Contacts of the helix formed by residues 392 - 422 (chain B) in PDB entry 6R7Z
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 LEU 392 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLU* 4.6 20.4 - - + +
283B GLU 4.2 5.6 - - - +
284B PRO* 4.8 0.2 - - - -
285B ARG* 3.5 8.7 - - - +
390B HIS 4.0 2.9 - - - +
391B ARG* 1.3 83.7 - - + +
393B GLU* 1.3 62.1 + - - +
394B SER* 4.0 10.5 - - - +
395B ALA* 4.3 15.2 - - + +
396B TYR* 3.4 20.6 + - - +
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Residues in contact with GLU 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B GLU 4.8 2.6 + - - +
285B ARG* 3.7 16.5 - - + +
286B PRO* 5.5 4.3 - - + -
392B LEU* 1.3 74.2 - - - +
394B SER* 1.3 54.9 + - - +
395B ALA 3.3 0.4 - - - -
396B TYR* 3.6 11.4 - - + +
397B GLN* 2.7 36.3 + - - +
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Residues in contact with SER 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 3.5 6.1 - - - +
393B GLU* 1.3 79.3 - - - +
395B ALA* 1.3 57.1 + - - +
397B GLN* 3.7 5.4 - - - +
398B ASN* 2.8 30.5 + - - +
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Residues in contact with ALA 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B HIS* 5.0 6.5 - - + -
391B ARG 5.7 0.7 - - - +
392B LEU* 4.3 18.5 + - + +
393B GLU 3.3 0.2 - - - -
394B SER* 1.3 75.4 - - - +
396B TYR* 1.3 60.4 + - - +
398B ASN* 3.3 5.3 + - - +
399B HIS* 2.7 48.1 + - + +
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Residues in contact with TYR 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ARG* 5.4 5.6 - - + -
382B GLU* 4.6 10.5 + - - +
385B THR* 3.7 42.2 - - - -
386B SER* 3.9 15.8 - - - -
390B HIS* 3.8 18.5 - - + +
392B LEU 3.4 19.2 + - - +
393B GLU* 3.4 13.0 + - + +
394B SER 3.3 0.2 - - - -
395B ALA* 1.3 79.9 - - - +
397B GLN* 1.3 67.7 + - + +
399B HIS* 4.0 4.2 - - - +
400B LEU* 3.1 28.8 + - + +
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Residues in contact with GLN 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B GLU 2.7 22.5 + - - +
394B SER* 3.7 6.7 - - - +
396B TYR* 1.3 80.0 - - + +
398B ASN* 1.3 50.5 + - - +
400B LEU* 3.4 5.0 + - - +
401B ILE* 2.7 36.8 + - - +
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Residues in contact with ASN 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B SER 2.8 22.1 + - - +
395B ALA* 3.3 8.0 + - - +
397B GLN* 1.3 71.0 - - - +
399B HIS* 1.3 65.2 + - + +
401B ILE* 3.3 6.7 + - - +
402B LEU* 2.8 30.1 + - - +
554B VAL* 5.7 10.3 - - + -
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Residues in contact with HIS 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ILE* 5.9 7.2 - - + -
385B THR* 5.4 7.6 - - - -
395B ALA* 2.7 39.1 + - + +
396B TYR* 4.1 4.7 - - - +
398B ASN* 1.3 78.0 - - + +
400B LEU* 1.3 61.3 + - - +
402B LEU* 3.2 7.1 + - - +
403B LYS* 2.9 29.8 + - - +
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Residues in contact with LEU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ALA* 5.5 8.2 - - + +
382B GLU* 6.2 2.0 - - - -
385B THR* 4.7 15.1 - - - -
396B TYR* 3.1 24.7 + - + +
397B GLN* 3.7 6.1 - - - +
399B HIS* 1.3 77.2 - - - +
401B ILE* 1.3 59.2 + - - +
403B LYS* 3.5 6.0 + - - +
404B VAL* 3.0 32.2 + - - +
495B PHE* 4.7 5.5 - - + -
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Residues in contact with ILE 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B GLN 2.7 22.5 + - - +
398B ASN* 3.7 7.9 - - - +
400B LEU* 1.3 73.4 - - - +
402B LEU* 1.3 57.8 + - - +
404B VAL* 4.2 0.2 - - - +
405B LEU* 2.9 33.7 + - - +
495B PHE* 4.4 20.7 - - + -
554B VAL* 6.0 4.9 - - + -
555B TRP* 5.2 11.4 - - + +
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Residues in contact with LEU 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ASN 2.8 19.1 + - - +
399B HIS* 3.2 8.7 + - - +
401B ILE* 1.3 76.8 - - - +
403B LYS* 1.3 61.6 + - - +
405B LEU* 4.0 3.7 - - - +
406B VAL* 3.1 25.5 + - - +
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Residues in contact with LYS 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B VAL* 6.0 6.5 - - + -
381B ALA* 4.5 19.1 - - + -
399B HIS 2.9 16.7 + - - +
400B LEU* 3.9 5.6 - - - +
402B LEU* 1.3 77.8 - - - +
404B VAL* 1.3 61.2 + - - +
406B VAL* 3.4 5.3 + - - +
407B PHE* 3.1 24.3 + - - +
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Residues in contact with VAL 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ARG* 6.4 2.0 - - + -
381B ALA* 5.5 6.7 - - + +
400B LEU 3.0 18.4 + - - +
401B ILE 4.2 1.3 - - - +
403B LYS* 1.3 73.8 - - - +
405B LEU* 1.3 60.2 + - - +
407B PHE* 3.5 5.4 + - - +
408B ASN* 2.9 33.0 + - - +
495B PHE* 3.6 27.6 - - + -
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Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B ILE 2.9 20.1 + - - +
402B LEU* 4.0 4.7 - - - +
404B VAL* 1.3 75.0 - - - +
406B VAL* 1.3 60.7 + - - +
408B ASN* 4.1 3.3 - - - +
409B PHE* 2.9 33.3 + - - +
555B TRP* 6.3 4.3 - - + -
558B ALA* 6.1 5.8 - - + -
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Residues in contact with VAL 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B LEU 3.1 18.6 + - - +
403B LYS* 3.7 5.2 - - - +
405B LEU* 1.3 77.2 - - - +
407B PHE* 1.3 62.4 + - - +
409B PHE* 3.9 4.9 - - - +
410B LEU* 3.1 25.1 + - - +
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Residues in contact with PHE 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B CYS* 4.2 22.9 - - + -
326B LEU* 5.2 3.8 - - + -
329B SER* 4.1 24.9 - - - -
373B MET* 3.4 42.2 - - + -
374B ASN* 3.6 17.5 - - + -
377B TYR* 3.6 21.3 - - + -
403B LYS 3.1 16.7 + - - +
404B VAL* 4.1 5.4 - - - +
406B VAL* 1.3 77.0 - - - +
408B ASN* 1.3 61.6 + - + +
410B LEU* 3.8 4.7 - - + +
411B ASN* 2.8 41.1 + - + +
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Residues in contact with ASN 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ASN* 6.2 4.0 - - + -
404B VAL 2.9 19.4 + - - +
405B LEU* 4.1 4.0 - - - +
407B PHE* 1.3 79.4 - - + +
409B PHE* 1.3 58.8 + - - +
411B ASN* 4.2 3.9 - - - +
412B CYS* 3.0 32.7 + - - +
499B LEU* 6.1 5.8 - - + +
503B LEU* 6.3 2.9 - - + -
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Residues in contact with PHE 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B LEU 2.9 18.8 + - - +
406B VAL* 3.9 5.4 - - - +
408B ASN* 1.3 76.8 - - - +
410B LEU* 1.3 57.2 + - - +
412B CYS* 4.9 2.0 - - - -
413B PHE* 2.9 37.4 + - + +
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LEU* 5.9 8.1 - - + -
329B SER* 5.9 6.3 - - - -
406B VAL 3.1 18.6 + - - +
407B PHE* 3.8 7.4 - - + +
409B PHE* 1.3 77.8 - - - +
411B ASN* 1.3 61.6 + - - +
414B ALA* 3.2 32.5 + - + +
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Residues in contact with ASN 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B SER* 5.5 8.0 - - - -
370B ILE* 4.8 25.7 - - + +
373B MET* 6.2 0.9 - - + -
374B ASN* 6.2 1.6 - - + -
407B PHE* 2.8 41.8 + - + +
408B ASN* 4.2 3.8 - - - +
410B LEU* 1.3 75.8 - - - +
412B CYS* 1.3 58.7 + - - +
414B ALA* 4.8 2.6 + - - +
415B SER 5.7 0.5 + - - -
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Residues in contact with CYS 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ASN 3.0 19.0 + - - +
409B PHE* 4.1 2.2 - - - +
411B ASN* 1.3 80.0 - - - +
413B PHE* 1.3 61.8 + - + +
414B ALA 3.5 0.6 + - - -
415B SER* 4.7 5.9 + - - -
416B LEU* 4.9 4.7 + - - +
503B LEU* 5.7 9.2 - - + -
507B TYR* 4.8 28.8 + - + +
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Residues in contact with PHE 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B PHE* 2.9 17.5 + - - +
410B LEU* 5.5 0.2 - - - -
412B CYS* 1.3 75.7 - - + +
414B ALA* 1.3 60.1 + - - +
415B SER 3.4 2.5 - - - -
416B LEU* 3.5 11.6 + - + +
417B PHE* 3.0 29.3 + - + +
510B LEU* 5.5 10.3 - - + -
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Residues in contact with ALA 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 6.3 1.3 - - - -
333B MET* 4.9 16.8 - - + -
337B PHE* 5.4 1.1 - - - -
410B LEU* 3.2 20.8 + - + +
411B ASN* 4.7 2.6 - - - +
412B CYS 3.5 1.4 - - - -
413B PHE* 1.3 78.1 - - - +
415B SER* 1.3 59.2 + - - +
417B PHE* 3.4 5.2 + - - +
418B TYR* 2.8 30.8 + - - +
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Residues in contact with SER 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B MET* 5.9 2.1 - - - +
336B TYR* 4.6 15.5 - - - -
337B PHE* 4.1 24.9 - - - -
411B ASN 5.7 0.8 + - - -
412B CYS 4.7 5.3 + - - -
413B PHE 3.4 0.4 - - - -
414B ALA* 1.3 79.3 - - - +
416B LEU* 1.3 57.4 + - - +
418B TYR* 3.4 1.6 + - - +
419B ILE* 2.8 30.3 + - - +
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Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B CYS 4.9 2.6 + - - +
413B PHE* 3.5 16.6 + - + +
414B ALA 3.3 0.2 - - - -
415B SER* 1.3 77.8 - - - +
417B PHE* 1.3 59.8 + - - +
419B ILE* 3.9 5.1 - - - +
420B ALA* 3.0 30.8 + - - +
433B LEU* 6.3 2.5 - - + -
510B LEU* 5.7 7.4 - - + +
511B PHE* 5.5 11.7 - - + -
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Residues in contact with PHE 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B PHE* 3.0 19.4 + - + +
414B ALA* 3.8 5.6 - - - +
416B LEU* 1.3 78.2 - - - +
418B TYR* 1.3 57.6 + - - +
420B ALA* 4.7 2.9 - - - -
421B PHE* 3.0 35.4 + - + +
422B VAL* 4.1 0.3 + - - +
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Residues in contact with TYR 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B PHE* 3.6 30.9 - - + -
414B ALA 2.8 18.7 + - - +
417B PHE* 1.3 74.4 - - - +
419B ILE* 1.3 63.8 + - - +
422B VAL* 3.3 16.5 + - + +
423B LEU* 3.2 21.5 + - - +
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Residues in contact with ILE 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B PHE* 4.8 6.7 - - + -
415B SER 2.8 17.8 + - - +
416B LEU* 4.0 6.1 - - - +
417B PHE 3.3 0.2 - - - -
418B TYR* 1.3 77.5 - - - +
420B ALA* 1.3 58.8 + - - +
423B LEU* 3.9 8.3 - - + +
424B LYS* 2.9 30.0 + - - -
425B ASP 3.8 6.5 + - - +
428B LEU* 5.8 0.9 - - + -
429B LEU* 4.5 24.4 - - + +
432B SER* 5.9 5.6 - - - -
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Residues in contact with ALA 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LEU 3.0 18.8 + - - +
417B PHE* 4.2 3.6 - - - +
419B ILE* 1.3 79.7 - - - +
421B PHE* 1.3 59.5 + - + +
422B VAL 3.7 0.2 - - - -
424B LYS* 3.9 16.0 - - - +
429B LEU* 5.7 4.2 - - + +
576B MET* 5.3 8.8 - - - +
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Residues in contact with PHE 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B PHE* 3.0 16.5 + - + +
420B ALA* 1.3 78.4 - - + +
422B VAL* 1.3 61.1 + - - +
424B LYS* 4.9 2.7 - - - -
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Residues in contact with VAL 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B TYR* 3.3 20.8 + - + +
420B ALA 3.7 0.4 - - - -
421B PHE* 1.3 80.8 - - - +
423B LEU* 1.3 67.2 + - - +
424B LYS* 3.4 2.8 - - - +
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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