Contacts of the helix formed by residues 564 - 592 (chain A) in PDB entry 3H3T
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 PRO 564 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A TRP* 5.8 1.3 - - + -
562A TRP* 3.6 25.3 - - + -
563A ALA* 1.3 85.8 - - + +
565A ALA* 1.3 60.8 + - - +
566A SER* 3.1 12.3 - - - +
567A VAL* 2.8 44.5 + - + +
568A LEU* 3.2 9.5 + - - +
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Residues in contact with ALA 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A GLY 5.9 0.9 - - - +
414A VAL* 3.4 31.9 - - + -
562A TRP* 5.1 2.4 - - - -
563A ALA 3.2 4.6 + - - -
564A PRO* 1.3 71.0 - - - +
566A SER* 1.3 55.5 - - - +
568A LEU* 4.6 2.5 - - - +
569A ARG* 2.9 55.3 + - - +
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Residues in contact with SER 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A PRO* 4.2 8.7 - - - +
565A ALA* 1.3 77.9 - - - +
567A VAL* 1.3 66.7 + - - +
569A ARG* 4.2 5.3 - - - +
570A ALA* 3.2 27.5 + - - +
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Residues in contact with VAL 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A TRP* 3.8 34.1 - - + -
474A PRO* 5.4 2.9 - - + -
564A PRO* 2.8 31.5 + - + +
566A SER* 1.3 85.5 + - - +
568A LEU* 1.3 67.2 + - + +
570A ALA* 3.2 5.7 + - - +
571A VAL* 3.0 26.8 + - + +
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Residues in contact with LEU 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ILE* 5.8 0.7 - - + -
414A VAL* 4.1 30.7 - - + +
473A TRP* 3.5 52.0 - - + -
559A PRO* 4.3 20.6 - - + -
561A GLY 5.2 0.4 - - - +
563A ALA* 3.6 34.5 - - + +
564A PRO 3.2 2.5 + - - +
565A ALA* 4.0 4.9 - - - +
567A VAL* 1.3 78.2 - - - +
569A ARG* 1.3 59.3 + - - +
571A VAL* 3.2 6.9 + - + +
572A ALA* 3.0 28.4 + - - +
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Residues in contact with ARG 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A ARG* 3.3 37.8 + - - +
407A GLU* 3.1 38.2 + - - +
408A VAL 4.1 7.9 + - - +
409A GLU* 5.5 3.2 - - - +
414A VAL* 4.2 13.8 - - + +
416A ASP* 2.6 42.5 + - - +
565A ALA* 2.9 42.9 + - - +
566A SER* 4.2 5.1 - - - +
568A LEU* 1.3 77.4 - - - +
570A ALA* 1.3 57.4 + - - +
572A ALA* 3.5 3.7 + - - +
573A LYS* 3.1 25.3 + - - +
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Residues in contact with ALA 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A SER 3.2 19.8 + - - +
567A VAL* 3.8 6.1 - - - +
568A LEU 3.2 0.4 - - - -
569A ARG* 1.3 76.8 - - - +
571A VAL* 1.3 60.3 + - + +
573A LYS* 3.8 11.6 - - - +
574A ARG* 3.1 30.8 + - - +
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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
----------------------------------------------------------
472A VAL* 3.5 52.9 - - + +
473A TRP* 4.6 12.1 - - + -
567A VAL* 3.0 21.7 + - + +
568A LEU* 3.6 7.0 - - - +
569A ARG 3.2 0.2 - - - -
570A ALA* 1.3 76.5 - - + +
572A ALA* 1.3 65.8 + - - +
574A ARG* 3.2 19.9 + - - +
575A GLU* 2.8 34.5 + - + +
600A 16H 4.2 11.0 - - + -
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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
----------------------------------------------------------
405A ARG* 4.8 6.1 - - - +
416A ASP* 6.6 0.7 - - + -
418A LEU* 4.7 8.6 - - + +
568A LEU 3.0 14.8 + - - +
569A ARG* 3.5 7.4 + - - +
571A VAL* 1.3 75.8 - - - +
573A LYS* 1.3 63.5 + - - +
576A TYR* 3.1 57.9 + - + +
577A PRO* 3.7 0.2 - - - +
600A 16H 5.1 3.8 - - + +
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Residues in contact with LYS 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A VAL* 3.9 41.9 + - + +
396A VAL* 3.9 11.8 - - + +
403A VAL* 6.2 1.6 - - - -
405A ARG* 3.8 28.1 - - - +
569A ARG 3.1 17.5 + - - +
570A ALA* 3.8 11.4 - - - +
572A ALA* 1.3 77.9 - - - +
574A ARG* 1.3 57.9 + - - +
577A PRO* 3.1 25.1 - - - +
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Residues in contact with ARG 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A VAL* 4.3 16.8 + - - +
570A ALA* 3.1 20.4 + - - +
571A VAL* 3.2 27.3 + - - +
573A LYS* 1.3 79.6 - - - +
575A GLU* 1.3 96.9 + - - +
577A PRO* 3.7 1.4 - - - +
578A LYS* 3.5 37.3 + - - +
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Residues in contact with GLU 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A THR* 4.4 3.3 + - - -
448A THR* 3.5 21.2 - - - +
472A VAL* 4.5 10.4 - - + +
571A VAL* 2.8 32.2 + - + +
572A ALA 4.5 0.2 - - - +
574A ARG* 1.3 112.1 + - - +
576A TYR* 1.3 64.2 + - - +
578A LYS* 3.4 25.5 + - - +
579A PHE* 3.0 24.8 + - - +
600A 16H 3.9 26.8 - - + +
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Residues in contact with TYR 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A VAL* 4.9 3.4 - - + -
418A LEU* 3.5 33.2 - - + -
553A TYR* 3.7 39.7 - + - -
555A ALA* 3.8 16.5 - - + +
557A VAL* 3.8 11.3 - - - +
572A ALA* 3.1 41.9 + - + +
575A GLU* 1.3 76.6 - - - +
577A PRO* 1.3 65.3 - - + +
579A PHE* 3.2 11.6 + + - -
580A LEU* 2.9 33.4 + - + +
600A 16H 3.7 52.6 - + + +
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Residues in contact with PRO 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A VAL* 3.8 34.3 - - + -
398A GLU* 5.7 2.2 - - - +
401A MET* 4.1 22.5 - - + +
403A VAL* 4.2 8.7 - - + -
572A ALA 3.7 2.5 - - - +
573A LYS* 3.1 28.0 - - - +
574A ARG 3.7 2.5 - - - +
576A TYR* 1.3 95.9 - - + +
578A LYS* 1.3 61.9 + - - +
580A LEU* 4.0 1.4 - - + +
581A LYS* 3.1 29.4 + - - +
----------------------------------------------------------
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Residues in contact with LYS 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A THR* 4.4 16.8 - - + +
574A ARG* 3.5 32.3 + - - +
575A GLU* 3.4 36.1 + - - +
576A TYR 3.2 0.8 - - - -
577A PRO* 1.3 75.1 - - - +
579A PHE* 1.3 66.4 + - - +
581A LYS* 4.1 4.0 - - - +
582A ARG* 3.2 33.0 + - + +
----------------------------------------------------------
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Residues in contact with PHE 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A PHE* 4.1 3.4 - + - -
445A TRP* 3.6 37.9 - + + -
446A GLU* 5.9 0.4 - - - +
447A THR* 5.9 3.4 - - - +
448A THR* 6.2 0.2 - - + -
527A MET* 4.0 15.0 - - + -
553A TYR* 3.5 44.2 - + - -
575A GLU 3.0 16.4 + - - +
576A TYR* 3.5 11.7 - + - -
578A LYS* 1.3 75.5 - - - +
580A LEU* 1.3 80.2 + - + +
582A ARG* 4.8 4.0 - - - +
583A PHE* 2.7 52.0 + + + +
600A 16H 3.7 32.3 - - + -
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Residues in contact with LEU 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A MET* 3.8 25.6 - - + -
403A VAL* 4.4 3.1 - - + -
420A ALA* 3.6 29.6 - - + -
422A HIS* 4.7 11.9 - - + -
527A MET* 5.3 3.8 - - + -
551A ILE* 5.0 10.5 - - + -
553A TYR* 4.4 20.4 - - + -
576A TYR* 2.9 27.6 + - + +
578A LYS 3.4 0.2 - - - -
579A PHE* 1.3 99.7 - - + +
581A LYS* 1.3 57.3 + - - +
583A PHE* 4.6 2.5 - - + -
584A THR* 2.9 47.5 + - + +
----------------------------------------------------------
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Residues in contact with LYS 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A GLU* 2.8 39.9 + - + +
401A MET* 4.3 12.7 - - + -
422A HIS* 5.3 5.4 - - - +
577A PRO 3.1 17.5 + - - +
578A LYS* 4.1 4.7 - - - +
580A LEU* 1.3 77.3 - - - +
582A ARG* 1.3 59.2 + - - +
584A THR* 3.3 5.1 + - - -
585A SER* 3.0 36.6 + - - +
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Residues in contact with ARG 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ASN 5.6 0.6 + - - -
444A ASP 3.8 14.6 + - - -
445A TRP* 3.0 35.8 + - - +
447A THR* 3.8 26.1 - - - +
578A LYS* 3.2 22.2 + - + +
579A PHE* 4.0 3.1 - - - +
581A LYS* 1.3 76.3 - - - +
583A PHE* 1.3 65.4 + - - +
585A SER* 3.8 4.4 - - - -
586A TYR* 3.1 24.2 + - + +
----------------------------------------------------------
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Residues in contact with PHE 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A VAL* 3.3 43.1 - - + -
435A TYR* 3.9 6.5 - - + -
436A PHE* 3.5 26.5 - + + -
445A TRP* 3.6 41.5 - + + +
527A MET* 3.8 21.8 - - + -
579A PHE* 2.7 39.6 + + + +
580A LEU* 4.1 3.4 - - + +
582A ARG* 1.3 72.2 - - - +
584A THR* 1.3 76.5 + - + +
586A TYR* 3.3 2.9 + + - +
587A VAL* 3.2 35.2 + - + +
----------------------------------------------------------
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Residues in contact with THR 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A HIS* 4.0 17.3 + - + -
424A VAL* 4.0 21.9 - - + +
432A VAL* 5.8 2.0 - - + -
551A ILE* 4.0 27.1 - - + -
580A LEU* 2.9 31.9 + - + +
581A LYS* 3.3 7.6 + - - -
583A PHE* 1.3 85.5 - - + +
585A SER* 1.3 69.1 + - - +
587A VAL* 3.2 8.7 + - - +
588A GLN* 3.1 25.4 + - - +
----------------------------------------------------------
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Residues in contact with SER 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A LYS* 3.0 21.5 + - - +
582A ARG* 3.8 6.1 - - - -
584A THR* 1.3 81.3 + - - +
586A TYR* 1.3 58.0 + - - +
588A GLN* 3.1 19.6 + - - +
589A GLU* 2.9 40.2 + - - +
----------------------------------------------------------
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Residues in contact with TYR 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A TYR* 3.7 23.8 - + - -
441A VAL* 3.6 17.0 - - + +
444A ASP* 2.7 45.8 + - + +
445A TRP* 4.1 32.1 - + + -
582A ARG* 3.1 19.6 + - + +
583A PHE* 3.4 8.3 - + - +
585A SER* 1.3 73.8 - - - +
587A VAL* 1.3 65.9 + - + +
589A GLU* 3.2 14.1 + - + +
590A LYS* 2.9 61.9 + - + +
----------------------------------------------------------
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Residues in contact with VAL 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A VAL* 3.8 20.4 - - + -
431A GLU 4.7 0.7 - - - -
432A VAL* 4.0 24.0 - - + +
435A TYR* 3.5 36.6 - - + -
583A PHE* 3.2 31.4 + - + +
584A THR* 3.2 8.5 + - - +
586A TYR* 1.3 80.8 - - + +
588A GLN* 1.3 63.0 + - - +
590A LYS* 3.2 4.2 + - - +
591A THR* 3.1 38.0 + - + +
----------------------------------------------------------
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Residues in contact with GLN 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A VAL* 3.6 18.0 - - + +
425A LYS* 2.8 27.2 + - - +
427A VAL* 3.7 23.1 - - + -
584A THR* 3.1 12.2 + - - +
585A SER* 3.1 24.9 + - - +
587A VAL* 1.3 77.6 - - - +
589A GLU* 1.3 63.1 + - + +
591A THR* 3.7 1.7 + - - -
592A ALA* 3.2 25.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A SER* 2.9 26.1 + - - +
586A TYR* 3.6 13.6 - - + +
588A GLN* 1.3 77.8 - - + +
590A LYS* 1.3 65.3 + - + +
591A THR 3.3 1.0 + - - -
592A ALA* 3.6 13.7 + - - +
----------------------------------------------------------
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Residues in contact with LYS 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A TYR* 3.6 25.6 + - + +
444A ASP* 4.5 6.9 + - - -
586A TYR* 2.9 56.8 + - + +
587A VAL 4.2 0.9 - - - +
589A GLU* 1.3 79.2 - - + +
591A THR* 1.3 58.9 + - - +
592A ALA 3.6 0.7 - - - -
594A LYS* 3.1 33.2 + - - +
----------------------------------------------------------
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Residues in contact with THR 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A GLY 4.0 1.4 + - - -
427A VAL* 3.9 11.1 - - - +
431A GLU* 3.9 17.3 - - + +
435A TYR* 3.7 26.5 - - + +
544A ARG* 2.9 43.4 + - - -
587A VAL* 3.1 23.3 + - + +
588A GLN 3.7 3.3 + - - -
590A LYS* 1.3 82.2 - - - +
592A ALA* 1.3 67.5 + - - +
594A LYS* 3.2 15.2 + - + -
----------------------------------------------------------
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Residues in contact with ALA 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ARG* 4.4 5.8 - - - +
588A GLN 3.2 17.9 + - - +
589A GLU* 3.6 11.3 + - - +
590A LYS 5.2 0.5 - - - +
591A THR* 1.3 78.3 - - - +
593A GLY* 1.3 58.3 + - - +
594A LYS* 3.1 9.0 + - - +
----------------------------------------------------------
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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