Contacts of the helix formed by residues 496 - 530 (chain A) in PDB entry 1G50
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 THR 496 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A GLY 5.6 0.2 - - - +
495A LEU* 1.3 74.0 - - - +
497A LEU* 1.3 57.8 + - - +
498A GLN* 2.9 12.0 + - + +
499A GLN* 2.5 63.5 + - + +
500A GLN* 2.4 33.3 + - - +
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Residues in contact with LEU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A THR* 1.3 73.6 - - - +
498A GLN* 1.3 58.4 + - - +
500A GLN* 2.8 37.4 + - - +
501A HIS* 2.9 31.1 + - + +
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Residues in contact with GLN 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A THR* 2.9 8.7 + - - +
497A LEU* 1.3 79.6 - - - +
499A GLN* 1.3 62.1 + - + +
501A HIS* 3.2 17.1 + - - +
502A GLN* 2.9 59.1 + - + +
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Residues in contact with GLN 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A GLY 4.0 2.8 - - - +
495A LEU* 2.9 33.4 - - + +
496A THR* 2.5 58.9 + - + +
498A GLN* 1.3 74.0 - - + +
500A GLN* 1.3 63.9 + - - +
502A GLN* 3.7 10.4 - - - +
503A ARG* 2.8 28.8 + - - +
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Residues in contact with GLN 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A ILE* 3.4 50.6 - - + +
490A MET* 3.7 29.0 - - + +
491A ALA* 3.9 16.7 - - - +
495A LEU* 3.1 15.7 + - + -
496A THR 2.4 36.5 + - - +
497A LEU* 2.8 24.3 + - - +
499A GLN* 1.3 79.3 - - - +
501A HIS* 1.3 64.8 + - + +
503A ARG 3.6 0.2 + - - -
504A LEU* 3.3 12.1 + - - +
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Residues in contact with HIS 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A ILE* 4.9 4.0 - - + -
497A LEU* 2.9 35.2 + - + +
498A GLN* 3.4 19.5 - - - +
500A GLN* 1.3 76.9 - - + +
502A GLN* 1.3 57.8 + - + +
503A ARG 2.7 1.2 + - - -
504A LEU* 2.7 35.2 + - - +
505A ALA* 3.1 9.4 + - - +
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Residues in contact with GLN 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A GLN* 2.9 52.5 + - + +
499A GLN* 3.8 10.6 - - - +
501A HIS* 1.3 80.6 - - + +
503A ARG* 1.3 53.5 + - - +
505A ALA* 3.5 9.5 - - - +
506A GLN* 2.5 43.0 + - - +
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Residues in contact with ARG 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A MET* 2.6 48.3 + - - +
439A ASN* 3.2 19.4 + - - +
440A LEU* 4.0 3.3 - - - +
441A GLN* 4.4 2.4 - - - +
444A GLU* 2.7 39.2 + - - -
490A MET* 3.4 22.8 - - - +
495A LEU* 4.5 11.9 - - + +
499A GLN 2.8 19.5 + - - +
501A HIS 2.7 4.8 + - - -
502A GLN* 1.3 68.7 - - - +
504A LEU* 1.3 65.3 + - - +
505A ALA 3.1 1.3 - - - -
506A GLN* 3.2 9.9 + - - +
507A LEU* 2.9 38.7 + - + +
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Residues in contact with LEU 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A THR* 4.0 28.3 - - + +
486A LEU* 3.8 38.4 - - + -
487A ILE* 4.1 13.5 - - + -
490A MET* 4.4 6.4 - - + +
500A GLN 3.3 9.4 + - - +
501A HIS* 2.7 17.5 + - - +
503A ARG* 1.3 74.4 - - - +
505A ALA* 1.3 66.7 + - - +
507A LEU* 3.5 6.1 + - - +
508A LEU* 3.1 43.2 + - + +
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Residues in contact with ALA 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A HIS 3.1 5.3 + - - +
502A GLN* 3.5 14.6 - - - +
503A ARG 3.1 0.2 - - - -
504A LEU* 1.3 80.5 - - - +
506A GLN* 1.3 68.1 + - + +
507A LEU 2.7 2.6 + - - -
508A LEU* 2.8 15.0 + - - -
509A LEU* 2.9 27.2 + - + -
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Residues in contact with GLN 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A ARG* 3.4 32.4 + - - +
438A MET* 3.3 27.6 - - + +
502A GLN* 2.5 38.2 + - - +
503A ARG* 3.5 6.5 - - - +
505A ALA* 1.3 76.7 - - + +
507A LEU* 1.3 64.0 + - - +
509A LEU* 3.9 11.6 + - + +
510A ILE* 3.3 22.9 + - - +
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Residues in contact with LEU 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A PHE* 5.6 2.0 - - + -
438A MET* 4.4 9.4 - - + -
440A LEU* 3.3 34.1 - - + -
444A GLU* 4.2 14.6 - - + +
448A LEU* 3.7 27.8 - - + +
486A LEU* 5.0 17.5 - - + -
490A MET* 5.0 4.3 - - + -
503A ARG* 2.9 42.7 + - + +
504A LEU* 3.6 8.5 - - - +
505A ALA 2.7 3.2 + - - -
506A GLN* 1.3 71.3 - - - +
508A LEU* 1.3 69.1 + - + +
510A ILE* 2.8 27.8 + - - +
511A LEU* 3.5 8.4 + - - +
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Residues in contact with LEU 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A LEU* 4.6 4.7 - - + -
451A ILE* 4.5 23.3 - - + -
483A THR* 5.7 3.1 - - - +
486A LEU* 5.3 0.4 - - + -
504A LEU* 3.2 43.1 - - + +
505A ALA* 2.8 9.9 + - - +
507A LEU* 1.3 76.5 - - + +
509A LEU* 1.3 55.3 + - + +
511A LEU* 2.7 53.4 + - + +
512A SER* 3.6 1.7 + - - -
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Residues in contact with LEU 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A ALA* 2.9 35.0 + - + +
506A GLN* 3.9 9.9 - - + +
508A LEU* 1.3 74.2 - - + +
510A ILE* 1.3 65.7 + - - +
512A SER* 2.8 27.2 + - - -
513A HIS* 3.7 1.0 + - - +
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Residues in contact with ILE 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A THR* 3.8 18.2 - - + -
434A ARG* 3.7 33.4 - - + +
435A PHE* 3.2 33.9 - - + -
438A MET* 4.5 6.7 - - - -
506A GLN 3.3 17.0 - - - +
507A LEU* 2.8 12.9 + - - +
509A LEU* 1.3 76.6 - - - +
511A LEU* 1.3 56.0 + - + +
513A HIS* 2.4 38.7 + - + +
514A ILE* 2.9 29.2 + - + -
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Residues in contact with LEU 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLU* 4.2 2.8 - - - +
435A PHE* 5.6 0.2 - - + -
448A LEU* 4.0 33.9 - - + -
451A ILE* 3.8 28.3 - - + -
452A ILE* 4.4 17.9 - - + -
507A LEU 3.6 9.2 - - - +
508A LEU* 2.7 34.8 + - + +
510A ILE* 1.3 73.2 - - + +
512A SER* 1.3 53.7 + - - -
514A ILE* 3.2 27.7 + - + +
515A ARG* 2.8 28.1 + - - +
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Residues in contact with SER 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A LEU 3.6 1.6 + - - -
509A LEU* 2.8 17.5 + - - -
510A ILE 2.7 2.0 + - - -
511A LEU* 1.3 75.9 - - - +
513A HIS* 1.3 62.7 + - - +
515A ARG* 3.1 10.9 - - - +
516A HIS* 2.8 28.2 + - - +
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Residues in contact with HIS 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A MET* 3.8 25.8 - - + +
430A ALA* 5.0 6.5 - - + -
431A THR* 3.4 28.1 + - - +
509A LEU 3.7 0.4 + - - +
510A ILE* 2.4 28.3 + - + +
512A SER* 1.3 78.2 + - - +
514A ILE* 1.3 49.0 + - - +
516A HIS* 3.1 18.1 + + - +
517A MET* 2.7 49.0 + - + +
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Residues in contact with ILE 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLU* 3.5 37.5 - - + +
388A MET* 5.0 3.5 - - + +
389A ILE* 4.6 24.9 - - + +
431A THR* 4.6 3.6 - - + -
435A PHE* 4.8 5.2 - - + -
452A ILE* 4.3 9.0 - - + -
510A ILE* 2.9 21.5 + - + +
511A LEU* 3.3 35.9 - - + +
512A SER 3.1 0.2 - - - -
513A HIS* 1.3 74.4 - - - +
515A ARG* 1.3 55.9 + - - +
517A MET* 2.9 22.1 + - + +
518A SER* 2.6 36.9 + - - -
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Residues in contact with ARG 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A CYS* 4.5 8.6 + - - -
385A GLU* 3.4 22.7 + - - +
455A ASN* 5.2 5.7 - - - +
456A SER* 3.0 44.8 + - - +
457A GLY 3.5 8.7 - - - +
511A LEU 2.8 13.2 + - - +
512A SER* 3.1 15.3 - - - +
514A ILE* 1.3 75.9 - - - +
516A HIS* 1.3 58.4 + - - +
518A SER* 3.6 1.9 + - - -
519A ASN* 3.0 47.7 + - - +
----------------------------------------------------------
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Residues in contact with HIS 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A MET* 4.1 21.8 - - - -
512A SER 2.8 13.0 + - - +
513A HIS* 3.1 21.8 - + - +
514A ILE 2.9 0.2 - - - -
515A ARG* 1.3 74.2 - - - +
517A MET* 1.3 68.0 + - - +
519A ASN* 3.0 14.0 + - - +
520A LYS* 3.0 54.2 + - + +
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Residues in contact with MET 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A MET* 3.4 21.6 - - + +
392A VAL* 5.1 0.9 - - + -
424A ILE* 5.1 0.2 - - - +
427A MET* 3.2 63.3 - - + +
428A LEU* 3.5 25.1 - - + -
431A THR* 3.2 24.0 - - + +
513A HIS* 2.7 22.4 + - + +
514A ILE* 3.5 33.4 - - + +
516A HIS* 1.3 70.7 - - - +
518A SER* 1.3 55.4 + - - +
520A LYS* 3.1 1.6 + - - +
521A GLY 2.7 32.4 + - - -
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Residues in contact with SER 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A CYS 5.6 1.0 + - - -
382A ALA 5.4 0.2 - - - -
384A LEU* 3.3 17.5 - - - +
385A GLU* 3.0 50.9 + - - +
388A MET* 3.8 11.8 - - - -
514A ILE 2.6 15.2 + - - -
515A ARG* 3.6 5.6 - - - -
517A MET* 1.3 73.4 - - - +
519A ASN* 1.3 63.4 + - - +
522A MET* 3.1 27.6 + - - +
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Residues in contact with ASN 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A ARG* 3.0 39.5 + - - +
516A HIS* 3.0 14.4 + - - +
518A SER* 1.3 79.5 - - - +
520A LYS* 1.3 71.8 + - + +
522A MET* 3.3 7.7 + - - +
523A GLU* 3.2 21.2 + - - +
547A HIS* 5.7 4.3 - - - -
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Residues in contact with LYS 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLU* 6.1 1.3 - - - +
424A ILE* 4.5 8.2 - - + +
427A MET* 4.1 17.0 - - + -
516A HIS* 3.0 47.1 + - + +
517A MET 3.6 5.2 - - - +
519A ASN* 1.3 76.7 - - + +
521A GLY* 1.3 68.8 + - - +
523A GLU* 2.9 29.9 + - - +
524A HIS* 3.0 10.9 + - - +
----------------------------------------------------------
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Residues in contact with GLY 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A LEU* 3.9 7.2 - - - -
388A MET* 4.8 0.7 - - - -
424A ILE* 3.8 21.4 - - - +
517A MET 2.7 19.5 + - - -
518A SER 4.0 0.9 - - - -
520A LYS* 1.3 71.3 - - - +
522A MET* 1.3 53.5 + - - +
524A HIS* 2.7 24.8 + - - +
525A LEU* 2.9 13.2 + - - +
600A EST 4.0 16.6 - - - +
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Residues in contact with MET 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A CYS 5.7 0.4 - - - +
383A TRP* 3.7 20.6 - - + +
384A LEU* 3.4 33.5 - - + +
518A SER* 3.1 15.0 + - - +
519A ASN* 3.3 12.8 - - - +
520A LYS 3.2 0.2 - - - -
521A GLY* 1.3 74.8 - - - +
523A GLU* 1.3 62.4 + - - +
525A LEU* 3.3 6.0 + - - +
526A TYR* 3.0 24.1 + - - +
544A LEU* 3.7 21.7 - - + +
547A HIS* 3.5 45.3 - - + +
549A LEU* 3.7 19.3 - - + -
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Residues in contact with GLU 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ASN 3.2 11.4 + - - +
520A LYS* 2.9 26.7 + - - +
522A MET* 1.3 79.3 - - - +
524A HIS* 1.3 65.2 + - - +
526A TYR* 3.3 6.1 + - - +
527A SER* 3.2 18.9 + - - -
549A LEU* 3.1 33.1 - - - +
550A HIS* 3.9 21.9 - - - +
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Residues in contact with HIS 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A MET* 4.1 4.9 - - + -
418A VAL* 4.1 0.2 - - - +
419A GLU 3.0 27.6 + - - -
420A GLY* 3.7 18.6 - - - -
421A MET* 3.7 24.3 - - - +
424A ILE* 3.8 18.2 - - + -
520A LYS 3.0 5.5 + - - +
521A GLY 2.7 15.3 + - - +
523A GLU* 1.3 69.8 - - - +
525A LEU* 1.3 54.0 + - - +
527A SER* 2.3 42.0 + - - -
528A MET* 3.0 35.5 + - + +
600A EST 2.7 27.9 + - + -
----------------------------------------------------------
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Residues in contact with LEU 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A MET* 5.0 1.3 - - - -
347A THR* 4.4 22.0 - - + -
383A TRP* 4.3 10.3 - - + -
521A GLY 2.9 12.9 + - - +
522A MET* 3.7 9.9 - - - +
524A HIS* 1.3 75.2 + - - +
526A TYR* 1.3 63.3 + - - +
528A MET* 3.0 7.3 + - + +
529A LYS* 3.0 22.5 + - + +
534A VAL* 4.4 13.2 - - + -
540A LEU* 4.0 34.3 - - + -
544A LEU* 4.3 19.1 - - + -
600A EST 3.5 38.4 - - + +
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Residues in contact with TYR 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A MET 3.0 17.8 + - - +
523A GLU* 3.7 7.6 - - - +
525A LEU* 1.3 77.3 - - - +
527A SER* 1.3 58.2 + - - +
529A LYS* 3.8 29.6 - - - +
530A CYS* 3.2 41.1 + - - +
544A LEU* 4.0 17.7 - - + +
545A ASP* 5.8 1.3 - - - -
548A ARG* 6.3 0.4 - - - -
549A LEU* 3.1 48.9 + - + -
550A HIS* 4.1 30.9 + + - -
----------------------------------------------------------
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Residues in contact with SER 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A GLU 3.2 10.5 + - - -
524A HIS* 2.3 35.7 + - - -
526A TYR* 1.3 72.5 - - - +
528A MET* 1.3 71.0 + - - +
529A LYS 3.1 1.6 - - - -
530A CYS* 3.3 12.3 + - - +
531A LYS* 3.0 33.3 + - - +
----------------------------------------------------------
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Residues in contact with MET 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLU* 4.4 16.8 - - - +
343A MET* 4.0 18.4 - - + -
418A VAL* 3.6 17.0 - - + -
419A GLU* 3.9 19.5 - - + +
524A HIS* 3.0 40.2 + - + +
525A LEU* 3.6 5.4 - - - +
527A SER* 1.3 89.2 + - - +
529A LYS* 1.3 61.5 + - - +
531A LYS* 3.2 42.7 + - + +
533A VAL* 3.4 16.0 + - + +
534A VAL* 3.1 22.8 - - + +
----------------------------------------------------------
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Residues in contact with LYS 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A LEU* 3.0 15.2 + - + +
526A TYR* 3.8 28.3 - - - +
528A MET* 1.3 75.1 - - - +
530A CYS* 1.3 58.9 + - - +
531A LYS 2.7 15.8 + - - -
532A ASN* 3.0 17.0 + - - +
534A VAL* 3.2 26.2 - - + +
541A LEU* 3.3 28.5 - - + +
544A LEU* 3.8 23.7 - - + +
545A ASP* 3.9 18.0 + - - -
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Residues in contact with CYS 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A TYR* 3.2 38.6 + - + +
527A SER* 3.3 10.2 + - - +
529A LYS* 1.3 82.2 - - - +
531A LYS* 1.3 61.9 + - - +
532A ASN* 3.6 6.9 + - - +
----------------------------------------------------------
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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