Contacts of the helix formed by residues 369 - 396 (chain G) in PDB entry 6V3O
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 369 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330G LEU 5.3 0.4 - - - +
331G SER* 2.8 43.1 + - - +
332G MET 3.9 4.3 - - - +
366G PRO* 3.3 26.2 + - + +
367G PRO 3.1 2.6 - - - -
368G ASN* 1.3 92.0 + - - +
370G PRO* 1.3 69.2 - - - +
371G TYR 3.5 1.6 - - - -
372G ARG* 3.2 36.7 + - + +
373G VAL* 3.3 15.8 + - - +
183H ARG* 5.6 1.7 + - - -
227H THR* 5.6 2.4 - - - +
1002H SO4 4.0 14.2 + - - -
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Residues in contact with PRO 370 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332G MET 3.3 17.7 - - - +
333G TRP* 3.7 14.1 - - - +
335G CYS* 3.6 35.9 - - + -
339G LEU* 4.6 4.5 - - + -
340G ARG* 4.5 9.0 - - - +
343G ALA* 4.2 21.1 - - + +
367G PRO 5.0 4.5 - - - +
368G ASN 3.6 7.4 - - - +
369G GLU* 1.3 86.0 - - - +
371G TYR* 1.3 64.9 + - + +
373G VAL* 3.0 16.6 + - + +
374G ILE* 3.1 18.0 + - - +
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Residues in contact with TYR 371 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330G LEU* 4.0 29.8 - - + +
332G MET* 3.9 34.5 - - + -
334G ARG 3.0 26.7 + - - -
335G CYS* 3.7 8.4 - - + -
339G LEU* 3.4 22.4 - - + -
369G GLU 3.5 0.4 - - - -
370G PRO* 1.3 78.5 - - + +
372G ARG* 1.3 55.9 + - - +
374G ILE* 3.4 7.3 + - - +
375G LEU* 3.0 38.7 + - + +
419G CYS* 3.7 21.1 - - + -
422G SER* 2.8 21.7 + - - -
423G LEU* 3.5 41.1 + - + +
426G CYS* 4.8 1.0 - - - +
428G ASP* 5.5 0.2 + - - -
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Residues in contact with ARG 372 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327G MET* 2.9 56.3 + - + +
328G PHE* 3.4 13.0 + - - +
330G LEU 4.4 5.7 + - - +
331G SER* 2.6 30.5 + - - -
366G PRO* 4.5 25.0 - - + +
369G GLU* 3.2 32.9 + - + +
370G PRO 3.1 1.0 - - - -
371G TYR* 1.3 80.1 - - - +
373G VAL* 1.3 59.3 + - + +
375G LEU 3.9 0.3 - - - -
376G GLY* 3.0 23.7 + - - -
185H SER* 3.8 6.1 - - - -
1002H SO4 2.9 38.3 + - - -
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Residues in contact with VAL 373 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343G ALA* 4.5 21.8 - - + +
346G LEU* 4.7 17.7 - - + +
347G HIS* 5.1 6.5 - - + +
365G ILE* 5.0 22.9 - - + -
366G PRO* 3.6 19.1 - - + +
367G PRO* 4.5 9.9 - - + +
369G GLU 3.3 17.0 - - - +
370G PRO* 3.0 8.4 + - + +
372G ARG* 1.3 75.4 - - + +
374G ILE* 1.3 67.7 + - - +
376G GLY* 3.5 1.8 + - - +
377G HIS* 3.2 21.5 + - - +
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Residues in contact with ILE 374 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339G LEU* 3.4 27.1 - - + -
342G ARG* 3.4 34.8 - - + +
343G ALA* 4.0 9.9 - - + +
346G LEU* 3.8 14.8 - - + -
370G PRO 3.1 11.0 + - - +
371G TYR 3.7 7.2 - - - +
373G VAL* 1.3 75.9 - - - +
375G LEU* 1.3 60.0 + - + +
377G HIS* 3.1 11.0 + - + +
378G VAL* 3.0 24.4 + - + +
415G PRO* 4.1 23.8 - - + +
418G LEU* 5.0 2.0 - - + -
419G CYS* 3.9 22.4 - - - -
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Residues in contact with LEU 375 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323G ILE* 3.4 25.0 - - + +
326G LEU* 3.9 33.0 - - + -
327G MET* 3.4 31.0 - - + +
330G LEU* 4.3 12.6 - - + -
371G TYR* 3.0 25.5 + - + +
374G ILE* 1.3 77.2 - - + +
376G GLY* 1.3 57.7 + - - +
378G VAL* 3.2 7.4 + - + +
379G ARG* 2.9 22.9 + - - +
416G LEU* 3.9 28.9 - - + -
419G CYS* 4.7 15.7 - - - -
436G LEU* 5.6 1.1 - - + -
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Residues in contact with GLY 376 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327G MET* 3.8 17.2 - - - +
372G ARG 3.0 18.4 + - - -
373G VAL* 3.9 1.8 - - - -
374G ILE 3.2 0.2 - - - -
375G LEU* 1.3 77.2 - - - +
377G HIS* 1.3 56.1 + - - +
379G ARG* 3.3 6.8 + - - +
380G ASP* 3.0 35.7 + - - +
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Residues in contact with HIS 377 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342G ARG* 5.4 10.5 + - - -
346G LEU* 4.4 36.0 - - + +
373G VAL 3.2 12.2 + - - +
374G ILE* 3.1 11.7 + - + +
376G GLY* 1.3 73.6 - - - +
378G VAL* 1.3 67.9 + - + +
380G ASP* 3.2 14.9 + - + +
381G LYS* 3.0 50.8 + - + +
406G PHE* 6.0 0.7 - + - -
415G PRO* 6.0 2.5 - - + -
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Residues in contact with VAL 378 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323G ILE* 4.0 14.4 - - + -
374G ILE 3.0 14.9 + - - +
375G LEU* 3.2 19.2 + - + +
377G HIS* 1.3 79.1 - - + +
379G ARG* 1.3 57.2 + - - +
381G LYS 3.4 0.9 + - - -
382G LEU* 2.9 35.7 + - + +
406G PHE* 3.7 14.1 - - + -
412G PHE* 3.6 31.4 - - + -
415G PRO* 3.7 34.3 - - + -
416G LEU* 4.7 2.7 - - + -
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Residues in contact with ARG 379 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320G ILE* 3.9 18.6 - - + +
323G ILE* 4.4 8.7 - - + +
324G GLU* 2.8 55.3 + - + +
327G MET* 4.7 15.3 - - - +
375G LEU 2.9 13.3 + - - +
376G GLY* 3.6 9.4 + - - +
377G HIS 3.3 0.2 - - - -
378G VAL* 1.3 78.0 - - - +
380G ASP* 1.3 73.5 + - - +
382G LEU* 3.3 5.0 + - - +
383G TYR* 2.9 45.8 + - + -
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Residues in contact with ASP 380 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376G GLY 3.0 16.7 + - - +
377G HIS* 3.2 18.5 + - + +
379G ARG* 1.3 90.4 + - - +
381G LYS* 1.3 63.6 + - - +
383G TYR* 3.1 19.2 + - - +
384G ASN* 3.2 22.6 + - - +
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Residues in contact with LYS 381 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342G ARG* 6.0 1.4 - - - +
377G HIS* 3.0 41.2 + - + +
380G ASP* 1.3 75.5 - - - +
382G LEU* 1.3 58.1 + - - +
384G ASN* 3.3 5.3 + - - +
385G THR* 3.0 31.1 + - - +
403G GLU 4.0 12.1 - - - -
404G SER* 3.2 23.5 - - - +
405G SER* 3.8 20.4 - - - -
406G PHE* 3.5 33.7 - - + -
411G GLU* 3.4 20.4 + - - -
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Residues in contact with LEU 382 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316G ALA* 4.0 11.9 - - + +
319G TYR* 3.9 31.2 - - + -
320G ILE* 3.3 28.3 - - + -
323G ILE* 4.1 11.2 - - + -
378G VAL* 2.9 36.3 + - + +
379G ARG* 4.4 0.2 - - - -
380G ASP 3.2 0.2 - - - -
381G LYS* 1.3 73.9 - - - +
383G TYR* 1.3 62.9 + - - +
385G THR* 2.2 36.3 + - + +
386G ARG* 3.0 10.4 + - - +
406G PHE* 3.9 19.5 - - + -
412G PHE* 4.1 14.1 - - + -
448G LEU* 5.1 7.0 - - + -
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Residues in contact with TYR 383 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320G ILE* 4.1 23.1 - - + +
324G GLU* 4.3 5.2 + - - -
379G ARG* 2.9 53.2 + - + -
380G ASP* 3.1 13.9 + - - +
382G LEU* 1.3 74.4 - - - +
384G ASN* 1.3 62.2 + - - +
386G ARG* 3.2 48.5 + - - +
387G GLU* 3.0 35.3 + - + +
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Residues in contact with ASN 384 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380G ASP* 3.2 18.5 + - - +
381G LYS* 3.7 3.1 - - - +
383G TYR* 1.3 79.2 - - - +
385G THR* 1.3 60.2 + - - +
387G GLU* 3.8 5.4 - - - +
388G ARG* 2.8 33.3 + - - +
400G ILE* 3.9 16.7 - - + +
404G SER* 3.2 36.7 + - - +
405G SER* 3.9 7.2 - - - +
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Residues in contact with THR 385 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G ARG* 6.1 0.2 - - - +
316G ALA* 3.9 10.0 - - - +
381G LYS 3.0 13.0 + - - +
382G LEU* 2.2 38.4 + - + +
384G ASN* 1.3 75.9 - - - +
386G ARG* 1.3 63.0 + - - +
388G ARG* 3.7 3.6 - - - +
389G ALA* 3.1 22.2 + - - +
405G SER* 3.4 10.7 - - - -
406G PHE* 3.0 48.5 - - + +
448G LEU* 6.2 1.3 - - + -
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Residues in contact with ARG 386 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G ARG 5.4 0.7 - - - -
313G MET* 3.8 25.0 - - + +
316G ALA* 3.7 14.1 - - + -
317G ASN* 3.3 37.4 + - - +
320G ILE* 5.1 5.1 - - - +
382G LEU 3.0 9.0 + - - +
383G TYR* 3.2 46.4 - - - +
384G ASN 3.2 0.2 - - - -
385G THR* 1.3 82.8 + - - +
387G GLU* 1.3 88.7 + - - +
389G ALA* 3.2 8.3 + - - +
390G ARG* 3.0 38.6 + - - +
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Residues in contact with GLU 387 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383G TYR* 3.0 22.6 + - + +
384G ASN* 3.9 3.6 - - - +
386G ARG* 1.3 102.9 + - - +
388G ARG* 1.3 60.4 + - - +
390G ARG* 2.7 42.8 + - - +
391G HIS* 2.9 39.9 + - + +
400G ILE* 3.6 23.3 - - + -
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Residues in contact with ARG 388 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384G ASN 2.8 21.0 + - - +
385G THR* 3.7 5.4 - - - +
387G GLU* 1.3 73.1 - - - +
389G ALA* 1.3 56.5 + - - +
391G HIS* 3.3 2.6 + - - +
392G LEU* 2.9 54.7 + - + +
398G SER* 3.6 33.2 + - - +
400G ILE* 2.5 42.4 + - + +
401G SER* 4.0 1.2 - - - +
402G ALA* 3.9 30.3 - - - +
405G SER* 3.8 17.0 - - - -
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Residues in contact with ALA 389 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309G LEU* 4.1 23.1 - - + +
312G ARG* 4.6 12.1 - - + -
313G MET* 3.6 20.7 - - + +
385G THR 3.1 14.0 + - - +
386G ARG* 3.2 8.0 + - - +
388G ARG* 1.3 73.1 - - - +
390G ARG* 1.3 65.7 + - - +
392G LEU* 3.4 11.8 + - - +
393G LEU* 3.0 23.2 + - - +
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Residues in contact with ARG 390 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313G MET* 3.5 36.5 - - + +
317G ASN* 5.6 3.0 - - - +
386G ARG* 3.0 29.1 + - - +
387G GLU* 2.7 49.9 + - - +
389G ALA* 1.3 76.8 - - - +
391G HIS* 1.3 63.7 + - + +
393G LEU* 3.2 5.8 + - + +
394G ALA* 3.0 30.0 + - + +
----------------------------------------------------------
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Residues in contact with HIS 391 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399F GLU* 2.3 43.8 + - - +
387G GLU* 2.9 30.0 + - - +
388G ARG 3.7 0.2 - - - +
390G ARG* 1.3 84.2 - - + +
392G LEU* 1.3 55.8 + - - +
394G ALA* 3.1 4.4 + - + +
395G SER* 2.4 43.4 + - - +
397G VAL 3.6 0.7 - - - -
398G SER* 3.6 20.1 + - - -
400G ILE* 4.4 18.0 - - + +
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Residues in contact with LEU 392 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305G ARG* 3.1 20.2 + - - +
309G LEU* 4.0 25.8 - - + -
388G ARG* 2.9 49.2 + - + +
389G ALA* 3.7 5.2 - - - +
391G HIS* 1.3 75.2 - - - +
393G LEU* 1.3 58.2 + - - +
396G GLY* 3.0 40.0 + - - +
397G VAL* 3.9 15.9 - - - -
398G SER* 3.9 8.3 - - - +
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Residues in contact with LEU 393 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305G ARG* 3.8 10.5 + - - +
306G ASP* 3.6 50.2 - - + +
309G LEU* 3.8 15.9 - - + +
310G LEU* 4.7 15.9 - - + +
313G MET* 5.2 5.8 - - + -
389G ALA 3.0 13.7 + - - +
390G ARG* 3.4 11.2 - - + +
391G HIS 3.1 0.2 - - - -
392G LEU* 1.3 80.4 - - - +
394G ALA* 1.3 65.1 + - + +
396G GLY 4.7 0.2 + - - -
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Residues in contact with ALA 394 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390G ARG* 3.0 19.5 + - + +
391G HIS* 3.1 4.9 + - + +
393G LEU* 1.3 82.4 - - + +
395G SER* 1.3 61.3 + - - +
----------------------------------------------------------
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Residues in contact with SER 395 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399F GLU* 4.2 13.5 + - - -
391G HIS* 2.4 25.6 + - - -
394G ALA* 1.3 77.7 - - - +
396G GLY* 1.3 55.4 + - - +
397G VAL* 2.3 46.8 + - - +
----------------------------------------------------------
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Residues in contact with GLY 396 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305G ARG* 4.4 14.4 + - - +
392G LEU* 3.0 32.4 + - - +
393G LEU 4.6 0.8 + - - -
394G ALA 3.9 0.4 - - - -
395G SER* 1.3 75.5 + - - +
397G VAL* 1.3 65.7 + - - +
----------------------------------------------------------
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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