Contacts of the helix formed by residues 384 - 408 (chain A) in PDB entry 5AM8
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 ASN 384 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A TRP 4.0 6.7 - - - +
202A TYR* 3.5 23.8 - - + -
382A GLY* 3.7 11.2 - - - -
383A ALA* 1.3 78.7 - - - +
385A PRO* 1.3 75.8 - - + +
386A GLY* 2.9 17.8 + - - -
387A PHE* 3.0 35.6 + - - +
388A HIS 3.5 2.4 + - - -
503A VAL* 4.4 6.9 - - - +
507A LEU* 5.5 0.2 - - - +
552A TRP* 3.2 44.9 - - + +
565A LEU* 5.8 0.8 - - - +
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Residues in contact with PRO 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A TRP* 4.1 37.2 - - + +
202A TYR* 3.6 22.4 - - + +
382A GLY* 5.6 1.1 - - - +
384A ASN* 1.3 88.5 - - + +
386A GLY* 1.3 55.1 + - - +
388A HIS* 3.2 10.9 + - + +
389A GLU* 3.1 29.5 + - - +
500A ARG* 3.7 31.2 - - + +
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Residues in contact with GLY 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TYR* 3.7 5.1 + - - -
384A ASN* 2.9 9.4 + - - -
385A PRO* 1.3 74.9 - - - +
387A PHE* 1.3 64.9 + - - +
389A GLU 3.2 1.6 + - - -
390A ALA* 2.9 25.1 + - - +
500A ARG* 3.4 22.0 - - - -
503A VAL* 4.0 13.7 - - - -
504A SER* 3.6 4.1 - - - -
507A LEU* 3.9 7.4 - - - -
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Residues in contact with PHE 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A TYR* 3.6 14.6 - + + +
383A ALA* 3.7 20.2 - - + +
384A ASN* 3.0 45.0 + - - +
386A GLY* 1.3 75.0 - - - +
388A HIS* 1.3 63.5 + - - +
390A ALA* 3.1 11.4 + - - +
391A ILE* 3.2 20.1 - - + +
507A LEU* 3.7 22.0 - - + -
511A PHE* 3.9 18.4 - + - -
543A VAL* 3.7 31.4 - - + -
552A TRP* 3.9 31.9 - + + -
555A VAL* 4.0 7.9 - - + -
556A LEU* 4.2 15.9 - - + -
559A MET* 5.7 0.2 - - - -
565A LEU* 6.1 0.2 - - + -
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Residues in contact with HIS 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A HIS 5.4 0.7 - - - +
365A HIS* 2.9 49.4 + - + +
368A TYR* 3.4 32.0 - + + +
369A TYR* 3.3 26.1 - + - -
372A TYR* 2.8 24.6 + - - -
381A ARG* 4.1 1.6 - - - -
382A GLY* 3.3 29.6 - - - -
384A ASN 3.5 3.8 + - - +
385A PRO* 3.2 15.2 + - + +
387A PHE* 1.3 78.5 - - - +
389A GLU* 1.3 63.9 + - - +
390A ALA 3.4 0.2 + - - -
391A ILE* 3.7 11.4 + - - +
392A GLY 5.1 0.5 + - - -
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Residues in contact with GLU 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A HIS* 2.9 49.4 + - + +
365A HIS* 3.1 19.2 + - - -
385A PRO 3.1 13.9 + - - +
386A GLY 3.2 2.0 + - - +
388A HIS* 1.3 78.2 - - - +
390A ALA* 1.3 58.3 + - - +
391A ILE 3.5 0.2 - - - -
392A GLY 4.9 0.7 + - - -
393A ASP* 3.9 5.9 + - - +
500A ARG* 3.5 34.0 + - + -
501A TYR* 3.2 33.2 + - + -
504A SER* 3.1 25.3 + - - -
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Residues in contact with ALA 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLY 2.9 16.1 + - - +
387A PHE 3.1 4.9 + - - +
389A GLU* 1.3 78.0 - - - +
391A ILE* 1.3 66.1 + - - +
392A GLY 3.5 0.4 - - - -
393A ASP* 3.4 5.7 + - - +
394A VAL* 3.1 25.6 + - - +
504A SER* 3.3 23.6 - - - +
507A LEU* 4.3 2.9 - - + -
508A GLN* 4.1 7.0 - - + +
511A PHE* 3.9 23.1 - - + -
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Residues in contact with ILE 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PHE* 4.7 9.0 - - + -
364A GLY* 3.8 24.7 - - - +
368A TYR* 3.6 26.5 - - + -
387A PHE* 3.2 21.1 - - - +
388A HIS 3.7 3.8 + - - +
389A GLU 3.5 2.0 - - - -
390A ALA* 1.3 78.3 - - - +
392A GLY* 1.3 64.3 + - - +
394A VAL* 3.2 16.4 + - - +
395A LEU* 3.6 10.0 + - - +
511A PHE* 4.2 16.6 - - + -
540A LEU* 4.3 24.7 - - + +
543A VAL* 5.0 5.4 - - + -
544A LEU* 3.6 29.4 - - + -
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Residues in contact with GLY 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PHE* 4.8 6.1 - - - -
360A HIS* 3.3 33.1 - - - +
361A HIS* 3.9 5.9 + - - +
364A GLY* 3.8 11.3 - - - -
388A HIS 5.1 0.6 + - - -
389A GLU 4.9 1.2 + - - -
390A ALA 3.5 0.2 - - - -
391A ILE* 1.3 77.0 - - - +
393A ASP* 1.3 61.4 + - - +
395A LEU* 3.3 6.2 + - - +
396A ALA* 3.0 26.9 + - - +
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Residues in contact with ASP 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A SER 5.2 0.7 - - - +
361A HIS* 2.8 38.2 + - - +
389A GLU 3.9 6.7 + - - +
390A ALA 3.4 6.2 + - - +
391A ILE 3.3 0.4 - - - -
392A GLY* 1.3 73.1 - - - +
394A VAL* 1.3 61.8 + - - +
396A ALA* 3.5 8.9 - - - +
397A LEU* 2.9 32.9 + - - +
432A LYS* 3.6 14.8 + - - +
504A SER* 4.3 0.3 + - - -
505A PHE* 3.7 14.7 - - - -
508A GLN* 2.9 36.9 + - - +
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Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ALA 3.1 17.5 + - - +
391A ILE* 3.5 8.1 - - - +
392A GLY 3.2 0.2 - - - -
393A ASP* 1.3 74.1 - - - +
395A LEU* 1.3 68.6 - - + +
397A LEU* 3.2 22.6 + - - +
398A SER* 3.6 4.7 + - - -
508A GLN* 3.6 23.1 - - + +
511A PHE* 3.6 23.6 - - + -
512A HIS* 4.2 22.8 + - + +
515A LEU* 3.7 28.7 - - + -
530A ILE* 4.6 7.2 - - + +
540A LEU* 6.0 2.9 - - + -
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Residues in contact with LEU 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A PHE* 3.6 39.1 - - + -
301A PHE* 3.6 46.9 - - + -
304A LEU* 4.1 11.4 - - + -
360A HIS* 4.5 9.0 - - + -
391A ILE* 3.6 14.8 + - + +
392A GLY* 3.3 8.8 + - - +
394A VAL* 1.3 77.8 - - + +
396A ALA* 1.3 58.2 + - - +
398A SER* 3.0 9.3 + - - +
399A VAL* 3.0 28.4 + - - +
530A ILE* 4.7 7.0 - - + -
540A LEU* 4.0 24.5 - - + -
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Residues in contact with ALA 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A SER* 4.3 24.9 + - - +
360A HIS* 4.2 15.4 - - + +
392A GLY 3.0 15.1 + - - +
393A ASP* 3.5 13.7 - - - +
394A VAL 3.2 0.2 - - - -
395A LEU* 1.3 72.3 - - - +
397A LEU* 1.3 66.2 + - - +
399A VAL* 3.7 10.4 - - + +
400A SER* 2.9 27.5 + - - -
431A GLU* 6.0 1.1 - - - +
432A LYS* 5.9 2.7 - - - +
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Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ASP 2.9 19.5 + - - +
394A VAL* 3.2 10.3 + - - +
396A ALA* 1.3 76.4 - - - +
398A SER* 1.3 60.5 + - - +
400A SER* 3.2 15.4 + - - -
401A THR* 3.5 14.3 - - - +
424A TYR* 3.6 2.6 + - - -
428A MET* 3.8 26.7 - - + -
432A LYS* 4.1 12.3 - - - -
508A GLN* 3.9 30.7 - - + +
509A PHE* 4.1 28.9 - - + -
512A HIS* 4.0 30.9 - - + +
573A TYR* 4.1 10.2 + - + +
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Residues in contact with SER 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A PHE* 3.5 13.5 - - - -
394A VAL 3.6 1.5 + - - -
395A LEU 3.0 10.9 + - - -
397A LEU* 1.3 76.2 - - - +
399A VAL* 1.3 62.6 + - - +
401A THR* 2.8 25.1 + - - -
404A HIS* 3.1 8.9 - - - +
512A HIS* 4.0 10.1 + - - -
528A CYS 3.8 11.1 + - - -
529A ASP* 3.3 22.3 - - - +
530A ILE* 3.0 29.4 + - - +
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Residues in contact with VAL 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A VAL* 6.2 1.3 - - + -
300A PHE* 3.5 25.4 - - + -
356A LEU* 4.6 16.6 - - + -
360A HIS* 3.5 35.9 - - + +
395A LEU 3.0 18.6 + - - +
396A ALA* 3.2 10.0 + - - +
398A SER* 1.3 77.2 - - - +
400A SER* 1.3 62.7 + - - +
401A THR 3.5 0.7 + - - -
404A HIS* 3.6 25.2 - - + +
405A LEU* 3.6 18.8 - - + +
408A ILE* 4.7 7.4 - - + -
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Residues in contact with SER 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 6.1 0.2 - - - +
353A MET* 4.5 14.5 - - - +
357A SER* 5.5 6.3 - - - -
396A ALA 2.9 14.4 + - - -
397A LEU 3.2 7.8 + - - -
398A SER 3.2 0.2 - - - -
399A VAL* 1.3 76.0 - - - +
401A THR* 1.3 66.5 + - - +
402A PRO* 3.4 0.7 - - - +
405A LEU* 3.3 20.2 - - - +
424A TYR* 2.7 37.1 + - - -
428A MET* 3.5 22.3 - - - +
431A GLU* 5.8 1.1 - - - -
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Residues in contact with THR 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A LEU 3.5 17.3 - - - +
398A SER 2.8 15.9 + - - +
400A SER* 1.3 79.6 + - - +
402A PRO* 1.3 74.7 - - - +
403A GLU* 4.1 11.7 - - - +
404A HIS* 2.9 21.5 + - - +
405A LEU* 3.0 10.6 + - - +
424A TYR* 3.6 9.4 - - - +
512A HIS* 6.1 0.2 - - - +
526A HIS 3.7 18.6 - - - +
527A GLN* 4.4 6.5 - - - -
528A CYS 3.6 20.4 - - - +
529A ASP* 4.4 3.8 - - - +
573A TYR* 5.7 0.2 - - - +
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Residues in contact with PRO 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 4.1 19.7 - - + -
400A SER 3.4 2.2 - - - +
401A THR* 1.3 86.0 - - - +
403A GLU* 1.3 56.7 + - - +
405A LEU* 3.6 5.4 - - + +
406A HIS* 2.9 29.1 + - - +
411A LEU* 3.9 22.4 - - + +
414A VAL* 3.9 29.6 - - + +
420A SER 6.0 0.4 - - - +
424A TYR* 3.8 29.8 - - + -
527A GLN* 6.4 2.0 - - + -
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Residues in contact with GLU 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A THR* 3.1 11.2 - - - +
402A PRO* 1.3 76.2 - - - +
404A HIS* 1.3 69.7 + - - +
406A HIS* 3.3 8.2 + - - +
407A LYS* 3.0 41.1 + - - +
414A VAL* 5.7 0.2 - - - +
521A TYR* 5.8 2.6 - - - -
527A GLN* 4.4 17.9 - - + +
529A ASP* 4.0 18.9 - - + +
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Residues in contact with HIS 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A VAL* 6.0 1.2 - - - +
300A PHE* 3.5 28.9 - + - -
398A SER 3.1 24.7 - - - +
399A VAL* 3.6 22.0 - - + +
401A THR* 2.9 9.7 + - - +
403A GLU* 1.3 78.1 - - - +
405A LEU* 1.3 63.3 + - - +
407A LYS* 3.0 18.0 + - + +
408A ILE* 3.0 42.4 + - + +
529A ASP* 2.8 26.8 + - - +
531A TYR* 3.7 27.6 - + - +
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Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 4.5 7.0 - - + +
279A VAL* 4.0 19.3 - - + -
353A MET* 3.9 20.9 - - + -
356A LEU* 5.6 2.5 - - + -
399A VAL* 3.6 22.9 - - + +
400A SER* 3.3 21.1 - - - +
401A THR 3.0 7.7 + - - +
402A PRO* 3.6 13.9 - - + +
404A HIS* 1.3 76.7 - - - +
406A HIS* 1.3 60.0 + - - +
408A ILE* 3.3 11.6 + - + +
409A GLY 3.1 4.0 + - - -
410A LEU* 3.0 53.4 + - + -
411A LEU* 3.9 18.6 - - + -
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Residues in contact with HIS 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A PRO 2.9 17.6 + - - +
403A GLU* 3.6 7.9 - - - +
404A HIS 3.1 0.2 - - - -
405A LEU* 1.3 74.5 - - - +
407A LYS* 1.3 71.6 + - + +
409A GLY* 3.1 13.7 + - - -
411A LEU* 2.8 30.3 + - + +
412A ASP* 4.3 9.2 - - - +
413A ARG* 3.4 60.8 + - + +
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Residues in contact with LYS 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A GLU* 3.0 35.3 + - - +
404A HIS* 3.0 11.2 + - + +
406A HIS* 1.3 82.7 - - + +
408A ILE* 1.3 63.6 + - + +
409A GLY 3.3 0.8 + - - -
529A ASP* 3.0 31.8 + - - +
531A TYR* 4.4 28.3 + - + +
532A ARG* 6.3 0.4 - - - +
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Residues in contact with ILE 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLN* 5.2 0.7 - - - +
288A TRP* 4.4 12.5 - - + -
296A VAL* 4.5 25.1 - - + -
356A LEU* 5.0 2.2 - - + -
399A VAL* 4.7 8.5 - - + -
404A HIS* 3.0 44.1 + - + +
405A LEU* 3.4 20.6 - - + +
406A HIS 3.2 0.2 - - - -
407A LYS* 1.3 80.2 - - + +
409A GLY* 1.3 58.7 + - - +
410A LEU* 3.4 29.9 + - + +
531A TYR* 5.9 5.2 - - + +
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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