Contacts of the helix formed by residues 467 - 494 (chain D) in PDB entry 3OS8
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 LYS 467 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371D THR* 5.5 8.5 - - + -
468D SER* 1.3 57.1 + - - +
469D LEU* 3.2 6.5 - - - +
470D GLU* 3.1 19.9 + - - +
471D GLU* 2.7 44.1 + - + +
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Residues in contact with SER 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374D ASP* 5.0 4.6 + - - -
461D PHE* 3.7 21.1 + - - +
467D LYS* 1.3 77.9 - - - +
469D LEU* 1.3 60.9 + - - +
471D GLU* 3.4 10.8 + - - +
472D LYS* 3.1 43.2 + - - +
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Residues in contact with LEU 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467D LYS 3.2 3.5 - - - +
468D SER* 1.3 77.4 - - - +
470D GLU* 1.3 62.9 + - - +
472D LYS* 3.3 19.3 + - + +
473D ASP* 3.0 34.0 + - - +
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Residues in contact with GLU 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467D LYS* 3.1 18.8 + - - +
469D LEU* 1.3 79.3 - - - +
471D GLU* 1.3 65.1 + - - +
473D ASP* 3.7 8.7 - - + +
474D HIS* 3.2 22.0 + - - +
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Residues in contact with GLU 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369D ASP 3.9 6.4 - - - +
370D LEU* 3.2 26.2 - - + +
371D THR* 2.9 35.5 + - + +
374D ASP* 2.7 30.7 - - - +
461D PHE* 4.2 7.4 - - + -
467D LYS* 2.7 29.0 + - + +
468D SER* 3.4 9.0 - - - +
469D LEU 3.2 0.2 - - - -
470D GLU* 1.3 81.3 - - - +
472D LYS* 1.3 57.9 + - - +
474D HIS* 3.4 5.3 + - - +
475D ILE* 3.0 33.9 + - - +
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Residues in contact with LYS 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458D VAL* 3.3 29.2 - - + +
459D TYR* 5.0 5.4 - - - +
461D PHE* 3.2 40.3 - - + +
468D SER* 3.1 23.8 + - - +
469D LEU* 3.3 21.3 + - + +
471D GLU* 1.3 76.4 - - - +
473D ASP* 1.3 65.8 + - - +
475D ILE* 3.3 8.2 + - - +
476D HIS* 2.9 41.8 + - + +
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Residues in contact with ASP 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469D LEU* 3.0 27.5 + - - +
470D GLU* 3.7 11.4 - - + +
471D GLU 3.4 0.2 - - - -
472D LYS* 1.3 74.6 - - - +
474D HIS* 1.3 58.3 + - - +
476D HIS* 3.1 9.1 + - - +
477D ARG* 2.9 42.4 + - - +
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Residues in contact with HIS 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D SER 4.8 8.7 + - - -
307D ALA* 5.2 1.6 - - + -
308D LEU* 4.5 22.1 - - + +
366D GLY* 3.2 32.3 + - - -
369D ASP* 3.2 32.5 + - + +
370D LEU* 3.9 15.0 - - + -
470D GLU* 3.2 15.8 + - + +
471D GLU* 3.6 7.4 - - - +
472D LYS 3.2 0.2 - - - -
473D ASP* 1.3 80.6 - - - +
475D ILE* 1.3 62.4 + - + +
477D ARG* 3.3 9.1 + - - +
478D VAL* 3.0 43.1 + - + +
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Residues in contact with ILE 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D LEU* 3.9 26.9 - - + -
378D LEU* 4.4 3.6 - - + -
454D LEU* 3.3 40.2 - - + +
458D VAL* 3.8 20.2 - - + -
461D PHE* 3.3 40.2 - - + -
471D GLU 3.0 18.7 + - - +
472D LYS 3.3 5.6 + - - +
474D HIS* 1.3 76.0 - - + +
476D HIS* 1.3 65.1 - - - +
478D VAL* 3.3 7.8 + - - +
479D LEU* 3.0 33.8 + - + +
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Residues in contact with HIS 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B ARG* 3.5 49.2 + - - +
506B GLN* 5.9 3.2 - - + +
455D ASN* 5.6 0.2 - - - -
458D VAL* 4.1 19.4 - - + +
459D TYR* 4.1 17.9 - + - -
472D LYS* 2.9 39.4 + - + +
473D ASP* 3.6 8.3 - - - +
475D ILE* 1.3 75.7 - - - +
477D ARG* 1.3 58.8 + - + +
479D LEU* 3.3 17.9 + - + +
480D ASP* 3.0 34.0 + - - +
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Residues in contact with ARG 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D LEU* 3.7 36.4 - - + +
473D ASP* 2.9 33.1 + - - +
474D HIS* 3.7 7.6 - - - +
475D ILE 3.3 0.2 - - - -
476D HIS* 1.3 73.9 - - + +
478D VAL* 1.3 64.6 + - - +
480D ASP* 3.3 13.2 + - - +
481D LYS* 3.1 19.8 + - - +
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Residues in contact with VAL 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D ALA* 4.6 6.1 - - + -
308D LEU* 4.2 11.0 - - + -
315D MET* 5.1 6.7 - - + -
365D PRO 3.5 18.4 - - - +
366D GLY* 4.2 10.3 - - - -
454D LEU* 3.4 26.2 - - + -
474D HIS* 3.0 44.4 + - + +
475D ILE* 3.3 5.8 + - - +
477D ARG* 1.3 74.8 - - - +
479D LEU* 1.3 63.9 + - - +
481D LYS* 2.9 15.5 + - - +
482D ILE* 2.9 19.4 + - + +
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Residues in contact with LEU 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B GLN* 6.5 0.4 - - + -
509B LEU* 4.2 20.9 - - + -
451D ILE* 4.0 39.9 - - + +
454D LEU* 3.9 24.5 - - + +
455D ASN* 4.4 15.5 - - + +
458D VAL* 5.4 0.2 - - + -
475D ILE* 3.0 34.0 + - + +
476D HIS* 3.5 22.0 - - + +
478D VAL* 1.3 77.1 - - - +
480D ASP* 1.3 58.2 + - - +
482D ILE* 3.1 7.5 + - + +
483D THR* 2.8 30.6 + - - +
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Residues in contact with ASP 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B GLN* 3.9 29.8 + - - +
506B GLN* 2.8 38.7 + - - +
476D HIS* 3.0 21.6 + - - +
477D ARG* 3.4 14.6 - - - +
478D VAL 3.2 0.2 - - - -
479D LEU* 1.3 77.2 - - - +
481D LYS* 1.3 58.0 + - - +
483D THR* 3.2 8.8 + - - -
484D ASP* 2.9 34.5 + - - +
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Residues in contact with LYS 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D ALA 4.1 6.5 - - - +
308D LEU* 2.8 36.1 + - + +
309D SER 4.3 0.6 - - - -
310D LEU 2.7 26.8 + - - +
311D THR* 4.8 5.4 - - - +
312D ALA* 5.2 1.1 - - - +
315D MET* 3.6 24.7 - - + -
477D ARG 3.1 10.7 + - - +
478D VAL* 2.9 13.1 + - - +
480D ASP* 1.3 78.0 - - - +
482D ILE* 1.3 55.8 + - - +
484D ASP* 3.3 19.3 + - + +
485D THR* 2.8 33.5 + - - +
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Residues in contact with ILE 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D MET* 4.4 19.5 - - + -
319D LEU* 5.5 1.1 - - + -
364D VAL* 5.5 2.0 - - + -
447D CYS* 3.8 28.7 - - + +
450D SER* 3.9 20.6 - - - -
451D ILE* 3.7 31.4 - - + +
454D LEU* 3.9 28.3 - - + -
478D VAL* 2.9 15.5 + - + +
479D LEU* 3.1 8.9 + - + +
481D LYS* 1.3 73.6 - - - +
483D THR* 1.3 60.8 - - - +
485D THR* 3.3 6.5 + - - -
486D LEU* 3.0 28.3 + - - +
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Residues in contact with THR 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B HIS* 3.4 33.4 - - + +
502B GLN* 4.0 9.4 - - + -
505B ALA* 3.4 21.9 - - + +
509B LEU* 6.0 1.0 - - - +
451D ILE* 5.5 3.8 - - - +
479D LEU 2.8 17.2 + - - -
480D ASP* 3.2 13.9 + - - -
482D ILE* 1.3 74.5 - - - +
484D ASP* 1.3 66.3 + - - +
486D LEU* 3.3 10.3 + - - +
487D ILE* 3.0 26.6 + - + +
504D LEU* 4.1 12.7 - - + +
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Residues in contact with ASP 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B GLN* 3.2 27.9 + - - +
502B GLN* 2.9 29.7 + - - +
312D ALA* 4.9 2.5 - - + -
480D ASP 2.9 16.9 + - - +
481D LYS* 3.4 28.3 - - + +
483D THR* 1.3 75.2 - - - +
485D THR* 1.3 58.0 + - - +
487D ILE* 3.3 7.3 + - - +
488D HIS* 2.9 30.1 + - - +
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Residues in contact with THR 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D ALA* 3.5 37.4 - - + +
315D MET* 3.5 24.8 - - + +
316D VAL* 3.5 20.2 - - + -
447D CYS* 3.9 14.6 - - - -
481D LYS* 2.8 20.8 + - - +
482D ILE* 3.5 10.8 - - - -
483D THR 3.2 0.2 - - - -
484D ASP* 1.3 76.1 - - - +
486D LEU* 1.3 63.7 + - - +
488D HIS* 3.1 4.0 + - - +
489D LEU* 2.9 23.4 + - + +
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Residues in contact with LEU 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444D GLU* 4.0 32.5 - - + +
447D CYS* 3.8 25.4 - - + -
448D LEU* 4.8 8.5 - - + -
451D ILE* 3.8 25.8 - - + -
482D ILE 3.0 18.7 + - - +
483D THR* 3.6 7.6 - - - +
485D THR* 1.3 75.0 - - - +
487D ILE* 1.3 63.4 + - - +
489D LEU* 3.2 9.1 + - + +
490D MET* 3.1 36.2 + - + +
504D LEU* 4.1 22.4 - - + -
507D LEU* 4.2 13.9 - - + -
508D LEU* 5.0 1.6 - - + -
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Residues in contact with ILE 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B HIS* 3.7 43.5 - - + +
483D THR* 3.0 16.5 + - + +
484D ASP* 3.7 9.2 - - - +
486D LEU* 1.3 74.6 - - + +
488D HIS* 1.3 59.1 + - - +
490D MET* 3.1 7.7 + - - +
491D ALA* 2.9 28.0 + - + +
500D GLN* 3.3 44.9 - - + +
504D LEU* 4.0 18.4 - - + -
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Residues in contact with HIS 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D ALA* 3.4 25.2 - - + +
313D ASP* 3.2 30.6 + - - -
484D ASP 2.9 14.0 + - - +
485D THR 3.4 7.9 - - - +
487D ILE* 1.3 77.8 - - - +
489D LEU* 1.3 62.1 + - - +
491D ALA* 3.3 7.1 + - + +
492D LYS* 2.8 43.6 + - + +
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Residues in contact with LEU 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D ASP* 5.7 2.5 - - - +
316D VAL* 3.9 26.9 - - + -
443D GLU* 3.8 47.8 - - + +
444D GLU* 4.3 13.5 - - + +
447D CYS* 4.3 5.4 - - - -
485D THR* 2.9 22.9 + - + +
486D LEU* 3.5 10.8 - - - +
488D HIS* 1.3 82.4 - - - +
490D MET* 1.3 58.1 + - + +
492D LYS* 3.5 7.5 + - + +
493D ALA* 2.9 28.2 + - - +
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Residues in contact with MET 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444D GLU* 4.1 14.6 - - - +
486D LEU* 3.1 31.9 + - + +
487D ILE* 3.1 8.7 + - - +
489D LEU* 1.3 74.1 - - + +
491D ALA* 1.3 64.8 + - - +
493D ALA* 3.2 4.8 + - - -
494D GLY 3.1 5.7 + - - -
495D LEU* 3.0 40.1 + - + +
500D GLN* 3.4 34.8 - - + +
503D ARG* 3.8 20.4 - - + -
504D LEU* 3.8 16.8 - - + +
507D LEU* 3.6 31.4 - - + -
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Residues in contact with ALA 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487D ILE* 2.9 16.6 + - + +
488D HIS* 3.8 8.7 - - + +
490D MET* 1.3 76.6 - - - +
492D LYS* 1.3 62.7 + - - +
494D GLY* 3.0 14.6 + - - -
495D LEU 4.2 2.1 - - - +
500D GLN* 3.4 28.6 - - - +
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Residues in contact with LYS 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488D HIS* 2.8 33.9 + - + +
489D LEU* 3.5 9.6 - - + +
491D ALA* 1.3 79.4 - - - +
493D ALA* 1.3 58.4 + - - +
494D GLY* 3.4 1.2 + - - -
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Residues in contact with ALA 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489D LEU 2.9 17.7 + - - +
490D MET* 3.2 8.5 + - - +
492D LYS* 1.3 77.1 - - - +
494D GLY* 1.3 58.8 + - - +
495D LEU* 3.6 13.7 - - + +
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Residues in contact with GLY 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491D ALA 3.0 13.5 + - - -
492D LYS 3.2 1.9 + - - -
493D ALA* 1.3 79.4 - - - +
495D LEU* 1.3 67.5 + - - +
496D THR* 3.6 4.5 + - - +
499D GLN* 4.7 1.2 - - - +
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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