Contacts of the helix formed by residues 413 - 441 (chain A) in PDB entry 5UNJ
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 TYR 413 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A GLY* 2.9 31.8 + - - +
402A SER 4.2 1.8 - - - +
403A ILE* 3.5 29.4 - - + -
411A VAL 3.5 2.0 + - - -
412A ASP* 1.3 71.2 - - - +
414A SER* 1.3 57.7 + - - +
416A ILE* 3.3 6.5 - - - +
417A ALA* 2.7 48.5 + - + +
425A ASN* 2.8 30.5 + - - -
428A MET* 3.7 13.8 - - + +
429A SER* 3.2 30.0 + - - -
432A GLN* 3.8 24.7 - - + -
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Residues in contact with SER 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ASP* 2.2 28.4 + - - -
413A TYR* 1.3 84.7 - - - +
415A ILE* 1.3 62.7 + - - +
417A ALA* 3.9 3.4 - - - +
418A SER* 2.9 29.3 + - - -
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Residues in contact with ILE 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A VAL* 6.1 2.2 - - + -
412A ASP* 3.0 32.1 + - + +
413A TYR 3.2 0.2 - - - -
414A SER* 1.3 79.8 - - - +
416A ILE* 1.3 64.1 + - + +
418A SER* 3.2 8.4 + - - -
419A GLN* 3.1 39.4 + - + +
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Residues in contact with ILE 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A THR* 5.3 2.9 - - + -
345A MET* 4.5 9.2 - - + -
403A ILE* 4.1 7.2 - - + -
405A LEU* 4.4 15.3 - - + -
411A VAL* 3.7 31.6 - - + -
412A ASP 3.2 11.8 + - - +
413A TYR* 3.3 15.5 - - - +
415A ILE* 1.3 77.3 - - + +
417A ALA* 1.3 63.6 + - - +
419A GLN* 3.3 17.4 + - - +
420A ALA* 2.9 27.8 + - - +
428A MET* 4.1 12.8 - - + -
601A RJW 3.7 37.0 - - + -
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Residues in contact with ALA 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A TYR* 2.7 38.2 + - + +
414A SER* 3.9 5.4 - - - +
416A ILE* 1.3 72.6 - - - +
418A SER* 1.3 65.9 + - - +
420A ALA* 3.2 15.7 + - - +
421A GLY* 3.3 15.1 + - - +
425A ASN* 3.3 33.2 - - - +
428A MET* 4.4 4.3 - - + -
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Residues in contact with SER 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A SER 2.9 19.7 + - - -
415A ILE* 3.4 10.2 - - - -
417A ALA* 1.3 76.3 - - - +
419A GLN* 1.3 64.2 + - - +
420A ALA 3.1 1.2 + - - -
421A GLY* 3.1 13.0 + - - -
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Residues in contact with GLN 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A THR* 3.5 43.9 + - + +
342A PHE* 4.8 7.8 + - - +
415A ILE* 3.1 25.9 + - + +
416A ILE* 3.3 22.0 + - - +
418A SER* 1.3 76.3 - - - +
420A ALA* 1.3 60.6 + - - +
421A GLY 3.6 0.2 + - - -
601A RJW 3.6 8.7 - - + +
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Residues in contact with ALA 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A PHE* 5.5 2.4 - - - +
416A ILE 2.9 17.0 + - - +
417A ALA 3.6 6.1 - - - +
418A SER 3.1 0.6 - - - -
419A GLN* 1.3 78.8 - - - +
421A GLY* 1.3 61.6 + - - +
424A LEU* 3.5 26.9 - - + +
425A ASN 4.4 0.2 - - - +
428A MET* 3.7 23.3 - - - -
516A TYR* 4.2 8.7 + - - -
601A RJW 3.5 25.1 - - + -
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Residues in contact with GLY 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ALA 3.3 4.2 + - - +
418A SER 3.1 13.9 + - - -
419A GLN 3.4 1.2 + - - -
420A ALA* 1.3 78.2 - - - +
422A ALA* 1.3 66.3 + - - -
423A THR 3.5 1.6 - - - -
424A LEU 4.2 0.2 - - - -
425A ASN* 3.0 25.7 + - - +
516A TYR* 5.5 2.5 - - - -
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Residues in contact with ALA 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A GLY* 1.3 72.7 - - - -
423A THR* 1.3 66.2 + - - +
425A ASN* 3.3 8.8 + - - +
426A ASN* 3.1 21.0 + - - +
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Residues in contact with THR 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A GLY 3.5 0.6 - - - -
422A ALA* 1.3 77.4 - - - +
424A LEU* 1.3 65.5 + - - +
426A ASN* 3.0 22.7 + - - +
427A LEU* 3.3 15.6 + - + +
516A TYR* 3.6 41.3 + - + -
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Residues in contact with LEU 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A PHE* 4.1 10.1 - - + -
420A ALA* 3.5 26.2 + - + +
421A GLY 3.7 1.6 + - - -
422A ALA 3.4 0.4 - - - -
423A THR* 1.3 79.2 - - - +
425A ASN* 1.3 59.0 + - - +
427A LEU* 3.0 16.3 + - + +
428A MET* 2.8 35.5 + - + +
513A ALA* 5.4 4.0 - - + +
516A TYR* 3.6 35.4 - - + -
517A LEU* 5.4 2.5 - - + -
601A RJW 3.8 69.8 - - + -
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Residues in contact with ASN 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A TYR* 2.8 31.0 + - - -
417A ALA* 3.3 31.1 - - + +
420A ALA* 4.4 0.4 - - - +
421A GLY 3.0 21.6 + - - +
422A ALA* 3.5 8.2 + - - +
424A LEU* 1.3 75.7 - - - +
426A ASN* 1.3 58.0 + - - +
428A MET* 3.3 10.3 + - - -
429A SER* 2.8 30.3 + - - -
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Residues in contact with ASN 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ALA 3.1 10.2 + - - +
423A THR* 3.0 14.2 + - - +
425A ASN* 1.3 78.3 - - - +
427A LEU* 1.3 68.9 + - - +
429A SER* 3.3 7.1 + - - -
430A HIS* 3.0 28.6 + - - +
512A GLN* 5.3 5.3 + - - +
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Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A THR* 3.3 19.7 + - + +
424A LEU* 3.0 20.2 + - + +
426A ASN* 1.3 83.8 - - - +
428A MET* 1.3 67.2 + - - +
430A HIS* 3.3 8.4 + - + +
431A ALA* 3.0 23.2 + - - +
509A ILE* 4.2 13.6 - - + +
512A GLN* 3.4 41.3 - - + +
513A ALA* 3.7 36.8 - - + +
516A TYR* 5.1 1.8 - - + -
601A RJW 3.7 16.4 - - + -
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Residues in contact with MET 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A HIS* 5.5 3.4 + - + +
403A ILE* 4.5 8.1 - - + -
413A TYR* 3.7 22.9 - - + +
416A ILE* 4.1 23.1 - - + -
417A ALA* 4.4 8.3 - - - -
420A ALA* 3.7 27.1 - - - -
424A LEU* 2.8 23.4 + - + +
425A ASN* 3.6 7.9 - - - +
427A LEU* 1.3 71.9 - - - +
429A SER* 1.3 58.1 + - - +
431A ALA* 3.3 3.6 + - - +
432A GLN* 2.9 31.9 + - - +
601A RJW 3.7 59.5 - - + -
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Residues in contact with SER 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A TYR* 3.2 13.0 + - - -
425A ASN* 2.8 23.2 + - - -
426A ASN* 3.6 8.7 - - - -
428A MET* 1.3 71.5 - - - +
430A HIS* 1.3 65.2 + - - +
432A GLN* 3.1 8.8 + - - +
433A GLU* 3.0 32.0 + - - +
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Residues in contact with HIS 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ASN* 3.0 15.8 + - - +
427A LEU* 3.6 12.3 - - + +
429A SER* 1.3 75.9 - - - +
431A ALA* 1.3 62.2 + - - +
433A GLU* 3.0 31.9 + - - +
434A LEU* 3.2 30.8 + - + +
505A GLU* 4.8 13.0 + - + +
508A ALA* 6.0 2.0 - - + +
509A ILE* 3.4 27.7 - - + +
512A GLN* 5.1 7.6 - - - -
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Residues in contact with ALA 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ILE* 4.9 2.2 - - + -
390A HIS* 4.4 6.7 - - + +
391A ILE* 4.1 24.1 - - + +
427A LEU 3.0 13.7 + - - +
428A MET 3.5 8.1 - - - +
430A HIS* 1.3 75.9 - - - +
432A GLN* 1.3 58.9 + - - +
434A LEU* 3.0 6.6 + - - +
435A VAL* 2.9 30.2 + - - +
509A ILE* 4.1 11.6 - - + +
601A RJW 4.0 20.2 - - + -
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Residues in contact with GLN 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A HIS* 4.1 7.1 + - - -
394A GLN* 3.7 19.3 - - - +
399A LYS 5.4 3.4 + - - -
401A GLY 6.0 1.4 - - - +
402A SER 4.4 7.9 + - - -
403A ILE* 3.2 27.1 - - + +
413A TYR* 3.8 20.9 - - + -
428A MET 2.9 18.9 + - - +
429A SER* 3.1 10.1 + - - +
431A ALA* 1.3 75.9 - - - +
433A GLU* 1.3 61.9 + - - +
435A VAL* 3.2 19.0 + - - +
436A ALA* 3.0 22.0 + - - +
439A ARG* 6.1 0.2 - - - +
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Residues in contact with GLU 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A SER* 3.0 23.5 + - - +
430A HIS* 3.0 27.9 + - - +
432A GLN* 1.3 77.1 - - + +
434A LEU* 1.3 65.3 + - + +
436A ALA* 3.2 8.4 + - - +
437A LYS* 3.1 39.9 + - - +
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Residues in contact with LEU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ILE* 4.0 15.3 - - + -
430A HIS* 3.3 39.7 - - + +
431A ALA 3.0 9.0 + - - +
433A GLU* 1.3 74.9 - - + +
435A VAL* 1.3 65.9 + - - +
437A LYS* 3.3 11.3 + - + +
438A LEU* 2.9 34.2 + - + +
502A ARG* 4.3 9.9 - - + +
505A GLU* 3.7 31.4 - - + +
506A ILE* 3.5 35.4 - - + +
509A ILE* 4.2 7.0 - - + -
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Residues in contact with VAL 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A HIS* 5.9 0.2 - - + -
391A ILE* 3.7 22.4 - - + +
394A GLN* 3.7 39.5 - - + -
395A VAL* 3.9 16.9 - - + +
431A ALA* 2.9 19.8 + - + +
432A GLN* 3.4 21.3 - - - +
434A LEU* 1.3 77.2 - - - +
436A ALA* 1.3 62.4 + - - +
438A LEU* 3.3 1.4 + - - +
439A ARG* 3.0 47.1 + - - +
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Residues in contact with ALA 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A GLN 3.0 11.8 + - - +
433A GLU* 3.2 9.8 + - - +
435A VAL* 1.3 78.0 - - - +
437A LYS* 1.3 64.2 + - + +
439A ARG* 3.5 10.8 + - - +
440A SER* 3.2 21.8 + - - -
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Residues in contact with LYS 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A GLU* 3.1 29.3 + - - +
434A LEU* 3.7 12.6 - - + +
436A ALA* 1.3 77.5 - - + +
438A LEU* 1.3 62.3 + - - +
440A SER* 2.7 23.6 + - - +
441A LEU* 3.1 16.0 + - + +
502A ARG* 4.6 31.6 - - - +
505A GLU* 5.3 4.0 - - - +
----------------------------------------------------------
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Residues in contact with LEU 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU* 5.7 1.3 - - + -
391A ILE* 3.6 31.4 - - + -
395A VAL* 4.1 4.7 - - + -
434A LEU* 2.9 21.6 + - + +
435A VAL 3.9 3.4 - - - +
437A LYS* 1.3 76.2 - - - +
439A ARG* 1.3 62.6 + - - +
441A LEU* 3.2 11.7 + - + +
443A PHE* 3.0 60.8 + - + +
451A LEU* 5.5 3.1 - - + -
499A LEU* 3.8 28.5 - - + -
502A ARG* 4.0 30.1 - - + -
506A ILE* 5.5 5.4 - - + -
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Residues in contact with ARG 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A GLN* 3.2 16.6 + - - +
395A VAL* 3.6 38.3 + - + +
396A VAL 4.6 2.4 + - - -
398A GLY* 2.6 31.7 + - - -
399A LYS* 4.4 7.8 + - - +
400A GLU* 5.1 7.3 + - - -
432A GLN* 6.1 0.2 - - - +
435A VAL* 3.0 34.4 + - - +
436A ALA* 3.6 9.9 - - - +
437A LYS 3.3 0.2 - - - -
438A LEU* 1.3 77.2 - - - +
440A SER* 1.3 58.6 + - - +
442A GLN* 2.9 23.0 + - - +
443A PHE 5.0 0.7 - - - +
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Residues in contact with SER 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ALA 3.2 9.5 + - - -
437A LYS* 2.7 24.3 + - - -
439A ARG* 1.3 79.3 - - - +
441A LEU* 1.3 63.5 + - - +
442A GLN* 3.5 5.4 + - - +
492A GLN* 3.9 11.8 + - - +
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Residues in contact with LEU 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LYS* 3.1 16.2 + - + +
438A LEU* 3.6 16.2 - - + +
439A ARG 3.1 1.0 - - - -
440A SER* 1.3 80.2 - - - +
442A GLN* 1.3 64.6 + - - +
443A PHE 4.5 1.3 - - - +
492A GLN* 3.4 32.7 - - + +
495A LYS* 3.0 32.0 + - + +
498A GLN* 3.9 45.1 - - + +
499A LEU* 4.4 15.3 - - + -
502A ARG* 4.4 9.9 - - - +
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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