Contacts of the helix formed by residues 379 - 409 (chain B) in PDB entry 6CNB
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 379 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLN* 3.3 35.4 - - + +
61B HIS* 5.0 1.3 - - + +
63B ASP* 6.3 0.2 - - + -
64B SER* 3.1 30.7 - - - +
194B ILE* 5.3 1.1 - - - -
196B VAL* 3.6 36.1 - - + -
377B LEU* 4.3 0.2 - - + -
378B GLU* 1.3 108.0 + - - +
380B ALA* 1.3 63.0 + - - +
381B GLY 3.2 1.1 - - - -
382B GLN* 3.9 4.0 + - - +
383B LEU* 3.9 8.4 - - - +
520B ILE* 3.7 44.9 - - + +
522B THR* 6.4 1.1 - - + -
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B HIS* 4.7 25.5 - - + +
64B SER* 4.6 0.4 - - - -
65B PHE* 5.4 5.2 - - + +
155B MET* 5.9 1.6 - - - -
185B PHE* 5.1 5.8 - - + -
194B ILE* 3.8 40.4 - - + +
196B VAL* 5.8 0.2 - - - +
379B LEU* 1.3 75.3 - - - +
381B GLY* 1.3 66.4 + - - +
382B GLN 3.5 0.2 - - - -
383B LEU* 3.8 3.1 - - - -
384B ILE* 3.1 30.8 + - + +
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Residues in contact with GLY 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER* 3.4 41.3 - - - -
65B PHE* 4.3 1.1 - - - -
67B TYR* 6.4 0.7 - - - -
68B PHE* 3.7 9.9 - - - -
72B ASP* 5.0 3.1 - - - +
379B LEU* 3.2 2.6 - - - +
380B ALA* 1.3 80.2 - - - +
382B GLN* 1.3 63.1 + - - +
384B ILE* 4.6 0.3 - - - +
385B SER* 3.5 21.3 + - - -
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Residues in contact with GLN 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER* 4.8 5.4 + - - -
67B TYR* 6.1 4.0 - - - -
72B ASP* 5.5 6.5 - - - +
378B GLU* 2.7 36.7 - - + +
379B LEU* 3.9 8.3 + - - +
381B GLY* 1.3 75.0 + - - +
383B LEU* 1.3 68.2 + - + +
385B SER* 3.8 6.1 - - - -
386B LEU* 3.0 33.1 + - + +
522B THR* 5.7 3.0 - - - +
523B ASP* 5.3 11.9 - - - +
605B GLY 5.9 0.6 - - - -
606B GLY* 5.3 10.9 - - - +
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ILE* 4.2 17.7 - - + -
195B LEU 5.0 0.9 - - - +
197B GLN* 3.7 26.2 - - + +
378B GLU* 2.9 34.7 + - - +
379B LEU 3.9 11.0 - - - +
380B ALA* 3.6 9.0 - - - +
381B GLY 3.3 0.8 - - - -
382B GLN* 1.3 76.5 - - + +
384B ILE* 1.3 65.2 + - + +
386B LEU* 3.0 14.0 + - + +
387B LEU* 2.9 22.0 + - - +
442B TRP* 3.4 36.3 - - + -
451B ARG* 4.3 15.7 - - - +
454B VAL* 4.4 5.6 - - + -
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Residues in contact with ILE 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 4.7 12.3 - - + -
68B PHE* 3.9 10.5 - - + -
152B MET* 3.5 28.7 - - + -
153B PRO* 6.5 0.2 - - + -
185B PHE* 3.4 37.0 - - + -
194B ILE* 3.6 21.5 - - + -
380B ALA* 3.1 14.0 + - + +
381B GLY* 4.6 1.8 - - - +
383B LEU* 1.3 77.6 - - - +
385B SER* 1.3 55.8 + - - +
387B LEU* 3.8 10.9 - - + +
388B PHE* 2.8 26.6 + - + +
433B LEU* 5.2 11.5 - - + +
437B ILE* 5.1 3.6 - - + -
442B TRP* 4.8 4.5 - - + -
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Residues in contact with SER 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 2.4 46.2 - - - -
72B ASP* 3.7 16.4 + - - +
76B ILE* 5.2 11.2 - - - -
381B GLY 3.5 6.9 + - - -
382B GLN* 3.8 9.4 - - - -
383B LEU 3.1 0.8 + - - -
384B ILE* 1.3 75.2 - - - +
386B LEU* 1.3 62.9 + - - +
388B PHE* 2.7 4.3 + - - +
389B GLU* 2.6 38.2 + - - +
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Residues in contact with LEU 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B GLN* 3.0 24.1 + - + +
383B LEU* 3.0 15.9 + - + +
385B SER* 1.3 79.7 - - - +
387B LEU* 1.3 65.2 + - - +
389B GLU* 3.4 25.3 - - - +
390B ASP* 3.3 24.0 + - - -
442B TRP* 6.0 1.1 - - + -
444B LEU* 4.3 17.9 - - + +
447B PHE* 4.3 27.4 - - + -
451B ARG* 5.4 6.7 - - - +
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B LEU 2.9 14.3 + - - +
384B ILE* 3.8 9.4 - - + +
386B LEU* 1.3 78.5 - - - +
388B PHE* 1.3 65.5 + - - +
390B ASP* 3.4 7.5 + - + +
391B LEU* 3.1 35.1 + - + +
433B LEU* 3.5 29.8 - - + -
436B ALA* 3.6 28.9 - - + -
437B ILE* 5.0 2.5 - - + +
442B TRP* 4.0 41.8 - - + -
443B SER 5.3 4.7 - - - +
444B LEU* 5.0 9.7 - - + +
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Residues in contact with PHE 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 4.4 7.0 - + + -
73B LEU* 3.6 33.2 - - + -
76B ILE* 4.1 18.8 - - + -
77B ILE* 5.5 4.9 - - + -
98B ILE* 6.0 2.7 - - + -
129B ILE* 5.6 11.2 - - + -
149B ILE* 5.4 5.6 - - + -
152B MET* 5.2 13.7 - - - -
384B ILE* 2.8 21.6 + - + +
385B SER* 2.7 14.2 + - - +
387B LEU* 1.3 70.0 - - - +
389B GLU* 1.3 61.6 + - - +
391B LEU* 2.6 30.0 + - - -
392B PHE* 2.8 41.3 + + + -
429B ILE* 3.5 28.3 - - + -
433B LEU* 5.5 9.0 - - + -
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Residues in contact with GLU 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 3.3 45.6 - - + +
224B THR* 5.6 2.4 - - - +
385B SER 2.6 14.7 + - - +
386B LEU* 3.4 35.0 - - - +
388B PHE* 1.3 79.2 - - - +
390B ASP* 1.3 65.0 + - - +
392B PHE* 4.2 2.7 - - - +
393B LYS* 2.8 30.8 + - - +
446B ARG* 4.8 19.6 + - - -
447B PHE* 5.1 5.4 - - - -
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Residues in contact with ASP 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B LEU 3.3 7.2 + - - +
387B LEU* 3.4 10.1 - - + +
388B PHE 2.7 3.8 + - - -
389B GLU* 1.3 75.3 - - - +
391B LEU* 1.3 64.1 + - + +
393B LYS* 2.7 26.2 + - - +
394B LYS* 2.8 15.7 + - - +
443B SER 4.5 4.7 - - - +
444B LEU* 3.1 44.5 - - - +
445B LYS* 4.6 2.2 - - - +
446B ARG* 3.3 35.7 + - - +
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LEU* 3.1 29.2 + - + +
388B PHE* 2.6 11.9 + - - +
390B ASP* 1.3 80.0 - - + +
392B PHE* 1.3 56.3 + - - +
394B LYS* 3.4 13.3 + - + +
395B PHE* 2.9 27.5 + - - +
428B ASN* 3.0 32.0 + - - +
429B ILE* 3.7 19.1 - - + +
432B GLY* 3.6 7.4 - - - +
433B LEU* 3.4 36.6 - - + +
443B SER 5.6 3.8 - - - +
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Residues in contact with PHE 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 4.3 18.4 - - + -
77B ILE* 4.2 23.3 - - + -
80B ASN* 4.2 19.7 - - + -
95B TYR* 3.9 32.3 - + - -
131B VAL* 6.0 3.6 - - + -
149B ILE* 5.3 10.5 - - + -
388B PHE* 2.8 45.9 + + + +
389B GLU 4.2 2.5 - - - +
391B LEU* 1.3 74.3 - - - +
393B LYS* 1.3 60.9 + - - +
395B PHE* 3.1 21.5 - + - +
396B ASN* 2.9 47.6 + - - +
429B ILE* 3.8 8.1 - - + +
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Residues in contact with LYS 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASN* 3.8 28.3 - - + +
389B GLU 2.8 21.6 + - - +
390B ASP* 2.7 16.4 + - - +
392B PHE* 1.3 74.8 - - + +
394B LYS* 1.3 56.7 + - - +
396B ASN* 2.9 10.2 + - + +
397B ASN* 2.9 61.9 + - - +
400B LYS* 5.7 0.2 - - - +
446B ARG* 3.7 31.5 - - - +
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Residues in contact with LYS 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ASP 2.8 11.4 + - - +
391B LEU* 3.7 15.3 - - + +
393B LYS* 1.3 74.9 - - - +
395B PHE* 1.3 62.3 + - - +
397B ASN* 4.5 8.7 - - + +
398B ASP* 2.9 44.2 + - - +
428B ASN* 4.0 13.7 - - + +
445B LYS* 4.5 24.0 - - - +
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Residues in contact with PHE 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B TYR* 3.8 17.3 - + - -
149B ILE* 4.3 28.3 - - + -
391B LEU 2.9 15.1 + - - +
392B PHE* 3.1 28.3 - + - +
394B LYS* 1.3 74.8 - - - +
396B ASN* 1.3 66.4 + - - +
398B ASP* 3.9 1.1 - - - +
399B PHE* 2.9 39.2 + + + +
422B ILE* 4.3 24.5 - - + -
425B HIS* 3.0 30.8 - + - -
426B SER* 3.8 9.4 - - - -
428B ASN* 3.2 33.7 - - - +
429B ILE* 4.8 7.0 - - + -
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Residues in contact with ASN 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASN* 4.9 7.4 - - + +
83B ILE* 3.5 29.5 - - + +
95B TYR* 2.5 33.0 + - - -
392B PHE* 2.9 43.8 + - - +
393B LYS* 2.9 14.4 + - + +
395B PHE* 1.3 79.6 - - - +
397B ASN* 1.3 68.2 + - - +
399B PHE* 3.1 5.0 + - - +
400B LYS* 2.9 31.7 + - - +
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Residues in contact with ASN 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B LYS* 2.9 53.7 + - - +
394B LYS* 4.0 8.0 - - + +
396B ASN* 1.3 72.8 - - - +
398B ASP* 1.3 68.0 + - - +
400B LYS* 3.2 39.8 + - - +
401B LEU* 3.4 7.1 + - - +
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Residues in contact with ASP 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LYS* 2.9 35.2 + - - +
397B ASN* 1.3 80.6 - - - +
399B PHE* 1.3 59.9 + - - +
401B LEU* 3.1 15.6 + - + +
402B SER* 2.9 23.7 + - - -
425B HIS* 3.1 31.1 + - + +
428B ASN* 5.5 1.3 + - - +
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Residues in contact with PHE 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 4.2 12.1 - - + -
91B PHE* 6.2 0.9 - + - -
93B LEU* 3.5 32.5 - - + -
95B TYR* 5.4 0.2 - - - -
395B PHE* 2.9 30.5 + + + +
396B ASN* 3.1 8.9 + - - +
398B ASP* 1.3 72.1 - - - +
400B LYS* 1.3 66.4 + - - +
402B SER* 3.3 3.8 + - - -
403B ILE* 2.9 32.6 + - + +
418B ALA 4.8 13.0 - - - -
419B LEU* 5.0 2.0 - - - -
421B SER* 3.8 20.9 - - - -
422B ILE* 3.4 46.2 - - + -
425B HIS* 3.2 22.3 - - + +
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Residues in contact with LYS 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU 5.5 0.7 - - - -
83B ILE* 4.0 40.6 - - + +
84B LEU 4.4 17.4 + - - +
85B SER* 4.7 7.4 - - - +
393B LYS* 5.7 0.4 - - - +
396B ASN* 2.9 17.1 + - - +
397B ASN* 3.2 32.4 + - - +
399B PHE* 1.3 75.5 - - - +
401B LEU* 1.3 56.1 + - - +
403B ILE* 2.4 39.2 + - - +
404B ASP* 2.9 14.1 + - - +
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Residues in contact with LEU 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B ASN 3.4 7.5 + - - +
398B ASP* 3.1 18.0 + - + +
400B LYS* 1.3 78.0 - - - +
402B SER* 1.3 60.1 + - - +
404B ASP* 3.6 26.4 + - + +
405B LYS* 3.6 30.4 + - + +
408B LYS* 5.5 0.5 - - - -
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Residues in contact with SER 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ASP 2.9 14.5 + - - -
399B PHE* 3.7 9.0 - - - -
400B LYS 3.0 0.4 - - - -
401B LEU* 1.3 77.4 - - - +
403B ILE* 1.3 64.7 + - - +
404B ASP 3.2 0.7 - - - -
405B LYS* 3.8 22.2 + - - +
406B VAL* 4.1 10.6 + - - +
421B SER* 4.8 13.6 - - - -
424B VAL* 6.0 1.0 - - - +
425B HIS* 3.9 19.9 + - - +
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Residues in contact with ILE 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 4.9 9.4 - - + -
85B SER* 3.4 19.1 - - - +
91B PHE* 4.5 18.2 - - + -
399B PHE* 2.9 25.6 + - + +
400B LYS* 2.4 39.5 + - - +
402B SER* 1.3 70.8 - - - +
404B ASP* 1.3 60.2 + - - +
406B VAL* 4.1 12.6 + - + +
407B LEU* 3.5 33.7 + - + +
418B ALA* 3.4 39.9 - - + +
421B SER* 5.5 6.3 - - - +
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Residues in contact with ASP 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B SER* 2.4 39.3 + - - -
87B VAL* 4.4 5.8 - - + +
400B LYS* 2.9 10.6 + - - +
401B LEU* 3.6 22.3 + - + +
402B SER 3.2 0.2 - - - -
403B ILE* 1.3 78.1 - - - +
405B LYS* 1.3 66.7 + - - +
406B VAL 3.2 0.2 - - - -
407B LEU* 2.8 16.6 + - - +
408B LYS* 2.9 33.5 + - + +
117P HIS* 4.7 16.7 - - - -
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Residues in contact with LYS 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B LEU* 3.6 31.2 + - + +
402B SER* 3.8 13.4 + - - +
403B ILE 3.5 0.4 - - - -
404B ASP* 1.3 77.8 - - - +
406B VAL* 1.3 64.9 + - + +
408B LYS* 3.4 36.6 + - + +
409B LYS* 4.3 5.2 + - - +
86R LYS* 3.4 29.8 - - - +
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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 SER 4.1 10.5 + - - +
403B ILE* 4.1 17.0 + - + +
404B ASP 3.2 0.8 - - - -
405B LYS* 1.3 79.2 - - + +
407B LEU* 1.3 69.7 + - + +
408B LYS 3.4 0.7 + - - -
409B LYS 4.1 5.0 + - - +
411B ASN* 5.4 0.9 - - - +
414B MET* 3.1 18.5 - - - +
415B GLU 5.3 1.1 - - - +
416B TYR* 3.8 36.4 - - + -
418B ALA* 5.8 4.3 - - + -
421B SER* 5.7 4.9 - - - +
----------------------------------------------------------
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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
----------------------------------------------------------
85B SER* 5.7 0.7 - - - +
87B VAL* 4.1 37.6 - - + +
88B ASP* 4.6 20.9 - - + +
91B PHE* 5.1 17.9 - - + -
403B ILE* 3.5 33.0 - - + +
404B ASP 2.8 11.0 + - - +
406B VAL* 1.3 82.2 - - + +
408B LYS* 1.3 62.8 + - - +
414B MET* 3.2 48.5 - - + +
415B GLU 5.0 5.6 - - - +
123P LYS* 5.2 1.0 + - - -
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Residues in contact with LYS 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B VAL* 5.8 1.1 - - - -
401B LEU 5.5 0.2 - - - -
404B ASP* 2.9 31.9 + - + +
405B LYS* 3.6 40.8 - - + +
406B VAL 3.2 1.0 - - - -
407B LEU* 1.3 81.0 - - - +
409B LYS* 1.3 77.3 + - + +
410B PRO* 3.4 11.4 - - - +
414B MET* 4.2 0.2 - - - +
119P HIS* 3.1 58.2 + - + +
123P LYS* 3.6 15.1 + - - -
----------------------------------------------------------
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Residues in contact with LYS 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B LYS 4.3 3.9 + - - +
406B VAL 4.1 3.8 + - - +
407B LEU 3.7 0.2 - - - -
408B LYS* 1.3 94.0 - - + +
410B PRO* 1.3 71.7 - - + +
411B ASN* 3.1 19.1 - - - +
414B MET* 3.3 9.9 - - - +
119P HIS* 5.9 3.4 - - + -
24X T 5.0 28.6 - - - +
25X T 5.1 7.3 + - - -
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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