Contacts of the helix formed by residues 466 - 497 (chain A) in PDB entry 1LVK
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 PHE 466 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 6.4 0.4 - - + -
465A SER* 1.3 79.8 + - - +
467A GLU* 1.3 69.3 + - + +
469A LEU* 3.1 7.5 + - + +
470A CYS* 3.0 42.6 + - - -
526A LEU* 4.0 15.5 - - + -
529A LEU* 3.5 23.6 - - + -
584A TRP* 3.1 42.2 - + + +
587A LYS* 3.8 35.0 - - + -
588A ASN* 4.3 2.2 - - - -
630A VAL* 4.0 25.6 - - + -
631A ALA* 4.1 23.8 - - + -
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Residues in contact with GLU 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 4.1 23.9 - - + +
459A GLU* 4.8 0.8 - - - +
465A SER* 3.9 5.2 - - - -
466A PHE* 1.3 87.8 + - + +
468A GLN* 1.4 68.7 + - - +
470A CYS* 3.3 10.0 + - - +
471A ILE* 3.1 29.9 + - - +
587A LYS* 3.2 40.6 + - - +
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Residues in contact with GLN 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A GLU* 2.9 34.8 + - + +
461A PHE* 3.5 22.8 - - + -
463A VAL 4.1 2.3 - - - +
464A ASN* 3.4 35.3 - - + +
465A SER* 2.8 38.6 + - - +
467A GLU* 1.4 84.1 + - - +
469A LEU* 1.3 66.5 + - - +
471A ILE* 3.5 5.7 + - - +
472A ASN* 2.9 30.3 + - - -
579A TYR* 3.8 4.0 - - + -
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Residues in contact with LEU 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A SER 3.1 7.6 + - - +
466A PHE* 3.1 12.0 + - + +
468A GLN* 1.3 78.4 - - - +
470A CYS* 1.3 55.0 + - - +
472A ASN* 3.2 0.7 + - - +
473A TYR* 2.7 36.4 + - - +
517A ILE* 4.1 31.9 - - + -
525A ILE* 3.9 20.6 - - + -
526A LEU* 4.2 18.4 - - + -
568A PHE* 4.9 1.3 - - + -
570A VAL* 4.8 5.8 - - + -
572A HIS* 4.6 1.6 - - - +
579A TYR* 3.4 38.5 - - + +
584A TRP* 3.7 29.2 - - + -
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Residues in contact with CYS 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 4.2 5.8 - - + -
466A PHE* 3.0 48.1 + - - -
467A GLU* 3.3 13.5 - - - +
469A LEU* 1.3 77.3 - - - +
471A ILE* 1.3 64.2 + - - +
473A TYR* 3.1 9.4 + - - +
474A THR* 2.9 19.4 + - - -
526A LEU* 5.6 4.9 - - - -
630A VAL* 6.2 0.2 - - - -
631A ALA* 5.8 0.2 - - - -
634A TYR* 3.0 52.3 + - + -
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Residues in contact with ILE 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 4.3 13.4 - - + +
455A ILE* 4.4 15.9 - - + -
456A SER* 3.9 20.2 - - - +
457A GLY 3.9 7.0 - - - +
459A GLU* 3.4 40.2 - - + +
467A GLU 3.1 9.8 + - - +
468A GLN 3.6 8.7 - - - +
470A CYS* 1.3 79.4 - - - +
472A ASN* 1.3 63.7 + - - +
474A THR* 3.3 6.9 + - + -
475A ASN* 2.9 49.1 + - - +
634A TYR* 3.6 11.2 + - - +
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Residues in contact with ASN 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A PHE* 3.4 22.9 - - + -
459A GLU 2.9 45.7 + - - -
468A GLN* 2.9 21.1 + - - +
469A LEU 3.7 1.1 - - - +
471A ILE* 1.3 79.7 - - - +
473A TYR* 1.3 57.7 + - - +
475A ASN 3.2 0.5 + - - -
476A GLU* 2.9 32.2 + - - +
572A HIS* 3.5 22.7 - - + +
577A VAL* 4.0 11.9 - - - +
579A TYR* 2.9 21.2 + - - +
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Residues in contact with TYR 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LEU* 2.7 14.8 + - + +
470A CYS* 3.1 10.1 - - - +
472A ASN* 1.3 74.2 - - - +
474A THR* 1.3 65.1 + - - +
476A GLU* 3.1 5.4 + - + +
477A LYS* 3.1 36.1 + - + +
514A ILE* 4.4 9.9 - - + -
517A ILE* 3.9 31.0 - - + -
518A ASP* 2.5 45.4 + - + +
526A LEU* 4.1 21.8 - - + -
572A HIS* 4.6 0.4 - - - -
634A TYR* 4.0 15.7 - + - -
635A LYS* 3.7 28.8 + - - +
638A LEU* 3.5 26.0 - - + +
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Residues in contact with THR 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A LEU* 6.0 0.2 - - + -
455A ILE* 4.9 6.5 - - + -
470A CYS 2.9 5.9 + - - -
471A ILE* 3.5 19.3 - - + +
473A TYR* 1.3 76.4 - - - +
475A ASN* 1.3 58.5 + - - +
477A LYS* 3.0 5.2 + - - +
478A LEU* 2.8 46.4 + - + +
634A TYR* 2.4 37.4 + - - -
638A LEU* 3.7 27.5 - - + +
641A LEU* 5.2 7.4 - - + -
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Residues in contact with ASN 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR* 4.6 5.2 - - - +
455A ILE* 4.9 0.2 - - - +
456A SER 2.9 23.1 + - - +
457A GLY* 3.2 30.8 + - - -
458A PHE* 3.6 29.2 + - + -
471A ILE* 2.9 32.5 + - - +
472A ASN 3.6 4.9 - - - +
473A TYR 3.2 0.2 - - - -
474A THR* 1.3 77.7 - - - +
476A GLU* 1.4 58.1 + - - +
478A LEU* 3.9 16.4 - - - +
479A GLN* 2.8 32.6 + - - +
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Residues in contact with GLU 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A PHE* 3.7 7.5 - - - -
472A ASN 2.9 19.1 + - - +
473A TYR* 3.1 10.1 + - - +
475A ASN* 1.4 75.3 - - - +
477A LYS* 1.3 59.6 + - - +
479A GLN* 3.5 1.7 + - - -
480A GLN* 3.0 25.8 + - - +
510A SER* 3.0 31.7 + - - -
513A THR* 3.5 22.0 + - + +
514A ILE* 3.8 18.6 - - + +
517A ILE* 4.9 2.0 - - + -
572A HIS* 2.8 31.4 + - + +
573A TYR* 2.9 31.7 + - - +
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Residues in contact with LYS 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A TYR* 3.1 18.3 + - + +
474A THR 3.0 9.5 + - - +
476A GLU* 1.3 80.1 - - - +
478A LEU* 1.4 59.4 + - - +
480A GLN* 3.3 9.7 + - - +
481A PHE* 2.9 28.4 + - - +
511A GLN* 5.9 0.2 - - - +
514A ILE* 4.0 29.8 - - + -
518A ASP* 3.8 22.9 + - - -
635A LYS 5.7 0.6 + - - -
638A LEU* 3.6 24.6 - - + +
639A ALA* 5.0 14.6 - - - +
642A MET* 3.9 28.0 - - + +
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Residues in contact with LEU 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 4.2 14.8 - - + -
178A THR* 4.5 13.7 - - + -
453A LEU* 4.1 20.0 - - + -
455A ILE* 4.6 2.9 - - + -
474A THR* 2.8 40.3 + - + +
475A ASN* 3.9 18.6 - - - +
477A LYS* 1.4 73.6 - - - +
479A GLN* 1.3 58.2 + - - +
481A PHE* 3.3 8.9 - - + +
482A PHE* 2.9 27.7 + - - +
641A LEU* 5.2 1.8 - - + -
642A MET* 3.6 27.1 - - + -
645A LEU* 3.8 20.0 - - + -
652A PHE* 5.0 1.6 - - + -
654A ARG* 5.6 4.2 + - - +
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Residues in contact with GLN 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PHE* 5.4 0.2 - - - -
458A PHE* 4.6 6.3 - - + -
475A ASN 2.8 17.9 + - - +
476A GLU* 4.0 4.9 - - - +
478A LEU* 1.3 79.1 - - - +
480A GLN* 1.3 56.0 + - - +
482A PHE* 3.2 17.7 + - - +
483A ASN* 2.9 64.5 + - - +
510A SER* 4.9 2.9 - - - +
573A TYR* 3.5 45.1 + - + -
654A ARG* 4.2 10.4 + - - +
678A CYS 5.1 0.2 - - - +
679A ASN 3.6 22.3 - - - +
680A GLY* 3.8 7.0 + - - -
683A GLU* 3.7 7.9 + - - -
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Residues in contact with GLN 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A GLU 3.0 19.0 + - - +
477A LYS* 3.3 11.1 + - - +
479A GLN* 1.3 74.7 - - - +
481A PHE* 1.3 61.4 + - - +
483A ASN* 3.3 7.7 + - - +
484A HIS* 2.9 55.7 + - + +
508A LEU* 4.7 7.8 - - + +
510A SER* 3.6 17.3 + - - +
511A GLN* 3.0 38.2 + - - +
514A ILE* 3.3 20.5 - - - +
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Residues in contact with PHE 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 4.3 14.6 - - + -
477A LYS 2.9 14.4 + - - +
478A LEU* 3.3 9.6 - - - +
480A GLN* 1.3 76.4 - - - +
482A PHE* 1.3 65.7 + - - +
484A HIS* 3.8 8.1 - - + +
485A HIS* 2.9 27.0 + - + +
642A MET* 3.8 18.2 - - + -
645A LEU* 3.6 38.6 - - + -
646A GLU* 3.5 34.1 - - - -
648A THR 5.2 0.4 - - - -
650A PRO* 3.7 35.7 - - + -
652A PHE* 3.8 19.5 - + - -
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Residues in contact with PHE 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.1 25.8 - - + -
122A PHE* 3.4 42.2 - + - -
478A LEU 2.9 13.9 + - - +
479A GLN* 3.2 26.4 + - - +
481A PHE* 1.3 77.1 - - - +
483A ASN* 1.3 58.6 + - - +
485A HIS* 3.0 2.3 + - - +
486A MET* 2.6 66.9 + - + -
652A PHE* 3.4 48.7 - + + -
654A ARG* 4.8 4.7 - - - +
680A GLY 5.2 2.9 - - - -
684A GLY* 5.3 2.9 - - - -
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Residues in contact with ASN 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A GLN* 2.9 47.5 + - - +
480A GLN* 3.8 7.6 - - - +
482A PHE* 1.3 84.5 - - - +
484A HIS* 1.3 67.3 + - + +
486A MET* 3.7 6.6 - - - +
487A PHE* 3.0 23.0 + - - +
510A SER* 5.8 2.2 + - - -
573A TYR* 4.4 3.0 - - - -
683A GLU* 3.4 26.2 + - - +
684A GLY* 6.1 0.3 - - - -
687A ILE* 4.7 8.8 - - - +
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Residues in contact with HIS 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A GLN* 2.9 44.4 + - + +
481A PHE* 3.8 7.4 - - + +
483A ASN* 1.3 78.9 - - + +
485A HIS* 1.3 64.6 + - - +
487A PHE* 3.0 25.3 - + + +
488A LYS* 3.2 21.2 + - + +
508A LEU* 4.4 22.7 - - + -
646A GLU* 6.1 1.6 - - - -
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Residues in contact with HIS 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.2 17.9 - - + +
481A PHE* 2.9 21.0 + - + +
482A PHE* 3.3 7.2 - + - +
484A HIS* 1.3 78.6 - - - +
486A MET* 1.3 64.4 + - - +
487A PHE 3.2 0.2 + - - -
488A LYS* 3.2 22.9 + - - +
489A VAL* 3.1 44.9 + - + +
649A ASN* 4.2 8.9 + - - -
650A PRO* 3.5 38.1 + - + +
652A PHE* 3.8 24.2 - + + -
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Residues in contact with MET 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 3.9 22.6 - - + +
482A PHE* 2.6 44.7 + - + +
483A ASN* 3.7 8.5 - - - +
485A HIS* 1.3 73.0 - - - +
487A PHE* 1.3 62.7 + - - +
489A VAL* 3.9 0.5 - - - +
490A GLU* 2.9 41.5 + - + +
684A GLY* 3.4 23.1 - - - +
687A ILE* 3.5 28.9 - - + -
688A THR* 3.1 28.5 - - - +
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Residues in contact with PHE 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ASN 3.0 13.0 + - - +
484A HIS* 3.0 18.4 - - + +
486A MET* 1.3 77.9 - - - +
488A LYS* 1.3 75.5 + - + +
490A GLU* 4.0 3.4 - - - +
491A GLN* 3.0 51.4 + - + +
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Residues in contact with LYS 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A HIS* 3.2 23.0 + - + +
485A HIS* 3.2 22.3 + - - +
487A PHE* 1.3 86.4 - - + +
489A VAL* 1.3 55.3 + - + +
491A GLN* 3.1 14.4 + - - +
492A GLU* 2.7 49.1 + - + +
646A GLU* 5.7 3.2 + - - -
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Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 3.6 39.5 - - + -
485A HIS* 3.1 34.5 + - + +
486A MET 4.2 1.6 - - - +
488A LYS* 1.3 79.7 - - + +
490A GLU* 1.3 67.7 + - + +
492A GLU* 3.6 23.7 - - - +
493A LYS* 3.2 23.2 + - - +
649A ASN* 6.0 0.7 - - - +
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Residues in contact with GLU 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 6.0 0.7 - - + -
486A MET* 2.9 39.0 + - + +
487A PHE* 4.0 4.0 - - - +
489A VAL* 1.3 80.6 - - + +
491A GLN* 1.3 67.0 + - - +
493A LYS* 3.3 5.6 + - - +
494A TYR* 3.1 32.5 + - + -
687A ILE* 5.9 0.8 - - + +
688A THR* 4.2 17.5 + - - -
695A ARG* 3.0 43.9 + - - -
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Residues in contact with GLN 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A PHE* 3.0 46.8 + - + +
488A LYS* 3.2 17.1 + - - +
490A GLU* 1.3 77.0 - - - +
492A GLU* 1.3 59.2 + - - +
494A TYR* 3.2 7.7 + - - +
495A LEU* 2.9 40.4 + - + +
----------------------------------------------------------
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Residues in contact with GLU 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A LYS* 2.7 33.2 + - + +
489A VAL* 3.6 24.9 - - - +
491A GLN* 1.3 76.0 - - + +
493A LYS* 1.3 59.0 + - - +
495A LEU* 3.2 7.3 + - - +
496A LYS* 2.9 47.2 + - + +
----------------------------------------------------------
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Residues in contact with LYS 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A VAL 3.2 14.5 + - - +
490A GLU* 3.6 9.6 - - - +
491A GLN 3.2 0.4 - - - -
492A GLU* 1.3 78.3 - - - +
494A TYR* 1.3 65.4 + - + +
495A LEU 3.1 0.5 + - - -
496A LYS* 3.2 15.1 + - + +
497A GLU* 3.3 16.4 + - + +
695A ARG* 3.8 33.2 - - - +
743A LYS* 3.0 47.1 - - - +
745A PHE* 4.2 14.4 - - + -
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Residues in contact with TYR 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A GLU* 3.1 23.9 + - + +
491A GLN* 3.6 9.9 - - - +
493A LYS* 1.3 79.0 - - + +
495A LEU* 1.3 57.5 + - + +
497A GLU* 3.5 2.0 + - - -
498A LYS 3.0 8.8 + - - -
499A ILE* 2.8 48.9 + - + +
500A ASN* 3.4 43.5 - - + +
691A GLY* 4.0 4.1 - - - -
692A PHE* 3.0 37.6 + + - +
695A ARG* 3.1 34.4 + - - -
745A PHE* 3.6 15.3 - + - -
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Residues in contact with LEU 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A GLN* 2.9 26.5 + - + +
492A GLU* 3.5 8.3 - - - +
494A TYR* 1.3 79.1 - - + +
496A LYS* 1.3 60.7 + - + +
497A GLU 3.2 1.4 + - - -
498A LYS* 3.5 11.6 + - - +
741A ILE* 5.4 0.7 - - - +
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Residues in contact with LYS 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A GLU* 2.9 32.6 + - + +
493A LYS* 3.2 7.8 + - + +
495A LEU* 1.3 74.9 - - + +
497A GLU* 1.3 66.4 + - + +
741A ILE* 3.4 20.2 - - - +
----------------------------------------------------------
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Residues in contact with GLU 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A LYS* 3.3 18.6 + - + +
495A LEU 3.2 0.6 - - - -
496A LYS* 1.3 83.4 - - + +
498A LYS* 1.3 73.3 + - - +
499A ILE* 4.1 16.2 - - + -
739A PHE 4.5 0.5 - - - +
740A GLY* 3.5 7.1 - - - -
741A ILE* 3.0 31.1 + - - +
742A THR* 3.0 36.8 + - - +
743A LYS* 2.9 46.2 + - - +
745A PHE* 3.9 17.2 - - + -
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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