Contacts of the helix formed by residues 438 - 461 (chain D) in PDB entry 6UZA
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 GLY 438 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D GLU* 3.8 14.6 - - - -
394D ASN* 4.9 4.2 - - - +
395D LEU* 6.3 1.8 - - - -
434D LYS 4.2 2.8 + - - -
435D ILE 3.2 13.1 + - - -
436D MET 4.3 0.2 - - - +
437D ARG* 1.3 82.1 - - - +
439D PRO* 1.3 74.5 - - - +
440D PHE 3.4 2.5 - - - -
441D MET* 3.8 2.9 + - - -
442D LYS* 3.2 23.8 + - - +
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Residues in contact with PRO 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D ARG* 4.6 7.0 - - - +
390D ILE 3.4 26.7 - - - +
391D TRP* 3.6 35.1 - - + +
393D GLU* 3.8 11.0 - - + +
437D ARG 4.4 1.1 - - - +
438D GLY* 1.3 84.6 - - - +
440D PHE* 1.3 56.4 + - - +
442D LYS* 3.4 4.4 + - + +
443D PHE* 2.9 28.1 + - - +
753D TYR* 3.9 25.3 - - + +
754D PHE* 3.6 21.8 - - + -
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Residues in contact with PHE 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391D TRP* 3.4 47.6 + + - +
392D TYR* 3.7 19.7 - + + -
395D LEU* 3.6 25.5 - - + +
398D LEU* 4.1 24.9 - - + -
406D LYS* 4.2 29.6 - - + -
409D VAL* 5.6 1.1 - - + -
438D GLY 3.4 0.4 - - - -
439D PRO* 1.3 77.1 - - - +
441D MET* 1.3 61.6 + - - +
443D PHE* 3.3 8.7 + + - +
444D VAL* 2.9 49.5 + - + +
1004D Y01 3.6 24.5 - - + -
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Residues in contact with MET 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395D LEU* 3.8 25.0 - - + +
398D LEU* 4.5 15.5 - - - -
409D VAL* 5.4 5.6 - - + -
413D VAL* 4.4 24.0 - - + -
420D LEU* 5.9 2.9 - - + -
432D MET* 6.2 3.6 - - + -
435D ILE* 3.5 40.2 - - + +
436D MET* 4.1 23.1 - - + +
438D GLY* 3.8 3.1 + - - +
439D PRO 3.4 0.4 - - - -
440D PHE* 1.3 75.6 - - - +
442D LYS* 1.3 61.4 + - - +
444D VAL* 3.7 14.7 - - + +
445D ALA* 2.9 29.2 + - + +
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Residues in contact with LYS 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D MET 4.6 4.1 + - - +
437D ARG 4.0 15.5 + - - -
438D GLY 3.2 21.8 + - - +
439D PRO* 3.5 5.6 - - + +
440D PHE 3.2 0.2 - - - -
441D MET* 1.3 77.4 - - - +
443D PHE* 1.3 57.6 + - - +
445D ALA* 3.4 4.4 + - - +
446D HIS* 3.0 41.2 + - + -
753D TYR* 3.3 28.0 + - + -
754D PHE 5.1 0.2 - - - -
755D GLU 3.4 18.4 + - - -
756D GLU* 5.0 1.8 - - - +
757D GLY 4.8 5.3 - - - +
758D ARG 3.6 17.2 + - - +
759D THR* 4.1 28.5 + - + +
1002D R0G 3.5 25.1 + - - +
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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
----------------------------------------------------------
391D TRP* 3.7 24.9 - + + -
439D PRO 2.9 16.7 + - - +
440D PHE* 3.5 15.7 - + - +
442D LYS* 1.3 75.7 - - - +
444D VAL* 1.3 63.0 + - + +
446D HIS* 3.4 1.8 + - + +
447D ALA* 2.9 29.1 + - + +
612D TYR 4.6 3.1 - - - -
613D ILE* 3.8 41.1 - - + -
616D ALA* 3.7 28.3 - - + -
749D LEU* 4.6 3.6 - - + -
753D TYR* 3.5 36.3 - + + -
1002D R0G 5.9 0.2 - + - -
1004D Y01 4.3 32.5 - - + -
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Residues in contact with VAL 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406D LYS 5.4 0.2 - - - +
409D VAL* 4.2 11.4 - - + +
410D VAL* 4.0 33.9 - - + +
413D VAL* 3.9 26.0 - - + -
440D PHE* 2.9 50.2 + - + +
441D MET* 3.7 15.7 - - + +
442D LYS 3.3 0.2 - - - -
443D PHE* 1.3 79.3 - - + +
445D ALA* 1.3 58.1 + - - +
447D ALA* 3.4 2.9 + - - +
448D ALA* 2.9 27.9 + - - +
1004D Y01 6.0 0.9 - - + -
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Residues in contact with ALA 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413D VAL* 4.2 20.9 - - + -
417D LEU* 4.5 3.7 - - + +
441D MET 2.9 17.0 + - - +
442D LYS* 3.7 7.0 - - - +
444D VAL* 1.3 78.0 - - - +
446D HIS* 1.3 57.5 + - + +
448D ALA* 3.3 1.7 + - - +
449D SER* 3.0 30.1 + - - -
759D THR 4.9 5.6 - - - +
761D PRO* 3.7 23.6 - - + +
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Residues in contact with HIS 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442D LYS* 3.0 38.9 + - + +
443D PHE 3.9 3.4 - - - +
445D ALA* 1.3 77.5 - - + +
447D ALA* 1.3 60.5 + - - +
449D SER* 3.9 2.6 + - - -
450D PHE* 3.7 13.7 + - - +
753D TYR* 4.5 5.6 - + - +
758D ARG* 3.5 26.4 + - + -
759D THR 4.4 4.8 + - - -
760D LEU 4.4 3.7 + - - -
761D PRO* 4.1 30.5 - - + +
762D VAL* 4.9 5.8 + - + +
1002D R0G 3.4 64.9 - + + -
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Residues in contact with ALA 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D VAL* 4.8 6.1 - - + -
443D PHE* 2.9 19.5 + - + +
444D VAL* 3.9 5.4 - - - +
446D HIS* 1.3 77.5 - - - +
448D ALA* 1.3 58.9 + - - +
450D PHE* 3.2 8.4 + - - +
451D THR* 3.0 30.2 + - - +
613D ILE* 4.2 22.7 - - + -
1002D R0G 4.5 0.4 - - - -
1004D Y01 4.1 27.3 - - + +
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Residues in contact with ALA 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D VAL* 3.6 25.0 - - - +
413D VAL* 3.9 11.9 - - + +
414D ALA* 3.6 17.8 - - - +
417D LEU* 4.8 2.2 - - + -
444D VAL 2.9 17.4 + - - +
445D ALA 3.3 4.7 + - - +
447D ALA* 1.3 75.9 - - - +
449D SER* 1.3 57.3 + - - +
450D PHE 3.1 0.2 - - - -
451D THR* 3.3 9.2 + - - -
452D ILE* 3.0 35.4 + - - +
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Residues in contact with SER 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417D LEU* 4.1 15.0 - - - +
445D ALA 3.0 17.0 + - - -
446D HIS* 4.2 5.2 - - - -
447D ALA 3.3 0.6 - - - -
448D ALA* 1.3 76.4 - - - +
450D PHE* 1.3 56.1 + - - +
452D ILE* 4.1 5.4 - - - -
453D PHE* 3.8 5.7 + - - +
501D TRP* 3.1 21.0 + - - -
761D PRO* 3.6 18.6 - - - -
762D VAL* 3.4 12.6 - - - +
763D PRO* 3.3 24.1 - - - +
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Residues in contact with PHE 450 (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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446D HIS 3.7 10.8 + - - +
447D ALA* 3.2 8.2 + - - +
448D ALA 3.1 0.6 - - - -
449D SER* 1.3 74.6 - - - +
451D THR* 1.3 63.5 + - - +
452D ILE 3.2 1.1 - - - -
453D PHE* 3.3 14.9 + + - +
454D LEU* 3.0 63.6 + - + +
505D MET* 6.2 1.6 - - + -
606D SER 3.5 26.2 - - - -
607D PHE* 4.7 0.7 - - - -
609D ARG* 3.7 35.0 - - + +
610D ILE* 3.7 30.3 - - + -
613D ILE* 4.5 16.4 - - + -
1002D R0G 4.5 12.1 - + + -
1004D Y01 5.1 5.6 - - + -
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Residues in contact with THR 451 (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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410D VAL* 4.4 6.5 - - - +
411D LEU* 4.3 18.8 - - + -
414D ALA* 4.8 7.9 - - + -
447D ALA 3.0 14.7 + - - -
448D ALA* 3.6 12.1 - - - -
450D PHE* 1.3 78.5 - - - +
452D ILE* 1.3 56.4 + - - +
454D LEU* 3.5 6.3 + - - +
455D GLY* 2.9 25.5 + - - -
1004D Y01 3.5 48.6 - - + +
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Residues in contact with ILE 452 (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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414D ALA* 3.3 35.4 - - + +
417D LEU* 3.8 29.2 - - + -
448D ALA 3.0 20.6 + - - +
449D SER* 4.4 3.1 - - - +
450D PHE 3.2 0.2 - - - -
451D THR* 1.3 75.9 - - - +
453D PHE* 1.3 57.2 + - - +
455D GLY* 3.2 2.5 + - - +
456D LEU* 2.9 37.3 + - + +
501D TRP* 3.6 30.1 - - + -
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Residues in contact with PHE 453 (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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449D SER 3.8 6.1 + - - +
450D PHE* 3.3 24.4 + + + +
452D ILE* 1.3 79.1 - - - +
454D LEU* 1.3 60.8 + - + +
456D LEU* 3.3 11.1 + - + +
457D LEU* 3.0 47.6 + - + +
498D ILE* 3.9 21.5 - - + -
501D TRP* 3.8 47.1 - + + +
502D VAL* 4.3 8.1 - - + -
505D MET* 4.3 19.7 - - + -
533D MET* 5.4 1.3 - - + -
537D PHE* 4.1 25.8 - + - -
606D SER* 4.2 15.3 - - - -
609D ARG* 6.4 0.7 - - - -
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Residues in contact with LEU 454 (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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450D PHE* 3.0 59.1 + - + +
451D THR* 3.9 4.5 - - - +
453D PHE* 1.3 79.7 - - + +
455D GLY* 1.3 57.8 + - - +
457D LEU* 3.3 7.2 + - + +
458D VAL* 3.0 32.6 + - - +
606D SER* 4.3 10.3 - - - +
607D PHE* 3.9 41.5 - - + -
610D ILE* 4.8 4.0 - - + -
1004D Y01 3.9 40.4 - - + -
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Residues in contact with GLY 455 (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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451D THR 2.9 15.3 + - - -
452D ILE* 3.2 4.4 + - - -
454D LEU* 1.3 75.9 - - - +
456D LEU* 1.3 57.6 + - - +
458D VAL* 3.4 2.5 + - - +
459D MET* 2.9 37.0 + - - +
1004D Y01 4.3 12.7 - - - +
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Residues in contact with LEU 456 (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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452D ILE* 2.9 24.9 + - + +
453D PHE* 3.6 8.1 - - + +
455D GLY* 1.3 77.4 - - - +
457D LEU* 1.3 58.8 + - - +
459D MET* 4.5 0.7 - - + +
460D ASN* 2.9 33.6 + - - +
493D TRP* 6.1 3.1 - - + -
494D MET* 3.8 28.2 - - + +
497D LEU* 3.8 33.4 - - + -
498D ILE* 4.2 17.7 - - + +
501D TRP* 4.1 26.7 - - + -
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Residues in contact with LEU 457 (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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650A ILE* 4.4 5.4 - - + +
654A ASN* 4.3 16.1 + - - +
453D PHE* 3.0 36.2 + - + +
454D LEU* 3.3 12.8 + - + +
456D LEU* 1.3 76.4 - - - +
458D VAL* 1.3 63.7 + - + +
460D ASN* 4.0 8.2 + - - +
461D ALA* 4.6 1.4 + - - +
498D ILE* 4.1 15.3 - - + -
537D PHE* 4.2 12.3 - - + -
599D TYR* 3.3 26.9 + - + +
603D VAL* 3.8 28.3 - - + +
606D SER* 3.3 27.4 - - - +
607D PHE* 4.9 5.8 - - + -
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Residues in contact with VAL 458 (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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650A ILE* 3.7 35.2 - - + +
653A PHE* 5.9 0.2 - - - -
454D LEU 3.0 20.5 + - - +
455D GLY* 3.8 5.8 - - - +
457D LEU* 1.3 80.9 - - + +
459D MET* 1.3 75.5 + - + +
460D ASN 3.2 2.1 + - - -
461D ALA* 3.7 9.0 + - - +
465D PHE* 3.9 28.9 - - + -
607D PHE* 5.0 2.7 - - + -
1004D Y01 3.8 25.1 - - + -
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Residues in contact with MET 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455D GLY* 2.9 21.1 + - - +
456D LEU* 4.9 0.4 - - + -
458D VAL* 1.3 84.8 - - + +
460D ASN* 1.3 63.6 + - - +
461D ALA 3.4 0.2 - - - -
462D ALA* 3.3 30.2 - - - +
465D PHE* 4.6 13.7 - - + -
494D MET* 3.3 27.9 - - + +
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Residues in contact with ASN 460 (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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654A ASN* 5.9 0.9 - - - +
456D LEU 2.9 18.2 + - - +
457D LEU 4.1 6.7 - - - +
458D VAL 3.2 1.0 - - - -
459D MET* 1.3 78.6 - - - +
461D ALA* 1.3 60.0 + - - +
462D ALA 3.2 4.7 + - - -
463D ASP* 4.9 1.0 + - - +
464D ARG* 5.1 1.6 + - - -
492D SER* 5.5 3.3 - - - -
494D MET* 3.7 20.9 - - - +
495D GLU* 4.5 13.2 + - - +
498D ILE* 4.1 17.1 - - + +
599D TYR* 3.1 29.0 + - - +
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Residues in contact with ALA 461 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A PHE* 3.6 12.9 - - + -
654A ASN* 3.6 22.2 - - - +
457D LEU 4.6 0.8 + - - +
458D VAL 3.7 5.9 + - - +
460D ASN* 1.3 79.5 - - + +
462D ALA* 1.3 57.6 + - - +
463D ASP 3.5 2.2 + - - -
464D ARG* 3.4 43.5 + - - +
465D PHE* 3.2 23.1 - - - -
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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