Contacts of the helix formed by residues 587 - 615 (chain F) in PDB entry 6BAA
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 VAL 587 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470F LEU* 4.9 8.1 - - + +
547F ASN* 4.9 16.4 - - + +
550F ILE* 5.9 4.3 - - + -
551F PRO* 3.9 29.8 - - + -
583F PHE 3.4 19.5 - - - +
584F HIS* 4.6 7.9 - - - +
585F ILE 3.0 2.2 + - - -
586F LEU* 1.3 78.9 - - - +
588F THR* 1.3 68.9 + - - +
590F LEU* 3.2 9.3 + - - +
591F PHE* 3.0 28.7 + - + +
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Residues in contact with THR 588 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444F GLN* 6.1 0.4 - - - +
584F HIS 4.9 3.6 + - - -
585F ILE 3.9 7.4 + - - -
587F VAL* 1.3 76.7 - - - +
589F PRO* 1.4 62.6 - - + +
591F PHE* 4.7 3.6 - - - +
592F LEU* 2.8 53.5 + - + +
1293F ASN* 5.7 2.9 + - - -
1297F TRP* 4.9 15.3 - - + -
2001F GBM 3.7 20.9 - - + -
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Residues in contact with PRO 589 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441F MET* 3.5 21.4 - - + +
444F GLN* 3.5 25.8 - - + +
445F ILE* 4.3 17.9 - - + -
585F ILE* 3.4 17.3 - - + +
586F LEU* 3.5 25.8 - - + +
587F VAL 3.5 3.1 - - - -
588F THR* 1.4 90.6 - - + +
590F LEU* 1.3 60.5 - - + +
592F LEU* 4.7 0.7 - - + -
593F LEU* 2.8 31.7 + - - +
2001F GBM 5.9 0.7 - - + -
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Residues in contact with LEU 590 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445F ILE* 3.7 28.7 - - + -
467F ILE* 3.6 38.4 - - + +
470F LEU* 3.7 26.0 - - + -
471F ALA* 4.6 14.7 - - + +
474F GLN* 3.1 13.5 - - - +
586F LEU* 3.2 24.2 - - + +
587F VAL* 3.2 4.6 + - - +
589F PRO* 1.3 76.2 - - + +
591F PHE* 1.3 61.6 + - - +
593F LEU* 3.0 22.6 + - + +
594F SER* 3.1 9.2 + - - -
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Residues in contact with PHE 591 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474F GLN* 3.5 21.8 - - + +
543F SER* 6.1 0.7 - - - -
544F ILE* 6.4 0.7 - - + -
547F ASN* 3.2 41.3 - - - +
587F VAL* 3.0 23.2 + - + +
588F THR* 4.2 3.4 - - - +
590F LEU* 1.3 76.6 - - - +
592F LEU* 1.3 76.3 + - + +
594F SER* 4.2 4.0 + - - -
595F SER* 4.1 9.5 + - - -
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Residues in contact with LEU 592 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434F LEU* 5.7 6.3 - - + -
437F ASN* 4.5 8.7 - - - +
441F MET* 5.1 0.4 - - - -
588F THR* 2.8 40.0 + - + +
589F PRO* 4.0 3.8 - - + +
591F PHE* 1.3 96.9 - - + +
593F LEU* 1.3 59.5 + - - +
595F SER* 2.5 27.7 + - - +
596F VAL* 3.0 15.9 + - + +
2001F GBM 3.2 59.7 - - + +
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Residues in contact with LEU 593 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437F ASN 4.9 1.6 - - - +
438F LEU* 5.8 4.3 - - + +
441F MET* 3.8 33.0 - - + -
442F PRO* 5.7 1.3 - - + -
445F ILE* 4.5 16.4 - - + -
471F ALA* 5.6 7.2 - - + -
589F PRO 2.8 18.4 + - - +
590F LEU* 3.0 12.1 + - + +
592F LEU* 1.3 76.6 - - - +
594F SER* 1.3 60.1 + - - +
596F VAL* 3.2 17.6 + - + +
597F VAL* 2.9 42.0 + - + +
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Residues in contact with SER 594 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471F ALA* 3.4 14.0 + - - +
474F GLN* 2.5 46.8 + - - +
475F TYR* 4.4 15.9 - - - +
478F ALA* 6.0 3.8 - - - +
590F LEU 3.1 4.5 + - - -
591F PHE 4.6 3.6 - - - -
592F LEU 3.3 0.2 - - - -
593F LEU* 1.3 76.9 - - - +
595F SER* 1.3 61.9 + - - +
597F VAL* 3.2 9.6 + - - +
598F ARG* 3.1 22.3 + - - +
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Residues in contact with SER 595 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434F LEU* 4.2 11.8 - - - +
591F PHE 4.1 5.6 + - - -
592F LEU* 2.5 33.2 + - - +
594F SER* 1.3 76.1 - - - +
596F VAL* 1.3 55.0 + - - +
598F ARG* 3.4 24.5 + - - +
599F SER* 2.4 40.3 + - - -
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Residues in contact with VAL 596 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431F PHE* 6.4 0.4 - - + -
434F LEU* 3.7 43.3 - - + +
437F ASN* 4.4 19.7 - - + +
438F LEU* 5.0 14.4 - - + +
592F LEU* 3.0 18.1 + - + +
593F LEU* 3.2 21.7 + - + +
595F SER* 1.3 83.2 + - - +
597F VAL* 1.3 56.4 + - + +
599F SER* 3.1 8.4 + - - -
600F THR* 2.9 39.0 + - + +
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Residues in contact with VAL 597 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475F TYR* 3.9 27.6 - - + -
593F LEU* 2.9 33.3 + - + +
594F SER* 3.5 10.1 - - - +
596F VAL* 1.3 76.2 - - + +
598F ARG* 1.3 61.6 + - - +
600F THR* 2.6 22.5 + - - +
601F VAL* 3.1 15.7 + - + +
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Residues in contact with ARG 598 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475F TYR* 5.2 9.1 - - + -
478F ALA* 3.4 42.6 + - + +
481F LEU* 4.5 13.5 - - - +
482F SER* 5.8 6.1 - - - -
594F SER 3.1 15.2 + - - +
595F SER* 3.8 20.6 + - - +
597F VAL* 1.3 76.9 - - - +
599F SER* 1.3 57.7 + - - +
601F VAL* 3.3 10.2 + - + +
602F LYS* 3.0 63.8 + - - +
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Residues in contact with SER 599 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427F GLN* 5.3 2.2 - - - +
430F TRP* 5.9 2.3 - - - +
431F PHE* 4.0 23.6 - - - +
434F LEU* 4.1 15.1 - - - +
595F SER* 2.4 24.5 + - - -
596F VAL* 3.3 10.2 - - - -
598F ARG* 1.3 78.1 + - - +
600F THR* 1.3 57.3 + - - +
602F LYS* 3.3 12.0 + - - +
603F ALA* 2.8 26.7 + - - +
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Residues in contact with THR 600 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431F PHE* 3.4 26.0 - - + -
438F LEU* 4.8 17.3 - - + -
596F VAL* 2.9 26.0 + - + +
597F VAL* 2.6 26.0 + - - +
599F SER* 1.3 74.9 - - - +
601F VAL* 1.3 63.7 + - - +
603F ALA* 3.3 8.0 - - - +
604F LEU* 3.0 31.3 + - - +
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Residues in contact with VAL 601 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475F TYR* 5.2 9.4 - - + +
597F VAL* 3.1 22.6 + - + +
598F ARG* 3.5 10.8 - - + +
600F THR* 1.3 77.0 + - - +
602F LYS* 1.3 64.6 + - + +
604F LEU* 3.2 10.2 + - - +
605F VAL* 3.1 30.9 + - + +
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Residues in contact with LYS 602 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424F ASP* 5.3 0.2 - - - +
427F GLN* 3.3 41.0 + - + +
598F ARG* 3.0 50.5 + - + +
599F SER* 3.5 10.1 - - - +
601F VAL* 1.3 77.6 - - + +
603F ALA* 1.3 57.9 + - - +
605F VAL* 3.3 10.4 + - - +
606F SER* 2.8 31.3 + - - -
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Residues in contact with ALA 603 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288F TRP* 5.6 1.0 + - + -
427F GLN* 6.0 2.2 - - - -
428F LEU* 5.4 6.1 - - + +
431F PHE* 3.7 31.4 - - + -
599F SER 2.8 14.8 + - - +
600F THR* 3.3 15.3 - - - +
601F VAL 3.2 0.2 - - - -
602F LYS* 1.3 74.9 - - - +
604F LEU* 1.3 72.2 + - + +
606F SER* 3.1 7.2 + - - +
607F VAL* 3.0 24.6 + - - +
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Residues in contact with LEU 604 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288F TRP* 4.0 26.9 - - + -
600F THR* 3.0 19.4 + - - +
601F VAL* 3.6 8.7 - - + +
603F ALA* 1.3 81.9 - - + +
605F VAL* 1.3 59.6 + - + +
607F VAL* 3.2 8.7 - - - +
608F GLN* 2.9 42.1 + - - +
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Residues in contact with VAL 605 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424F ASP* 5.0 6.5 - - - +
601F VAL* 3.1 21.9 + - + +
602F LYS* 3.4 11.4 - - + +
603F ALA 3.1 0.6 - - - -
604F LEU* 1.3 78.1 - - + +
606F SER* 1.3 58.3 + - - +
608F GLN* 3.2 14.2 + - - +
609F LYS* 2.9 51.1 + - + +
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Residues in contact with SER 606 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420F LEU* 5.4 0.3 - - - +
424F ASP* 3.0 53.5 + - - +
427F GLN* 3.8 6.7 - - - +
428F LEU* 4.3 19.9 - - - +
602F LYS 2.8 17.4 + - - -
603F ALA* 3.1 6.5 + - - -
605F VAL* 1.3 76.6 - - - +
607F VAL* 1.3 57.3 + - - +
609F LYS* 3.3 1.7 + - - +
610F LEU* 2.9 29.8 + - - +
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Residues in contact with VAL 607 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284F ALA 5.5 5.2 - - - +
287F ILE* 4.8 17.7 - - + -
288F TRP* 3.4 55.2 - - + +
291F LEU* 5.9 0.4 - - + -
428F LEU* 5.5 4.6 - - + +
603F ALA 3.0 15.7 + - - +
604F LEU* 3.2 16.4 - - - +
606F SER* 1.3 76.1 - - - +
608F GLN* 1.3 59.6 + - + +
610F LEU* 3.8 6.6 - - + -
611F SER* 2.8 44.5 + - - +
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Residues in contact with GLN 608 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604F LEU* 2.9 34.9 + - - +
605F VAL* 3.5 15.0 - - + +
607F VAL* 1.3 80.8 - - + +
609F LYS* 1.3 61.9 + - + +
611F SER* 3.4 6.5 + - - -
612F GLU* 3.0 35.3 + - - +
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Residues in contact with LYS 609 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420F LEU* 3.9 12.2 - - + +
424F ASP* 3.8 21.8 - - - +
605F VAL* 2.9 36.2 + - + +
606F SER 4.0 1.3 - - - +
608F GLN* 1.3 77.7 - - + +
610F LEU* 1.3 60.8 + - - +
612F GLU* 3.2 32.4 + - - +
613F PHE* 2.9 27.5 + - - +
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Residues in contact with LEU 610 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F ILE* 4.7 25.8 - - + -
291F LEU* 6.3 0.2 - - + -
391F ILE* 4.6 23.1 - - + -
394F LYS* 6.2 4.9 - - + -
395F ILE* 4.2 27.4 - - + -
420F LEU* 4.6 8.4 - - + +
428F LEU* 5.6 6.5 - - + -
606F SER 2.9 17.9 + - - +
607F VAL* 4.0 6.7 - - + +
609F LYS* 1.3 74.4 - - - +
611F SER* 1.3 60.6 + - - +
613F PHE* 4.6 11.7 - - + -
614F LEU* 2.9 37.6 + - + +
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Residues in contact with SER 611 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F ILE* 4.4 16.0 - - - +
607F VAL* 2.8 33.2 + - - +
608F GLN* 3.6 7.4 - - - -
610F LEU* 1.3 76.6 - - - +
612F GLU* 1.3 64.7 + - - +
614F LEU* 4.0 1.1 - - - +
615F SER* 3.2 21.5 + - - -
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Residues in contact with GLU 612 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608F GLN* 3.0 22.6 + - - +
609F LYS* 3.3 41.6 + - - +
610F LEU 3.2 0.2 - - - -
611F SER* 1.3 79.7 - - - +
613F PHE* 1.3 62.6 + - - +
615F SER* 3.3 19.1 - - - +
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Residues in contact with PHE 613 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395F ILE* 3.8 25.1 - - + -
398F LYS* 2.6 55.3 + - + -
399F ILE* 3.8 25.1 - - + -
402F MET* 5.4 9.9 - - + -
417F ILE* 4.6 25.1 - - + -
420F LEU* 3.9 23.8 - - + -
609F LYS 2.9 16.0 + - - +
610F LEU* 3.3 12.8 + - + +
612F GLU* 1.3 77.2 - - - +
614F LEU* 1.3 52.8 + - + +
615F SER 2.9 4.5 - - - +
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Residues in contact with LEU 614 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270F PHE* 6.3 2.5 - - + -
287F ILE* 4.8 14.4 - - + -
394F LYS* 6.0 8.5 - - + -
398F LYS* 3.2 24.9 + - + +
610F LEU* 2.9 26.7 + - + +
611F SER 4.0 2.0 - - - +
613F PHE* 1.3 75.7 - - + +
615F SER* 1.3 62.1 + - - +
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Residues in contact with SER 615 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398F LYS* 2.5 26.8 + - - -
402F MET* 5.6 0.2 - - - +
611F SER 3.2 11.7 + - - -
612F GLU* 3.3 16.8 - - - +
613F PHE 2.9 6.1 - - - +
614F LEU* 1.3 79.1 - - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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