Contacts of the helix formed by residues 431 - 455 (chain D) in PDB entry 5YD6
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 PRO 431 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429D ASP 4.4 2.2 - - - +
430D LEU* 1.4 87.4 - - + +
432D LYS* 1.3 66.1 + - - +
433D ALA 3.2 1.8 - - - +
434D ASP* 3.0 30.6 + - - +
435D GLN* 3.1 10.2 + - - +
519D LYS* 4.4 22.9 - - + -
520D GLU* 3.9 28.9 - - + -
523D ARG* 5.5 2.5 - - - -
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Residues in contact with LYS 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D ARG* 5.0 14.3 - - - +
430D LEU 3.5 1.8 + - - -
431D PRO* 1.3 70.5 - - - +
433D ALA* 1.3 57.9 + - - +
435D GLN* 3.2 21.8 + - + +
436D ASP* 2.8 63.2 + - - +
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Residues in contact with ALA 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431D PRO* 3.2 1.2 - - + +
432D LYS* 1.3 79.2 - - - +
434D ASP* 1.3 58.5 + - - +
436D ASP* 3.5 7.0 + - - +
437D LEU* 2.8 31.2 + - - +
519D LYS* 4.0 31.4 - - + -
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Residues in contact with ASP 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D LEU* 4.5 11.3 - - + +
431D PRO* 3.0 21.4 + - + +
433D ALA* 1.3 73.9 - - - +
435D GLN* 1.3 57.9 + - - +
437D LEU* 4.1 5.9 - - - +
438D LEU* 2.7 41.4 + - - +
517D GLY 4.3 1.9 - - - +
518D LEU* 3.4 23.9 - - + +
519D LYS* 2.8 33.0 + - - +
520D GLU* 3.1 34.1 + - - +
524D VAL* 5.0 1.5 - - + +
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Residues in contact with GLN 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422D GLU* 4.4 13.7 + - - +
427D PHE* 3.4 60.4 + - + +
428D ALA* 3.6 16.9 - - - +
430D LEU* 3.2 20.4 - - + +
431D PRO 3.1 11.2 + - - +
432D LYS* 3.3 24.1 - - + +
434D ASP* 1.3 76.5 - - - +
436D ASP* 1.3 54.6 + - - +
438D LEU* 5.1 0.2 - - - -
439D PHE* 2.8 38.0 + - - +
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Residues in contact with ASP 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D ARG* 5.2 7.1 + - - -
432D LYS* 2.8 57.5 + - - +
433D ALA* 3.8 6.3 - - - +
435D GLN* 1.3 76.5 - - - +
437D LEU* 1.3 55.9 + - - +
439D PHE* 3.2 7.2 + - - +
440D GLU* 2.7 57.2 + - - +
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Residues in contact with LEU 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433D ALA 2.8 22.0 + - - +
434D ASP* 3.7 4.7 - - - +
436D ASP* 1.3 71.5 - - - +
438D LEU* 1.3 56.5 + - - +
440D GLU* 4.0 3.3 - - + +
441D SER* 2.7 48.7 + - - +
515D ARG* 3.9 15.5 - - + -
516D HIS 3.9 9.4 - - - +
517D GLY 3.8 31.6 - - - +
518D LEU* 3.8 20.6 - - + +
594D ASP 5.3 9.2 - - - +
595D THR* 5.7 3.1 - - - +
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Residues in contact with LEU 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427D PHE* 3.9 13.9 - - + -
430D LEU* 3.6 30.7 - - + -
434D ASP 2.7 25.6 + - - +
435D GLN 3.8 2.2 - - - +
437D LEU* 1.3 72.8 - - - +
439D PHE* 1.3 64.5 + - - +
441D SER* 4.1 2.9 - - - -
442D ALA* 3.1 27.7 + - - +
511D MET* 3.4 28.3 - - + +
512D VAL* 4.7 6.1 - - + -
513D THR 3.4 26.0 - - - +
515D ARG* 3.9 8.9 + - + -
518D LEU* 3.7 21.1 - - + -
524D VAL* 4.0 15.9 - - + -
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Residues in contact with PHE 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D MET* 3.5 25.1 - - + -
417D ILE* 3.7 30.1 - - + -
418D ARG* 3.7 54.1 - - + -
421D ALA* 5.0 2.5 - - + -
427D PHE* 4.6 5.2 - - + -
435D GLN 2.8 22.4 + - - +
436D ASP* 3.7 5.4 - - - +
438D LEU* 1.3 72.8 - - - +
440D GLU* 1.3 63.5 + - + +
442D ALA* 3.6 1.0 - - - +
443D PHE* 2.8 51.9 + + + +
446D LEU* 5.1 0.8 - - + +
511D MET* 3.8 17.6 - - - -
591D LEU* 4.1 20.9 - - + -
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Residues in contact with GLU 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D ASP* 2.7 41.0 + - - +
437D LEU* 4.1 3.6 - - + +
439D PHE* 1.3 82.4 - - + +
441D SER* 1.3 58.9 - - - +
442D ALA 3.4 0.3 + - - -
443D PHE* 3.5 2.1 + - - +
590D LYS* 4.7 4.9 + - - -
591D LEU* 3.4 40.3 - - + +
594D ASP* 2.6 41.1 - - + +
595D THR* 3.7 13.2 + - - +
601D 8SU 2.8 31.2 + - - +
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Residues in contact with SER 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437D LEU* 2.7 37.9 + - - +
438D LEU 4.1 0.2 - - - -
440D GLU* 1.3 76.5 - - - +
442D ALA* 1.3 57.3 + - - +
443D PHE 3.5 0.2 - - - -
445D GLU* 4.0 1.6 - - - +
515D ARG* 3.3 41.5 + - - -
595D THR* 3.8 11.7 + - - -
601D 8SU 3.3 42.0 - - - +
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Residues in contact with ALA 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438D LEU 3.1 17.8 + - - +
439D PHE 4.2 0.2 - - - +
441D SER* 1.3 76.1 - - - +
443D PHE* 1.3 67.9 + - - +
444D LEU 3.3 2.2 - - - -
445D GLU* 3.0 11.3 + - + +
446D LEU* 2.9 27.9 + - + +
510D ALA 3.4 26.9 - - - +
511D MET* 3.8 15.5 - - + -
515D ARG* 3.5 8.1 - - - +
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Residues in contact with PHE 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D LEU* 3.3 32.8 - - + -
413D SER* 4.3 0.9 - - - -
414D MET* 3.5 28.0 - - + -
417D ILE* 3.9 24.9 - - + -
439D PHE* 2.8 32.8 + + + +
440D GLU 3.5 6.2 + - - +
442D ALA* 1.3 75.3 - - - +
444D LEU* 1.3 70.8 + - + +
446D LEU* 3.0 10.5 + - - +
447D PHE* 2.8 34.1 + + + -
591D LEU* 4.1 15.3 - - + -
601D 8SU 3.4 44.4 - - + +
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Residues in contact with LEU 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D LEU* 3.6 29.6 - - + -
442D ALA 3.3 0.6 - - - -
443D PHE* 1.3 82.2 - - + +
445D GLU* 1.3 61.4 + - - +
447D PHE* 3.6 4.5 - - + +
448D VAL* 3.0 35.3 + - - +
482D TRP* 4.0 20.2 - - + -
566D CYS* 3.5 36.6 - - - +
569D GLY 4.0 6.1 - - - -
570D LEU* 3.7 17.3 - - - +
573D ILE* 4.3 7.0 - - + -
601D 8SU 3.1 38.0 + - + +
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Residues in contact with GLU 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441D SER 4.0 6.5 - - - +
442D ALA* 3.0 10.0 + - - +
444D LEU* 1.3 77.2 - - - +
446D LEU* 1.3 58.1 + - - +
448D VAL* 3.3 0.4 + - - -
449D LEU* 2.9 28.4 + - - +
510D ALA* 4.4 14.6 - - + +
515D ARG* 3.8 15.0 + - - -
559D LEU* 4.4 4.5 - - - +
562D LEU* 3.2 42.6 - - + +
563D ARG* 2.7 49.9 + - - -
566D CYS* 3.7 23.3 - - + +
601D 8SU 4.2 3.0 - - + -
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Residues in contact with LEU 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417D ILE* 3.9 26.0 - - + -
420D TRP* 3.4 45.8 - - + -
439D PHE 5.1 1.1 - - - +
442D ALA* 2.9 35.5 + - + +
443D PHE* 3.4 7.0 - - - +
445D GLU* 1.3 74.3 - - - +
447D PHE* 1.3 66.3 + - - +
449D LEU* 4.6 3.6 - - + -
450D ARG* 3.1 39.5 + - - +
507D ALA* 3.6 23.3 - - + +
510D ALA* 4.5 6.5 - - + -
511D MET* 4.0 10.5 - - + -
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Residues in contact with PHE 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409D LEU 3.3 28.5 - - - -
410D LEU* 3.7 27.6 - - + -
413D SER* 3.5 23.1 - - - -
417D ILE* 3.6 11.3 - - + +
443D PHE* 2.8 21.9 + + + +
444D LEU* 3.6 12.1 - - + +
446D LEU* 1.3 72.7 - - - +
448D VAL* 1.3 73.2 + - + +
450D ARG* 4.2 2.0 - - - +
451D LEU* 3.2 38.2 + - + +
454D ARG* 5.2 3.3 + - - -
464D PHE* 4.0 29.2 - + - -
465D CYS 6.2 0.2 - - - -
479D PHE* 4.1 20.2 - + - -
482D TRP* 4.8 7.0 - + - -
486D ILE* 5.6 0.4 - - + -
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Residues in contact with VAL 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444D LEU 3.0 19.9 + - - +
445D GLU* 3.9 3.4 - - - +
446D LEU 3.3 0.2 - - - -
447D PHE* 1.3 80.9 - - + +
449D LEU* 1.3 61.4 + - - +
451D LEU* 3.7 5.0 - - - +
452D ALA* 2.8 28.8 + - - +
482D TRP* 3.4 37.2 - - + +
486D ILE* 4.3 19.0 - - + +
489D PHE* 4.5 5.4 - - + -
562D LEU* 3.8 10.5 - - + -
565D LEU* 3.6 35.7 - - + +
566D CYS* 5.6 0.9 - - - +
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Residues in contact with LEU 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445D GLU 2.9 16.6 + - - +
446D LEU* 4.0 5.6 - - + +
448D VAL* 1.3 75.8 - - - +
450D ARG* 1.3 60.0 + - + +
452D ALA* 3.1 6.5 + - - +
453D TYR* 2.8 30.1 + - - +
489D PHE* 3.9 26.0 - - + -
493D LEU* 4.1 12.1 - - + +
503D PHE* 3.4 24.7 - - + -
506D ILE* 4.0 15.9 - - + +
507D ALA* 3.7 36.1 - - + +
510D ALA* 4.5 3.6 - - + -
558D LYS* 5.8 1.3 - - + -
562D LEU* 3.7 23.7 - - + +
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Residues in contact with ARG 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D HIS* 4.3 4.5 - - + +
375D SER* 2.7 45.0 + - - -
376D ASN* 3.0 21.1 - - - +
416D ILE* 3.6 17.0 - - - +
417D ILE* 3.6 25.1 - - - +
420D TRP* 4.2 18.5 - - - -
446D LEU* 3.1 35.5 + - + +
447D PHE* 4.5 1.8 - - - +
449D LEU* 1.3 77.0 - - + +
451D LEU* 1.3 61.7 + - - +
453D TYR* 3.4 2.3 + - - +
454D ARG* 3.1 53.7 + - - +
465D CYS* 4.5 5.5 - - - +
503D PHE* 4.0 23.3 - - + -
507D ALA* 5.3 3.8 - - + -
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Residues in contact with LEU 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447D PHE* 3.2 35.9 + - + +
448D VAL* 3.7 3.1 - - - +
450D ARG* 1.3 74.5 - - - +
452D ALA* 1.3 64.2 + - - +
454D ARG* 3.9 9.3 - - - +
455D SER* 2.7 46.1 + - - +
462D LEU* 3.7 24.7 - - + -
463D ILE 3.3 31.4 - - - +
464D PHE* 3.8 30.5 - - + -
479D PHE* 5.1 2.0 - - + -
486D ILE* 4.0 19.7 - - + -
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Residues in contact with ALA 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448D VAL* 2.8 21.5 + - + +
449D LEU 3.4 5.4 - - - +
451D LEU* 1.3 77.1 - - - +
453D TYR* 1.3 57.0 + - - +
455D SER 4.0 0.7 + - - -
486D ILE* 4.7 4.7 - - + +
489D PHE* 3.6 31.0 - - + -
490D SER* 2.6 41.4 + - - +
493D LEU* 3.8 5.2 - - + -
494D GLN* 2.9 14.9 - - - +
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Residues in contact with TYR 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ARG* 4.4 3.5 + - - -
372D HIS* 4.1 19.1 - + - -
449D LEU 2.8 7.9 + - - +
450D ARG 3.8 3.6 - - - +
451D LEU 3.2 0.4 - - - -
452D ALA* 1.3 78.0 - - - +
454D ARG* 1.3 60.6 + - + +
493D LEU* 4.0 13.7 - - + -
494D GLN* 3.3 20.1 - - + +
498D ILE* 2.8 36.3 + - + -
499D ASP* 3.4 15.6 - - - -
500D ILE* 3.4 14.3 + - + +
503D PHE* 3.5 64.2 - + + -
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Residues in contact with ARG 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376D ASN* 2.6 39.3 + - - -
377D PRO* 3.6 18.8 - - - +
379D MET* 3.4 44.6 - - + +
447D PHE* 5.2 3.2 + - - -
450D ARG* 3.1 35.3 + - - +
451D LEU* 3.9 18.3 - - - +
453D TYR* 1.3 78.1 - - - +
455D SER* 1.3 67.5 + - - +
463D ILE* 3.0 31.5 + - + +
464D PHE* 3.4 4.8 + - - +
465D CYS* 3.3 41.5 - - - +
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Residues in contact with SER 455 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451D LEU* 2.7 28.0 + - - +
452D ALA* 4.0 0.8 + - - -
453D TYR 3.6 0.8 - - - +
454D ARG* 1.3 81.0 - - - +
456D ASN* 1.3 59.9 + - - +
457D PRO* 3.3 4.8 - - - +
461D LYS 3.1 12.1 - - - -
462D LEU* 3.2 9.6 - - - +
463D ILE* 2.9 30.6 + - - +
490D SER* 4.3 12.1 - - - -
494D GLN* 2.8 22.5 + - - +
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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