Contacts of the helix formed by residues 397 - 419 (chain Q) in PDB entry 1HI0
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 ALA 397 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135Q PHE* 6.4 0.7 - - + -
283Q ILE* 4.2 2.2 - - + +
287Q ALA* 4.1 15.7 - - + -
291Q ARG* 4.3 0.7 - - - +
357Q PHE* 4.4 20.4 - - + -
395Q GLN* 2.9 16.8 + - - +
396Q GLY* 1.3 75.3 - - - +
398Q THR* 1.3 66.0 + - - +
399Q ASP* 2.9 13.7 + - - -
400Q LEU* 2.9 24.2 + - + -
401Q MET* 3.0 14.5 + - + +
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Residues in contact with THR 398 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E C 5.3 1.6 + - - -
329Q ASP* 6.1 0.2 - - - -
391Q LEU* 3.1 44.3 - - + +
392Q SER 2.9 35.9 - - - +
393Q SER* 3.1 21.4 + - - +
395Q GLN* 3.3 19.0 + - + +
396Q GLY 3.9 0.2 - - - -
397Q ALA* 1.3 75.5 - - - +
399Q ASP* 1.3 57.6 + - - +
401Q MET* 4.0 1.1 - - - -
402Q GLY* 3.1 10.0 + - - -
667Q GTP 3.8 24.2 + - - -
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Residues in contact with ASP 399 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291Q ARG* 2.7 49.4 + - - +
295Q TYR* 4.1 9.4 + - - -
397Q ALA 3.5 5.9 - - - +
398Q THR* 1.3 75.0 + - - +
400Q LEU* 1.3 69.8 + - - +
402Q GLY 3.4 0.3 + - - -
403Q THR* 2.9 34.8 + - - +
451Q LYS* 5.1 14.9 + - - -
452Q SER* 3.6 12.4 + - - +
629Q GLN 6.1 1.8 - - - +
667Q GTP 4.2 7.6 + - - +
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Residues in contact with LEU 400 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134Q MET* 4.8 8.7 - - + +
135Q PHE* 5.3 4.7 - - + -
287Q ALA* 3.6 40.6 - - + +
290Q VAL* 3.7 29.4 - - + -
291Q ARG* 4.2 13.2 - - + -
294Q ILE* 4.0 23.8 - - + -
295Q TYR* 5.7 1.1 - - - +
397Q ALA* 2.9 12.3 + - + +
399Q ASP* 1.3 92.7 + - - +
401Q MET* 1.3 70.0 + - + +
403Q THR* 3.1 4.3 + - - +
404Q LEU* 2.7 37.1 + - - +
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Residues in contact with MET 401 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134Q MET* 6.4 0.2 - - - -
135Q PHE* 4.6 16.6 - - + -
332Q TRP* 3.0 46.0 + - + -
337Q ARG* 5.9 0.2 - - - -
340Q ILE* 3.9 22.0 - - + -
357Q PHE* 3.6 33.7 - - + -
361Q LEU* 4.3 4.7 - - + -
391Q LEU* 3.7 20.6 - - + -
395Q GLN* 4.4 6.5 - - - +
397Q ALA* 3.0 18.4 + - + +
398Q THR 4.1 0.2 - - - +
400Q LEU* 1.3 87.9 - - + +
402Q GLY* 1.3 63.1 + - - +
404Q LEU* 3.8 6.4 - - + +
405Q LEU* 3.0 15.6 + - - +
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Residues in contact with GLY 402 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328Q HIS* 3.4 27.6 - - - -
332Q TRP* 4.0 2.2 - - - -
391Q LEU* 3.8 1.0 - - - +
398Q THR 3.1 13.2 + - - -
399Q ASP 3.8 2.7 - - - -
401Q MET* 1.3 81.2 - - - +
403Q THR* 1.3 56.3 + - - +
405Q LEU* 3.6 0.9 - - - +
406Q MET* 2.9 35.0 + - - +
452Q SER* 3.9 10.1 - - - -
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Residues in contact with THR 403 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134Q MET* 4.2 10.1 - - + -
294Q ILE* 5.0 4.3 - - + +
302Q PHE* 3.4 41.1 - - + -
399Q ASP* 2.9 25.5 + - - +
400Q LEU* 3.6 7.7 - - - +
402Q GLY* 1.3 73.2 - - - +
404Q LEU* 1.3 62.4 + - - +
405Q LEU 3.1 0.2 + - - -
406Q MET 3.3 0.3 + - - -
407Q SER* 2.7 37.6 + - - +
450Q SER* 4.9 2.7 - - - +
451Q LYS* 4.2 7.2 - - - +
452Q SER* 3.2 23.9 + - - +
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Residues in contact with LEU 404 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127Q PHE* 4.4 11.7 - - + +
130Q ALA* 3.5 35.4 - - + -
131Q VAL* 3.9 8.3 - - + +
134Q MET* 3.2 35.1 - - - +
135Q PHE* 5.1 4.7 - - + -
336Q LEU* 4.2 14.1 - - + -
340Q ILE* 3.9 28.5 - - + -
400Q LEU 2.7 22.4 + - - +
401Q MET* 3.8 9.2 - - + +
403Q THR* 1.3 72.5 - - - +
405Q LEU* 1.3 65.1 + - - +
407Q SER* 5.0 2.0 - - - -
408Q ILE* 3.6 18.7 + - - +
440Q TRP* 5.9 1.1 - - - -
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Residues in contact with LEU 405 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127Q PHE* 4.0 11.6 - - + -
328Q HIS* 3.8 7.4 - - + -
332Q TRP* 3.5 31.6 - - + +
333Q PRO* 4.0 16.2 - - + -
335Q TRP* 5.2 1.8 - - + -
336Q LEU* 3.4 28.9 - - + +
401Q MET 3.0 8.3 + - - +
402Q GLY 3.6 1.3 - - - +
404Q LEU* 1.3 81.0 - - - +
406Q MET* 1.3 82.0 + - - +
408Q ILE* 3.5 2.4 + - - +
409Q THR* 3.0 37.8 + - - +
485Q TYR* 5.1 4.7 - - + -
486Q MET* 3.8 22.2 - - + -
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Residues in contact with MET 406 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325Q VAL* 3.2 32.5 - - + -
328Q HIS* 3.7 20.2 - - + +
402Q GLY 2.9 16.9 + - - +
403Q THR 4.3 0.2 - - - +
405Q LEU* 1.3 96.2 - - - +
407Q SER* 1.3 59.9 + - - +
409Q THR* 3.9 7.0 - - + -
410Q TYR* 2.8 54.5 + - + +
452Q SER 3.1 29.6 - - - +
453Q ASP* 4.1 1.1 - - - -
486Q MET* 3.6 13.0 - - + -
488Q ILE* 3.9 15.7 - - + -
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Residues in contact with SER 407 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302Q PHE* 3.7 14.1 - - - -
403Q THR* 2.7 22.9 + - - +
404Q LEU* 4.5 1.6 - - - -
406Q MET* 1.3 72.9 - - - +
408Q ILE* 1.3 63.1 + - - +
410Q TYR* 4.3 1.5 - - - -
411Q LEU* 3.0 21.7 + - - +
439Q TYR* 4.9 0.5 - - - -
440Q TRP* 2.9 31.4 + - - -
448Q GLN* 2.6 41.1 + - - +
450Q SER* 4.4 4.4 + - - -
452Q SER 5.2 0.2 + - - -
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Residues in contact with ILE 408 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126Q LEU* 3.8 36.6 - - + +
127Q PHE* 3.5 41.1 - - + -
130Q ALA* 3.7 24.2 - - + -
404Q LEU 3.6 13.0 + - - +
405Q LEU 3.5 1.0 + - - -
406Q MET 3.3 0.2 - - - -
407Q SER* 1.3 73.2 - - - +
409Q THR* 1.3 67.4 + - - +
411Q LEU* 3.1 8.2 + - + +
412Q VAL* 2.8 30.5 + - + +
436Q LEU* 3.9 24.9 - - + -
440Q TRP* 4.4 6.7 - - + +
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Residues in contact with THR 409 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127Q PHE* 4.5 2.4 - - - -
405Q LEU* 3.0 38.5 + - - +
406Q MET* 3.2 25.9 + - + -
408Q ILE* 1.3 78.4 - - - +
410Q TYR* 1.3 58.4 + - + +
412Q VAL* 3.3 7.5 + - - +
413Q MET* 2.8 26.7 + - + +
483Q SER* 3.5 27.8 + - - +
485Q TYR* 3.8 20.9 - - + +
486Q MET* 4.7 2.2 - - - +
488Q ILE* 4.6 7.9 - - + -
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Residues in contact with TYR 410 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323Q THR* 3.4 24.5 + - - -
325Q VAL* 3.2 15.1 - - - +
406Q MET* 2.8 55.1 + - + +
407Q SER* 4.3 1.6 - - - -
409Q THR* 1.3 69.2 - - + +
411Q LEU* 1.3 68.1 + - - +
413Q MET* 3.1 29.7 + - + +
414Q GLN* 2.9 27.5 + - - +
448Q GLN* 3.6 13.7 - - - +
450Q SER* 4.8 1.6 - - - -
452Q SER 4.1 4.5 - - - -
453Q ASP 2.8 24.6 + - - -
455Q ALA* 3.5 25.1 - - + -
457Q LEU* 3.5 23.5 - - + +
488Q ILE* 4.3 7.0 - - + -
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Residues in contact with LEU 411 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126Q LEU* 3.9 30.7 - - + -
407Q SER 3.0 15.3 + - - +
408Q ILE* 3.5 12.3 - - + +
410Q TYR* 1.3 74.5 - - - +
412Q VAL* 1.3 60.2 + - - +
414Q GLN* 2.9 7.1 + - - +
415Q LEU* 2.8 36.3 + - + +
435Q PHE* 4.0 20.4 - - + -
436Q LEU* 4.0 21.3 - - + -
439Q TYR* 3.7 41.5 - - + -
446Q ILE* 3.9 14.6 - - + -
448Q GLN* 4.1 0.4 + - - -
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Residues in contact with VAL 412 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122Q ARG* 3.7 14.4 - - - +
123Q ASP* 3.5 36.3 - - - +
126Q LEU* 4.1 20.0 - - + -
408Q ILE* 2.8 26.6 + - + +
409Q THR* 3.5 10.8 - - - +
411Q LEU* 1.3 74.6 - - - +
413Q MET* 1.3 66.9 + - - +
414Q GLN 3.1 0.2 + - - -
415Q LEU* 3.1 7.4 + - - +
416Q ASP* 2.8 34.9 + - - +
483Q SER* 5.7 0.4 - - - +
484Q PRO* 5.3 3.8 - - + -
485Q TYR* 4.3 13.2 - - + -
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Residues in contact with MET 413 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323Q THR* 5.2 1.1 - - - -
409Q THR* 2.8 13.4 + - + +
410Q TYR* 3.1 41.2 + - + +
412Q VAL* 1.3 75.9 - - - +
414Q GLN* 1.3 61.8 + - + +
416Q ASP* 4.6 1.6 - - - -
417Q HIS* 3.2 32.6 + - + +
457Q LEU* 4.0 11.7 - - + -
471Q LEU* 4.1 17.7 - - + +
475Q LEU* 5.1 4.7 - - - -
482Q PRO* 3.5 53.8 - - + +
483Q SER* 4.6 4.5 + - - -
488Q ILE* 3.8 24.5 - - + -
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Residues in contact with GLN 414 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410Q TYR 2.9 13.6 + - - +
411Q LEU* 2.9 7.7 + - - +
413Q MET* 1.3 75.0 - - - +
415Q LEU* 1.3 67.0 + - - +
418Q THR* 2.8 39.6 + - - +
419Q ALA* 3.2 2.0 + - - -
439Q TYR* 2.7 36.8 + - - -
446Q ILE* 3.8 16.9 - - + +
447Q ARG 3.4 11.1 + - - -
457Q LEU* 3.9 14.7 - - + +
458Q GLY 3.3 24.9 + - - -
459Q TRP* 3.5 31.1 - - + -
471Q LEU* 4.9 1.3 - - + -
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Residues in contact with LEU 415 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122Q ARG* 3.5 42.8 - - - +
126Q LEU* 3.9 19.7 - - + -
411Q LEU* 2.8 37.3 + - + +
412Q VAL* 3.6 7.0 - - - +
414Q GLN* 1.3 76.9 - - - +
416Q ASP* 1.3 64.6 + - - +
419Q ALA* 3.2 22.0 + - - +
420Q PRO* 3.6 12.0 - - - +
422Q LEU* 4.0 27.6 - - + -
423Q ASN* 4.1 4.9 + - - +
426Q ILE* 3.9 9.9 - - + -
435Q PHE* 4.5 6.3 - - + -
446Q ILE* 4.3 10.1 - - + -
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Residues in contact with ASP 416 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122Q ARG* 2.6 32.8 + - - +
123Q ASP* 5.2 0.5 - - - +
412Q VAL* 2.8 32.4 + - - +
413Q MET* 4.4 1.2 - - - -
415Q LEU* 1.3 75.3 - - - +
417Q HIS* 1.3 79.9 + - + +
420Q PRO* 5.2 3.3 - - - +
482Q PRO 5.2 2.3 - - - +
484Q PRO* 4.8 12.3 - - - +
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Residues in contact with HIS 417 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413Q MET* 3.2 28.1 + - + +
416Q ASP* 1.3 89.9 + - + +
418Q THR* 1.3 70.7 + - + +
420Q PRO* 5.2 1.1 - - - -
467Q GLY* 3.7 12.6 - - - +
470Q ARG* 4.2 13.2 + - + +
471Q LEU* 4.0 21.3 - - + +
474Q MET* 3.1 37.1 - - + +
480Q VAL* 5.8 1.1 - - + -
482Q PRO* 3.0 30.2 + - + +
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Residues in contact with THR 418 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414Q GLN 2.8 26.0 + - - +
415Q LEU 3.5 1.0 + - - -
417Q HIS* 1.3 88.2 - - + +
419Q ALA* 1.3 61.0 + - - +
420Q PRO* 3.5 8.5 - - - +
421Q HIS* 4.0 2.3 + - - -
446Q ILE* 4.0 2.1 - - - +
459Q TRP* 3.1 25.9 + - + +
463Q ARG 4.6 0.7 - - - +
464Q ALA* 3.1 38.0 - - - +
467Q GLY* 3.2 9.2 - - - +
468Q GLY* 3.2 27.4 - - - +
470Q ARG* 5.6 0.4 - - - +
471Q LEU* 4.3 5.8 - - + -
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Residues in contact with ALA 419 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414Q GLN 3.2 3.8 + - - +
415Q LEU* 3.2 18.5 + - + +
418Q THR* 1.3 87.9 + - - +
420Q PRO* 1.3 54.0 - - - +
421Q HIS* 3.0 17.7 - - + -
422Q LEU* 2.7 56.6 + - + +
423Q ASN 3.9 1.2 + - - -
446Q ILE* 4.6 5.6 - - + -
464Q ALA* 4.0 6.7 - - + -
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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