Contacts of the helix formed by residues 467 - 495 (chain A) in PDB entry 3NYL
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 ARG 467 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A ALA 5.6 0.6 + - - -
463A ALA* 5.2 5.3 - - + +
465A PRO* 2.7 20.1 + - + +
466A PRO* 1.3 67.0 - - - +
468A PRO* 1.3 71.3 - - - +
469A ARG* 3.1 5.2 - - + +
470A HIS* 2.7 36.4 + - + +
471A VAL* 3.4 5.8 + - - +
535A VAL* 4.4 0.7 - - - -
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Residues in contact with PRO 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A PRO 2.5 21.2 - - - +
467A ARG* 1.3 73.1 - - - +
469A ARG* 1.3 63.1 + - - +
470A HIS 3.1 1.2 + - - -
471A VAL* 3.2 11.6 + - - +
472A PHE* 3.4 10.7 + - - +
535A VAL* 3.0 30.5 - - + -
538A GLU* 3.7 34.5 - - + -
539A ILE* 3.6 9.5 - - + +
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Residues in contact with ARG 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ARG* 2.9 4.7 + - + -
468A PRO* 1.3 79.0 - - + +
470A HIS* 1.3 60.5 + - - +
472A PHE* 3.9 6.6 - - - +
473A ASN* 3.4 18.4 + - - +
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Residues in contact with HIS 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A ALA* 4.3 13.2 - - + -
467A ARG* 2.7 29.4 + - + +
469A ARG* 1.3 70.9 - - - +
471A VAL* 1.3 66.7 + - - +
472A PHE 3.1 1.8 - - - -
473A ASN* 2.8 19.1 + - - +
474A MET* 2.9 14.6 + - - +
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Residues in contact with VAL 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A TYR* 4.3 12.4 - - + -
460A ALA* 4.0 14.1 - - + +
461A LEU* 3.9 42.4 - - + +
466A PRO* 5.3 2.7 - - + -
467A ARG 4.0 6.7 - - - +
468A PRO 3.2 1.1 + - - +
470A HIS* 1.3 77.7 - - + +
472A PHE* 1.3 52.0 + - - +
474A MET* 3.2 2.9 + - - +
475A LEU* 2.8 40.7 + - + +
529A LEU* 4.2 5.4 - - + -
535A VAL* 3.5 28.5 - - + -
539A ILE* 3.2 24.0 - - + -
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Residues in contact with PHE 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A PRO 3.4 6.7 + - - +
469A ARG* 3.9 10.1 - - - +
470A HIS 3.1 0.4 - - - -
471A VAL* 1.3 77.2 - - - +
473A ASN* 1.3 69.9 + - - +
475A LEU* 2.9 10.1 + - + -
476A LYS* 2.8 32.7 + - + +
539A ILE* 3.9 24.8 - - + +
542A GLU* 3.9 38.1 - - + -
543A VAL* 4.1 6.3 - - + -
546A LEU* 3.5 37.0 - - + -
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Residues in contact with ASN 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ARG 3.4 11.7 + - - +
470A HIS* 2.8 18.1 + - - +
472A PHE* 1.3 81.7 - - - +
474A MET* 1.3 61.2 + - - +
476A LYS* 3.8 9.0 + - - +
477A LYS* 3.8 16.3 + - - +
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Residues in contact with MET 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ALA 3.7 11.6 - - - +
456A ASN* 3.9 16.9 - - + +
457A TYR* 3.8 27.3 - - - +
460A ALA* 4.2 8.1 - - + -
470A HIS 2.9 13.0 + - - +
471A VAL 3.9 4.3 - - - +
473A ASN* 1.3 73.7 - - - +
475A LEU* 1.3 59.8 + - - +
477A LYS* 3.5 9.9 - - - +
478A TYR 3.4 14.0 + - - -
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Residues in contact with LEU 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A TYR* 3.5 35.6 - - + +
471A VAL* 2.8 24.6 + - + +
472A PHE* 2.9 11.3 + - + +
474A MET* 1.3 70.1 - - - +
476A LYS* 1.3 70.0 + - - +
477A LYS 3.0 1.8 - - - -
478A TYR* 2.8 16.8 + - + +
479A VAL* 2.9 34.6 + - + -
526A LEU* 4.3 15.3 - - + -
529A LEU* 4.2 19.7 - - + -
539A ILE* 5.3 1.3 - - + -
543A VAL* 4.8 17.3 - - + -
546A LEU* 4.5 11.4 - - + -
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Residues in contact with LYS 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A PHE* 2.8 28.2 + - + +
473A ASN* 4.1 8.1 - - - +
475A LEU* 1.3 73.1 - - - +
477A LYS* 1.3 76.9 + - + +
479A VAL* 3.8 1.6 - - - +
480A ARG* 2.8 48.4 + - + +
546A LEU* 3.9 34.3 - - + +
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Residues in contact with LYS 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ALA* 3.5 17.3 - - + +
473A ASN 3.8 8.2 + - - +
474A MET* 3.5 13.0 + - - +
476A LYS* 1.3 103.3 - - + +
478A TYR* 1.3 62.1 + - - +
480A ARG* 3.6 4.9 - - + +
481A ALA* 3.2 16.3 + - - +
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Residues in contact with TYR 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ARG* 3.2 35.1 + - + -
453A ALA* 3.5 15.9 - - + +
454A LEU* 3.8 27.4 - - + -
457A TYR* 4.5 7.0 - + + -
474A MET 3.4 10.0 + - - +
475A LEU* 2.8 13.4 + - + +
477A LYS* 1.3 74.6 - - - +
479A VAL* 1.3 74.8 + - + +
480A ARG 3.0 3.4 - - - -
481A ALA* 2.9 6.9 + - - +
482A GLU* 2.7 54.2 + - - +
521A ARG 3.0 22.7 + - - -
522A MET* 3.0 19.9 - - + -
525A SER* 3.0 26.8 - - - -
526A LEU* 5.2 3.4 - - + -
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Residues in contact with VAL 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A LEU* 2.9 39.7 + - + +
476A LYS* 4.0 4.5 - - - +
478A TYR* 1.3 83.3 - - + +
480A ARG* 1.3 58.2 + - - +
483A GLN* 3.0 44.5 + - - +
522A MET* 3.4 28.5 - - + +
526A LEU* 4.5 13.0 - - + -
546A LEU* 5.1 18.6 - - + +
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Residues in contact with ARG 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A LYS* 2.8 35.7 + - + +
477A LYS* 3.6 8.5 - - + +
479A VAL* 1.3 74.6 - - - +
481A ALA* 1.3 54.5 + - - +
483A GLN* 2.8 18.2 + - - +
484A LYS* 2.7 34.2 + - - +
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Residues in contact with ALA 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A LEU* 5.0 4.0 - - - +
449A ARG* 4.0 15.7 - - + +
450A ARG* 3.8 29.6 - - - +
453A ALA* 4.7 0.2 - - + -
477A LYS 3.2 10.0 + - - +
478A TYR* 2.9 8.9 + - - +
480A ARG* 1.3 78.1 - - - +
482A GLU* 1.3 65.0 + - - +
484A LYS* 2.9 10.6 + - - +
485A ASP* 2.8 24.5 + - - +
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Residues in contact with GLU 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ARG* 2.7 41.8 + - - +
478A TYR* 2.7 38.5 + - + +
479A VAL* 4.1 0.4 - - - -
481A ALA* 1.3 75.2 - - - +
483A GLN* 1.3 59.0 + - - +
485A ASP* 3.1 7.0 + - - +
486A ARG* 2.8 27.0 + - - +
518A ILE* 3.7 14.7 - - + +
521A ARG* 3.2 28.9 + - - +
522A MET* 3.1 43.0 - - + +
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Residues in contact with GLN 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A VAL* 3.0 36.2 + - + +
480A ARG* 2.8 20.8 + - - +
482A GLU* 1.3 74.0 - - - +
484A LYS* 1.3 63.9 + - - +
485A ASP 3.0 1.1 - - - -
486A ARG* 3.0 39.2 + - - +
487A GLN* 2.8 24.8 + - - +
522A MET* 4.5 5.4 - - + -
546A LEU* 4.7 14.0 - - - +
547A LEU* 6.0 0.2 - - - -
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Residues in contact with LYS 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A LEU* 3.8 20.5 - - + +
480A ARG 2.7 14.9 + - - +
481A ALA* 3.4 12.1 - - - +
483A GLN* 1.3 73.5 - - - +
485A ASP* 1.3 57.0 + - - +
487A GLN* 3.6 7.3 + - - +
488A HIS* 3.0 28.9 + - - +
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Residues in contact with ASP 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A GLU* 3.1 24.6 - - - +
446A LEU* 3.5 30.3 - - + +
447A ASN* 4.3 1.3 + - - +
450A ARG* 5.7 1.6 - - + -
481A ALA 2.8 11.4 + - - +
482A GLU* 3.3 13.2 - - - +
484A LYS* 1.3 75.8 - - - +
486A ARG* 1.3 70.5 + - - +
488A HIS* 3.2 1.2 + - - +
489A THR* 2.8 24.8 + - - -
514A HIS* 2.8 18.0 - - - -
518A ILE* 2.8 27.1 - - + +
521A ARG* 3.6 11.1 + - - +
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Residues in contact with ARG 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A GLU 2.8 11.5 + - - +
483A GLN* 3.1 51.7 + - - +
485A ASP* 1.3 77.4 - - - +
487A GLN* 1.3 67.5 + - - +
489A THR* 3.1 9.7 + - - -
490A LEU* 3.2 16.6 + - + +
515A LEU* 4.3 11.0 - - + +
518A ILE* 3.6 20.6 - - + +
519A TYR* 3.1 50.8 + - + +
522A MET* 5.8 7.7 - - - -
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Residues in contact with GLN 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A GLN 2.8 14.6 + - - +
484A LYS* 3.6 11.4 - - - +
486A ARG* 1.3 72.5 - - - +
488A HIS* 1.3 58.2 + - - +
490A LEU* 2.9 35.1 + - - +
491A LYS* 3.1 25.3 + - + +
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Residues in contact with HIS 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A MET* 3.1 50.4 + - + +
442A VAL* 3.6 20.6 - - + +
443A GLU* 3.7 31.5 + - + -
446A LEU* 3.4 28.4 - - + +
484A LYS 3.0 11.6 + - - +
485A ASP 3.8 1.6 - - - +
487A GLN* 1.3 70.1 - - - +
489A THR* 1.3 66.4 + - - +
491A LYS* 3.2 15.6 + - + +
492A HIS* 3.1 22.5 + - + +
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Residues in contact with THR 489 (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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443A GLU* 4.4 4.0 + - - -
485A ASP* 2.8 19.9 + - - -
486A ARG 3.5 8.3 - - - -
488A HIS* 1.3 75.0 - - - +
490A LEU* 1.3 57.6 + - - +
492A HIS* 3.1 10.9 + - + +
493A PHE 3.0 22.5 + - - -
511A VAL* 3.5 38.6 - - + +
514A HIS* 3.3 28.7 + - + +
515A LEU* 4.2 14.6 - - + -
518A ILE* 3.5 7.3 - - - +
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Residues in contact with LEU 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ARG* 3.2 11.5 + - + +
487A GLN* 2.9 17.6 + - - +
489A THR* 1.3 76.8 - - - +
491A LYS* 1.3 65.3 + - + +
493A PHE* 3.0 21.0 + - + +
494A GLU* 3.0 43.4 + - + +
511A VAL* 5.4 0.2 - - - -
512A MET* 6.2 1.8 - - + -
515A LEU* 4.9 20.2 - - + -
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Residues in contact with LYS 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A MET* 4.7 7.0 - - + -
487A GLN* 3.1 31.1 + - + +
488A HIS* 3.4 23.1 - - + +
490A LEU* 1.3 77.6 - - - +
492A HIS* 1.3 60.7 + - - +
494A GLU* 3.6 15.7 + - - +
495A HIS* 3.1 35.3 + - + +
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Residues in contact with HIS 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A GLU* 2.7 41.6 + - - -
439A MET* 3.9 36.5 + - + +
440A ALA* 6.5 0.2 - - - -
488A HIS* 3.1 15.2 + - + +
489A THR* 3.2 13.6 - - - +
490A LEU 3.0 0.2 - - - -
491A LYS* 1.3 76.2 - - - +
493A PHE* 1.3 68.6 + - - +
495A HIS* 2.7 16.2 + - + -
496A VAL* 3.5 3.2 + - + +
507A ILE* 4.0 10.9 - - + +
511A VAL* 3.5 23.9 - - + +
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Residues in contact with PHE 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A THR 3.0 7.7 + - - +
490A LEU* 3.2 22.4 - - + +
492A HIS* 1.3 78.3 - - - +
494A GLU* 1.3 69.3 + - + +
496A VAL* 3.0 22.6 + - + +
508A ARG* 3.5 35.9 - - + -
511A VAL* 3.7 31.1 - - + +
512A MET* 3.4 31.6 - - + -
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Residues in contact with GLU 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A LEU* 3.0 36.8 + - + +
491A LYS* 3.9 14.4 + - - +
493A PHE* 1.3 83.9 - - + +
495A HIS* 1.3 59.6 + - + +
496A VAL 3.1 4.8 + - - -
497A ARG* 3.8 15.4 + - - +
----------------------------------------------------------
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Residues in contact with HIS 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ARG* 6.1 2.7 - - - -
432A GLN* 5.7 4.5 - - - +
435A VAL* 4.3 22.8 - - + +
436A GLU* 4.2 8.4 - - - +
439A MET* 3.1 31.7 - - + +
491A LYS* 3.1 20.9 + - + +
492A HIS* 2.7 24.5 + - + +
494A GLU* 1.3 72.6 + - + +
496A VAL* 1.3 56.4 + - - +
497A ARG* 2.9 15.7 + - - +
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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