Contacts of the helix formed by residues 392 - 424 (chain A) in PDB entry 2DFS
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 SER 392 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ASP* 3.1 43.6 + - - -
348A CYS* 4.5 0.7 - - - -
391A ILE* 1.4 76.7 - - - +
393A LYS* 1.4 63.1 + - - +
394A LEU* 4.1 5.2 + - - +
395A HIS* 2.9 40.0 + - - +
396A ALA* 3.2 19.2 + - - +
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Residues in contact with LYS 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLU* 2.5 41.5 + - - -
340A PHE* 2.6 30.4 + - + +
342A SER* 4.6 24.2 - - - +
346A ASP* 4.0 4.9 + - - -
347A SER 4.6 2.4 + - - -
348A CYS* 4.3 15.6 - - + +
392A SER* 1.4 73.4 - - - +
394A LEU* 1.3 67.4 + - + +
396A ALA* 3.3 3.8 + - - +
397A ILE* 3.3 40.0 + - + +
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Residues in contact with LEU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A SER* 3.4 6.6 + - - +
393A LYS* 1.3 79.5 - - + +
395A HIS* 1.4 62.4 + - + +
397A ILE* 3.4 16.5 + - + +
398A ASN* 3.0 36.1 + - - +
569A LYS* 6.2 1.3 - - - +
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Residues in contact with HIS 395 (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 14.7 - - + +
392A SER* 2.9 31.9 + - - +
394A LEU* 1.4 81.6 - - + +
396A ALA* 1.3 59.9 + - - +
398A ASN* 3.8 10.0 + - - +
399A ALA* 3.2 14.7 + - - +
516A PRO* 5.9 6.3 + - + +
573A TYR* 2.9 30.3 + - - +
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Residues in contact with ALA 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A PHE* 3.9 20.5 - - + -
348A CYS* 3.7 27.6 - - - -
375A LEU* 3.8 11.0 - - - +
391A ILE* 3.6 18.0 - - + +
392A SER 3.2 5.4 + - - +
393A LYS 3.3 9.4 + - - +
395A HIS* 1.3 74.4 - - - +
397A ILE* 1.3 57.1 + - - +
399A ALA* 3.3 4.6 + - - +
400A ARG* 2.9 28.8 + - - +
576A GLN* 5.7 0.2 + - - -
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Residues in contact with ILE 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLU* 4.8 3.1 - - - +
340A PHE* 3.9 19.1 - - + -
393A LYS* 3.3 42.9 + - + +
394A LEU* 3.4 18.4 + - + +
396A ALA* 1.3 74.9 - - - +
398A ASN* 1.4 66.2 + - - +
400A ARG* 3.2 33.3 + - - +
401A ASP* 3.1 29.6 + - - +
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Residues in contact with ASN 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LEU* 3.0 23.1 + - - +
395A HIS* 4.0 10.7 - - - +
397A ILE* 1.4 79.3 - - - +
399A ALA* 1.3 56.6 + - - +
401A ASP* 3.7 8.7 + - - +
402A ALA* 3.0 27.0 + - - +
405A LYS* 5.8 0.2 - - - -
566A GLU* 2.8 25.2 + - - +
569A LYS* 2.8 45.6 + - + +
570A ASP* 5.8 0.2 - - - -
571A THR 5.3 1.5 + - - -
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Residues in contact with ALA 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A HIS 3.2 16.1 + - - +
396A ALA* 3.6 5.4 - - - +
398A ASN* 1.3 77.2 - - - +
400A ARG* 1.4 57.5 + - - +
402A ALA* 3.3 8.3 + - - +
403A LEU* 2.9 30.0 + - - +
571A THR 4.5 3.8 - - - -
572A VAL* 5.1 0.9 - - - +
573A TYR* 3.4 41.7 - - + +
576A GLN* 3.9 13.0 - - - +
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Residues in contact with ARG 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A VAL* 5.5 0.2 - - - +
286A HIS* 2.9 31.5 + - - -
287A TYR* 3.5 11.1 + - - +
335A LEU* 3.6 37.7 - - + +
336A GLY 3.2 20.2 + - - -
338A VAL* 4.0 19.6 + - + -
340A PHE* 4.4 15.0 - - + -
375A LEU* 5.2 9.6 - - + +
396A ALA 2.9 17.0 + - - +
397A ILE* 3.2 27.9 + - - +
399A ALA* 1.4 70.3 - - - +
401A ASP* 1.3 91.3 + - - +
403A LEU* 3.3 8.5 + - - +
404A ALA* 3.0 26.5 + - - +
576A GLN* 5.2 1.0 - - - +
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Residues in contact with ASP 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A VAL* 4.1 31.9 - - + +
287A TYR* 3.4 6.7 + - - -
397A ILE* 3.1 21.2 + - - +
398A ASN* 3.8 9.2 + - - +
400A ARG* 1.3 113.5 + - - +
402A ALA* 1.3 60.7 + - - +
404A ALA* 3.4 1.4 + - - +
405A LYS* 2.9 42.1 + - - +
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Residues in contact with ALA 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A ASN 3.0 19.2 + - - +
399A ALA 3.3 6.3 + - - +
401A ASP* 1.3 76.1 - - - +
403A LEU* 1.3 55.5 + - - +
405A LYS* 3.8 11.5 - - - +
406A HIS* 2.9 29.7 + - - +
569A LYS 5.5 0.2 - - - +
570A ASP* 3.9 9.5 - - - +
571A THR 3.6 17.7 - - - +
572A VAL* 3.6 30.2 - - - +
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Residues in contact with LEU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU* 4.2 20.2 - - + -
360A PHE* 5.0 2.2 - - + -
371A MET* 4.8 12.8 - - + -
375A LEU* 5.2 4.3 - - + -
399A ALA 2.9 12.9 + - - +
400A ARG* 3.5 9.4 - - - +
402A ALA* 1.3 72.6 - - - +
404A ALA* 1.4 58.9 + - - +
406A HIS* 3.2 5.8 + - + +
407A ILE* 2.9 44.8 + - + +
572A VAL* 4.0 21.7 - - + +
576A GLN* 4.2 33.2 - - + +
577A ILE* 4.5 9.4 - - + -
580A LEU* 4.1 26.0 - - + -
593A PHE* 6.4 0.7 - - + -
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Residues in contact with ALA 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A VAL* 4.2 4.9 - - + +
250A VAL* 3.9 6.1 - - + -
287A TYR* 3.5 40.4 - - + +
332A ILE* 4.0 15.1 - - + +
335A LEU* 4.3 11.8 - - + +
400A ARG 3.0 10.6 + - - +
401A ASP 3.4 5.1 + - - +
403A LEU* 1.4 73.4 - - - +
405A LYS* 1.3 60.9 + - - +
407A ILE* 3.5 5.0 + - - +
408A TYR* 3.2 25.6 + - - +
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Residues in contact with LYS 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LYS* 3.3 47.3 - - + +
247A SER* 4.4 3.7 - - - +
249A VAL* 4.3 14.1 - - + +
250A VAL* 4.1 20.9 - - + -
401A ASP* 2.9 32.6 + - - +
402A ALA 3.8 6.1 - - - +
404A ALA* 1.3 73.2 - - - +
406A HIS* 1.4 63.1 + - - +
408A TYR* 3.7 2.2 + - - +
409A ALA* 3.2 24.1 + - - +
566A GLU 5.0 2.0 + - - -
567A LYS* 4.0 12.5 + - - +
569A LYS 2.8 23.6 + - - -
570A ASP* 2.6 30.7 + - - +
636A VAL* 4.0 1.4 - - - +
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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
----------------------------------------------------------
246A LYS* 5.0 6.0 - - - +
402A ALA 2.9 21.7 + - - +
403A LEU* 3.2 10.7 + - + +
405A LYS* 1.4 73.6 - - - +
407A ILE* 1.3 63.0 + - + +
409A ALA* 3.3 5.4 + - - +
410A ASN* 2.9 40.5 + - - +
570A ASP* 6.2 0.2 - - - -
572A VAL* 4.1 16.8 - - + -
577A ILE* 3.7 32.5 - - + +
593A PHE* 3.4 30.0 - + - -
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Residues in contact with ILE 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ILE* 3.5 32.1 - - + -
332A ILE* 3.9 15.9 - - + -
335A LEU* 4.7 10.1 - - + -
360A PHE* 5.0 2.0 - - + -
364A MET* 4.3 13.7 - - + -
403A LEU* 2.9 38.2 + - + +
404A ALA* 4.0 3.6 - - - +
405A LYS 3.5 0.2 - - - -
406A HIS* 1.3 71.9 - - + +
408A TYR* 1.4 57.2 + - - +
410A ASN* 3.4 1.9 + - - +
411A LEU* 2.9 27.5 + - - +
580A LEU* 3.8 25.1 - - + -
589A LEU* 5.1 0.7 - - + -
592A LEU* 4.5 9.8 - - + +
593A PHE* 4.1 22.2 - - + -
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Residues in contact with TYR 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ILE* 2.7 42.1 + - + +
244A LEU* 4.6 12.3 - - + -
249A VAL* 3.8 23.8 - - + -
259A TYR* 3.4 33.7 - + - +
261A ILE* 4.0 4.7 - - + +
262A PHE* 3.5 33.2 - + - -
329A LEU* 3.8 20.6 - - + -
332A ILE* 4.1 9.3 - - + +
404A ALA 3.2 17.5 + - - +
405A LYS 4.0 4.0 - - - +
407A ILE* 1.4 76.3 - - - +
409A ALA* 1.4 56.3 + - - +
411A LEU* 3.4 4.7 + - + +
412A PHE* 2.9 44.8 + + + +
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Residues in contact with ALA 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 5.0 9.2 - - + -
246A LYS* 4.3 17.9 - - - +
405A LYS 3.2 16.8 + - - +
406A HIS* 3.3 6.7 + - - +
408A TYR* 1.4 79.2 - - - +
410A ASN* 1.3 61.9 + - - +
412A PHE* 3.5 6.1 - - - +
413A ASN* 3.0 35.9 + - - +
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Residues in contact with ASN 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A HIS* 2.9 44.9 + - - +
407A ILE 3.9 3.1 - - - +
409A ALA* 1.3 76.6 - - - +
411A LEU* 1.3 58.5 + - - +
413A ASN* 3.4 13.0 + - - +
414A TRP* 2.9 27.5 + - - +
592A LEU* 2.8 43.9 + - + +
593A PHE* 3.8 9.0 - - + +
594A GLN 5.1 1.4 - - - +
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ILE* 3.9 33.0 - - + +
328A ILE* 3.9 40.6 - - + -
329A LEU* 4.0 22.0 - - + -
332A ILE* 5.1 1.8 - - + -
407A ILE 2.9 20.9 + - - +
408A TYR* 3.8 6.1 - - + +
410A ASN* 1.3 70.5 - - - +
412A PHE* 1.4 60.7 + - - +
414A TRP* 3.3 6.9 + - + +
415A ILE* 3.1 34.3 + - + +
588A LEU* 4.1 12.8 - - + -
592A LEU* 4.1 24.3 - - + +
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Residues in contact with PHE 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A MET* 4.2 8.1 - - + -
206A ILE* 3.6 55.9 - - + +
207A GLY* 4.0 3.4 - - - -
220A PHE* 4.1 20.2 - + + -
241A THR* 3.7 27.6 - - + -
244A LEU* 3.8 42.4 - - + -
408A TYR* 2.9 25.2 + + + +
409A ALA* 3.5 7.0 - - - +
411A LEU* 1.4 76.1 - - - +
413A ASN* 1.4 71.0 + - - +
415A ILE* 3.6 4.5 + - - +
416A VAL* 3.3 27.8 + - + +
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Residues in contact with ASN 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A THR* 4.6 6.9 + - - -
409A ALA* 3.0 21.9 + - - +
410A ASN* 3.4 15.1 + - - +
412A PHE* 1.4 83.0 - - - +
414A TRP* 1.4 58.3 + - - +
416A VAL* 3.1 9.7 + - - +
417A ASP* 2.9 36.8 + - - +
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Residues in contact with TRP 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ILE* 4.5 8.7 - - + -
321A TYR* 3.3 44.4 - + + -
325A ILE* 4.2 25.6 - - + -
410A ASN 2.9 17.2 + - - +
411A LEU* 3.3 7.2 + - + +
413A ASN* 1.4 74.3 - - - +
415A ILE* 1.3 73.2 + - + +
417A ASP* 3.4 11.6 + - + +
418A HIS* 3.0 69.0 + + + +
588A LEU* 3.5 27.4 - - + +
591A GLU* 4.1 23.4 + - + +
592A LEU* 3.7 14.4 - - + -
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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
----------------------------------------------------------
202A ILE* 3.8 28.3 - - + -
203A MET* 5.2 2.5 - - - -
206A ILE* 4.0 35.7 - - + -
317A ILE* 4.7 9.3 - - + +
325A ILE* 4.0 40.8 - - + -
411A LEU* 3.1 23.1 + - + +
412A PHE* 3.9 4.7 - - - +
413A ASN 3.4 0.2 - - - -
414A TRP* 1.3 83.6 - - + +
416A VAL* 1.4 56.7 + - - +
418A HIS* 3.3 3.2 + - - +
419A VAL* 2.8 42.0 + - + +
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Residues in contact with VAL 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A MET* 3.9 22.7 - - + -
206A ILE* 5.1 0.9 - - + -
239A MET* 3.8 24.7 - - + +
241A THR* 3.9 33.7 - - + +
412A PHE* 3.3 15.5 + - + +
413A ASN* 3.1 10.1 + - - +
415A ILE* 1.4 75.7 - - - +
417A ASP* 1.4 61.8 + - - +
419A VAL* 3.5 6.3 + - - +
420A ASN* 3.0 43.9 + - - +
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Residues in contact with ASP 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ASN* 2.9 29.6 + - - +
414A TRP* 3.6 14.3 - - + +
416A VAL* 1.4 70.9 - - - +
418A HIS* 1.3 62.0 + - + +
420A ASN* 3.3 13.5 + - - +
421A LYS* 3.3 45.0 + - - +
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Residues in contact with HIS 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU 4.5 4.9 - - - +
317A ILE* 4.9 16.6 - - + +
321A TYR* 5.6 6.5 - + - -
414A TRP* 3.0 67.9 + + + +
415A ILE* 4.1 2.9 - - - +
417A ASP* 1.3 76.8 - - + +
419A VAL* 1.4 62.4 + - - +
421A LYS* 2.9 55.0 + - + +
422A ALA* 3.6 6.6 + - - +
591A GLU* 5.7 0.2 + - - -
----------------------------------------------------------
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Residues in contact with VAL 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A SER* 3.8 26.9 - - - -
202A ILE* 4.2 23.8 - - + -
203A MET* 5.4 4.3 - - - -
239A MET* 3.8 18.2 - - + -
315A LEU* 4.1 13.4 - - + +
317A ILE* 4.7 7.2 - - + -
415A ILE* 2.8 39.3 + - + +
416A VAL* 3.8 6.7 - - - +
418A HIS* 1.4 69.7 - - - +
420A ASN* 1.3 63.5 + - - +
422A ALA* 3.2 18.0 + - - +
423A LEU* 3.5 17.1 + - + +
----------------------------------------------------------
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Residues in contact with ASN 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ALA 4.4 0.9 - - - +
238A ASN* 3.5 18.4 + - - +
239A MET* 2.8 51.6 + - - +
416A VAL* 3.0 27.2 + - - +
417A ASP* 3.3 16.2 + - - +
418A HIS 3.3 0.2 - - - -
419A VAL* 1.3 75.7 - - - +
421A LYS* 1.3 57.4 + - + +
423A LEU* 2.9 7.7 + - - +
424A HIS* 2.8 47.3 + - + -
----------------------------------------------------------
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Residues in contact with LYS 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ASP* 3.3 29.3 - - - +
418A HIS* 2.9 55.0 + - + +
420A ASN* 1.3 75.1 - - + +
422A ALA* 1.3 57.4 + - - +
423A LEU 3.4 0.4 + - - -
424A HIS* 4.3 23.1 + - + +
----------------------------------------------------------
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Residues in contact with ALA 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LYS* 4.8 13.5 - - - +
315A LEU* 3.4 49.6 - - + +
418A HIS 3.6 2.5 + - - +
419A VAL 3.2 10.4 + - - +
420A ASN 3.2 0.6 - - - -
421A LYS* 1.3 76.2 - - - +
423A LEU* 1.3 60.0 + - - +
424A HIS 3.7 2.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A VAL* 3.6 19.5 - - + +
195A LYS* 4.1 18.6 - - + -
196A VAL* 3.4 36.3 - - + +
199A SER* 5.7 1.1 - - - +
224A ILE* 4.9 4.9 - - + -
236A GLY* 3.5 5.7 - - - -
237A ALA* 3.0 58.4 + - + +
238A ASN* 4.3 7.0 - - - +
239A MET* 4.9 7.6 - - + +
315A LEU* 5.9 1.6 - - + -
419A VAL* 3.7 16.8 - - + +
420A ASN* 2.9 13.6 + - - +
422A ALA* 1.3 77.1 - - - +
424A HIS* 1.3 64.6 + - - +
----------------------------------------------------------
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Residues in contact with HIS 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ILE 5.1 0.9 - - - +
236A GLY* 4.9 0.2 - - - -
237A ALA 4.1 8.6 + - - +
238A ASN* 3.4 26.4 + - + -
420A ASN* 2.8 38.7 + - + +
421A LYS* 4.4 19.2 - - + +
422A ALA 3.7 3.2 - - - +
423A LEU* 1.3 81.0 + - - +
425A SER* 1.3 64.1 + - - +
426A THR* 5.9 0.2 - - - +
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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