Contacts of the helix formed by residues 398 - 422 (chain B) in PDB entry 5FWP
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 398 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B GLU* 3.3 33.3 + - - +
395B LEU* 4.7 10.9 + - - -
396B GLN 3.7 1.0 - - - -
397B GLN* 1.3 68.4 - - - +
399B LYS* 1.3 62.9 + - - +
400B ILE 3.0 2.2 - - - -
401B LEU* 2.8 26.1 + - - +
402B LYS* 3.3 8.5 + - - -
17E ASP* 5.2 0.9 + - - -
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Residues in contact with LYS 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B GLN* 3.0 13.4 + - - +
398B SER* 1.3 80.9 + - - +
400B ILE* 1.3 60.9 + - - +
402B LYS* 3.1 15.7 + - + +
403B VAL* 3.0 26.5 + - - +
10E ILE* 3.1 47.0 + - + +
11E GLU* 5.9 0.2 - - - +
12E VAL* 3.7 11.7 + - + +
15E ASP* 2.6 35.8 + - - +
18E GLU* 2.8 23.5 + - - -
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Residues in contact with ILE 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 4.1 11.2 - - + -
386B LEU* 4.0 17.3 - - + -
387B PRO* 3.4 39.0 - - + -
395B LEU* 4.9 8.5 - - + -
396B GLN 4.0 0.9 - - - +
397B GLN* 3.0 23.9 + - + +
399B LYS* 1.3 78.6 - - - +
401B LEU* 1.3 57.6 + - - +
403B VAL* 3.2 9.3 + - + +
404B ILE* 2.9 42.4 + - + +
7E TRP* 4.1 16.8 - - + +
10E ILE* 3.4 21.3 - - + -
119E LEU* 5.7 2.9 - - + -
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Residues in contact with LEU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B LEU* 3.6 22.4 - - + -
363B MET* 5.3 7.4 - - - -
365B SER* 4.1 13.0 - - - +
368B GLU* 3.6 35.2 - - + +
369B LEU* 3.4 43.5 - - + +
395B LEU* 5.3 10.7 - - + +
398B SER* 2.8 15.7 + - - +
400B ILE* 1.3 80.0 - - - +
402B LYS* 1.3 57.5 + - - +
404B ILE* 3.2 14.0 + - + +
405B ARG* 2.8 28.3 + - - +
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Residues in contact with LYS 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B GLU* 2.8 30.7 + - + +
398B SER* 3.3 13.8 + - - +
399B LYS* 3.1 15.8 + - - +
401B LEU* 1.3 75.1 - - - +
403B VAL* 1.3 63.2 - - - +
405B ARG* 3.3 24.1 + - - +
406B LYS* 3.0 31.3 + - - +
12E VAL* 3.9 21.5 - - + -
15E ASP* 3.4 34.2 + - - +
16E GLU* 3.4 26.5 - - - +
17E ASP* 2.8 25.9 + - - +
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Residues in contact with VAL 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 3.8 16.6 - - + -
399B LYS 3.0 19.2 + - - +
400B ILE* 3.4 8.3 - - - +
402B LYS* 1.3 74.1 - - - +
404B ILE* 1.3 65.1 + - - +
406B LYS* 3.3 7.1 + - + +
407B ASN* 3.2 26.3 + - - +
10E ILE* 3.9 13.9 - - + -
11E GLU 5.1 0.2 - - - +
12E VAL* 4.0 9.0 - - + -
115E ASN* 4.9 2.0 - - - -
116E VAL* 3.9 30.5 - - + +
119E LEU* 3.8 35.7 - - + -
120E SER* 5.5 0.2 - - - +
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Residues in contact with ILE 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 3.8 29.8 - - + -
329B PHE* 4.0 21.0 - - + -
355B LEU* 5.6 3.6 - - + -
369B LEU* 3.7 11.4 - - + -
381B VAL* 4.7 11.2 - - + -
383B SER* 6.0 2.5 - - - -
386B LEU* 5.1 11.0 - - + -
395B LEU* 6.1 1.3 - - + -
400B ILE* 2.9 34.0 + - + +
401B LEU* 3.4 18.8 - - + +
403B VAL* 1.3 71.0 - - - +
405B ARG* 1.3 66.9 + - - +
407B ASN* 3.2 7.3 + - - +
408B ILE* 2.9 41.6 + - + +
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Residues in contact with ARG 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ASP 5.2 1.0 + - - -
368B GLU* 3.2 31.0 + - - +
369B LEU 3.0 25.1 - - - +
370B ILE 4.2 2.7 + - - -
371B PRO* 3.9 27.6 - - + -
401B LEU 2.8 12.4 + - - +
402B LYS* 3.3 25.1 + - - +
404B ILE* 1.3 76.6 - - - +
406B LYS* 1.3 59.1 + - - +
408B ILE* 3.0 5.8 + - - +
409B VAL* 2.8 36.1 + - + +
14E ASP* 3.7 30.9 + - - -
16E GLU* 2.9 42.0 + - - -
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Residues in contact with LYS 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B LYS 3.0 16.5 + - - +
403B VAL* 3.5 8.3 - - + +
404B ILE 3.3 0.2 - - - -
405B ARG* 1.3 84.3 - - - +
407B ASN* 1.3 63.8 + - - +
409B VAL* 3.4 8.5 + - - +
410B LYS* 3.1 35.0 + - - +
12E VAL* 4.3 8.5 - - + -
13E SEP 2.8 42.2 + - - -
14E ASP* 3.2 41.5 + - - +
116E VAL* 3.7 27.4 - - + -
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Residues in contact with ASN 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PHE* 3.8 22.7 - - + -
323B VAL* 4.3 8.6 - - + +
327B LEU* 4.4 5.3 - - - +
329B PHE* 5.1 1.1 - - + -
403B VAL* 3.2 22.6 + - - +
404B ILE* 3.2 9.2 + - - +
406B LYS* 1.3 77.4 - - - +
408B ILE* 1.3 61.4 + - - +
410B LYS* 3.3 22.2 + - - +
411B LYS* 3.2 24.8 + - - +
116E VAL* 3.9 23.9 + - - +
120E SER* 3.8 20.2 + - - -
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Residues in contact with ILE 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PHE* 4.5 15.9 - - + -
329B PHE* 5.1 2.0 - - + -
333B LEU* 4.0 21.1 - - + -
353B ILE* 5.1 1.1 - - + -
369B LEU* 3.6 37.5 - - + +
370B ILE* 4.3 16.8 - - + -
374B LEU* 5.9 0.4 - - + -
381B VAL* 4.3 16.2 - - + -
404B ILE* 2.9 27.8 + - + +
405B ARG* 3.4 6.7 - - - +
407B ASN* 1.3 73.9 - - - +
409B VAL* 1.3 54.7 + - + +
411B LYS* 3.0 5.8 + - - +
412B CYS* 2.8 50.4 + - - -
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Residues in contact with VAL 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ILE* 6.1 0.2 - - + -
371B PRO* 3.6 35.9 - - + -
373B TYR* 4.4 9.2 - - - +
374B LEU* 4.0 9.4 - - + -
405B ARG* 2.8 21.9 + - + +
406B LYS* 3.5 10.3 - - - +
408B ILE* 1.3 76.5 - - + +
410B LYS* 1.3 65.9 + - + +
412B CYS* 3.1 6.8 + - - +
413B LEU* 2.9 42.2 + - + +
447B ASN* 3.9 20.0 - - - +
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Residues in contact with LYS 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B LYS* 3.1 21.7 + - - +
407B ASN* 3.4 27.6 + - - +
409B VAL* 1.3 81.3 - - + +
411B LYS* 1.3 61.3 + - + +
413B LEU* 3.5 10.2 + - + +
414B GLU* 3.1 34.5 + - - +
447B ASN* 6.1 0.7 - - - +
450B ARG* 5.1 0.9 + - - -
116E VAL* 4.1 21.6 + - - +
117E ASP* 5.1 4.2 + - - -
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Residues in contact with LYS 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LYS* 3.0 26.0 + - - +
321B PHE* 3.6 37.7 - - + -
333B LEU* 4.3 14.6 - - + -
407B ASN 3.2 12.3 + - - +
408B ILE 3.0 8.1 + - - +
410B LYS* 1.3 76.8 - - + +
412B CYS* 1.3 60.9 + - - +
414B GLU* 3.1 28.8 + - - +
415B LEU* 3.0 26.2 + - - +
122E ASP* 2.8 29.8 + - - -
125E SER* 3.1 18.0 + - - +
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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
----------------------------------------------------------
333B LEU* 3.9 13.7 - - - -
353B ILE* 6.2 0.2 - - - -
370B ILE* 6.0 0.9 - - - -
374B LEU* 4.3 11.7 - - + -
377B ILE* 3.5 34.1 - - + -
408B ILE* 2.8 40.1 + - - -
409B VAL* 3.1 8.9 + - - +
411B LYS* 1.3 76.7 - - - +
413B LEU* 1.3 58.3 + - + +
415B LEU* 3.2 9.3 + - - +
416B PHE* 2.9 45.1 + - + -
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Residues in contact with LEU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B TYR* 5.5 2.5 - - + +
374B LEU* 6.0 1.6 - - + -
409B VAL* 2.9 33.9 + - + +
410B LYS* 3.6 10.1 - - + +
412B CYS* 1.3 77.4 - - + +
414B GLU* 1.3 56.8 + - - +
416B PHE* 3.3 16.9 + - + +
417B SER* 2.9 31.4 + - - -
447B ASN* 3.6 28.5 - - + +
450B ARG* 3.3 40.6 + - + +
451B LEU* 3.7 31.6 - - + -
454B LEU* 5.0 2.5 - - + +
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Residues in contact with GLU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LYS* 2.9 25.2 + - - +
410B LYS* 3.1 23.0 + - - +
411B LYS* 3.1 30.4 + - - +
412B CYS 3.3 0.2 - - - -
413B LEU* 1.3 77.2 - - - +
415B LEU* 1.3 61.7 + - - +
417B SER* 3.2 3.2 + - - -
418B GLU* 3.0 33.0 + - - +
450B ARG* 3.5 17.7 - - - +
125E SER* 4.3 0.9 + - - -
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ALA* 4.2 19.7 - - + -
318B VAL 4.4 1.3 - - - +
319B LYS* 3.8 31.1 - - + +
333B LEU* 4.7 10.1 - - + +
335B ILE* 3.5 34.8 - - + -
377B ILE* 6.5 0.7 - - + -
411B LYS 3.0 14.5 + - - +
412B CYS* 3.2 12.1 + - - +
414B GLU* 1.3 75.8 - - - +
416B PHE* 1.3 52.1 + - + +
418B GLU* 3.3 6.1 + - - +
419B LEU* 2.8 35.0 + - - +
127E SER* 3.9 24.7 - - - -
128E MET 4.4 5.6 - - - +
129E VAL* 4.8 6.5 - - + -
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Residues in contact with PHE 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ILE* 3.7 26.5 - - + -
374B LEU* 3.7 27.1 - - + -
376B PHE* 3.8 20.6 - + - -
377B ILE* 4.0 10.5 - - + -
412B CYS* 2.9 29.5 + - + -
413B LEU* 3.4 18.6 - - + +
415B LEU* 1.3 77.5 - - + +
417B SER* 1.3 52.3 + - - +
419B LEU* 3.3 7.5 + - + +
420B ALA* 2.8 33.4 + - - +
426B TYR* 4.2 2.9 - - + -
429B PHE* 3.6 31.0 - + + -
437B LEU* 6.4 0.2 - - + -
451B LEU* 5.3 3.1 - - + -
454B LEU* 3.7 32.4 - - + +
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Residues in contact with SER 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B LEU 2.9 6.6 + - - -
414B GLU* 3.2 9.4 + - - -
416B PHE* 1.3 76.4 - - - +
418B GLU* 1.3 59.2 + - - +
420B ALA* 3.1 11.0 + - - +
421B GLU* 3.1 28.8 + - - +
450B ARG* 2.8 35.6 + - - -
453B GLU* 5.1 1.9 + - - -
454B LEU* 4.5 8.4 - - - +
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Residues in contact with GLU 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LYS* 5.4 2.3 + - - -
414B GLU* 3.0 24.1 + - - +
415B LEU* 3.8 6.3 - - + +
417B SER* 1.3 73.5 - - - +
419B LEU* 1.3 65.8 + - - +
421B GLU* 3.1 37.9 + - - +
422B ASP* 3.3 6.6 + - - +
127E SER* 2.6 37.5 + - - -
129E VAL* 4.7 8.1 - - + +
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 4.2 10.1 - - + -
317B ALA* 4.9 2.0 - - + -
335B ILE* 4.0 19.5 - - + -
415B LEU* 2.8 18.1 + - + +
416B PHE* 3.4 7.6 - - + +
418B GLU* 1.3 77.9 - - - +
420B ALA* 1.3 55.3 + - - +
422B ASP* 2.9 32.3 + - - +
425B ASN* 4.1 18.4 - - + +
426B TYR* 3.3 13.7 - - + +
429B PHE* 3.5 43.1 - - + -
129E VAL* 3.7 38.5 - - + +
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Residues in contact with ALA 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B PHE 2.8 14.2 + - - +
417B SER* 3.1 11.9 + - - +
419B LEU* 1.3 73.1 - - - +
421B GLU* 1.3 65.8 + - - +
422B ASP 3.3 0.5 + - - -
423B LYS* 3.4 14.7 + - - +
426B TYR* 3.6 21.4 - - + +
454B LEU* 4.1 11.2 - - + -
456B ARG* 4.1 21.4 + - - +
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Residues in contact with GLU 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B SER 3.1 15.9 + - - +
418B GLU* 3.1 30.3 + - - +
420B ALA* 1.3 74.5 - - - +
422B ASP* 1.3 60.0 + - - +
423B LYS* 2.9 10.6 + - - +
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Residues in contact with ASP 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B GLU 3.3 6.3 + - - +
419B LEU* 2.9 16.2 + - - +
420B ALA 3.7 0.2 - - - -
421B GLU* 1.3 74.3 - - - +
423B LYS* 1.3 50.9 + - - +
424B GLU* 3.4 8.0 + - - +
425B ASN* 2.9 25.6 + - + +
426B TYR 2.8 27.9 + - - -
129E VAL* 3.7 10.1 - - + +
131E THR* 2.5 33.9 + - - +
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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