Contacts of the helix formed by residues 465 - 495 (chain B) in PDB entry 4S15
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 GLY 465 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B GLU* 2.8 14.5 + - - +
464B ASP* 1.3 77.5 - - - +
466B ILE* 1.3 63.7 + - - +
467B LEU 3.6 0.7 - - - -
468B THR* 4.1 11.6 - - - -
469B LYS* 3.4 20.6 + - - +
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Residues in contact with ILE 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B MET* 3.7 34.3 - - + +
415B LEU* 4.9 0.7 - - + -
457B LEU* 3.7 30.3 - - + -
462B ARG* 3.7 33.9 - - + +
463B GLU* 3.2 34.2 + - + +
464B ASP 3.4 0.2 - - - -
465B GLY* 1.3 77.4 - - - +
467B LEU* 1.3 67.9 + - - +
469B LYS* 3.1 10.3 + - + +
470B LEU* 2.9 22.5 + - + +
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Residues in contact with LEU 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B GLN* 4.3 23.8 - - + +
453B LEU* 4.1 27.8 - - + -
454B GLN* 3.8 41.5 - - + +
457B LEU* 3.9 18.9 - - + +
464B ASP 4.5 6.5 + - - +
466B ILE* 1.3 77.7 - - - +
468B THR* 1.3 65.3 + - - +
470B LEU* 3.1 5.6 + - + +
471B ILE* 3.0 47.4 + - + +
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Residues in contact with THR 468 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B ASP 4.3 8.3 + - - -
465B GLY* 4.0 13.0 + - - -
466B ILE 3.2 0.6 - - - -
467B LEU* 1.3 79.5 - - - +
469B LYS* 1.3 63.1 + - - +
471B ILE* 3.4 8.3 + - - +
472B CYS* 3.2 29.6 + - - -
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Residues in contact with LYS 469 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B SER* 4.8 2.8 + - - -
412B SER* 4.3 11.3 + - - -
413B MET* 3.8 37.9 - - + -
465B GLY 3.4 13.4 + - - +
466B ILE* 3.1 13.3 + - + +
468B THR* 1.3 80.1 - - - +
470B LEU* 1.3 62.2 + - - +
472B CYS* 3.3 11.4 + - + +
473B LYS* 3.2 50.6 + - - +
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Residues in contact with LEU 470 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU* 4.0 11.2 - - + -
413B MET* 3.8 24.0 - - + -
415B LEU* 3.9 34.1 - - + -
419B GLU* 5.6 0.4 - - + +
423B PHE* 3.5 35.8 - - + -
453B LEU* 4.3 18.2 - - + -
457B LEU* 4.2 27.4 - - + -
466B ILE* 2.9 13.1 + - + +
467B LEU* 3.1 11.4 + - + +
469B LYS* 1.3 77.4 - - - +
471B ILE* 1.3 63.3 + - + +
473B LYS* 3.1 18.4 + - + +
474B VAL 3.4 5.2 + - - -
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Residues in contact with ILE 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B PHE* 5.5 1.1 - - + -
426B PHE* 3.7 36.3 - - + -
450B GLN* 4.7 10.1 - - - +
453B LEU* 5.8 1.6 - - + -
467B LEU* 3.0 36.7 + - + +
468B THR* 3.8 7.6 - - - +
470B LEU* 1.3 77.0 - - + +
472B CYS* 1.3 62.9 + - - +
474B VAL* 3.2 22.3 + - + +
475B SER* 4.1 3.1 + - - -
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Residues in contact with CYS 472 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B THR* 3.2 26.8 + - - -
469B LYS* 3.4 13.9 - - + +
470B LEU 3.2 0.2 - - - -
471B ILE* 1.3 78.6 - - - +
473B LYS* 1.3 63.7 + - + +
474B VAL 3.2 1.2 + - - -
475B SER* 3.2 17.0 + - - -
476B THR* 3.6 9.7 + - - -
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Residues in contact with LYS 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B PHE* 4.1 19.0 - - + -
409B SER* 3.2 43.3 + - - +
410B LEU* 4.4 13.5 - - + +
413B MET* 4.6 3.6 - - - -
423B PHE* 4.3 10.5 - - + -
469B LYS* 3.2 46.4 + - - +
470B LEU* 3.1 15.6 + - - +
472B CYS* 1.3 75.8 - - + +
474B VAL* 1.3 58.5 + - - +
476B THR* 3.1 14.2 + - + +
477B LEU* 2.8 32.9 + - - +
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Residues in contact with VAL 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B GLU* 5.5 2.0 - - - +
423B PHE* 4.0 16.8 - - + -
426B PHE* 4.0 22.4 - - + -
427B VAL* 4.1 14.4 - - + -
470B LEU 3.7 10.1 - - - +
471B ILE* 3.3 18.4 - - + +
472B CYS 3.1 0.4 - - - -
473B LYS* 1.3 77.0 - - - +
475B SER* 1.3 63.9 + - - +
477B LEU* 3.3 11.7 + - - +
478B ARG* 3.1 47.5 + - + +
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Residues in contact with SER 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ILE 4.1 2.3 + - - -
472B CYS* 3.2 11.9 + - - -
474B VAL* 1.3 80.0 - - - +
476B THR* 1.3 62.1 + - - +
478B ARG* 3.4 11.7 + - - +
479B ALA* 3.2 21.0 + - - +
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Residues in contact with THR 476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B PHE* 4.0 25.5 - - + -
406B PHE* 3.8 27.1 - - + -
472B CYS 3.7 9.7 + - - -
473B LYS* 3.1 19.8 + - + +
475B SER* 1.3 77.6 - - - +
477B LEU* 1.3 58.9 + - - +
479B ALA* 3.1 6.5 + - - +
480B LEU* 2.9 29.5 + - + +
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Residues in contact with LEU 477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B GLU* 3.5 40.2 - - + +
365B PHE* 3.7 17.7 - - + -
366B ILE* 3.7 28.9 - - + -
406B PHE* 3.5 26.0 - - + -
423B PHE* 4.2 9.6 - - + -
427B VAL* 4.1 16.6 - - + -
473B LYS 2.8 16.5 + - - +
474B VAL* 3.5 9.6 - - - +
476B THR* 1.3 76.7 - - - +
478B ARG* 1.3 58.2 + - - +
480B LEU* 3.3 6.5 + - + +
481B CYS* 3.0 34.7 + - - -
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Residues in contact with ARG 478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B GLU* 3.4 19.3 + - - +
427B VAL 5.4 0.2 + - - -
430B SER* 2.8 19.6 + - - -
432B ASP* 2.6 49.1 + - - -
433B ARG* 3.4 24.0 - - - +
474B VAL* 3.1 35.1 + - - +
475B SER* 3.7 10.5 - - - +
476B THR 3.2 0.4 - - - -
477B LEU* 1.3 76.1 - - - +
479B ALA* 1.3 57.5 + - - +
481B CYS* 3.5 2.7 + - - +
482B GLY* 2.9 26.7 + - - -
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Residues in contact with ALA 479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B PHE* 4.1 18.8 - - + -
475B SER 3.2 11.8 + - - +
476B THR* 3.1 10.2 + - - +
478B ARG* 1.3 76.1 - - - +
480B LEU* 1.3 59.3 + - - +
482B GLY* 3.8 1.6 - - - +
483B ARG* 2.9 30.5 + - - +
486B GLU* 5.4 0.2 - - - +
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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
----------------------------------------------------------
365B PHE* 4.0 29.8 - - + -
399B PHE* 3.6 16.6 - - + -
402B PHE* 3.6 30.9 - - + -
403B VAL* 3.8 35.0 - - + +
406B PHE* 3.6 43.3 - - + -
476B THR* 2.9 13.1 + - + +
477B LEU* 3.5 10.5 - - + +
479B ALA* 1.3 76.3 - - - +
481B CYS* 1.3 57.7 + - - +
483B ARG* 3.2 2.2 + - - -
484B HIS* 3.0 23.9 + - - +
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Residues in contact with CYS 481 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ALA 4.9 5.4 - - - +
361B LEU* 3.8 23.5 - - + +
362B GLU* 3.4 42.4 - - + +
365B PHE* 4.0 6.1 - - - -
477B LEU 3.0 21.0 + - - +
478B ARG* 4.0 4.3 - - - +
480B LEU* 1.3 72.7 - - - +
482B GLY* 1.3 67.4 + - - +
484B HIS* 3.2 10.4 + - - +
485B THR* 3.1 25.0 + - - -
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Residues in contact with GLY 482 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B ARG 2.9 18.9 + - - -
479B ALA* 3.8 2.2 - - - -
481B CYS* 1.3 76.0 - - - +
483B ARG* 1.3 56.7 + - - +
485B THR* 3.4 8.0 + - - -
486B GLU* 3.1 34.5 + - - +
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Residues in contact with ARG 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ASP* 3.3 38.7 + - - +
399B PHE* 3.7 29.2 - - + +
402B PHE* 3.8 33.2 - - - +
479B ALA 2.9 17.1 + - - +
480B LEU* 3.6 5.2 - - - +
481B CYS 3.2 0.2 - - - -
482B GLY* 1.3 75.7 - - - +
484B HIS* 1.3 66.5 + - - +
486B GLU* 3.2 26.3 + - + +
487B LYS* 3.0 33.2 + - + +
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Residues in contact with HIS 484 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B TRP* 5.4 0.2 - + - -
327B ILE* 4.3 9.6 - - + +
361B LEU* 3.4 31.4 - - + +
365B PHE* 5.1 2.2 - + + -
399B PHE* 3.7 18.7 - + + -
480B LEU 3.0 13.3 + - - +
481B CYS 3.4 8.6 + - - +
483B ARG* 1.3 75.9 - - - +
485B THR* 1.3 62.2 + - - +
487B LYS* 3.3 3.4 + - - +
488B LEU* 2.9 38.3 + - + +
507B TYR* 2.9 39.2 + + - -
511B PHE* 4.1 22.0 - + - -
601B 4D8 4.2 25.1 - - + +
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Residues in contact with THR 485 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B CYS 3.1 12.6 + - - -
482B GLY* 3.6 10.7 - - - -
484B HIS* 1.3 79.7 + - - +
486B GLU* 1.3 65.8 + - - +
488B LEU* 3.8 7.1 - - - +
489B MET* 2.9 46.5 + - + +
511B PHE* 4.9 14.1 + - - +
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Residues in contact with GLU 486 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B ALA 5.4 0.2 - - - +
482B GLY 3.1 19.1 + - - +
483B ARG* 3.4 34.0 + - - +
485B THR* 1.3 75.2 - - - +
487B LYS* 1.3 70.0 + - + +
489B MET* 4.2 3.3 - - - +
490B ALA* 3.2 22.9 + - - +
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Residues in contact with LYS 487 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B TRP* 3.6 21.5 - - + -
395B GLY 5.0 4.4 + - - +
396B CYS* 3.9 32.8 - - + +
399B PHE* 4.5 15.9 - - + +
483B ARG* 3.0 25.7 + - + +
484B HIS* 3.8 5.2 - - - +
486B GLU* 1.3 84.3 - - + +
488B LEU* 1.3 60.9 + - - +
490B ALA* 3.4 8.0 + - + +
491B PHE* 2.9 29.6 + - - +
601B 4D8 5.0 2.2 - - + -
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Residues in contact with LEU 488 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B TRP* 3.6 17.2 - - + -
484B HIS* 2.9 23.1 + - + +
485B THR* 3.8 4.9 - - - +
487B LYS* 1.3 76.3 - - - +
489B MET* 1.3 68.0 + - + +
491B PHE* 3.2 4.8 + - + +
492B LYS* 2.8 27.5 + - + +
499B VAL* 5.0 4.9 - - + -
503B PHE* 4.0 15.9 - - + -
507B TYR* 3.5 44.0 - - + +
511B PHE* 3.7 24.9 - - + -
512B THR* 3.7 17.3 - - + -
----------------------------------------------------------
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Residues in contact with MET 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B THR* 2.9 33.5 + - + +
486B GLU* 4.2 3.8 - - - +
488B LEU* 1.3 91.9 - - + +
490B ALA* 1.3 58.0 + - - +
492B LYS* 3.4 21.5 + - - +
493B ALA* 3.0 27.5 + - - +
511B PHE 3.0 28.7 - - - +
512B THR* 3.6 23.8 - - + +
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Residues in contact with ALA 490 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B GLU 3.2 18.6 + - - +
487B LYS* 3.6 12.3 - - + +
489B MET* 1.3 75.1 - - - +
491B PHE* 1.3 65.2 + - - +
493B ALA* 3.4 14.9 + - - +
494B ILE* 3.5 22.3 + - + +
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Residues in contact with PHE 491 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ARG* 4.1 5.2 - - + -
317B GLU* 3.7 24.2 - - + -
320B TRP* 3.5 55.9 - + + -
487B LYS 2.9 17.6 + - - +
488B LEU* 3.5 5.6 - - + +
490B ALA* 1.3 77.0 - - - +
492B LYS* 1.3 59.1 + - - +
494B ILE* 3.0 5.6 + - - -
495B TYR* 2.8 67.5 + + + -
498B ILE* 4.2 6.3 - - + -
499B VAL* 3.8 18.8 - - + -
503B PHE* 3.6 26.7 - + - -
----------------------------------------------------------
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Residues in contact with LYS 492 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B LEU* 2.8 18.3 + - + +
489B MET* 3.7 22.9 - - - +
490B ALA 3.3 0.2 - - - -
491B PHE* 1.3 75.3 - - - +
493B ALA* 1.3 61.8 + - - +
495B TYR 4.4 0.9 - - - +
496B PRO* 3.1 33.8 - - + +
499B VAL* 4.0 41.1 - - + -
512B THR* 4.1 29.8 + - + -
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Residues in contact with ALA 493 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B MET 3.0 13.8 + - - +
490B ALA* 3.5 13.2 - - - +
491B PHE 3.2 0.2 - - - -
492B LYS* 1.3 76.5 - - - +
494B ILE* 1.3 62.3 + - + +
496B PRO* 4.0 7.3 - - - +
----------------------------------------------------------
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Residues in contact with ILE 494 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ARG* 5.1 11.2 - - - +
490B ALA* 3.5 17.0 + - + +
491B PHE* 3.0 7.2 + - - +
493B ALA* 1.3 79.6 - - + +
495B TYR* 1.3 90.7 + - + +
496B PRO* 3.3 9.6 - - - +
----------------------------------------------------------
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Residues in contact with TYR 495 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ARG* 4.2 26.2 + - - +
317B GLU* 3.6 38.3 + - + -
491B PHE* 2.8 50.9 + + + +
492B LYS 3.5 3.1 - - - -
494B ILE* 1.3 105.4 - - + +
496B PRO* 1.3 65.0 - - - +
497B ASP 3.3 2.5 - - - -
498B ILE* 3.2 26.6 + - + -
499B VAL* 3.3 14.7 + - - +
----------------------------------------------------------
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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