Contacts of the helix formed by residues 469 - 498 (chain C) in PDB entry 5MKF
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C ILE* 4.2 21.1 - - + -
239C TYR* 5.6 9.0 - + - -
240C GLY* 4.0 27.8 - - - -
466C VAL* 3.6 3.5 + - + +
468C THR* 1.3 85.2 - - + +
470C ASP* 1.3 66.6 + - - +
471C PHE 3.5 0.4 - - - -
472C PHE* 3.2 32.2 + + + +
473C LEU* 3.2 32.7 + - + -
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Residues in contact with ASP 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C LYS* 5.3 2.1 + - - -
464C ARG* 2.9 29.3 + - - +
465C TYR* 3.0 21.0 - - - -
466C VAL* 3.2 30.2 + - + +
469C PHE* 1.3 75.2 - - - +
471C PHE* 1.3 58.0 + - + +
472C PHE 2.9 4.9 - - - -
473C LEU* 2.5 25.9 + - - +
474C ALA* 2.4 55.5 + - - +
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Residues in contact with PHE 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C TYR* 5.4 17.3 - + + -
466C VAL 4.2 2.7 - - - -
467C THR* 3.3 51.4 - - + -
468C THR 4.8 3.1 - - - +
469C PHE 3.5 0.4 - - - -
470C ASP* 1.3 79.3 - - + +
472C PHE* 1.3 64.9 + - + +
474C ALA* 4.6 2.9 - - + +
475C ALA* 3.1 28.4 - - - +
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Residues in contact with PHE 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C THR 4.8 8.7 + - - -
469C PHE* 3.2 36.0 + + + +
470C ASP 2.9 0.6 - - - -
471C PHE* 1.3 85.8 - - + +
473C LEU* 1.3 60.5 + - - +
475C ALA* 4.0 1.5 - - - +
476C CYS* 3.0 28.6 + - - +
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Residues in contact with LEU 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C ILE* 4.4 17.9 - - + -
237C LEU* 4.1 34.3 - - + -
240C GLY 4.4 4.3 - - - +
241C MET* 3.8 30.3 - - + +
461C LYS* 4.1 11.2 - - - +
464C ARG* 6.2 1.6 - - - +
469C PHE* 3.2 24.4 + - + +
470C ASP* 2.5 25.8 + - - +
472C PHE* 1.3 72.3 - - - +
474C ALA* 1.3 54.7 + - - +
476C CYS* 2.9 8.5 + - + +
477C GLU* 2.4 38.8 + - + +
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Residues in contact with ALA 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C ARG* 5.3 3.4 - - + +
465C TYR* 4.2 16.2 - - + -
470C ASP* 2.4 50.0 + - - +
471C PHE* 4.9 2.7 - - + -
473C LEU* 1.3 70.6 - - - +
475C ALA* 1.3 56.7 + - - +
477C GLU* 3.0 27.9 + - + +
478C ILE* 3.0 14.6 + - - +
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Residues in contact with ALA 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C PHE* 3.1 23.5 + - - +
472C PHE* 4.2 2.2 - - - +
473C LEU 3.3 0.2 - - - -
474C ALA* 1.3 79.0 - - - +
476C CYS* 1.3 57.6 + - - +
478C ILE* 3.1 26.8 - - + +
479C ILE* 3.1 16.8 - - + +
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Residues in contact with CYS 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C VAL* 3.7 32.1 - - - -
236C ILE* 5.2 11.7 - - + -
237C LEU* 5.3 5.8 - - - +
472C PHE 3.0 19.8 + - - +
473C LEU* 2.9 11.5 + - + +
475C ALA* 1.3 74.0 - - - +
477C GLU* 1.3 59.2 + - - +
478C ILE 3.4 0.2 - - - -
479C ILE* 3.2 19.8 + - + +
480C PHE* 2.9 25.8 + - - +
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Residues in contact with GLU 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C LEU* 6.0 6.7 - - + -
464C ARG* 4.2 21.7 + - - +
473C LEU* 2.4 29.9 + - + +
474C ALA* 3.1 19.5 - - + +
476C CYS* 1.3 70.4 - - - +
478C ILE* 1.3 77.3 + - - +
480C PHE* 2.9 31.2 + - + +
481C CYS* 3.2 15.3 + - - +
525C ASN* 5.1 6.1 + - - +
526C ILE* 3.8 26.0 - - - +
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Residues in contact with ILE 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C ALA 3.0 6.1 + - - +
475C ALA* 3.1 24.7 - - - +
477C GLU* 1.3 89.6 + - - +
479C ILE* 1.3 64.9 + - + +
481C CYS* 3.2 22.3 - - - -
482C PHE* 3.0 23.5 + - + +
526C ILE* 5.8 5.6 - - + -
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Residues in contact with ILE 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C VAL* 5.9 5.4 - - + -
475C ALA* 3.1 19.3 - - + +
476C CYS* 3.2 26.6 + - + +
477C GLU 3.1 0.6 - - - -
478C ILE* 1.3 81.2 - - + +
480C PHE* 1.3 50.9 + - - +
482C PHE* 3.2 12.6 + - + +
483C PHE* 2.6 41.8 + - + +
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Residues in contact with PHE 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C PHE* 3.4 23.1 - + - -
233C VAL* 4.5 15.0 - - + -
234C LEU* 3.4 36.6 - - + -
237C LEU* 5.3 10.8 - - + -
476C CYS 2.9 10.8 + - - +
477C GLU* 2.9 17.1 + - + +
479C ILE* 1.3 76.1 - - - +
481C CYS* 1.3 62.2 + - + +
483C PHE* 2.7 25.1 + - - +
484C ILE* 3.0 44.1 + - + +
518C SER* 5.4 9.0 - - - -
522C ILE* 5.0 14.4 - - + -
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Residues in contact with CYS 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C GLU* 3.2 13.4 + - - +
478C ILE* 3.2 46.2 - - - -
480C PHE* 1.3 87.6 - - + +
482C PHE* 1.3 60.5 + - - +
484C ILE* 3.9 4.6 + - - +
485C PHE* 3.3 21.0 + - - +
522C ILE* 4.6 27.4 - - + +
526C ILE* 5.8 3.6 - - + -
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Residues in contact with PHE 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478C ILE* 3.0 20.9 + - + +
479C ILE* 3.4 12.6 - - + +
481C CYS* 1.3 76.7 - - - +
483C PHE* 1.3 72.0 + + + +
485C PHE* 3.0 33.1 + + - +
486C TYR* 3.1 19.9 + + + +
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Residues in contact with PHE 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C THR* 3.5 42.4 - - + -
227C TYR* 4.2 4.3 - + - -
229C LEU* 6.1 3.6 - - + -
230C PHE* 3.3 51.8 - + + -
233C VAL* 6.4 1.6 - - + -
479C ILE* 2.6 27.6 + - + +
480C PHE* 2.7 12.5 + - - +
482C PHE* 1.3 78.0 - + + +
484C ILE* 1.3 64.5 + - + +
486C TYR* 3.0 25.0 - + + +
487C TYR* 3.6 20.7 + + - -
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Residues in contact with ILE 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C PHE* 3.8 16.8 - - + -
480C PHE* 3.0 70.7 + - + +
481C CYS* 4.4 3.6 - - - +
483C PHE* 1.3 74.3 - - + +
485C PHE* 1.3 56.3 + - - +
486C TYR 3.0 1.8 - - - -
487C TYR* 2.8 9.5 + - + +
488C VAL* 2.5 53.1 + - + +
515C VAL* 5.1 9.9 - - + -
518C SER* 4.3 21.3 - - - +
519C VAL* 5.2 0.4 - - + -
522C ILE* 4.4 15.3 - - + -
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Residues in contact with PHE 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C CYS 3.3 15.0 + - - +
482C PHE* 3.0 30.2 + + + +
484C ILE* 1.3 77.9 - - - +
486C TYR* 1.3 65.3 + - - +
488C VAL* 3.4 25.8 + - + +
489C VAL* 3.6 23.0 + - + +
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Residues in contact with TYR 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C ARG* 5.2 13.5 + - - +
223C GLU* 6.2 0.3 - - - +
226C THR* 5.0 9.8 - - + +
482C PHE* 3.1 18.0 + + + +
483C PHE* 3.0 20.0 - + + +
484C ILE 3.0 0.2 - - - -
485C PHE* 1.3 83.4 - - - +
487C TYR* 1.3 103.9 + + - +
488C VAL 3.0 0.7 + - - -
489C VAL* 3.2 1.6 + - - +
490C GLU* 3.0 47.4 + - + +
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Residues in contact with TYR 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C GLU* 3.4 24.5 + - + +
226C THR* 2.6 37.3 + - - +
227C TYR* 3.3 31.3 - + - +
483C PHE* 4.0 21.8 - + - +
484C ILE* 2.8 11.3 + - + +
486C TYR* 1.3 105.6 - + - +
488C VAL* 1.3 66.3 + - - +
490C GLU* 3.9 17.5 - - - -
491C GLU* 2.7 62.8 - - + +
515C VAL* 5.6 2.9 - - + -
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Residues in contact with VAL 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C ILE* 2.5 44.7 + - + +
485C PHE* 3.4 21.3 - - + +
486C TYR 3.0 0.2 + - - -
487C TYR* 1.3 77.1 - - - +
489C VAL* 1.3 69.1 + - + +
491C GLU* 4.3 1.2 - - - +
492C ILE* 3.1 37.3 + - + +
515C VAL* 4.8 16.1 - - + +
519C VAL* 5.0 9.2 - - + -
522C ILE* 5.9 0.9 - - + -
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Residues in contact with VAL 489 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485C PHE* 4.2 26.0 - - + +
486C TYR 3.2 5.3 + - - +
488C VAL* 1.3 82.2 - - + +
490C GLU* 1.3 68.0 + - - +
491C GLU 3.1 1.8 - - - -
492C ILE* 3.0 20.2 + - + +
493C LEU* 3.2 28.1 + - + +
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Residues in contact with GLU 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C GLU* 5.0 10.5 - - - +
486C TYR* 3.0 48.3 + - + +
487C TYR* 3.9 16.8 - - + -
489C VAL* 1.3 77.3 - - - +
491C GLU* 1.3 71.5 + - - +
493C LEU* 3.7 27.3 + - + +
494C GLU* 4.3 13.1 + - - +
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Residues in contact with GLU 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C TYR* 2.9 26.2 + - - -
487C TYR* 2.7 44.6 + - + +
488C VAL 4.3 1.1 - - - +
489C VAL 3.1 0.8 - - - -
490C GLU* 1.3 78.1 - - - +
492C ILE* 1.3 65.9 + - + +
493C LEU 3.2 2.5 + - - -
494C GLU* 3.5 9.6 + - - +
495C ILE* 3.2 23.1 + - + +
511C ASP 5.1 4.6 - - - +
514C ILE* 6.2 0.2 - - - +
515C VAL* 3.3 27.9 - - - +
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Residues in contact with ILE 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C VAL* 3.1 30.9 + - + +
489C VAL* 3.0 12.6 + - + +
491C GLU* 1.3 76.0 - - + +
493C LEU* 1.3 56.8 + - + +
495C ILE* 2.8 18.1 + - + +
496C ARG* 2.7 46.5 + - + +
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Residues in contact with LEU 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C VAL* 3.2 26.3 + - + +
490C GLU* 3.7 22.4 - - + +
491C GLU 3.2 0.4 - - - -
492C ILE* 1.3 77.0 - - + +
494C GLU* 1.3 59.0 + - + +
496C ARG* 3.1 41.8 - - - +
497C ILE* 2.9 39.5 + - + +
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Residues in contact with GLU 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490C GLU* 5.1 12.6 - - - +
491C GLU* 3.5 10.3 + - - +
492C ILE 3.3 0.4 - - - -
493C LEU* 1.3 76.0 - - + +
495C ILE* 1.3 63.8 + - + +
497C ILE* 4.5 1.1 - - - +
498C HIS* 2.8 52.7 + - + +
501C HIS* 6.1 3.8 - - + -
502C TYR* 4.2 2.6 - - + -
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Residues in contact with ILE 495 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C GLU* 3.2 18.2 - - + +
492C ILE* 2.8 22.6 + - + +
494C GLU* 1.3 80.1 - - + +
496C ARG* 1.3 62.1 + - - +
498C HIS 3.2 12.1 - - - +
499C LYS* 4.2 2.9 - - - +
502C TYR* 3.5 50.9 + - + +
508C ASN* 5.3 4.5 - - - +
512C VAL* 5.0 16.8 - - + -
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Residues in contact with ARG 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492C ILE* 2.7 25.3 + - + +
493C LEU* 3.1 43.5 - - - +
495C ILE* 1.3 76.0 - - - +
497C ILE* 1.3 102.9 + - - +
498C HIS 4.5 1.4 - - - -
499C LYS* 4.6 4.0 + - - +
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Residues in contact with ILE 497 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493C LEU* 2.9 26.2 + - + +
494C GLU* 4.6 0.7 - - - -
496C ARG* 1.3 119.5 - - - +
498C HIS* 1.3 79.1 + - + +
499C LYS* 3.6 2.9 + - - +
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Residues in contact with HIS 498 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C GLU* 2.8 43.1 + - + +
495C ILE 3.2 2.8 - - - +
497C ILE* 1.3 91.8 - - + +
499C LYS* 1.3 61.4 + - - +
501C HIS* 3.4 44.8 - + + +
502C TYR* 3.0 19.4 - - + +
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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