Contacts of the helix formed by residues 382 - 415 (chain B) in PDB entry 3JQZ
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 GLU 382 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LYS 3.6 15.7 - - - +
379B PRO* 3.0 5.6 + - + +
381B VAL* 1.3 83.3 - - + +
383B GLU* 1.3 61.6 + - - +
384B PRO 3.3 2.2 - - - -
385B GLN* 3.0 18.1 + - + +
386B ASN* 2.7 47.6 + - - +
389B LYS* 4.1 14.3 + - - +
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Residues in contact with GLU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ARG* 5.1 0.5 + - - -
379B PRO* 2.5 24.6 + - + +
380B LEU* 4.2 13.2 - - + +
382B GLU* 1.3 79.9 + - - +
384B PRO* 1.3 77.9 - - + +
386B ASN* 3.0 25.3 + - - +
387B LEU* 3.2 15.8 + - - +
485B ARG* 2.8 38.8 + - - -
489B SER* 5.7 2.8 - - - -
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Residues in contact with PRO 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LEU* 4.3 11.9 - - + -
348B ARG* 4.3 17.7 - - - +
380B LEU* 3.0 25.4 - - - +
381B VAL 4.0 0.9 - - - -
382B GLU 3.5 3.4 - - - +
383B GLU* 1.3 98.8 - - + +
385B GLN* 1.3 63.7 + - - +
386B ASN 2.8 4.5 - - - -
387B LEU* 2.7 15.3 + - + -
388B ILE* 2.9 18.5 + - + +
446B MET* 3.7 24.2 - - + -
450B GLU* 5.1 1.1 - - - +
485B ARG* 3.8 14.6 - - - +
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Residues in contact with GLN 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ASP* 5.3 2.9 - - - +
341B TYR* 4.6 15.1 + - - -
345B LEU* 5.7 0.2 - - + -
381B VAL 3.2 23.2 + - - +
382B GLU* 3.0 20.1 + - + +
384B PRO* 1.3 79.3 - - + +
386B ASN* 1.3 56.5 + - - +
388B ILE* 3.7 10.3 - - + +
389B LYS* 2.9 33.8 + - - +
446B MET* 4.4 18.9 - - + +
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Residues in contact with ASN 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B GLU* 2.7 30.1 + - - +
383B GLU* 3.0 17.5 + - - +
384B PRO 2.8 0.6 + - - -
385B GLN* 1.3 73.5 - - - +
387B LEU* 1.3 78.0 + - - +
389B LYS* 3.2 17.2 + - - +
390B GLN* 2.7 57.9 + - - +
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLU* 3.2 19.4 + - - +
384B PRO 2.7 11.8 + - - +
386B ASN* 1.3 103.3 - - - +
388B ILE* 1.3 59.7 + - + +
390B GLN* 4.7 14.4 - - - +
391B ASN* 2.7 52.1 + - - +
410B ARG* 6.3 0.9 - - - +
485B ARG* 4.2 16.4 - - - +
489B SER* 5.4 10.8 - - - +
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Residues in contact with ILE 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B PRO* 2.9 21.5 + - + +
385B GLN* 3.7 9.0 - - - +
387B LEU* 1.3 75.3 - - + +
389B LYS* 1.3 66.1 - - - +
391B ASN* 4.3 2.1 - - - +
392B CYS* 3.2 35.1 + - - +
445B ARG* 3.8 20.9 - - + +
446B MET* 3.4 45.5 - - + +
449B ALA* 3.8 25.8 - - + -
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Residues in contact with LYS 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B GLU* 4.1 18.8 + - - +
385B GLN* 2.9 18.5 + - - +
386B ASN* 3.2 23.7 + - - +
388B ILE* 1.3 77.8 - - - +
390B GLN* 1.3 72.3 + - + +
392B CYS* 3.4 3.9 + - - +
393B GLU* 3.4 32.6 + - + +
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Residues in contact with GLN 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ASN* 2.7 46.6 + - - +
387B LEU* 4.2 16.1 - - - +
389B LYS* 1.3 78.0 - - + +
391B ASN* 1.3 59.0 + - - +
393B GLU* 2.8 40.4 + - - +
394B LEU* 3.1 10.5 + - - +
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Residues in contact with ASN 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LEU* 2.7 45.9 + - - +
388B ILE* 4.4 2.2 - - - +
390B GLN* 1.3 81.1 - - - +
392B CYS* 1.3 52.6 + - - +
394B LEU* 3.3 14.5 + - - +
395B PHE* 2.7 35.0 + - - +
403B PHE* 3.9 27.0 - - + -
407B LEU* 5.8 0.2 - - - +
410B ARG* 4.3 17.1 + - - +
438B CYS* 5.0 0.4 - - - -
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Residues in contact with CYS 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ILE* 3.2 30.4 + - - +
389B LYS* 3.7 4.5 - - - +
390B GLN 2.8 1.2 + - - -
391B ASN* 1.3 73.8 - - - +
393B GLU* 1.3 65.3 + - - +
395B PHE* 3.2 2.3 + - - +
396B GLU* 3.0 31.8 + - - +
437B CYS* 6.0 0.2 - - - -
438B CYS* 2.0 50.0 - - + -
445B ARG* 4.0 26.5 - - - +
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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
----------------------------------------------------------
389B LYS* 3.4 28.9 - - + +
390B GLN* 2.8 18.8 + - - +
392B CYS* 1.3 72.1 - - - +
394B LEU* 1.3 62.7 + - - +
396B GLU* 3.1 18.2 + - - +
397B GLN* 3.2 31.5 + - - +
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Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B GLN 3.1 8.0 + - - +
391B ASN* 3.5 18.8 - - - +
393B GLU* 1.3 79.7 - - - +
395B PHE* 1.3 62.7 + - - +
397B GLN* 3.2 18.2 + - + +
398B LEU* 3.2 37.3 + - + +
403B PHE* 3.6 24.2 - - + -
406B ALA* 5.4 5.8 - - + -
410B ARG* 4.4 16.4 - - - +
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Residues in contact with PHE 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ASN 2.7 20.8 + - - +
392B CYS* 3.4 9.4 - - - +
394B LEU* 1.3 73.7 - - - +
396B GLU* 1.3 70.4 + - + +
397B GLN 2.8 6.2 + - - -
399B GLY* 2.8 26.7 + - - -
400B GLU* 4.2 20.4 - - + -
403B PHE* 3.8 29.8 - + + -
431B GLY 3.3 19.3 - - - -
434B GLY* 3.4 19.7 - - - -
435B SER* 3.1 46.9 - - - -
438B CYS* 4.5 4.7 - - + -
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Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B CYS* 3.0 22.3 + - - +
393B GLU* 3.1 8.3 + - - +
395B PHE* 1.3 85.0 - - + +
397B GLN* 1.3 64.7 + - - +
399B GLY 5.0 0.2 - - - -
438B CYS* 3.1 30.4 - - + +
445B ARG* 5.2 1.1 + - - -
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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* 3.2 30.1 + - - +
394B LEU* 3.5 14.4 - - + +
395B PHE 2.9 0.6 - - - -
396B GLU* 1.3 80.3 - - - +
398B LEU* 1.3 72.6 + - + +
399B GLY 3.7 0.4 - - - -
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LEU* 3.2 38.3 + - + +
397B GLN* 1.3 87.6 - - + +
399B GLY* 1.3 63.0 + - - +
402B LYS* 3.2 57.7 + - + +
403B PHE* 3.8 11.9 - - + +
406B ALA* 4.6 10.3 - - + -
545B LYS* 6.3 1.8 - - - -
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Residues in contact with GLY 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 2.8 23.9 + - - -
397B GLN 3.7 1.2 - - - +
398B LEU* 1.3 83.9 - - - +
400B GLU* 1.3 67.3 + - - -
401B TYR 3.5 0.7 - - - -
403B PHE* 3.0 19.8 + - - +
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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
----------------------------------------------------------
395B PHE* 4.2 13.9 - - + -
399B GLY* 1.3 72.5 - - - +
401B TYR* 1.3 65.1 + - - +
403B PHE* 3.4 2.0 - - - +
404B GLN* 2.9 41.6 + - - +
431B GLY 3.3 16.4 - - - +
432B LYS* 3.0 38.6 - - - +
435B SER* 3.6 19.5 + - - +
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Residues in contact with TYR 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B GLY 3.5 0.6 - - - -
400B GLU* 1.3 80.1 - - - +
402B LYS* 1.3 78.2 + - + +
404B GLN* 3.2 14.4 + - - +
405B ASN* 3.0 55.4 + - - +
522B GLN* 3.5 50.9 - - + +
525B LYS* 3.6 35.0 + - + +
526B GLN* 4.1 18.6 - - + +
548B MET* 5.2 4.7 - - + +
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Residues in contact with LYS 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B LEU* 3.2 47.8 + - + +
399B GLY 3.7 1.2 + - - -
400B GLU 3.4 0.2 - - - -
401B TYR* 1.3 95.9 - - + +
403B PHE* 1.3 60.6 + - - +
405B ASN* 3.4 9.3 + - + +
406B ALA* 3.3 20.3 + - - +
541B LYS* 6.0 0.2 - - - -
545B LYS* 4.2 26.5 - - - +
549B ASP* 5.5 3.6 - - - -
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Residues in contact with PHE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ASN* 3.9 35.4 - - + -
394B LEU* 3.6 42.0 - - + -
395B PHE* 3.8 27.4 - + - -
398B LEU* 3.8 11.6 - - + +
399B GLY 3.0 23.5 + - - +
400B GLU* 3.4 2.9 - - - +
402B LYS* 1.3 75.3 - - - +
404B GLN* 1.3 64.3 + - - +
406B ALA* 3.2 15.0 + - + +
407B LEU* 3.3 32.4 + - + +
410B ARG* 5.8 0.9 - - - -
430B LEU 4.3 4.9 - - - -
431B GLY* 3.7 28.0 - - - -
434B GLY* 5.6 1.8 - - - -
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Residues in contact with GLN 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B GLU* 2.9 40.1 + - - +
401B TYR* 3.5 16.0 - - - +
403B PHE* 1.3 75.7 - - - +
405B ASN* 1.3 51.6 + - - +
407B LEU* 2.9 12.9 + - - +
408B LEU* 2.7 38.9 + - + +
427B SER* 4.3 7.0 - - - +
428B ARG* 2.8 46.0 + - - +
431B GLY* 3.5 17.7 - - - +
432B LYS* 3.7 9.5 - - - +
526B GLN* 3.6 22.5 + - - +
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Residues in contact with ASN 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B TYR* 3.0 39.5 + - - +
402B LYS* 3.5 13.3 - - + +
403B PHE 3.2 0.4 - - - -
404B GLN* 1.3 76.3 - - - +
406B ALA* 1.3 62.9 + - - +
408B LEU* 3.1 8.1 + - - +
409B VAL* 3.0 29.9 + - - +
526B GLN* 2.8 34.2 + - - +
529B LEU* 4.3 11.0 - - + +
541B LYS* 4.4 13.3 - - - +
548B MET* 4.2 21.0 - - - +
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Residues in contact with ALA 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LEU* 5.4 5.4 - - + -
398B LEU* 4.6 12.8 - - + -
402B LYS 3.3 8.7 + - - +
403B PHE* 3.2 14.4 + - + +
405B ASN* 1.3 78.5 - - - +
407B LEU* 1.3 59.4 + - + +
409B VAL* 3.7 3.8 + - - +
410B ARG* 3.2 35.2 + - - +
541B LYS* 4.5 19.4 - - + +
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Residues in contact with LEU 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ASN* 5.8 0.2 - - - +
403B PHE* 3.3 37.4 + - + +
404B GLN* 2.9 9.9 + - - +
406B ALA* 1.3 76.8 - - + +
408B LEU* 1.3 65.9 + - - +
409B VAL 2.9 2.1 + - - -
410B ARG* 3.4 33.2 - - - +
411B TYR* 2.9 52.1 + - + +
427B SER* 4.2 13.5 - - - +
430B LEU* 3.7 33.0 - - + -
431B GLY* 4.1 6.3 - - - +
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Residues in contact with LEU 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B GLN* 2.7 16.5 + - + +
405B ASN* 3.1 12.8 + - - +
407B LEU* 1.3 72.7 - - - +
409B VAL* 1.3 52.0 + - - +
412B THR* 2.7 36.7 + - - +
423B LEU* 3.8 10.0 - - + +
424B VAL* 3.8 9.6 - - + -
427B SER* 3.4 28.7 + - - +
428B ARG* 5.3 0.7 - - + +
526B GLN* 3.3 56.8 - - + +
529B LEU* 4.7 13.5 - - + -
530B VAL* 3.5 26.3 - - + +
533B VAL* 5.0 1.7 - - - +
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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
----------------------------------------------------------
405B ASN 3.0 16.1 + - - +
406B ALA 3.8 5.6 - - - +
407B LEU 2.9 0.4 - - - -
408B LEU* 1.3 76.6 - - - +
410B ARG* 1.3 68.8 + - - +
412B THR* 3.2 17.4 - - - +
413B LYS* 3.2 23.4 + - - +
529B LEU* 3.8 20.4 - - + -
533B VAL* 4.5 4.5 - - + -
541B LYS* 3.8 35.0 - - + +
544B LEU* 3.7 28.0 - - + -
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Residues in contact with ARG 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ASN* 4.3 15.2 + - - +
394B LEU* 4.4 20.2 - - - +
403B PHE* 5.8 0.8 - - - -
406B ALA* 3.2 22.1 + - - +
407B LEU* 3.0 29.2 + - - +
409B VAL* 1.3 76.2 - - - +
411B TYR* 1.3 71.1 + - - +
412B THR 2.9 9.5 + - - -
413B LYS* 2.9 17.6 + - - +
414B LYS* 3.2 41.8 + - + +
----------------------------------------------------------
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Residues in contact with TYR 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B LEU* 2.9 40.2 + - + +
410B ARG* 1.3 89.0 - - + +
412B THR* 1.3 59.3 + - - +
414B LYS* 3.5 34.2 + - + +
415B VAL* 3.2 32.9 + - + +
423B LEU* 4.3 5.1 - - + +
426B VAL* 5.9 4.7 - - + -
427B SER* 4.7 11.4 - - - +
430B LEU* 4.2 25.1 - - + +
457B LEU* 5.5 7.4 - - + +
460B LEU* 6.0 5.4 - - + -
488B PHE* 4.8 25.2 - + + +
489B SER* 4.6 12.0 + - - -
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Residues in contact with THR 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B LEU 2.7 26.0 + - - +
409B VAL 3.2 9.4 - - - +
410B ARG 2.9 1.0 + - - -
411B TYR* 1.3 76.6 - - - +
413B LYS* 1.3 63.6 + - - +
414B LYS 3.2 0.2 - - - -
416B PRO* 2.9 35.3 - - - +
423B LEU* 3.2 26.1 - - - +
530B VAL* 4.0 16.9 - - - +
533B VAL* 3.3 35.7 - - + -
534B LYS* 4.3 9.3 - - + +
----------------------------------------------------------
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Residues in contact with LYS 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B VAL* 3.3 27.5 - - + +
410B ARG* 2.9 9.2 + - - +
412B THR* 1.3 79.8 - - - +
414B LYS* 1.3 65.9 + - - +
416B PRO* 3.4 14.3 - - - +
493B VAL* 3.6 33.6 - - + -
494B ASP* 3.8 4.2 + - - +
533B VAL* 3.9 19.3 - - + -
537B PRO* 3.1 32.9 + - + +
538B LYS* 4.5 2.8 - - - +
539B ALA 3.7 23.8 + - - +
540B THR* 4.3 5.9 - - - +
541B LYS 5.1 1.0 - - - +
544B LEU* 4.7 4.8 - - - +
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Residues in contact with LYS 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B ARG* 3.2 31.5 + - + +
411B TYR* 3.5 43.6 + - + +
413B LYS* 1.3 78.2 - - + +
415B VAL* 1.3 64.4 + - + +
416B PRO* 3.6 1.8 - - - +
472B ARG* 2.8 25.6 + - - -
488B PHE 4.0 13.3 + - - +
489B SER* 4.7 9.5 + - - +
491B LEU* 3.2 41.0 + - + +
492B GLU 3.6 14.6 - - - +
493B VAL* 3.3 10.8 - - + +
494B ASP* 4.0 0.2 - - - +
----------------------------------------------------------
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Residues in contact with VAL 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B TYR* 3.2 20.2 + - + +
412B THR 3.3 3.3 - - - +
414B LYS* 1.3 86.8 - - + +
416B PRO* 1.3 66.3 - - - +
417B GLN* 3.0 6.1 - - - +
418B VAL* 3.0 33.7 + - + +
423B LEU* 4.1 6.3 - - + +
470B SER* 4.3 4.3 - - - +
472B ARG* 3.7 14.4 - - - +
473B VAL* 3.5 28.5 - - + -
491B LEU* 4.0 17.5 - - + -
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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