* 4.5 18.2 - - + -
738A LYS* 4.4 19.3 - - + -
741A MET* 3.7 39.0 - - + -
742A VAL* 3.7 18.8 - - + -
745A LEU* 4.0 21.5 + - + +
746A GLY 3.5 26.0 + - - -
747A PRO 4.3 1.8 + - - -
748A ARG* 3.5 63.7 + - + +
749A PRO* 4.1 3.5 - - + +
750A PHE* 4.9 0.5 - - - -
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Residues in contact with TYR 584 (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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580A VAL* 3.3 24.2 + - + +
583A TRP* 1.3 105.6 - + - +
585A LEU* 1.3 62.2 + - - +
715A LEU* 4.1 22.0 - - + +
719A LYS* 3.6 42.0 + - + -
722A ASP* 2.7 33.7 + - - -
745A LEU* 3.9 19.3 + - + +
749A PRO* 4.6 16.1 - - + +
750A PHE* 3.3 20.9 - - - -
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Residues in contact with LEU 585 (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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581A ALA* 3.3 23.8 + - + +
583A TRP 3.6 1.1 + - - -
584A TYR* 1.3 81.2 + - - +
586A GLU* 1.3 61.3 + - - +
587A HIS 3.7 0.4 - - - -
588A ALA* 4.0 13.8 + - + +
623A ASP* 4.1 19.7 - - - +
626A CYS* 3.7 33.9 - - + +
627A MET* 5.1 0.2 - - + -
711A ARG* 3.8 33.2 - - + +
712A THR* 6.2 0.9 - - + -
715A LEU* 3.8 26.9 - - + -
748A ARG* 3.0 23.4 + - - -
750A PHE* 3.8 1.8 - - - -
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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