Contacts of the helix formed by residues 469 - 498 (chain B) in PDB entry 5MKE
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 469 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B VAL* 3.3 11.7 - - + +
468B THR* 1.3 94.5 + - - +
470B ASP* 1.3 66.2 + - - +
471B PHE 3.3 2.5 - - - -
472B PHE* 2.9 52.9 + + + +
473B LEU* 3.3 7.5 + - + +
331C CYS* 4.7 16.4 - - - -
346C ASP* 6.1 0.4 - - - -
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Residues in contact with ASP 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B ARG* 2.9 15.7 - - - +
465B TYR* 3.1 27.5 + - - -
466B VAL* 3.0 44.4 + - - +
468B THR 3.3 1.8 - - - -
469B PHE* 1.3 75.2 - - - +
471B PHE* 1.3 67.0 + - + +
473B LEU* 2.6 20.0 + - - +
474B ALA* 2.2 49.5 + - - +
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Residues in contact with PHE 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B TYR* 6.2 2.2 - + - -
466B VAL 4.9 5.4 - - - -
467B THR 5.8 2.0 - - - -
468B THR 4.4 11.2 - - - +
469B PHE 3.3 0.8 - - - -
470B ASP* 1.3 90.7 - - + +
472B PHE* 1.3 64.1 + - + +
474B ALA* 3.8 15.0 - - + -
475B ALA* 3.1 23.5 + - - +
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Residues in contact with PHE 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ILE* 5.7 2.5 - - - +
468B THR 5.8 0.4 - - - -
469B PHE* 2.9 52.7 + + + +
470B ASP 2.9 0.2 + - - -
471B PHE* 1.3 84.5 - - + +
473B LEU* 1.3 58.4 + - - +
475B ALA* 3.2 19.9 - - - +
476B CYS* 4.1 6.1 + - - -
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Residues in contact with LEU 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ILE* 6.0 3.6 - - + -
237B LEU* 4.2 14.4 - - + +
240B GLY* 5.7 6.1 - - - +
241B MET* 5.6 13.7 - - + +
461B LYS* 5.9 5.4 - - + +
464B ARG* 3.4 37.2 - - + +
466B VAL* 3.6 26.9 - - + -
469B PHE* 3.3 5.5 + - + +
470B ASP* 2.6 39.9 + - - +
472B PHE* 1.3 73.0 - - - +
474B ALA* 1.3 67.6 - - + +
475B ALA 3.0 4.8 + - - -
476B CYS* 3.6 11.4 + - - -
477B GLU* 3.1 23.0 + - + +
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Residues in contact with ALA 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B ASP* 2.2 54.6 + - - +
471B PHE* 3.8 13.5 - - + -
473B LEU* 1.3 67.3 - - + +
475B ALA* 1.3 66.4 + - - +
477B GLU* 3.6 17.7 + - + +
478B ILE* 4.0 13.9 + - - +
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Residues in contact with ALA 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B PHE 3.1 22.2 + - - +
472B PHE* 3.2 13.5 - - - +
473B LEU 3.0 0.6 - - - -
474B ALA* 1.3 81.4 - - - +
476B CYS* 1.3 62.0 + - + +
477B GLU 3.3 0.2 + - - -
478B ILE* 4.4 2.6 + - - +
479B ILE* 3.1 27.0 + - + +
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Residues in contact with CYS 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B VAL* 4.1 26.7 - - + -
236B ILE* 4.5 19.7 - - - -
237B LEU* 4.3 16.8 - - - -
472B PHE 4.4 7.2 - - - -
473B LEU* 3.7 12.3 - - - -
475B ALA* 1.3 78.2 - - + +
477B GLU* 1.3 65.6 + - - +
479B ILE* 3.2 17.5 - - + +
480B PHE* 3.0 24.1 + - - +
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Residues in contact with GLU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU* 4.9 0.7 - - + -
464B ARG* 3.4 39.0 + - + +
473B LEU* 3.1 20.3 + - + +
474B ALA* 3.6 14.4 - - - +
475B ALA 3.2 2.0 - - - -
476B CYS* 1.3 74.0 - - - +
478B ILE* 1.3 89.6 + - - +
479B ILE 2.9 6.3 + - - -
480B PHE* 3.0 45.0 + - + -
481B CYS* 3.8 6.2 + - - +
526B ILE* 3.7 24.9 - - - +
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Residues in contact with ILE 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B ALA 4.0 12.4 + - - +
475B ALA 4.5 3.8 - - - +
477B GLU* 1.3 91.8 + - - +
479B ILE* 1.3 60.4 + - + +
481B CYS* 3.0 36.9 - - - -
482B PHE* 3.1 16.1 - - + -
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Residues in contact with ILE 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B VAL* 6.3 1.8 - - + -
475B ALA* 3.1 25.1 - - + +
476B CYS* 3.2 18.4 - - + +
477B GLU 2.9 1.2 - - - -
478B ILE* 1.3 82.0 - - + +
480B PHE* 1.3 70.2 + - + +
482B PHE* 3.1 39.8 - - + -
483B PHE* 3.3 12.4 + - + +
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Residues in contact with PHE 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PHE* 3.5 28.0 - + + -
233B VAL* 4.4 9.6 - - + -
234B LEU* 4.8 7.9 - - + -
237B LEU* 3.5 29.6 - - + -
464B ARG* 5.4 3.6 - - - -
476B CYS 3.0 19.3 + - - +
477B GLU* 3.0 46.2 - - + -
479B ILE* 1.3 79.0 - - + +
481B CYS* 1.3 67.3 + - + +
483B PHE* 2.6 28.3 + - - -
484B ILE* 2.9 32.8 + - + +
522B ILE* 5.3 11.7 - - + -
525B ASN* 6.0 4.7 - - - -
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Residues in contact with CYS 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B GLU* 3.8 5.6 + - - +
478B ILE* 3.0 51.8 - - - -
480B PHE* 1.3 94.0 - - + +
482B PHE* 1.3 61.8 + - - +
484B ILE* 4.8 2.6 - - - +
485B PHE* 3.2 20.1 + - - +
522B ILE* 5.7 15.0 - - + +
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Residues in contact with PHE 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B ILE* 3.1 28.0 - - + -
479B ILE* 3.1 37.5 - - + -
481B CYS* 1.3 82.5 - - - +
483B PHE* 1.3 70.5 + + + +
485B PHE* 3.2 23.7 - - + +
486B TYR* 3.2 45.8 + + + +
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Residues in contact with PHE 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR* 3.5 26.2 - - + -
230B PHE* 3.4 44.6 - + + -
479B ILE* 3.3 11.2 + - + +
480B PHE* 2.6 27.6 + - - +
482B PHE* 1.3 71.9 - + + +
484B ILE* 1.3 63.4 + - + +
486B TYR* 2.8 44.6 + + - +
487B TYR* 3.2 44.0 + + - -
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Residues in contact with ILE 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PHE* 3.3 42.2 - - + -
234B LEU* 5.6 1.1 - - + -
480B PHE* 2.9 46.8 + - + +
481B CYS* 4.8 2.0 - - - +
483B PHE* 1.3 74.6 - - + +
485B PHE* 1.3 50.7 + - - +
487B TYR* 2.6 45.8 + - + +
488B VAL* 2.7 25.9 + - + +
514B ILE* 6.4 1.8 - - + -
518B SER* 4.5 23.3 - - - +
522B ILE* 4.5 16.4 - - + -
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Residues in contact with PHE 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B CYS 3.2 19.0 + - - +
482B PHE* 3.2 22.0 - - + +
483B PHE 3.1 0.2 - - - -
484B ILE* 1.3 77.8 - - - +
486B TYR* 1.3 74.3 + + - +
488B VAL* 3.3 31.2 + - + +
489B VAL* 3.8 19.7 + - + +
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Residues in contact with TYR 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B PHE* 3.2 48.7 + + + +
483B PHE* 2.8 27.9 + + - +
485B PHE* 1.3 91.6 - + - +
487B TYR* 1.3 64.9 + - + +
488B VAL 3.3 0.3 + - - -
489B VAL* 3.8 1.7 + - - +
490B GLU* 3.7 23.7 + - - +
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Residues in contact with TYR 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B GLU* 4.7 6.7 - - + -
226B THR* 2.7 34.0 + - - -
227B TYR* 4.2 31.1 + + - -
230B PHE* 5.0 7.0 - + - -
483B PHE* 3.2 27.7 - + - -
484B ILE* 2.6 40.6 + - + +
486B TYR* 1.3 73.1 - - + +
488B VAL* 1.3 61.8 + - - +
490B GLU* 2.9 29.9 - - - +
491B GLU* 2.6 29.5 - - - +
515B VAL* 5.8 1.9 - - - +
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Residues in contact with VAL 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B ILE* 2.7 30.8 + - + +
485B PHE* 3.3 26.9 - - + +
486B TYR 3.2 0.6 - - - -
487B TYR* 1.3 76.4 - - - +
489B VAL* 1.3 71.4 + - + +
491B GLU* 4.0 1.6 + - - +
492B ILE* 3.1 36.0 + - + +
515B VAL* 5.4 14.3 - - + +
518B SER* 5.9 0.2 - - - +
519B VAL* 5.0 17.5 - - + -
522B ILE* 6.0 2.0 - - + -
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Residues in contact with VAL 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B PHE* 3.8 20.8 + - + +
486B TYR 3.8 3.7 + - - +
487B TYR 3.5 0.2 - - - -
488B VAL* 1.3 86.4 - - + +
490B GLU* 1.3 67.4 + - - +
492B ILE* 2.8 27.1 + - + +
493B LEU* 3.2 13.4 + - + +
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Residues in contact with GLU 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B GLU* 5.4 2.1 - - - +
227B TYR* 5.5 0.5 + - - -
486B TYR* 3.7 16.4 + - - +
487B TYR* 2.9 37.5 - - - +
488B VAL 3.4 0.2 - - - -
489B VAL* 1.3 79.9 - - - +
491B GLU* 1.3 86.5 + - - +
493B LEU* 3.8 8.2 + - - +
494B GLU* 3.4 24.3 + - - +
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Residues in contact with GLU 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B TYR* 5.3 4.5 + - - -
487B TYR* 2.6 32.2 - - - +
488B VAL 4.2 1.5 - - - +
489B VAL 3.3 0.2 - - - -
490B GLU* 1.3 95.2 - - - +
492B ILE* 1.3 60.5 + - + +
493B LEU 3.2 0.4 - - - -
494B GLU* 2.8 42.3 + - + +
495B ILE* 2.9 18.8 + - + +
512B VAL* 4.9 20.4 - - + -
515B VAL* 5.5 8.7 - - + +
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Residues in contact with ILE 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B VAL* 3.1 37.0 - - + +
489B VAL* 2.8 24.0 + - + +
491B GLU* 1.3 76.9 - - - +
493B LEU* 1.3 62.1 + - - +
495B ILE* 3.1 35.5 + - + +
496B ARG* 3.9 5.5 + - - +
515B VAL* 5.9 6.7 - - + -
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Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B VAL* 3.2 11.5 + - + +
490B GLU* 3.9 10.3 - - - +
491B GLU 3.2 0.2 - - - -
492B ILE* 1.3 76.4 - - - +
494B GLU* 1.3 61.5 + - + +
495B ILE 3.1 0.7 + - - -
496B ARG* 3.4 7.6 + - + +
497B ILE* 3.1 45.6 + - + +
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Residues in contact with GLU 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B GLU* 3.4 19.2 - - - +
491B GLU* 2.8 32.4 + - + +
493B LEU* 1.3 74.8 - - + +
495B ILE* 1.3 58.0 + - - +
496B ARG 3.5 0.2 - - - -
497B ILE* 3.7 21.3 - - + -
498B HIS* 3.0 35.1 + - + +
502B TYR* 5.3 0.5 - - - -
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Residues in contact with ILE 495 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B GLU* 2.9 15.7 + - + +
492B ILE* 3.2 35.4 - - + +
493B LEU 3.1 0.8 - - - -
494B GLU* 1.3 79.5 - - - +
496B ARG* 1.3 64.0 + - + +
498B HIS 2.6 25.9 - - - +
499B LYS* 3.6 7.9 + - + +
502B TYR* 4.5 20.0 - - + +
512B VAL* 6.3 2.9 - - + -
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Residues in contact with ARG 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B ILE 3.9 4.0 + - - +
493B LEU* 3.4 10.0 + - + +
495B ILE* 1.3 81.6 - - + +
497B ILE* 1.3 64.6 + - - +
498B HIS* 4.5 1.0 - - - -
499B LYS* 5.0 5.1 + - - +
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Residues in contact with ILE 497 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B LEU* 3.1 46.0 + - + +
494B GLU* 3.7 21.5 - - + +
496B ARG* 1.3 77.6 - - - +
498B HIS* 1.3 90.8 + - + +
499B LYS 4.1 0.7 + - - -
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Residues in contact with HIS 498 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B GLU* 3.0 19.4 + - + +
495B ILE 2.6 17.5 - - - +
497B ILE* 1.3 105.3 - - + +
499B LYS* 1.3 58.1 + - - +
501B HIS* 3.0 50.0 + + + -
502B TYR* 3.0 22.7 - - + +
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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