Contacts of the helix formed by residues 494 - 531 (chain S) in PDB entry 6CNB
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 494 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625R ARG* 3.4 16.4 - - - +
493S GLY* 1.3 78.6 + - - -
495S VAL* 1.3 58.9 + - - +
496S ALA 3.6 1.1 - - - -
497S ASP* 3.5 30.3 - - + +
498S PHE* 2.5 45.9 + - - +
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Residues in contact with VAL 495 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625R ARG* 3.2 61.7 - - + +
628R ILE* 3.8 18.6 - - + -
629R GLY* 3.5 21.3 - - - +
492S ILE* 3.8 28.9 - - + +
493S GLY 4.1 1.6 - - - +
494S THR* 1.3 70.9 - - - +
496S ALA* 1.3 61.6 + - + +
498S PHE* 3.8 2.3 - - - +
499S ASN* 2.9 33.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA 496 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625R ARG* 3.9 10.8 - - - +
495S VAL* 1.3 81.0 - - + +
497S ASP* 1.3 65.4 + - - +
499S ASN* 3.3 14.5 - - - +
500S GLU* 3.3 22.7 + - - +
----------------------------------------------------------
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Residues in contact with ASP 497 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625R ARG* 5.5 3.3 + - - -
494S THR* 3.5 28.9 - - + +
495S VAL 3.1 0.8 - - - -
496S ALA* 1.3 81.7 - - - +
498S PHE* 1.3 60.1 + - - +
500S GLU* 3.5 4.1 + - - +
501S LYS* 2.9 29.4 + - - +
----------------------------------------------------------
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Residues in contact with PHE 498 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632R ALA* 5.5 9.4 - - + -
633R ASP* 6.1 1.6 - - - -
493S GLY 4.4 3.4 - - - +
494S THR* 2.5 34.3 + - - +
495S VAL* 4.2 1.1 - - - +
497S ASP* 1.3 71.0 - - - +
499S ASN* 1.3 64.9 + - - +
501S LYS* 3.8 24.2 - - + -
502S LEU* 2.9 66.3 + - + +
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Residues in contact with ASN 499 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628R ILE* 3.2 29.2 - - - +
632R ALA* 3.6 26.3 - - - +
635R LEU* 4.7 11.4 - - + +
495S VAL* 2.9 25.9 + - - +
496S ALA* 3.3 19.7 - - - +
498S PHE* 1.3 80.1 - - - +
500S GLU* 1.3 59.6 + - - +
502S LEU* 3.8 2.8 - - - +
503S ILE* 2.9 40.9 + - + +
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Residues in contact with GLU 500 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496S ALA 3.3 12.7 + - - +
497S ASP* 4.3 2.5 - - - +
499S ASN* 1.3 78.8 - - - +
501S LYS* 1.3 57.6 + - - +
503S ILE* 3.6 16.9 - - + +
504S GLU* 2.9 32.9 + - + +
----------------------------------------------------------
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Residues in contact with LYS 501 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497S ASP 2.9 20.5 + - - +
498S PHE* 3.7 23.3 - - + +
499S ASN 3.1 0.2 - - - -
500S GLU* 1.3 76.9 - - - +
502S LEU* 1.3 59.3 + - - +
504S GLU* 3.1 10.3 + - - +
505S LEU* 2.9 25.0 + - + +
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Residues in contact with LEU 502 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632R ALA* 5.3 4.5 - - + +
636R LEU* 3.6 38.6 - - + -
498S PHE* 2.9 56.0 + - + +
499S ASN* 3.9 2.5 - - - +
501S LYS* 1.3 75.2 - - - +
503S ILE* 1.3 56.8 + - + +
505S LEU* 3.2 31.6 + - + +
506S GLN* 2.9 32.5 + - + +
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Residues in contact with ILE 503 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635R LEU* 5.3 9.2 - - + -
639R GLU* 3.1 42.6 - - - +
642R ARG* 5.2 0.4 - - - +
499S ASN* 2.9 33.3 + - + +
500S GLU* 3.6 15.0 - - + +
502S LEU* 1.3 76.8 - - + +
504S GLU* 1.3 57.0 + - - +
506S GLN* 2.9 16.5 + - - +
507S ASN* 2.9 35.4 + - - +
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Residues in contact with GLU 504 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500S GLU* 2.9 22.7 + - + +
501S LYS* 3.1 7.6 + - - +
503S ILE* 1.3 73.6 - - + +
505S LEU* 1.3 61.6 + - - +
507S ASN* 3.1 20.3 + - + +
508S GLU* 2.9 23.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 505 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501S LYS* 2.9 12.4 + - + +
502S LEU* 3.2 32.8 - - + +
503S ILE 3.1 0.2 - - - -
504S GLU* 1.3 73.2 - - - +
506S GLN* 1.3 57.2 + - + +
507S ASN 3.0 4.5 - - - -
508S GLU* 2.8 46.5 + - + +
509S HIS* 2.9 16.3 + - + +
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Residues in contact with GLN 506 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636R LEU* 3.5 18.1 + - + +
639R GLU* 3.4 34.4 - - - +
640R SER* 2.3 45.0 + - - +
643R LEU* 3.3 19.0 - - + +
502S LEU* 2.9 23.7 + - + +
503S ILE* 3.2 13.3 - - - +
505S LEU* 1.3 75.1 - - + +
507S ASN* 1.3 52.1 + - - +
508S GLU 3.3 0.2 - - - -
509S HIS* 4.6 3.8 - - - +
510S LYS* 2.7 35.6 + - - +
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Residues in contact with ASN 507 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642R ARG* 5.6 3.3 + - - -
503S ILE* 2.9 26.9 + - - +
504S GLU* 3.2 25.0 - - + +
505S LEU 3.0 0.4 - - - -
506S GLN* 1.3 78.3 - - - +
508S GLU* 1.3 57.4 + - - +
510S LYS* 3.4 30.4 + - + +
511S HIS* 2.9 28.8 + - - +
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Residues in contact with GLU 508 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504S GLU 2.9 10.1 + - - +
505S LEU* 2.8 33.3 + - + +
507S ASN* 1.3 76.0 - - - +
509S HIS* 1.3 60.1 + - - +
511S HIS* 3.9 3.7 - - - +
512S HIS* 2.9 27.1 + - + +
----------------------------------------------------------
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Residues in contact with HIS 509 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P ARG* 4.4 16.6 + - - -
133P TYR* 5.8 8.1 - + - -
643R LEU* 4.7 7.0 - - + -
505S LEU* 2.9 13.9 + - + +
506S GLN* 4.6 4.5 - - - +
508S GLU* 1.3 74.4 - - - +
510S LYS* 1.3 60.8 + - - +
512S HIS* 3.4 25.6 - + - -
513S MET* 2.9 66.8 + - + +
516S ILE* 6.1 0.4 - - + -
----------------------------------------------------------
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Residues in contact with LYS 510 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642R ARG* 5.2 12.7 - - - +
643R LEU* 3.5 21.1 - - + +
646R GLU* 3.1 36.0 - - - +
506S GLN 2.7 21.5 + - - +
507S ASN* 3.4 28.3 + - + +
508S GLU 3.2 0.2 - - - -
509S HIS* 1.3 73.4 - - - +
511S HIS* 1.3 61.7 + - - +
513S MET* 3.0 6.9 + - - +
514S LYS* 2.9 27.1 + - + +
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Residues in contact with HIS 511 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507S ASN 2.9 21.5 + - - +
508S GLU* 4.1 3.8 + - - +
510S LYS* 1.3 74.5 - - - +
512S HIS* 1.3 56.7 + - - +
514S LYS* 3.4 42.1 + - - +
515S GLU* 2.9 40.0 + - + +
----------------------------------------------------------
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Residues in contact with HIS 512 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508S GLU* 2.9 21.5 + - + +
509S HIS* 3.4 37.0 - + - +
511S HIS* 1.3 79.0 + - - +
513S MET* 1.3 56.9 + - + +
515S GLU* 3.0 19.9 + - - +
516S ILE* 2.9 58.7 + - + +
----------------------------------------------------------
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Residues in contact with MET 513 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P ARG* 4.4 19.5 - - + +
151P TYR* 4.0 21.3 - - + +
643R LEU* 4.7 11.9 - - + -
647R ALA* 3.6 31.4 - - + -
509S HIS* 2.9 56.8 + - + +
510S LYS* 3.0 5.1 + - - +
512S HIS* 1.3 74.4 - - + +
514S LYS* 1.3 60.4 + - - +
516S ILE* 3.9 7.5 - - + +
517S GLU* 2.9 32.5 + - - +
----------------------------------------------------------
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Residues in contact with LYS 514 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646R GLU* 5.1 12.5 + - - +
510S LYS* 2.9 13.0 + - + +
511S HIS* 3.4 44.4 + - - +
513S MET* 1.3 75.5 - - - +
515S GLU* 1.3 57.7 + - - +
517S GLU* 3.6 14.9 - - - +
518S GLU* 2.9 31.6 + - + +
----------------------------------------------------------
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Residues in contact with GLU 515 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511S HIS* 2.9 27.8 + - + +
512S HIS* 3.0 27.2 + - - +
514S LYS* 1.3 75.4 - - - +
516S ILE* 1.3 62.7 + - + +
518S GLU* 2.8 30.8 + - - +
519S ALA* 2.9 14.4 + - + +
----------------------------------------------------------
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Residues in contact with ILE 516 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152P SER* 4.1 35.2 - - - +
153P LEU* 5.3 1.6 - - + +
509S HIS* 6.1 0.2 - - + -
512S HIS* 2.9 52.2 + - + +
513S MET* 4.4 5.8 - - + +
515S GLU* 1.3 78.1 - - + +
517S GLU* 1.3 57.8 + - - +
519S ALA* 3.6 7.2 + - + +
520S LYS* 2.9 27.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU 517 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646R GLU* 5.3 6.8 - - - +
649R ILE* 4.4 18.0 - - - +
650R ALA* 4.7 16.8 - - + +
513S MET 2.9 22.1 + - - +
514S LYS* 3.6 15.9 - - - +
516S ILE* 1.3 79.2 - - - +
518S GLU* 1.3 55.8 + - - +
520S LYS* 3.1 22.0 - - + +
521S ASN* 2.9 36.4 + - - +
----------------------------------------------------------
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Residues in contact with GLU 518 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514S LYS* 2.9 19.1 + - + +
515S GLU* 2.8 20.1 + - - +
517S GLU* 1.3 74.4 - - - +
519S ALA* 1.3 61.3 + - - +
520S LYS 3.0 0.9 - - - -
521S ASN* 2.8 29.1 + - + +
522S THR* 2.9 14.0 + - - +
----------------------------------------------------------
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Residues in contact with ALA 519 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153P LEU* 5.0 3.0 - - - +
515S GLU* 2.9 13.1 + - + +
516S ILE* 4.1 7.4 - - + +
518S GLU* 1.3 76.9 - - - +
520S LYS* 1.3 57.8 + - - +
522S THR* 3.1 31.7 + - - +
523S ALA* 3.3 9.4 + - - +
----------------------------------------------------------
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Residues in contact with LYS 520 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135P LYS* 3.6 11.5 - - - +
151P TYR* 3.4 19.0 + - - -
152P SER 3.2 18.8 - - - +
153P LEU* 3.5 19.7 - - + +
154P GLN* 3.3 46.9 + - + +
650R ALA* 3.4 29.0 - - + +
516S ILE 2.9 15.5 + - - +
517S GLU* 3.1 25.8 - - + +
518S GLU 3.0 0.2 - - - -
519S ALA* 1.3 78.3 - - - +
521S ASN* 1.3 60.2 + - - +
523S ALA* 4.1 2.8 + - - +
524S LYS* 3.5 17.7 + - - +
----------------------------------------------------------
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Residues in contact with ASN 521 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154P GLN* 5.8 2.1 + - - -
517S GLU* 2.9 26.5 + - - +
518S GLU* 2.8 17.0 + - + +
520S LYS* 1.3 79.5 - - - +
522S THR* 1.3 65.8 + - - +
524S LYS* 3.1 38.7 + - + +
525S GLU* 3.3 8.0 + - - +
----------------------------------------------------------
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Residues in contact with THR 522 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518S GLU* 2.9 8.2 + - - +
519S ALA* 3.1 24.3 + - - +
521S ASN* 1.3 75.1 - - - +
523S ALA* 1.3 60.0 + - - +
524S LYS 3.0 0.7 + - - -
525S GLU* 3.0 7.9 + - - +
526S GLU* 2.9 34.0 + - + +
----------------------------------------------------------
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Residues in contact with ALA 523 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102P ARG* 5.1 17.3 - - - +
153P LEU* 5.3 8.7 - - + -
519S ALA 3.3 9.5 + - - +
520S LYS 4.6 3.6 - - - +
522S THR* 1.3 79.1 - - - +
524S LYS* 1.3 57.5 + - - +
525S GLU 3.3 0.2 - - - -
526S GLU* 3.6 21.3 - - + +
527S ASP* 2.9 44.4 + - - +
----------------------------------------------------------
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Residues in contact with LYS 524 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154P GLN* 5.6 10.4 - - - +
233P VAL* 6.1 5.8 - - - -
520S LYS 3.5 14.9 + - - +
521S ASN* 3.1 33.6 + - + +
522S THR 3.0 0.8 - - - -
523S ALA* 1.3 80.1 - - - +
525S GLU* 1.3 60.9 + - - +
527S ASP* 3.8 5.5 + - - +
528S GLN* 3.4 31.4 + - - +
----------------------------------------------------------
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Residues in contact with GLU 525 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521S ASN 3.3 5.3 + - - +
522S THR* 3.0 7.7 + - - +
524S LYS* 1.3 77.7 - - - +
526S GLU* 1.3 66.1 + - - +
527S ASP 3.2 0.4 - - - -
528S GLN* 2.9 24.0 + - + +
529S THR* 2.9 26.3 + - - +
----------------------------------------------------------
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Residues in contact with GLU 526 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522S THR* 2.9 23.5 + - + +
523S ALA* 3.6 21.6 + - + +
525S GLU* 1.3 77.5 - - - +
527S ASP* 1.3 61.7 + - - +
529S THR* 3.1 10.5 + - - +
530S ALA* 2.9 26.6 + - + +
----------------------------------------------------------
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Residues in contact with ASP 527 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102P ARG* 5.6 4.8 + - - -
155P PRO* 4.3 19.4 - - - +
523S ALA* 2.9 29.2 + - - +
524S LYS* 4.0 5.7 - - - +
526S GLU* 1.3 78.4 - - - +
528S GLN* 1.3 62.1 + - - +
530S ALA* 3.0 10.7 + - - +
531S GLN* 2.9 40.3 + - + +
----------------------------------------------------------
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Residues in contact with GLN 528 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233P VAL* 5.0 13.1 - - - +
234P GLU* 3.6 26.9 + - - +
524S LYS* 3.4 27.4 + - - +
525S GLU* 2.9 26.0 + - + +
527S ASP* 1.3 78.2 - - + +
529S THR* 1.3 62.3 + - - +
531S GLN* 3.6 23.1 + - - +
532S ARG* 3.7 21.5 + - - +
----------------------------------------------------------
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Residues in contact with THR 529 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525S GLU* 2.9 18.6 + - - +
526S GLU* 3.4 11.5 - - - -
528S GLN* 1.3 77.6 - - - +
530S ALA* 1.3 63.6 + - - +
532S ARG* 3.3 39.3 + - - +
533S LEU* 4.5 3.3 + - - +
----------------------------------------------------------
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Residues in contact with ALA 530 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526S GLU* 2.9 14.1 + - + +
527S ASP* 3.0 14.7 + - - +
529S THR* 1.3 78.2 - - - +
531S GLN* 1.3 62.3 + - + +
532S ARG 3.1 1.2 + - - -
533S LEU* 3.1 30.5 + - + +
----------------------------------------------------------
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Residues in contact with GLN 531 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156P SER 5.7 2.6 + - - -
158P ASP 6.0 2.0 - - - +
527S ASP* 2.9 26.9 + - + +
528S GLN* 3.9 19.1 - - - +
529S THR 3.3 0.4 - - - -
530S ALA* 1.3 76.4 - - - +
532S ARG* 1.3 57.3 + - - +
533S LEU 3.0 15.0 + - - +
----------------------------------------------------------
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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