Contacts of the helix formed by residues 473 - 505 (chain B) in PDB entry 3DYQ
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 PRO 473 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B THR* 3.2 20.6 - - + +
470B LYS 5.0 1.8 - - - +
471B LEU 3.7 7.6 - - - +
472B PHE* 1.3 86.7 - - - +
474B MET* 1.3 74.6 + - + +
475B VAL 3.1 0.2 - - - -
476B GLU* 3.1 21.9 + - - +
477B GLU* 4.4 0.9 + - - +
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Residues in contact with MET 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 3.3 43.7 - - + +
271B CYS* 4.4 7.9 - - - -
272B SER* 6.0 2.0 - - - +
472B PHE* 3.7 29.8 - - + +
473B PRO* 1.3 88.3 - - + +
475B VAL* 1.3 63.7 + - - +
476B GLU 3.2 1.0 + - - -
477B GLU* 3.5 7.1 + - - +
478B ILE* 3.5 24.3 + - + +
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Residues in contact with VAL 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B MET* 4.9 4.5 - - - -
270B LEU* 4.2 15.9 - - + -
271B CYS* 3.7 29.6 - - - -
465B PHE* 4.1 24.2 - - + +
468B VAL* 4.5 9.6 - - + -
469B THR* 3.5 16.2 - - - +
472B PHE* 2.9 21.8 + - + +
474B MET* 1.3 76.9 - - - +
476B GLU* 1.3 58.5 + - - +
479B MET* 2.8 41.8 + - + +
480B LEU* 3.3 4.0 + - + +
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Residues in contact with GLU 476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B THR* 3.6 24.1 + - + +
473B PRO 3.1 14.5 + - - +
475B VAL* 1.3 78.6 - - - +
477B GLU* 1.3 65.1 + - - +
480B LEU* 3.1 31.8 + - + +
481B GLN* 3.2 9.5 + - - +
484B TRP* 4.0 28.9 - - + -
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Residues in contact with GLU 477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B PRO 4.4 0.8 + - - +
474B MET* 3.5 8.7 + - - +
475B VAL 3.4 0.2 - - - -
476B GLU* 1.3 80.6 - - - +
478B ILE* 1.3 79.0 + - + +
481B GLN* 3.4 23.8 - - + +
482B PRO* 4.0 1.2 - - - +
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Residues in contact with ILE 478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PRO* 3.5 32.8 - - + +
270B LEU* 3.7 35.0 - - + -
407B VAL 4.6 1.9 - - - +
474B MET* 3.5 16.9 + - + +
476B GLU 3.3 0.6 - - - -
477B GLU* 1.3 100.8 - - + +
479B MET* 1.3 61.3 + - + +
482B PRO* 3.1 17.4 - - - +
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Residues in contact with MET 479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PRO* 5.4 2.0 - - + -
263B MET* 4.3 15.5 - - + +
267B MET* 2.9 40.4 - - + -
270B LEU* 3.4 29.8 - - + -
407B VAL* 3.6 30.1 - - + +
465B PHE* 3.7 25.6 - - + -
475B VAL* 2.8 26.0 + - + +
478B ILE* 1.3 85.9 - - + +
480B LEU* 1.3 64.2 + - - +
482B PRO* 3.3 11.2 - - - +
483B LEU* 3.3 22.8 + - - +
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Residues in contact with LEU 480 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B ILE* 3.9 27.8 - - + +
465B PHE* 3.9 25.8 - - + -
466B GLU* 4.1 24.5 - - + -
469B THR* 3.7 24.7 - - + +
475B VAL 3.3 3.1 + - - +
476B GLU* 3.1 27.4 + - + +
479B MET* 1.3 75.0 - - - +
481B GLN* 1.3 60.8 + - - +
483B LEU* 2.9 9.2 + - + +
484B TRP* 2.8 56.9 + - + +
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Residues in contact with GLN 481 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B GLU 3.2 7.9 + - - +
477B GLU* 3.4 19.3 - - + +
480B LEU* 1.3 75.2 - - - +
482B PRO* 1.3 70.4 - - + +
484B TRP* 3.0 34.3 + - + +
485B GLU* 2.9 63.1 + - - +
----------------------------------------------------------
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Residues in contact with PRO 482 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLU 4.2 3.8 - - - +
407B VAL 3.3 27.6 - - - +
408B ARG 4.9 4.5 - - - +
409B PRO* 6.2 0.2 - - + -
477B GLU 4.0 1.3 - - - +
478B ILE 3.1 25.1 - - - +
479B MET* 3.3 15.5 - - - +
481B GLN* 1.3 96.5 - - + +
483B LEU* 1.3 56.3 + - - +
485B GLU* 3.3 15.4 + - + +
486B SER* 2.9 29.8 + - - -
----------------------------------------------------------
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Residues in contact with LEU 483 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLU* 3.7 37.9 - - + +
407B VAL* 3.9 9.2 - - + +
457B ILE* 3.7 10.8 - - + +
461B LEU* 3.9 32.3 - - + +
462B ILE* 4.2 11.4 - - + +
465B PHE* 3.6 33.2 - - + -
479B MET 3.3 15.2 + - - +
480B LEU* 2.9 18.9 + - + +
482B PRO* 1.3 78.8 - - - +
484B TRP* 1.3 59.4 - - - +
486B SER* 3.4 2.4 + - - -
487B ARG* 3.0 28.4 + - - +
----------------------------------------------------------
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Residues in contact with TRP 484 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B ILE* 3.8 20.5 - - + +
466B GLU* 5.3 3.6 + - - -
476B GLU* 4.0 30.7 - - + -
480B LEU* 2.8 46.8 + - + +
481B GLN* 3.0 41.9 + - + +
483B LEU* 1.3 69.6 - - - +
485B GLU* 1.3 65.1 - - - +
487B ARG* 3.2 40.5 + - - +
488B ASP* 3.0 31.3 + - - +
----------------------------------------------------------
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Residues in contact with GLU 485 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B GLN* 2.9 47.8 + - - +
482B PRO* 3.6 17.2 - - + +
484B TRP* 1.3 75.2 - - - +
486B SER* 1.3 58.0 + - - +
488B ASP* 3.3 7.0 + - - +
489B ARG* 2.9 30.2 + - - +
----------------------------------------------------------
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Residues in contact with SER 486 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLU* 2.6 35.0 + - - -
410B MET* 6.5 1.3 - - - -
457B ILE* 3.4 8.1 - - - +
482B PRO 2.9 17.7 + - - -
483B LEU* 3.8 4.7 - - - -
485B GLU* 1.3 73.8 - - - +
487B ARG* 1.3 68.2 + - - +
489B ARG* 3.2 8.2 + - - +
490B TYR* 2.8 40.6 + - - -
----------------------------------------------------------
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Residues in contact with ARG 487 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B ILE* 4.9 3.5 - - + +
457B ILE* 3.8 21.4 - - + +
458B LYS* 4.0 28.7 - - + +
462B ILE* 4.0 10.4 - - + +
483B LEU 3.0 17.8 + - - +
484B TRP* 3.2 44.1 + - - +
486B SER* 1.3 78.1 - - - +
488B ASP* 1.3 83.1 + - - +
490B TYR* 3.1 2.9 + - - +
491B GLU* 2.8 50.7 + - + +
----------------------------------------------------------
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Residues in contact with ASP 488 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B TRP* 3.0 18.8 + - - +
485B GLU* 3.7 6.8 - - - +
487B ARG* 1.3 106.6 + - - +
489B ARG* 1.3 66.8 - - - +
491B GLU* 3.6 10.9 + - - +
492B GLU* 3.1 24.3 + - - +
495B ARG* 4.8 1.6 + - - -
----------------------------------------------------------
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Residues in contact with ARG 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B MET* 3.8 48.2 - - - +
414B GLU* 3.9 19.0 + - - +
485B GLU 2.9 18.8 + - - +
486B SER* 3.5 8.5 - - - +
488B ASP* 1.3 76.9 - - - +
490B TYR* 1.3 92.4 + - + +
492B GLU* 3.2 8.1 + - - +
493B LEU* 2.9 51.5 + - + +
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Residues in contact with TYR 490 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLU* 3.6 16.5 + - - -
414B GLU* 3.8 14.5 - - + +
417B VAL* 3.6 20.0 - - + +
449B LYS* 4.3 21.7 - - + +
450B ALA* 3.7 19.4 - - - +
453B GLN* 3.9 19.3 - - + -
454B ILE* 3.5 27.7 - - + +
457B ILE* 4.0 2.5 - - + -
486B SER* 2.8 42.5 + - - +
487B ARG* 3.8 2.9 - - - +
489B ARG* 1.3 102.2 + - - +
491B GLU* 1.3 65.2 + - - +
493B LEU* 3.3 19.3 + - + +
494B LYS 3.0 17.8 + - - -
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Residues in contact with GLU 491 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B ILE* 3.9 21.3 - - + +
458B LYS* 2.8 36.9 + - - -
487B ARG* 2.8 43.5 + - + +
488B ASP* 4.0 10.2 - - - +
490B TYR* 1.3 70.0 - - - +
492B GLU* 1.3 58.0 + - - +
494B LYS* 3.1 4.6 + - - +
495B ARG* 2.9 47.8 + - - +
----------------------------------------------------------
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Residues in contact with GLU 492 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B ASP 3.1 19.1 + - - +
489B ARG* 3.2 7.8 + - - +
491B GLU* 1.3 74.8 - - - +
493B LEU* 1.3 66.8 + - + +
495B ARG* 3.2 33.9 + - - +
496B ILE* 3.1 46.1 + - + +
----------------------------------------------------------
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Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LYS* 6.4 0.4 - - + -
450B ALA* 4.3 9.9 - - + -
489B ARG* 2.9 49.2 + - + +
490B TYR* 3.3 31.4 + - + +
492B GLU* 1.3 74.2 - - + +
494B LYS* 1.3 57.8 + - - +
496B ILE* 3.2 20.8 + - + +
497B ASP* 2.8 37.3 + - - +
----------------------------------------------------------
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Residues in contact with LYS 494 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B ALA* 4.0 8.0 - - + +
451B THR* 4.2 24.2 - - + -
454B ILE* 3.8 21.5 - - + -
490B TYR 3.0 13.5 + - - +
491B GLU* 3.1 7.8 + - - +
493B LEU* 1.3 73.6 - - - +
495B ARG* 1.3 60.5 + - - +
497B ASP* 4.2 7.4 - - + -
498B ASP* 2.5 66.8 + - - +
----------------------------------------------------------
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Residues in contact with ARG 495 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B ASP 4.8 1.4 + - - -
491B GLU* 2.9 24.1 + - - +
492B GLU* 3.2 47.4 + - - +
494B LYS* 1.3 75.6 - - - +
496B ILE* 1.3 56.6 + - + +
498B ASP* 3.6 8.2 + - - +
499B ALA* 3.1 24.9 + - - +
----------------------------------------------------------
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Residues in contact with ILE 496 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B GLU* 3.1 38.8 + - + +
493B LEU* 3.4 21.5 - - + +
494B LYS 3.1 0.4 - - - -
495B ARG* 1.3 75.1 - - + +
497B ASP* 1.3 71.9 + - - +
498B ASP 3.1 1.3 - - - -
499B ALA* 2.8 19.3 + - + +
500B MET* 2.9 27.7 + - + +
----------------------------------------------------------
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Residues in contact with ASP 497 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B THR* 4.4 22.5 + - + +
450B ALA* 4.4 11.3 - - - +
493B LEU* 2.8 28.0 + - - +
494B LYS* 3.7 8.2 - - + +
496B ILE* 1.3 73.6 - - - +
498B ASP* 1.3 60.2 + - - +
500B MET* 3.0 6.9 + - - +
501B LYS* 2.8 54.8 + - + +
----------------------------------------------------------
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Residues in contact with ASP 498 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B LYS* 2.5 55.1 + - - +
495B ARG* 3.6 7.5 - - - +
497B ASP* 1.3 79.4 - - - +
499B ALA* 1.3 59.3 + - - +
501B LYS* 3.8 13.3 - - - +
502B GLU* 2.9 31.4 + - - +
----------------------------------------------------------
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Residues in contact with ALA 499 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B ARG 3.1 13.3 + - - +
496B ILE* 2.8 14.7 + - + +
498B ASP* 1.3 75.2 - - - +
500B MET* 1.3 58.5 + - + +
502B GLU* 4.0 5.0 - - - +
503B LEU* 3.1 28.1 + - - +
----------------------------------------------------------
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Residues in contact with MET 500 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B ILE* 2.9 28.7 + - + +
497B ASP* 3.3 8.7 - - - +
499B ALA* 1.3 73.7 - - - +
501B LYS* 1.3 79.8 + - - +
503B LEU* 2.6 31.1 + - - +
504B GLN* 3.1 26.4 + - - +
----------------------------------------------------------
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Residues in contact with LYS 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B THR* 6.1 2.0 - - - +
497B ASP* 2.8 66.0 + - + +
498B ASP* 3.8 15.9 - - - +
500B MET* 1.3 81.0 - - - +
502B GLU* 1.3 62.7 + - - +
504B GLN* 3.2 12.5 + - - +
505B LYS* 3.3 42.2 + - - +
----------------------------------------------------------
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Residues in contact with GLU 502 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B ASP 2.9 19.7 + - - +
499B ALA* 4.0 6.5 - - - +
501B LYS* 1.3 77.2 - - - +
503B LEU* 1.3 62.2 + - - +
504B GLN 3.3 0.7 + - - -
505B LYS* 3.7 21.1 + - - +
----------------------------------------------------------
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Residues in contact with LEU 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B ALA 3.1 20.3 + - - +
500B MET* 2.6 30.8 + - + +
502B GLU* 1.3 73.0 - - - +
504B GLN* 1.3 63.1 + - - +
505B LYS 5.0 0.2 - - - +
----------------------------------------------------------
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Residues in contact with GLN 504 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B MET* 3.1 37.7 + - - +
501B LYS* 3.8 8.5 + - - +
503B LEU* 1.3 85.1 - - - +
505B LYS* 1.3 82.3 + - + +
----------------------------------------------------------
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Residues in contact with LYS 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B LYS* 3.3 49.8 + - - +
502B GLU* 3.7 19.6 - - - +
503B LEU 5.0 0.3 - - - +
504B GLN* 1.3 100.1 + - + +
----------------------------------------------------------
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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