Contacts of the helix formed by residues 489 - 520 (chain A) in PDB entry 5I4E
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 SER 489 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A LEU* 3.8 18.0 - - - +
488A ASN* 1.3 76.0 - - - +
490A PHE* 1.3 69.5 + - - +
491A GLU* 3.2 14.6 - - - -
492A GLN* 3.0 13.7 + - - +
493A LEU 3.1 16.8 + - - -
605A TYR* 3.6 2.1 - - - -
606A LYS 3.9 3.1 + - - -
608A ASN 4.0 4.5 + - - -
610A TRP* 3.1 28.5 + - - +
613A LYS* 3.2 19.9 + - - -
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Residues in contact with PHE 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A SER* 1.3 77.9 + - - +
491A GLU* 1.3 69.6 + - + +
493A LEU* 3.4 6.0 + - + +
494A CYS* 3.1 45.6 + - - +
551A LEU* 4.2 15.9 - - + -
554A LEU* 3.5 28.5 - - + -
610A TRP* 3.1 36.7 - + + +
613A LYS* 4.3 28.9 - - + -
614A ASN* 3.9 18.8 - - + -
670A VAL* 4.0 21.5 - - + -
671A GLY* 4.5 10.1 - - - -
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Residues in contact with GLU 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 5.2 3.3 - - - +
287A GLU* 3.8 37.2 - - + +
289A SER* 3.0 19.7 + - - +
489A SER* 3.3 12.5 - - - -
490A PHE* 1.3 82.2 + - + +
492A GLN* 1.3 64.7 + - - +
494A CYS* 3.4 7.3 + - - +
495A ILE* 3.1 35.8 + - + +
613A LYS* 2.9 41.9 + - - +
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Residues in contact with GLN 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ARG* 3.9 7.3 - - - +
287A GLU* 4.1 9.5 + - - -
483A GLU* 2.8 36.3 + - + +
485A PHE* 3.2 22.5 - - + -
487A LEU* 4.1 2.3 - - - +
488A ASN* 3.5 34.3 - - + +
489A SER* 3.0 30.7 + - - +
491A GLU* 1.3 78.1 - - - +
493A LEU* 1.3 60.9 + - - +
495A ILE* 4.5 2.5 - - - +
496A ASN* 3.0 41.5 + - - +
605A TYR* 3.9 2.5 - - + -
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Residues in contact with LEU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A SER 3.1 9.6 + - - +
490A PHE* 3.7 13.5 - - + +
491A GLU 3.3 0.2 - - - -
492A GLN* 1.3 78.0 - - - +
494A CYS* 1.3 55.1 + - - +
496A ASN* 4.2 0.2 - - - +
497A TYR* 3.0 31.2 + - - +
541A ILE* 4.4 26.0 - - + -
550A LEU* 4.9 13.5 - - + -
551A LEU* 4.3 25.1 - - + -
554A LEU* 6.0 0.4 - - + -
594A PHE* 5.2 2.7 - - + -
596A VAL* 4.7 6.1 - - + -
598A HIS* 4.6 2.9 - - + -
605A TYR* 3.5 37.1 - - + +
610A TRP* 3.6 30.3 - - + -
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Residues in contact with CYS 494 (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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285A LEU* 3.5 31.4 - - + -
490A PHE* 3.1 49.5 + - - +
491A GLU* 3.6 4.5 - - - +
492A GLN 3.3 0.2 - - - -
493A LEU* 1.3 75.3 - - - +
495A ILE* 1.3 56.1 + - - +
497A TYR* 3.7 7.1 + - - +
498A THR* 2.7 32.9 + - - -
551A LEU* 5.1 9.9 - - - -
670A VAL* 5.5 1.1 - - - -
671A GLY* 5.7 2.0 - - - -
674A TYR* 3.8 20.0 - - + -
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Residues in contact with ILE 495 (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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261A ARG* 4.0 13.9 - - - +
285A LEU* 5.6 5.6 - - + -
287A GLU* 5.7 3.4 - - + -
480A ALA* 3.3 31.4 - - + +
481A GLY 2.9 29.2 - - - +
483A GLU* 3.4 27.4 - - + +
491A GLU* 3.1 28.6 + - + +
492A GLN* 4.0 3.6 - - - +
494A CYS* 1.3 74.9 - - + +
496A ASN* 1.3 65.8 + - - +
498A THR* 3.2 8.2 + - - -
499A ASN* 2.8 33.2 + - - +
674A TYR* 5.5 0.7 - - - -
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Residues in contact with ASN 496 (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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482A PHE* 3.1 28.6 - - + -
483A GLU* 3.0 44.3 + - - +
492A GLN* 3.0 18.8 + - - +
493A LEU 4.2 0.7 - - - +
495A ILE* 1.3 76.5 - - - +
497A TYR* 1.4 56.1 + - - +
499A ASN* 3.2 4.2 + - - +
500A GLU* 2.9 30.7 + - - +
598A HIS* 3.9 13.2 + - + -
599A TYR* 4.5 1.2 - - - -
603A VAL* 3.9 8.7 - - - +
605A TYR* 3.0 25.7 + - - +
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Residues in contact with TYR 497 (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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493A LEU* 3.0 21.0 + - + +
494A CYS* 3.7 10.1 - - - +
495A ILE 3.3 0.2 - - - -
496A ASN* 1.4 74.9 - - - +
498A THR* 1.3 56.5 + - - +
500A GLU* 3.2 10.1 + - + +
501A LYS* 3.0 48.8 + - + +
538A ILE* 4.4 7.2 - - + -
541A ILE* 3.6 35.9 - - + -
542A GLU* 2.4 48.9 + - + +
551A LEU* 4.3 16.6 - - + -
598A HIS* 4.9 0.8 - - - -
674A TYR* 4.4 15.0 - + - -
675A LYS* 3.6 18.3 + - + +
678A LEU* 3.8 21.6 - - + +
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Residues in contact with THR 498 (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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479A ILE* 3.9 29.9 - - + +
480A ALA 5.4 1.1 - - - +
494A CYS 2.7 13.2 + - - -
495A ILE* 3.2 10.4 + - - -
497A TYR* 1.3 73.9 - - - +
499A ASN* 1.4 64.4 + - - +
501A LYS* 3.6 2.4 + - - +
502A LEU* 3.2 22.3 + - - +
674A TYR* 2.6 35.1 + - - +
678A LEU* 3.8 28.8 - - + +
681A LEU* 6.1 0.2 - - + -
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Residues in contact with ASN 499 (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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198A GLY 3.5 11.8 + - - +
204A LYS* 5.6 0.2 - - - +
479A ILE* 4.5 13.1 - - - +
480A ALA 2.8 24.2 + - - -
481A GLY* 3.4 7.8 - - - -
482A PHE* 2.9 32.7 + - + +
495A ILE* 2.8 28.3 + - - +
496A ASN 3.2 7.1 + - - +
498A THR* 1.4 73.0 - - - +
500A GLU* 1.3 65.2 + - - +
502A LEU* 3.2 5.1 + - - +
503A GLN 3.0 19.6 + - - -
599A TYR* 2.8 28.0 + - + +
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Residues in contact with GLU 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A ASN 2.9 11.0 + - - +
497A TYR* 3.3 13.7 - - + +
499A ASN* 1.3 75.9 - - - +
501A LYS* 1.3 56.1 + - - +
503A GLN 3.2 0.3 + - - -
504A GLN* 3.0 24.8 + - - +
534A LEU* 3.2 31.8 - - + +
537A CYS* 3.6 26.8 - - - +
538A ILE* 3.6 26.0 - - + -
541A ILE* 5.7 1.1 - - + -
597A LEU 4.6 0.2 - - - +
598A HIS* 3.4 17.9 + - - +
599A TYR* 2.9 52.2 + - + -
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Residues in contact with LYS 501 (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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497A TYR* 3.0 36.8 + - + +
498A THR 3.9 5.4 - - - +
499A ASN 3.3 0.2 - - - -
500A GLU* 1.3 72.9 - - - +
502A LEU* 1.3 59.1 + - - +
504A GLN* 3.6 2.7 + - - +
505A LEU* 3.1 24.8 + - - +
538A ILE* 3.6 33.8 - - + +
542A GLU* 3.3 29.7 + - - +
678A LEU* 3.8 25.8 - - + -
679A SER* 5.6 5.5 + - - +
682A MET* 4.6 25.1 - - + +
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Residues in contact with LEU 502 (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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195A LEU* 4.2 26.0 - - + -
196A CYS 4.2 11.2 - - - +
197A THR* 3.7 27.4 - - + -
477A LEU* 3.8 23.3 - - + -
479A ILE* 3.3 29.8 - - + -
498A THR 3.2 15.6 + - - +
499A ASN* 3.2 7.2 + - - +
501A LYS* 1.3 72.0 - - - +
503A GLN* 1.3 64.8 + - - +
505A LEU* 3.0 17.1 + - + +
506A PHE* 3.0 20.6 + - - +
682A MET* 5.7 4.5 - - + +
685A LEU* 5.3 0.4 - - + -
692A PHE* 4.5 3.5 - - + -
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Residues in contact with GLN 503 (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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197A THR* 5.4 1.8 - - - +
499A ASN 3.0 12.3 + - - +
500A GLU 3.5 8.1 - - - +
502A LEU* 1.3 75.4 - - - +
504A GLN* 1.3 57.5 + - - +
506A PHE* 3.1 10.5 + - - +
507A ASN* 2.9 50.4 + - - +
532A LEU* 5.1 1.2 - - + +
534A LEU* 3.8 16.8 - - + -
599A TYR* 4.0 18.1 - - + +
694A ARG* 2.7 29.7 + - - +
718A CYS 3.5 18.4 + - - +
719A ASN* 3.0 31.4 + - - +
720A GLY* 4.9 0.4 - - - -
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Residues in contact with GLN 504 (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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500A GLU 3.0 8.7 + - - +
501A LYS* 3.8 5.4 - - - +
502A LEU 3.2 0.2 - - - -
503A GLN* 1.3 72.8 - - - +
505A LEU* 1.4 55.4 + - - +
507A ASN* 3.2 24.1 + - - +
508A HIS* 2.8 45.3 + - + +
512A VAL* 5.7 4.4 - - - +
532A LEU 5.1 0.2 + - - -
533A ASP* 3.6 16.2 + - - -
534A LEU* 2.8 32.8 + - + +
535A GLN* 4.9 1.1 - - - +
538A ILE* 3.5 30.7 - - + -
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Residues in contact with LEU 505 (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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195A LEU* 3.8 26.7 - - + -
501A LYS 3.1 14.3 + - - +
502A LEU* 3.0 17.5 + - + +
504A GLN* 1.4 72.3 - - - +
506A PHE* 1.3 63.2 + - - +
508A HIS* 4.4 14.6 - - + -
509A THR* 2.7 42.4 + - - +
682A MET* 4.5 18.4 - - + +
685A LEU* 3.9 31.4 - - + -
686A SER* 5.8 6.5 - - - +
690A PRO* 5.9 2.7 - - + -
692A PHE* 4.3 4.5 - - + -
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Residues in contact with PHE 506 (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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141A PHE* 3.7 39.3 - + - -
197A THR* 5.5 0.7 - - + -
502A LEU 3.0 10.5 + - - +
503A GLN* 3.1 29.1 + - - +
505A LEU* 1.3 75.2 - - - +
507A ASN* 1.4 57.7 + - - +
509A THR* 3.2 1.4 + - - -
510A MET* 2.8 66.6 + - + +
511A PHE* 4.4 9.4 - + - -
692A PHE* 3.7 37.8 - + + -
694A ARG* 3.2 28.0 - - - +
719A ASN 3.3 14.8 - - - -
720A GLY 3.8 12.1 - - - -
724A GLY* 4.7 0.9 - - - -
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Residues in contact with ASN 507 (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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503A GLN* 2.9 39.8 + - - +
504A GLN* 3.2 31.1 + - - +
506A PHE* 1.4 77.4 - - - +
508A HIS* 1.3 56.5 + - - +
511A PHE* 2.9 46.7 + - + +
512A VAL* 3.6 4.0 + - - +
532A LEU* 3.3 47.5 + - - +
533A ASP 3.9 1.0 - - - +
534A LEU* 4.1 11.3 - - - +
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Residues in contact with HIS 508 (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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504A GLN* 2.8 30.3 + - + +
505A LEU* 4.0 13.9 - - + +
507A ASN* 1.3 73.2 - - - +
509A THR* 1.3 58.8 + - - +
512A VAL* 3.2 39.5 + - + +
513A LEU* 2.8 60.7 + - + +
516A GLU* 5.2 2.2 - - - -
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Residues in contact with THR 509 (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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505A LEU* 2.7 35.9 + - - +
506A PHE 3.8 2.7 - - - -
508A HIS* 1.3 77.7 - - - +
510A MET* 1.3 64.2 + - - +
513A LEU* 3.9 29.6 - - + +
514A GLU* 3.9 8.7 + - - +
690A PRO* 3.8 30.6 - - + +
692A PHE* 4.1 14.8 - - + -
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Residues in contact with MET 510 (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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140A LEU* 4.9 21.3 - - + +
141A PHE* 3.7 32.5 - - + -
506A PHE* 2.8 49.8 + - + +
509A THR* 1.3 82.9 - - - +
511A PHE* 1.3 76.7 + - + +
514A GLU* 3.3 18.4 - - - +
692A PHE* 5.2 5.8 - - + -
724A GLY* 3.8 18.8 - - - +
727A ILE* 3.6 22.6 - - + +
728A CYS* 5.9 1.6 - - + -
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Residues in contact with PHE 511 (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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506A PHE* 4.4 5.8 - + - -
507A ASN* 2.9 41.2 + - + +
510A MET* 1.3 91.5 - - + +
512A VAL* 1.3 63.3 + - + +
514A GLU* 4.3 2.9 - - - -
515A GLN* 2.8 38.7 + - - +
527A PHE* 4.2 1.6 - - + -
528A LEU 5.7 0.2 - - - +
530A PHE* 3.4 32.5 - + + -
532A LEU* 3.5 35.7 - - + +
720A GLY 4.3 2.9 - - - -
723A GLU* 3.4 27.6 - - + -
724A GLY* 3.5 20.4 - - - -
727A ILE* 3.6 11.7 - - + -
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Residues in contact with VAL 512 (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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504A GLN* 5.7 4.3 - - - +
507A ASN 3.6 3.3 + - - +
508A HIS* 3.2 42.3 + - + +
511A PHE* 1.3 77.1 - - + +
513A LEU* 1.4 56.7 - - - +
515A GLN* 3.3 3.3 + - - +
516A GLU* 2.8 63.9 + - + +
527A PHE* 5.1 15.3 - - + -
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Residues in contact with LEU 513 (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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508A HIS* 2.8 45.0 + - + +
509A THR* 3.9 29.4 - - + +
512A VAL* 1.4 71.3 - - - +
514A GLU* 1.4 62.1 + - - +
516A GLU* 4.0 18.0 - - + +
517A GLU* 3.1 24.9 + - - +
520A ARG* 5.5 3.7 + - - +
735A ARG* 5.2 1.5 + - - -
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Residues in contact with GLU 514 (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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140A LEU* 5.5 8.1 - - - +
509A THR 3.9 8.2 + - - +
510A MET 3.3 27.4 - - - +
511A PHE* 4.6 1.6 - - - +
512A VAL 3.3 1.4 - - - +
513A LEU* 1.4 78.1 - - - +
515A GLN* 1.3 62.3 + - - +
517A GLU* 3.3 16.2 + - - +
518A TYR* 2.7 47.5 + - + +
727A ILE* 4.3 15.5 - - + +
732A PHE 3.5 11.4 - - - +
733A PRO* 4.0 11.6 - - - +
735A ARG* 3.0 28.3 + - - +
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Residues in contact with GLN 515 (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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511A PHE* 2.8 31.6 + - - +
512A VAL 3.3 2.0 + - - +
514A GLU* 1.3 72.9 - - + +
516A GLU* 1.4 63.6 + - - +
518A TYR* 3.2 12.5 + - + +
519A GLN* 3.2 21.0 + - - +
525A TRP* 2.9 29.5 + - + +
527A PHE* 3.2 30.1 - - + -
528A LEU* 2.7 49.3 + - - +
530A PHE* 4.7 0.8 - - - -
727A ILE* 4.2 21.6 - - + +
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Residues in contact with GLU 516 (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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508A HIS* 5.2 1.7 - - - -
512A VAL* 2.8 46.3 + - + +
513A LEU* 4.0 20.1 - - + +
514A GLU 3.4 0.2 - - - -
515A GLN* 1.4 72.4 - - - +
517A GLU* 1.3 56.3 + - - +
519A GLN* 3.5 7.6 + - - +
520A ARG* 3.0 42.2 + - - +
527A PHE* 6.0 3.6 - - + -
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Residues in contact with GLU 517 (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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513A LEU 3.1 12.7 + - - +
514A GLU 3.4 11.0 - - - +
516A GLU* 1.3 74.2 - - - +
518A TYR* 1.4 65.0 + - + +
520A ARG* 3.0 38.7 + - - +
521A GLU* 3.2 38.0 + - - +
735A ARG* 3.4 35.8 + - - +
784A LYS* 4.1 17.7 + - - -
786A PHE* 4.2 10.5 - - + -
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Residues in contact with TYR 518 (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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514A GLU* 2.7 50.2 + - + +
515A GLN* 3.2 15.4 + - + +
517A GLU* 1.4 75.0 - - + +
519A GLN* 1.4 64.0 + - - +
521A GLU 3.2 9.4 + - - -
523A ILE* 3.2 38.8 + - + +
525A TRP* 3.7 57.2 - + + -
727A ILE* 4.8 1.4 + - + -
731A GLY* 3.5 3.9 - - - -
732A PHE* 2.8 35.6 + + + -
735A ARG* 5.8 0.2 - - - -
786A PHE* 3.8 36.1 - + - -
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Residues in contact with GLN 519 (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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515A GLN 3.2 12.1 + - - +
516A GLU* 3.7 10.8 - - - +
517A GLU 3.4 0.2 - - - -
518A TYR* 1.4 73.5 - - - +
520A ARG* 1.3 61.6 + - - +
521A GLU 3.2 1.0 + - - -
522A GLY* 3.2 14.7 + - - -
523A ILE 5.4 2.5 - - - +
525A TRP* 5.1 8.0 - - - +
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Residues in contact with ARG 520 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513A LEU* 5.5 3.2 + - - +
516A GLU* 3.0 42.0 + - - +
517A GLU* 3.0 35.4 + - - +
518A TYR 3.3 0.2 - - - -
519A GLN* 1.3 74.6 - - - +
521A GLU* 1.3 63.9 + - + +
522A GLY 3.5 0.2 - - - -
782A GLN* 5.1 4.5 - - - +
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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
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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