Contacts of the helix formed by residues 390 - 415 (chain B) in PDB entry 3SV1
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 390 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B PRO* 1.3 78.6 - - - +
391B LYS* 1.3 54.7 + - - +
392B ASN* 2.8 21.7 - - - +
393B ILE* 2.6 44.0 + - - +
394B ARG* 2.8 6.7 + - - -
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Residues in contact with LYS 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B PRO 4.1 1.0 + - - -
390B SER* 1.3 71.0 - - - +
392B ASN* 1.3 55.3 + - - +
393B ILE 3.0 2.2 - - - -
394B ARG* 3.9 12.6 - - + -
395B MET* 2.8 30.0 - - - +
460B TYR* 5.3 8.1 - - + +
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Residues in contact with ASN 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B SER* 2.8 15.4 - - - +
391B LYS* 1.3 78.4 - - - +
393B ILE* 1.3 56.9 + - + +
395B MET* 3.1 25.0 - - - +
396B MET* 3.5 8.0 - - - +
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Residues in contact with ILE 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B GLU* 3.1 28.5 - - - +
389B PRO* 3.1 25.8 - - + -
390B SER* 2.6 34.7 + - - +
392B ASN* 1.3 80.4 - - + +
394B ARG* 1.3 53.0 + - - +
395B MET 2.8 4.7 - - - -
396B MET* 2.6 31.0 + - + +
397B GLN* 2.6 46.4 + - + +
496B LYS* 4.9 4.7 - - - +
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Residues in contact with ARG 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B SER* 5.3 4.8 + - - -
387B ARG 5.2 0.4 + - - -
388B ASN* 4.6 16.4 - - - +
389B PRO* 4.0 26.3 - - + +
390B SER 2.8 19.3 + - - +
391B LYS* 4.1 5.6 - - - -
393B ILE* 1.3 72.1 - - - +
395B MET* 1.3 60.9 + - - +
397B GLN* 2.9 30.1 + - - +
398B ALA* 3.2 22.5 + - - +
459B SER* 2.4 48.3 + - - -
460B TYR* 3.3 40.4 - - + +
471B MET* 4.8 10.8 - - - +
500B MET* 4.6 6.3 - - - +
758E GLU* 5.1 4.9 - - - +
762E TYR* 4.1 15.0 - - - -
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Residues in contact with MET 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B LYS 2.8 26.7 + - - +
392B ASN* 3.1 21.3 - - - +
393B ILE 2.8 0.2 - - - -
394B ARG* 1.3 79.2 - - - +
396B MET* 1.3 69.3 + - - +
398B ALA* 3.3 3.4 + - - +
399B GLN* 2.7 83.2 + - + +
460B TYR* 3.6 17.2 + - - +
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Residues in contact with MET 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B LEU* 6.1 0.4 - - + -
392B ASN 3.5 6.7 - - - +
393B ILE* 2.6 42.2 + - + +
395B MET* 1.3 88.1 - - - +
397B GLN* 1.3 92.9 + - + +
399B GLN* 3.2 10.3 + - - +
400B GLU* 3.1 27.9 + - - +
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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
----------------------------------------------------------
383B LEU* 3.7 24.6 - - + +
384B LEU 4.0 10.7 + - - -
385B SER* 2.9 32.6 + - - +
386B GLU* 4.2 6.1 + - - -
389B PRO* 4.3 3.5 - - - +
393B ILE* 2.6 27.1 + - + +
394B ARG* 2.9 39.7 + - - +
396B MET* 1.3 91.5 - - + +
398B ALA* 1.3 65.4 + - - +
400B GLU* 2.8 6.5 + - - +
401B ALA* 2.8 25.8 + - - +
471B MET* 4.4 9.0 - - - +
496B LYS* 5.6 0.2 - - - +
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Residues in contact with ALA 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ARG 3.2 12.9 + - - +
395B MET* 3.5 8.5 - - - +
397B GLN* 1.3 78.1 - - - +
399B GLN* 1.3 56.0 + - + +
400B GLU 2.7 12.3 + - - -
401B ALA* 3.1 3.4 + - - +
402B VAL* 3.1 23.0 + - - +
460B TYR* 4.0 20.0 - - + +
462B ALA* 4.7 5.8 - - + -
464B ILE* 6.4 0.2 - - + -
469B VAL* 4.3 29.8 - - + +
471B MET* 4.9 2.8 - - - -
502B CYS* 5.1 3.1 - - - -
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Residues in contact with GLN 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B MET* 2.7 62.7 + - + +
396B MET* 3.3 11.1 - - - +
398B ALA* 1.3 70.8 - - - +
400B GLU* 1.3 57.3 + - - +
402B VAL* 2.8 21.9 - - - +
403B SER* 3.8 6.6 + - - -
464B ILE* 6.5 1.3 - - + -
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Residues in contact with GLU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B LEU* 6.0 1.6 - - + -
396B MET* 3.1 19.7 + - - +
397B GLN* 2.8 10.7 + - - +
398B ALA 2.7 4.0 + - - -
399B GLN* 1.3 72.9 - - + +
401B ALA* 1.3 54.7 + - - +
402B VAL 2.5 6.0 + - - -
403B SER* 2.4 34.5 + - - -
404B ARG* 2.8 14.5 + - - +
407B ARG* 3.2 32.7 + - - -
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Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B THR* 3.1 39.8 - - + +
383B LEU* 4.6 7.7 - - + +
397B GLN 2.8 16.3 + - - +
398B ALA* 3.7 4.0 - - - +
400B GLU* 1.3 72.1 - - - +
402B VAL* 1.3 62.6 + - - +
404B ARG* 3.3 5.3 - - - +
405B VAL* 3.2 13.2 + - - +
469B VAL* 4.8 1.8 - - + -
502B CYS* 3.5 30.7 - - + -
504B VAL* 4.0 1.5 - - - +
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Residues in contact with VAL 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ALA 3.1 8.9 + - - +
399B GLN* 2.8 31.6 - - - +
400B GLU 2.5 4.8 + - - -
401B ALA* 1.3 74.4 - - - +
403B SER* 1.3 65.8 + - - +
405B VAL* 2.8 10.2 + - - +
406B LYS* 2.6 57.8 + - + -
467B ILE* 4.3 14.1 - - + -
469B VAL* 4.3 13.0 - - + -
504B VAL* 3.9 26.4 - - + +
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Residues in contact with SER 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B GLN 3.8 9.4 + - - -
400B GLU* 2.4 27.9 + - - -
402B VAL* 1.3 74.1 - - - +
404B ARG* 1.3 69.3 + - - +
406B LYS* 4.2 10.8 - - - +
407B ARG* 2.7 58.0 + - - +
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Residues in contact with ARG 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B SER 4.0 12.8 + - - -
381B THR* 3.0 28.9 + - - +
400B GLU* 2.8 11.0 + - - +
401B ALA* 3.3 14.4 - - - +
403B SER* 1.3 77.9 - - - +
405B VAL* 1.3 53.0 + - - +
407B ARG* 4.4 3.6 - - - +
408B MET* 2.6 71.3 + - - +
372C ILE* 3.4 23.3 - - - +
374C ALA* 5.5 1.6 - - - +
431C ASP* 3.1 28.3 + - - -
444C ALA* 5.0 5.9 + - - +
447C GLN* 2.7 36.8 + - - +
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Residues in contact with VAL 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LEU* 3.7 17.5 - - + -
379B GLY* 3.3 30.1 - - - +
380B SER* 2.7 46.2 - - - +
401B ALA 3.2 9.2 + - - +
402B VAL 2.8 11.4 + - - +
404B ARG* 1.3 74.4 - - - +
406B LYS* 1.3 56.8 + - - +
408B MET* 2.9 20.6 + - - +
409B GLN* 2.7 31.8 + - + +
504B VAL* 3.9 12.1 - - + -
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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
----------------------------------------------------------
378B LEU* 4.6 23.2 - - + +
402B VAL* 2.6 43.1 + - + +
403B SER* 4.2 8.3 - - - +
405B VAL* 1.3 73.1 - - + +
407B ARG* 1.3 60.2 + - + +
409B GLN* 3.1 9.6 + - - +
410B LYS* 3.0 29.4 + - - +
413B LYS* 6.2 0.4 - - - +
467B ILE* 4.8 11.9 - - + +
504B VAL* 5.5 0.2 - - + -
506B GLU* 5.4 3.8 + - - -
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Residues in contact with ARG 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B GLU* 3.2 35.6 + - - -
403B SER* 2.7 47.2 + - - +
404B ARG* 4.4 1.0 - - - +
406B LYS* 1.3 69.6 - - + +
408B MET* 1.3 62.9 + - - +
409B GLN 2.9 5.9 + - - -
410B LYS* 3.0 17.5 + - - +
411B ALA 3.3 7.8 + - - -
369C ASP* 3.6 33.9 + - - +
370C GLY 3.3 26.0 - - - +
371C ILE* 3.8 0.7 - - - -
372C ILE* 3.4 33.2 + - + +
433C PHE* 3.9 17.4 - - - -
440C LYS* 6.2 0.6 - - - +
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Residues in contact with MET 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LEU 3.8 15.9 - - - +
379B GLY* 4.9 4.5 - - - -
380B SER 5.8 0.2 - - - +
404B ARG* 2.6 46.5 + - - +
405B VAL* 2.9 30.0 + - - +
407B ARG* 1.3 71.6 - - - +
409B GLN* 1.3 75.6 + - + +
411B ALA* 3.9 5.1 - - - +
412B ALA* 3.3 24.4 + - + +
426B THR 5.5 1.1 - - - +
372C ILE* 3.5 21.7 - - + +
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Residues in contact with GLN 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LEU* 3.3 28.2 - - + +
405B VAL* 2.7 13.0 + - + +
406B LYS* 3.2 11.9 - - - +
407B ARG 2.9 0.4 - - - -
408B MET* 1.3 97.2 - - + +
410B LYS* 1.3 59.6 + - - +
411B ALA 3.0 1.3 - - - -
412B ALA* 2.7 23.4 + - - +
413B LYS* 2.9 43.2 + - - +
426B THR* 2.7 48.5 - - - +
427B LEU* 3.9 5.3 + - - +
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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
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406B LYS 3.0 19.0 + - - +
407B ARG* 3.0 6.0 + - + +
409B GLN* 1.3 74.3 - - - +
411B ALA* 1.3 62.8 + - - +
413B LYS* 3.5 13.8 + - + +
414B ILE* 3.1 28.2 + - - +
365C GLU 4.4 0.6 + - - -
366C ASP* 2.7 69.8 + - - +
369C ASP* 3.2 31.8 + - - +
370C GLY 4.3 2.6 - - - +
371C ILE* 3.2 17.9 - - + -
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Residues in contact with ALA 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B ARG 3.3 2.7 + - - +
408B MET 3.9 3.6 - - - +
409B GLN 3.0 0.6 - - - -
410B LYS* 1.3 79.2 - - - +
412B ALA* 1.3 65.8 + - - +
414B ILE* 3.4 9.2 + - - +
415B LYS* 3.2 19.1 + - - +
371C ILE* 3.9 20.8 - - + +
372C ILE 3.8 26.7 - - - +
373C PHE* 4.1 26.5 - - + -
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Residues in contact with ALA 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B MET* 3.3 13.8 + - + +
409B GLN* 2.7 28.5 + - + +
411B ALA* 1.3 76.0 - - - +
413B LYS* 1.3 56.0 + - - +
415B LYS* 2.7 32.4 + - - +
416B LYS* 3.5 4.9 + - - +
426B THR* 4.0 22.4 - - - -
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Residues in contact with LYS 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B LYS* 6.2 0.2 - - - +
409B GLN* 2.9 43.5 + - - +
410B LYS* 3.9 12.8 - - + +
412B ALA* 1.3 72.7 - - - +
414B ILE* 1.3 62.4 + - + +
416B LYS* 3.1 19.3 + - - +
417B LYS* 3.4 8.8 + - - +
425B GLN* 6.3 0.7 - - - -
426B THR* 4.6 12.7 - - - +
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Residues in contact with ILE 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LYS 3.1 19.5 + - - +
411B ALA* 3.6 6.5 - - - +
412B ALA 3.0 0.4 + - - -
413B LYS* 1.3 74.9 - - + +
415B LYS* 1.3 56.0 + - - +
416B LYS 3.0 5.6 - - - -
417B LYS* 3.1 32.1 + - + +
418B ALA* 4.0 2.4 + - - +
366C ASP* 4.5 20.4 - - + +
367C LEU* 6.0 2.0 - - + -
371C ILE* 4.1 25.8 - - + -
373C PHE* 5.0 12.6 - - + -
512C LEU* 6.0 4.0 - - + -
516C SER* 6.4 1.6 - - - -
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Residues in contact with LYS 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ALA 3.2 10.0 + - - +
412B ALA* 2.7 18.7 + - - +
414B ILE* 1.3 71.7 - - - +
416B LYS* 1.3 55.7 + - - +
417B LYS 3.4 1.6 - - - -
418B ALA* 4.2 15.3 + - - +
419B ASN* 5.2 0.5 - - - +
373C PHE* 5.3 7.9 - - + -
509C ASP* 5.4 9.6 - - + +
512C LEU* 5.8 11.0 - - + -
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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