Contacts of the helix formed by residues 462 - 491 (chain X) in PDB entry 5IJO
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 GLU 462 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459X LEU 4.7 1.2 + - - -
460X LEU 3.2 0.6 - - - -
461X ARG* 1.4 81.9 - - + +
463X ILE* 1.3 77.1 - - - +
464X LYS* 2.9 4.7 - - - +
465X GLN* 3.3 30.5 - - + +
466X HIS* 3.8 7.5 + - + +
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Residues in contact with ILE 463 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459X LEU 4.4 7.5 + - - +
460X LEU* 2.6 26.4 + - + +
462X GLU* 1.3 69.9 - - - +
464X LYS* 1.4 61.2 + - - +
466X HIS* 3.4 1.4 + - - +
467X LEU* 3.1 13.9 + - - +
385Y LEU* 5.8 8.1 - - + -
474Z ILE* 4.0 26.8 - - + +
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Residues in contact with LYS 464 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6U PHE* 5.3 12.4 - - + +
460X LEU 3.9 0.6 + - - -
461X ARG* 2.6 22.4 + - + +
462X GLU* 2.5 10.9 - - + -
463X ILE 1.4 69.3 - - - +
465X GLN* 1.4 83.3 - - + +
467X LEU* 2.8 12.1 + - - +
468X LYS 3.7 3.0 + - - -
470Z PRO* 5.6 0.4 + - - +
473Z GLN* 6.1 3.9 - - - +
474Z ILE* 4.7 5.1 - - - +
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Residues in contact with GLN 465 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462X GLU* 3.3 16.4 - - + +
463X ILE 3.2 1.2 - - - -
464X LYS* 1.4 91.2 - - + +
466X HIS* 1.3 67.2 + - + +
468X LYS* 2.6 27.1 + - - +
469X GLN 3.8 0.7 + - - -
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Residues in contact with HIS 466 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462X GLU* 3.8 6.2 + - + +
463X ILE* 3.4 6.4 + - - +
464X LYS 3.1 2.2 + - - -
465X GLN* 1.3 77.0 - - + +
467X LEU* 1.3 68.8 - - - +
469X GLN* 3.4 12.1 + - + +
470X GLN* 3.5 7.6 + - - +
389Y MET* 6.2 4.3 - - + -
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Residues in contact with LEU 467 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463X ILE 3.1 9.8 + - - +
464X LYS 2.8 12.2 + - - +
466X HIS* 1.3 83.7 - - - +
468X LYS* 1.4 60.9 + - - +
470X GLN* 3.0 16.2 + - + +
471X GLN* 3.2 9.2 + - - +
474Z ILE* 5.9 4.9 - - + +
477Z ILE* 5.2 15.0 - - + -
478Z LEU* 5.6 9.0 - - + -
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Residues in contact with LYS 468 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5U GLY* 6.2 0.7 - - - -
6U PHE* 4.8 20.2 - - + +
464X LYS 3.7 2.8 + - - -
465X GLN* 2.6 21.0 + - - +
467X LEU* 1.4 47.9 - - - +
469X GLN* 1.4 53.8 - - + +
471X GLN* 2.8 26.5 + - - +
472X GLU* 3.3 8.7 + - - +
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Residues in contact with GLN 469 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465X GLN 3.8 2.0 + - - -
466X HIS* 3.4 8.2 + - + +
467X LEU 2.9 1.2 - - - -
468X LYS* 1.4 77.9 - - + +
470X GLN* 1.4 70.1 + - - +
471X GLN 3.0 0.9 + - - -
472X GLU* 3.0 13.7 + - - +
473X GLY* 3.4 7.6 + - - -
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Residues in contact with GLN 470 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466X HIS 3.5 7.6 + - - +
467X LEU* 3.0 12.8 + - + +
469X GLN* 1.4 79.5 - - - +
471X GLN* 1.4 59.6 + - - +
472X GLU 3.0 0.2 - - - -
473X GLY* 3.3 2.5 + - - +
474X LEU* 3.2 20.3 + - - +
392Y ILE* 5.8 8.5 - - + -
481Z HIS* 5.5 11.5 - - + +
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Residues in contact with GLN 471 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9U LEU* 5.7 9.0 - - + -
467X LEU 3.2 7.9 + - - +
468X LYS* 2.8 19.8 + - - +
470X GLN* 1.4 71.5 - - - +
472X GLU* 1.3 60.7 + - - +
474X LEU* 3.1 7.1 + - - +
475X SER* 3.1 18.2 + - - -
481Z HIS* 6.0 4.7 - - - +
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Residues in contact with GLU 472 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468X LYS 3.3 5.1 + - - +
469X GLN* 3.0 9.2 + - - +
470X GLN 3.0 0.8 - - - -
471X GLN* 1.3 82.2 - - - +
473X GLY* 1.3 67.7 + - - +
475X SER* 3.0 13.3 + - - +
476X HIS* 3.1 13.0 + - - +
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Residues in contact with GLY 473 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469X GLN 3.4 6.7 + - - -
470X GLN* 3.3 6.7 + - - -
471X GLN 3.2 0.4 - - - -
472X GLU* 1.3 79.9 - - - +
474X LEU* 1.4 64.7 + - - +
476X HIS* 3.2 6.6 + - - +
477X LEU* 3.1 18.4 + - - +
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Residues in contact with LEU 474 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470X GLN 3.2 11.0 + - - +
471X GLN* 3.1 9.7 + - - +
472X GLU 2.9 0.6 - - - -
473X GLY* 1.4 79.7 - - - +
475X SER* 1.4 63.1 + - - +
477X LEU* 3.3 6.7 + - - +
478X ILE* 3.1 23.2 + - - +
481Z HIS* 5.2 11.0 - - + +
484Z SER* 4.7 19.8 - - - -
485Z LEU* 5.4 5.6 - - + +
488Z ILE* 5.7 1.0 - - - +
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Residues in contact with SER 475 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471X GLN 3.1 8.6 + - - -
472X GLU* 3.0 10.7 + - - -
474X LEU* 1.4 79.4 - - - +
476X HIS* 1.3 62.7 + - - +
478X ILE* 3.3 5.3 + - - +
479X SER* 3.1 22.3 + - - -
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Residues in contact with HIS 476 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472X GLU 3.1 12.5 + - - +
473X GLY* 3.7 8.7 - - - +
474X LEU 3.2 0.2 - - - -
475X SER* 1.3 77.0 - - - +
477X LEU* 1.4 63.2 + - - +
479X SER* 3.2 4.9 + - - -
480X ILE* 3.1 21.9 + - - +
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Residues in contact with LEU 477 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473X GLY 3.1 13.8 + - - +
474X LEU* 3.3 8.4 + - - +
476X HIS* 1.4 75.1 - - - +
478X ILE* 1.4 62.0 + - - +
480X ILE* 3.2 6.8 + - - +
481X ILE* 3.0 21.7 + - - +
399Y LEU* 6.1 4.3 - - + -
400Y ALA* 5.9 6.7 - - + +
403Y LEU* 5.2 12.9 - - + +
488Z ILE* 4.6 14.3 - - + +
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Residues in contact with ILE 478 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474X LEU 3.1 14.5 + - - +
475X SER* 4.0 5.8 - - - +
476X HIS 3.2 0.4 - - - -
477X LEU* 1.4 72.1 - - - +
479X SER* 1.4 68.1 + - - +
481X ILE* 3.1 4.8 + - - +
482X LYS* 2.9 22.0 + - - +
484Z SER* 5.7 6.5 - - - +
487Z TRP* 6.5 0.7 - - + -
488Z ILE* 4.7 16.8 - - + +
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Residues in contact with SER 479 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475X SER 3.1 13.8 + - - -
476X HIS* 3.9 7.6 - - - -
478X ILE* 1.4 78.3 - - - +
480X ILE* 1.4 55.6 + - - +
482X LYS* 3.4 5.0 + - - +
483X ASP* 3.0 27.2 + - - +
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Residues in contact with ILE 480 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476X HIS 3.1 16.1 + - - +
477X LEU* 3.2 6.7 + - - +
478X ILE 3.1 0.2 - - - -
479X SER* 1.4 74.8 - - - +
481X ILE* 1.3 65.0 + - - +
483X ASP* 3.4 6.2 + - - +
484X ASP* 3.1 22.3 + - - +
403Y LEU* 5.8 6.3 - - + -
407Y HIS* 5.5 1.4 - - - +
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Residues in contact with ILE 481 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477X LEU 3.0 14.3 + - - +
478X ILE* 3.1 7.1 + - - +
480X ILE* 1.3 71.8 - - - +
482X LYS* 1.3 70.9 + - - +
484X ASP* 3.2 7.9 - - + +
485X LEU* 2.9 23.2 + - - +
403Y LEU* 5.2 9.3 - - + +
488Z ILE* 4.9 8.3 - - + +
491Z ASN* 5.3 6.7 - - + -
492Z SER* 4.7 25.8 - - - +
495Z LEU* 5.9 0.9 - - - +
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Residues in contact with LYS 482 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478X ILE 2.9 16.0 + - - +
479X SER* 3.7 4.3 - - - +
481X ILE* 1.3 81.5 - - - +
483X ASP* 1.3 64.1 + - - +
484X ASP 3.1 0.5 + - - -
485X LEU* 3.4 5.1 + - - +
486X GLU* 3.3 13.9 + - - +
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Residues in contact with ASP 483 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479X SER 3.0 16.9 + - - +
480X ILE* 3.4 5.8 + - - +
481X ILE 3.3 0.4 - - - -
482X LYS* 1.3 57.5 - - - +
484X ASP* 1.4 50.0 + - - +
486X GLU* 2.8 19.7 + - - +
487X ASP* 2.9 17.7 + - - +
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Residues in contact with ASP 484 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480X ILE 3.1 18.2 + - - +
481X ILE* 3.2 12.1 - - + +
482X LYS 3.2 0.2 - - - -
483X ASP* 1.4 66.9 - - - +
485X LEU* 1.3 75.8 - - - +
486X GLU 2.9 1.7 + - - -
487X ASP* 3.2 11.1 + - - +
488X ILE* 3.1 15.8 + - - +
403Y LEU* 5.1 1.3 - - - +
406Y ILE* 4.8 8.7 - - + -
407Y HIS* 4.2 30.7 - - + +
410Y VAL* 3.9 6.7 - - - +
495Z LEU* 5.3 4.3 - - + -
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Residues in contact with LEU 485 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481X ILE 2.9 11.8 + - - +
482X LYS* 3.9 4.7 - - + +
483X ASP 3.3 0.2 - - - -
484X ASP* 1.3 90.4 - - - +
486X GLU* 1.3 62.7 + - - +
488X ILE* 3.1 16.7 - - + +
489X LYS* 3.1 19.4 + - - +
495Z LEU* 4.8 13.7 - - + +
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Residues in contact with GLU 486 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482X LYS 3.3 6.8 + - - +
483X ASP* 2.8 17.7 + - - +
485X LEU* 1.3 69.7 - - - +
487X ASP* 1.3 77.7 - - - +
488X ILE 2.7 2.4 + - - -
489X LYS* 4.9 6.5 - - + +
490X LEU* 3.2 17.8 + - - +
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Residues in contact with ASP 487 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483X ASP 2.9 11.9 + - - +
484X ASP* 3.5 11.4 - - - +
486X GLU* 1.3 66.9 - - - +
488X ILE* 1.4 48.3 + - - +
490X LEU* 2.8 25.9 + - - +
491X VAL* 3.2 5.5 + - - +
407Y HIS 5.5 1.1 - - - +
410Y VAL* 4.0 20.2 - - + -
411Y LYS* 5.2 4.0 - - + +
414Y LYS* 5.4 11.6 - - + +
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Residues in contact with ILE 488 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484X ASP 3.1 6.0 + - - +
485X LEU* 3.1 29.6 - - + +
486X GLU 2.7 8.9 - - - -
487X ASP* 1.4 59.9 - - - +
489X LYS* 1.3 55.0 + - - +
490X LEU 2.8 6.3 - - - -
491X VAL* 2.9 27.6 + - + +
492X GLU 3.0 7.3 + - - -
410Y VAL* 4.3 8.6 - - + +
495Z LEU* 5.8 5.4 - - + -
498Z LYS* 6.5 0.9 - - + -
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Residues in contact with LYS 489 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485X LEU 3.1 13.0 + - - +
486X GLU* 4.5 6.7 - - + +
488X ILE* 1.3 71.1 - - - +
490X LEU* 1.3 64.0 + - - +
492X GLU* 2.5 36.6 + - + +
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Residues in contact with LEU 490 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486X GLU 3.2 9.2 + - - +
487X ASP* 2.8 20.0 + - - +
488X ILE 2.8 0.8 - - - -
489X LYS* 1.3 86.3 - - - +
491X VAL* 1.3 47.7 + - - +
492X GLU* 2.9 1.0 + - - +
493X HIS* 2.4 30.9 + - - +
414Y LYS* 6.2 2.7 - - + -
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Residues in contact with VAL 491 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487X ASP 3.2 6.5 + - - +
488X ILE* 2.9 23.9 + - + +
490X LEU* 1.3 73.7 - - - +
492X GLU* 1.2 62.3 + - - +
493X HIS* 2.6 24.5 + - + +
410Y VAL* 5.3 4.0 - - - +
413Y LEU* 4.3 23.8 - - + -
414Y LYS* 5.5 3.4 - - + +
502Z VAL* 6.3 2.0 - - + -
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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