Contacts of the helix formed by residues 468 - 493 (chain A) in PDB entry 3V98
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 TYR 468 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A PHE 4.5 0.8 + - - -
237A LEU* 3.1 43.3 - - + -
238A ASN* 4.0 0.2 - - - -
242A PRO 2.6 22.8 + - - -
454A ILE* 4.5 5.4 - - + -
457A ARG* 2.9 21.4 + - - -
459A MET* 3.7 50.5 - - + -
465A ILE* 4.0 7.4 + - + +
466A PRO 3.5 4.0 + - - -
467A TYR* 1.3 74.6 - - - +
469A PHE* 1.3 59.5 + - - +
470A TYR* 3.7 20.0 - + - -
471A ARG* 3.3 36.7 + - + +
472A ASP* 3.1 30.4 + - - +
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Residues in contact with PHE 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TYR* 4.1 14.6 - + - -
238A ASN* 2.8 39.3 + - - +
466A PRO 4.4 5.4 - - - -
467A TYR* 4.1 31.6 - + + -
468A TYR* 1.3 71.5 - - - +
470A TYR* 1.3 63.0 + - - +
472A ASP* 4.2 11.2 - - - -
473A ASP* 2.9 30.0 + - - -
651A ARG* 3.6 37.9 - - + +
655A LEU* 3.3 41.3 - - + -
659A TYR* 4.0 23.6 - - + -
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Residues in contact with TYR 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU 3.4 18.8 - - - +
238A ASN* 3.6 3.0 + - - -
242A PRO* 3.6 36.1 - - + -
243A VAL* 3.6 14.2 - - + +
450A PHE* 3.3 29.8 - + - -
454A ILE* 4.4 6.3 - - + -
457A ARG* 4.9 1.6 - - - -
468A TYR* 3.7 12.1 - + + -
469A PHE* 1.3 77.8 - - - +
471A ARG* 1.3 59.4 + - - +
474A GLY* 3.0 27.2 + - - -
544A PHE* 6.3 0.4 - + - -
549A GLN* 2.8 32.1 + - - -
552A ALA* 3.8 19.1 - - + -
553A VAL* 5.4 0.7 - - + -
659A TYR* 3.4 33.6 - - + +
662A LEU* 3.7 9.8 - - + +
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Residues in contact with ARG 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A PHE* 3.7 10.2 - - - -
454A ILE* 3.9 22.4 - - + -
459A MET 3.0 29.4 + - - -
460A GLU* 4.1 7.6 - - - +
461A SER 3.2 14.8 + - - -
462A LYS* 3.6 23.0 - - - +
465A ILE* 2.8 33.7 + - - +
466A PRO 4.3 3.6 + - - -
468A TYR* 3.3 41.5 + - + +
469A PHE 3.2 0.4 - - - -
470A TYR* 1.3 79.7 - - - +
472A ASP* 1.3 91.2 + - - +
474A GLY 3.2 0.9 + - - -
475A LEU* 2.9 42.1 + - + +
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Residues in contact with ASP 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LYS* 3.1 24.3 + - - +
466A PRO 4.4 6.8 - - - +
468A TYR 3.1 15.0 + - - +
469A PHE* 3.3 17.3 + - - +
471A ARG* 1.3 106.9 + - - +
473A ASP* 1.3 69.3 + - - +
475A LEU* 3.3 9.9 + - - +
476A LEU* 3.3 20.0 + - + +
651A ARG* 4.6 4.3 + - - +
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Residues in contact with ASP 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A PHE 2.9 13.3 + - - +
472A ASP* 1.3 74.7 - - - +
474A GLY* 1.3 66.4 + - - +
476A LEU* 3.3 13.0 + - - +
477A VAL* 3.1 26.7 + - - +
644A ILE* 5.3 0.3 - - - +
647A VAL* 5.6 1.6 - - - +
648A ILE* 3.7 26.2 - - + +
651A ARG* 2.8 41.5 + - - -
659A TYR* 3.5 16.5 - - - +
662A LEU* 3.8 22.6 + - + +
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Residues in contact with GLY 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A PHE* 3.5 17.9 - - - -
470A TYR 3.0 21.4 + - - -
473A ASP* 1.3 76.7 - - - +
475A LEU* 1.3 56.1 + - - +
477A VAL* 3.4 1.8 + - - -
478A TRP* 2.9 30.8 + - - +
544A PHE* 3.6 12.5 - - - -
662A LEU* 3.7 12.0 - - - +
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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
----------------------------------------------------------
450A PHE* 3.4 19.5 - - + -
451A PRO* 4.1 27.8 - - + -
454A ILE* 5.1 5.2 - - + -
460A GLU* 5.7 2.0 - - - +
462A LYS* 3.9 28.0 - - - +
471A ARG* 2.9 35.1 + - + +
472A ASP 3.6 4.9 - - - +
474A GLY* 1.3 75.3 - - - +
476A LEU* 1.3 64.9 + - + +
478A TRP* 3.7 3.1 - - - +
479A GLU* 3.1 31.5 + - + +
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Residues in contact with LEU 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ASP 3.5 13.7 - - - +
473A ASP* 3.3 16.0 + - - +
475A LEU* 1.3 81.3 - - + +
477A VAL* 1.3 62.3 + - - +
479A GLU* 3.3 6.0 + - + +
480A ALA* 3.0 18.5 + - - +
644A ILE* 3.5 37.6 - - + +
647A VAL* 3.9 31.2 - - + -
648A ILE* 5.3 0.4 - - + -
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Residues in contact with VAL 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A ASP 3.1 17.4 + - - +
474A GLY* 3.9 3.4 - - - +
476A LEU* 1.3 71.9 - - - +
478A TRP* 1.3 66.1 + - - +
480A ALA* 3.3 2.6 + - - +
481A ILE* 3.1 37.3 + - + +
544A PHE* 4.2 4.0 - - + -
548A ALA* 3.9 23.8 - - + -
617A LEU* 4.0 17.0 - - + -
641A LEU* 5.0 2.0 - - + -
644A ILE* 4.1 13.9 - - + -
662A LEU* 3.9 23.3 - - + +
664A PRO* 4.5 12.3 - - + -
667A ILE* 4.3 7.6 - - + -
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Residues in contact with TRP 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A LEU 3.7 10.5 - - - -
449A CYS* 3.7 24.2 - - + -
450A PHE* 3.5 22.0 - - + -
451A PRO* 3.5 34.9 - - + +
474A GLY 2.9 18.6 + - - +
475A LEU* 3.7 7.0 - - - +
477A VAL* 1.3 77.1 - - - +
479A GLU* 1.3 74.3 + - + +
481A ILE* 3.3 4.6 + - - +
482A ARG* 2.9 35.8 + - + +
537A GLU* 5.0 9.2 - - + -
540A THR* 3.7 34.3 - - + +
541A VAL* 3.9 16.2 - - + -
544A PHE* 3.5 41.2 - + + -
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Residues in contact with GLU 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A PRO* 4.9 5.2 - - - +
475A LEU* 3.1 22.8 + - + +
476A LEU* 3.8 5.2 - - + +
478A TRP* 1.3 90.7 + - + +
480A ALA* 1.3 61.9 + - - +
482A ARG* 3.6 13.0 - - - +
483A THR* 2.9 37.9 + - - +
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Residues in contact with ALA 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A LEU 3.0 13.5 + - - +
477A VAL 3.6 8.3 - - - +
478A TRP 3.3 0.2 - - - -
479A GLU* 1.3 76.8 - - - +
481A ILE* 1.3 62.1 + - - +
483A THR* 3.5 6.8 + - - +
484A PHE* 3.1 22.0 + - - +
637A PHE* 3.6 10.6 - - + -
640A ASN* 4.6 16.1 + - + +
641A LEU* 4.1 16.6 - - + -
644A ILE* 3.9 18.2 - - + -
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Residues in contact with ILE 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A VAL* 3.1 34.3 + - + +
478A TRP 3.7 4.0 - - - +
480A ALA* 1.3 75.7 - - + +
482A ARG* 1.3 58.6 + - - +
484A PHE* 3.3 3.0 + - + +
485A THR* 2.9 34.8 + - + +
540A THR* 3.8 25.1 - - + -
543A ILE* 3.9 26.7 - - + -
544A PHE* 3.9 30.3 - - + -
547A SER* 4.2 6.7 - - - +
617A LEU* 4.4 3.1 - - + -
637A PHE* 4.0 24.7 - - + -
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Residues in contact with ARG 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A TRP* 2.9 29.5 + - - +
479A GLU* 3.2 19.3 + - - +
481A ILE* 1.3 76.6 - - - +
483A THR* 1.3 62.1 + - - +
485A THR* 3.1 2.1 + - - -
486A ALA* 3.0 30.5 + - - +
533A GLU* 3.6 34.6 + - - +
536A SER* 2.8 37.7 + - - -
537A GLU* 3.7 29.4 + - - +
540A THR* 3.3 26.2 + - + +
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Residues in contact with THR 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A GLU* 2.9 22.8 + - - +
480A ALA* 3.7 7.4 - - - -
482A ARG* 1.3 78.9 - - - +
484A PHE* 1.3 63.0 + - - +
486A ALA* 3.4 6.1 + - - +
487A GLU* 3.1 41.2 + - + +
640A ASN* 4.5 17.3 - - - +
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Residues in contact with PHE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A LEU* 3.7 31.0 - - + -
480A ALA 3.1 16.2 + - - +
481A ILE* 3.3 5.6 + - + +
483A THR* 1.3 77.3 - - - +
485A THR* 1.3 70.7 + - + +
487A GLU* 3.2 7.7 + - - +
488A VAL* 3.1 33.4 + - + +
543A ILE* 5.2 6.3 - - + -
620A TYR* 3.9 17.7 - + - -
633A ALA* 3.8 10.1 - - + -
634A MET* 3.8 42.8 - - + -
637A PHE* 3.6 46.9 - + + +
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Residues in contact with THR 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A LEU* 4.5 6.1 - - + -
481A ILE* 2.9 24.3 + - + +
482A ARG 3.1 6.4 + - - -
484A PHE* 1.3 78.9 - - + +
486A ALA* 1.3 56.8 + - - +
488A VAL* 3.3 8.2 + - - +
489A VAL* 2.9 35.0 + - - +
536A SER* 3.0 24.8 + - - -
539A LEU* 3.9 21.3 - - + +
540A THR* 3.2 11.3 + - - +
543A ILE* 3.8 29.2 - - + -
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Residues in contact with ALA 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ARG* 3.0 25.1 + - + +
483A THR* 3.6 7.2 - - - +
485A THR* 1.3 78.4 + - - +
487A GLU* 1.3 56.9 + - + +
489A VAL* 3.3 3.0 + - - +
490A ASP* 3.0 40.3 + - - +
536A SER* 3.6 17.3 - - - +
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Residues in contact with GLU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A THR* 3.1 34.2 + - + +
484A PHE* 3.2 9.0 + - - +
486A ALA* 1.3 76.6 - - + +
488A VAL* 1.3 64.0 + - - +
490A ASP* 3.4 7.5 + - - +
491A ILE* 3.2 30.5 + - + +
633A ALA* 3.6 20.1 - - + +
636A ARG* 3.0 47.4 + - - +
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Residues in contact with VAL 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A PRO* 5.3 4.0 - - + +
395A LEU* 4.5 19.7 - - + -
484A PHE* 3.1 40.8 + - + +
485A THR* 3.7 9.4 - - - +
487A GLU* 1.3 75.6 - - - +
489A VAL* 1.3 66.8 + - + +
491A ILE* 3.2 18.6 + - - +
492A TYR* 3.4 26.4 + - + +
539A LEU* 6.0 0.4 - - + -
625A PHE* 4.5 16.6 - - + -
630A VAL* 4.2 15.0 - - + -
633A ALA* 4.6 4.0 - - + -
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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
----------------------------------------------------------
392A ILE* 6.4 0.2 - - + -
485A THR 2.9 23.0 + - - +
486A ALA* 3.7 5.8 - - - +
487A GLU 3.3 0.2 - - - -
488A VAL* 1.3 77.7 - - + +
490A ASP* 1.3 58.3 + - - +
491A ILE 3.2 0.2 + - - -
492A TYR 3.3 0.5 + - - -
493A TYR* 2.9 39.3 + - + +
532A ARG* 3.7 41.5 - - + +
535A LEU* 3.8 34.5 - - + -
536A SER* 4.3 8.1 - - - +
539A LEU* 3.8 15.3 - - + -
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Residues in contact with ASP 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ALA* 3.0 26.4 + - - +
487A GLU* 3.8 6.6 - - - +
488A VAL 3.3 0.2 - - - -
489A VAL* 1.3 76.7 - - - +
491A ILE* 1.3 63.3 + - + +
493A TYR 3.4 10.7 - - - +
494A GLU* 5.2 0.9 - - - -
532A ARG* 3.2 49.3 + - - +
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Residues in contact with ILE 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A GLU* 3.2 20.3 + - + +
488A VAL* 3.4 12.6 - - - +
489A VAL 3.1 0.6 - - - -
490A ASP* 1.3 80.3 - - + +
492A TYR* 1.3 85.4 + - + +
494A GLU* 4.8 6.2 - - - +
629A PRO* 3.8 47.1 - - + +
630A VAL* 3.8 10.5 - - + +
633A ALA* 4.5 5.8 - - + -
636A ARG* 5.7 2.0 - - - +
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Residues in contact with TYR 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ALA* 3.5 34.1 - - + -
118A LEU* 3.6 20.0 - - + +
120A ARG* 4.8 1.0 + - - -
391A PRO* 3.8 26.7 - - + -
488A VAL* 3.4 18.6 + - + +
489A VAL 3.3 2.0 + - - -
491A ILE* 1.3 97.2 - - + +
493A TYR* 1.3 68.9 + - + +
494A GLU* 3.1 13.6 - - - +
625A PHE* 3.7 28.3 - + - -
627A GLU* 2.6 32.6 + - - +
629A PRO* 5.9 0.3 - - - +
630A VAL* 3.8 19.0 + - + +
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Residues in contact with TYR 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 3.8 20.2 - - + -
390A HIS* 3.4 16.8 - - - -
391A PRO* 4.9 3.1 - - + -
392A ILE* 3.6 15.3 - - + +
489A VAL* 2.9 30.3 + - + +
490A ASP 3.4 8.6 - - - +
492A TYR* 1.3 86.4 - - + +
494A GLU* 1.3 62.3 + - - +
495A GLY 4.2 2.0 - - - +
498A VAL* 3.7 20.2 - - + -
499A VAL* 3.5 39.7 - - + -
502A ASP* 2.8 28.0 + - + -
505A LEU* 4.2 2.5 - - + +
532A ARG* 2.9 28.6 + - + -
535A LEU* 3.8 17.3 - - + -
----------------------------------------------------------
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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