Contacts of the helix formed by residues 374 - 399 (chain G) in PDB entry 1GLE
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 ASN 374 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332G PHE* 3.1 50.3 - - - +
333G ALA* 4.6 1.0 - - - -
335G LYS* 3.8 25.3 - - - +
336G VAL* 3.9 20.0 - - + +
372G ASN* 3.2 14.0 + - - +
373G ALA* 1.3 80.2 - - - +
375G HIS* 1.3 65.3 + - - +
376G ILE 3.3 0.2 + - - -
377G ILE* 3.8 7.8 - - - +
378G ARG* 3.3 21.7 + - - +
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Residues in contact with HIS 375 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336G VAL* 3.8 17.7 - - + +
338G ASN* 3.1 30.2 + - - -
339G THR* 3.2 21.7 - - - +
340G ASN* 3.1 32.0 + - + +
342G VAL* 4.5 1.8 - - + -
370G GLY 4.1 4.5 - - - -
371G VAL* 3.4 15.8 - - + -
372G ASN* 2.7 53.7 + - - +
374G ASN* 1.3 71.8 - - - +
376G ILE* 1.3 58.3 + - - +
378G ARG* 3.3 5.0 + - - +
379G ALA* 2.9 29.9 + - - +
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Residues in contact with ILE 376 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315G TRP* 6.0 2.0 - - + -
316G LEU* 5.1 6.5 - - + -
320G MET* 6.3 1.8 - - + -
322G LEU* 4.7 16.2 - - + -
342G VAL* 4.6 12.1 - - + -
344G VAL* 5.0 1.6 - - + -
364G ILE* 4.8 23.1 - - + -
367G LEU* 4.7 12.3 - - + -
371G VAL* 4.1 16.6 - - + +
372G ASN* 3.3 18.4 + - - +
373G ALA* 3.5 10.1 - - - +
375G HIS* 1.3 75.2 - - - +
377G ILE* 1.3 67.4 + - - +
379G ALA* 3.1 12.8 + - - +
380G THR* 3.0 22.9 + - - +
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Residues in contact with ILE 377 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316G LEU* 3.7 27.8 - - + +
322G LEU* 4.5 16.4 - - + +
323G ILE* 3.8 25.8 - - + -
329G SER* 4.1 32.8 - - - +
332G PHE* 4.0 21.8 - - + -
333G ALA* 4.1 4.7 - - + +
373G ALA* 3.0 18.9 + - + +
374G ASN* 3.8 9.4 - - - +
375G HIS 3.4 0.2 - - - -
376G ILE* 1.3 74.3 - - - +
378G ARG* 1.3 59.7 + - - +
380G THR* 2.6 27.2 + - - -
381G LEU* 2.8 12.8 + - + +
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Residues in contact with ARG 378 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333G ALA* 3.2 42.1 + - + -
334G THR* 4.8 2.8 - - - +
336G VAL* 3.9 13.5 - - - -
337G GLN* 3.1 46.3 + - - +
338G ASN* 4.0 11.0 - - - +
339G THR* 3.8 10.8 - - + -
374G ASN 3.3 11.1 + - - +
375G HIS 4.0 1.8 - - - +
376G ILE 3.3 0.6 - - - -
377G ILE* 1.3 82.0 - - - +
379G ALA* 1.3 58.1 + - - +
381G LEU* 3.5 4.9 - - - +
382G GLU* 2.6 52.4 + - + +
417G PHE* 3.7 31.4 - - + -
421G PHE* 4.7 6.3 - - - -
482G ARG* 5.6 4.8 - - - +
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Residues in contact with ALA 379 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339G THR* 3.8 18.4 - - + -
342G VAL* 4.0 20.2 - - + +
343G TYR* 4.7 0.6 - - - -
344G VAL* 3.3 28.8 + - + +
375G HIS 2.9 13.6 + - - +
376G ILE 3.3 7.0 - - - +
377G ILE 3.0 0.2 - - - -
378G ARG* 1.3 77.8 - - - +
380G THR* 1.3 62.4 + - - +
382G GLU* 3.1 5.9 + - - +
383G SER* 3.0 21.7 + - - -
386G TYR* 5.6 0.2 - - - -
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Residues in contact with THR 380 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G SER* 3.3 36.7 - - - +
313G ILE* 3.8 13.5 - - + -
315G TRP* 5.4 1.6 - - + -
316G LEU* 3.9 23.6 - - + +
344G VAL* 3.2 22.4 - - + +
348G PHE* 6.4 0.2 - - + -
376G ILE* 3.0 13.2 + - - +
377G ILE 2.6 12.3 + - - -
379G ALA* 1.3 74.5 - - - +
381G LEU* 1.3 61.6 + - - +
383G SER* 2.5 27.4 + - - +
384G ILE* 3.6 5.5 + - - +
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Residues in contact with LEU 381 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313G ILE* 3.5 32.1 - - + -
329G SER* 4.0 29.4 - - - +
330G GLU* 4.9 0.2 - - - -
333G ALA* 4.1 3.1 - - + -
377G ILE* 2.8 15.0 + - + +
378G ARG* 3.1 8.9 + - - +
380G THR* 1.3 75.9 - - - +
382G GLU* 1.3 64.6 + - - +
384G ILE* 3.1 29.0 + - + +
415G ASN* 3.7 27.4 - - - +
417G PHE* 4.0 28.5 - - + -
418G LEU* 3.8 17.5 - - + +
504G ADP 4.9 3.1 - - + -
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Residues in contact with GLU 382 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338G ASN* 5.6 0.2 - - - -
339G THR* 3.7 21.8 + - - +
343G TYR* 4.6 5.3 - - + -
378G ARG* 2.6 51.1 + - + +
379G ALA* 3.1 6.3 + - - +
381G LEU* 1.3 75.9 - - - +
383G SER* 1.3 63.4 + - - +
384G ILE 2.9 1.4 + - - -
385G ALA* 3.0 15.2 + - - +
386G TYR* 2.9 47.2 + - + -
417G PHE* 5.0 4.0 - - + -
421G PHE* 3.5 38.4 - - + -
482G ARG* 5.4 5.0 + - - -
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Residues in contact with SER 383 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G SER* 5.1 0.9 + - - -
344G VAL* 3.3 27.0 + - - +
346G PRO* 3.5 27.9 - - - +
379G ALA 3.0 7.6 + - - -
380G THR* 2.5 25.9 + - - +
382G GLU* 1.3 72.7 - - - +
384G ILE* 1.3 58.0 + - - +
386G TYR* 2.8 11.9 + - - +
387G GLN* 2.7 41.0 + - - +
486G TRP* 4.0 5.2 - - - -
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Residues in contact with ILE 384 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G TYR* 3.7 33.2 - - + -
269G CYS* 4.1 11.6 - - - -
308G MET 5.2 1.3 - - - +
309G ALA* 3.7 38.1 - - + +
310G GLY* 4.4 1.6 - - - +
312G SER* 5.7 1.6 - - - -
313G ILE* 4.5 7.9 - - + -
346G PRO* 6.3 0.2 - - + -
380G THR 3.9 7.0 - - - +
381G LEU* 3.4 26.9 - - + +
382G GLU 2.9 1.2 - - - -
383G SER* 1.3 81.4 - - - +
385G ALA* 1.3 62.7 + - - +
387G GLN* 3.2 7.5 + - - +
388G THR* 2.9 24.0 + - - -
412G ALA* 5.4 5.2 - - + -
418G LEU* 4.1 22.2 - - + -
504G ADP 5.8 0.7 - - + -
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Residues in contact with ALA 385 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381G LEU 4.0 1.0 + - - -
382G GLU 3.0 10.9 + - - +
384G ILE* 1.3 75.9 - - - +
386G TYR* 1.3 65.4 + - - +
388G THR 3.7 0.2 - - - -
389G ARG* 2.9 21.1 + - - +
418G LEU* 4.3 5.8 - - + +
421G PHE* 3.6 30.7 - - + -
422G GLN* 3.2 37.8 + - - +
425G ILE* 3.8 6.0 - - + +
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Residues in contact with TYR 386 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343G TYR* 3.8 19.8 + + - -
379G ALA 5.6 0.2 - - - -
382G GLU* 2.9 61.3 + - + -
383G SER* 2.8 7.0 + - - +
385G ALA* 1.3 79.3 - - - +
387G GLN* 1.3 64.2 + - - +
389G ARG* 3.0 7.3 + - - +
390G ASP* 2.8 25.3 + - - +
421G PHE* 3.8 8.6 - + - -
425G ILE* 3.4 27.8 - - + -
482G ARG* 3.6 39.8 + - - +
483G TYR* 3.8 19.5 - + - -
486G TRP* 3.3 39.9 - + + +
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Residues in contact with GLN 387 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G CYS* 6.0 0.7 - - + -
306G VAL* 3.4 37.3 - - + +
307G PHE 5.3 0.2 - - - +
308G MET 3.0 23.5 + - - +
346G PRO* 3.9 25.9 + - - +
351G LEU* 4.7 15.0 - - - +
355G TYR* 5.9 2.9 - - + -
383G SER* 2.7 21.5 + - - +
384G ILE* 3.6 6.2 + - + +
386G TYR* 1.3 75.3 - - - +
388G THR* 1.3 64.9 + - - +
390G ASP* 2.7 22.6 + - - +
391G VAL* 2.9 14.6 + - - +
486G TRP* 3.5 24.4 - - + -
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Residues in contact with THR 388 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263G ASN* 3.3 32.0 + - - +
265G TYR* 3.5 9.7 + - - +
269G CYS* 4.2 6.8 - - - -
271G MET* 4.2 9.0 - - + -
306G VAL* 5.1 2.0 - - - +
384G ILE 2.9 16.0 + - - -
385G ALA 3.5 1.8 - - - -
387G GLN* 1.3 77.2 - - - +
389G ARG* 1.3 68.6 + - - +
391G VAL* 3.0 8.3 + - - +
392G LEU* 2.9 19.8 + - + +
406G LEU* 4.6 5.8 - - + -
422G GLN* 3.1 32.5 + - - +
426G LEU* 4.8 2.9 - - + -
----------------------------------------------------------
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Residues in contact with ARG 389 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385G ALA 2.9 15.1 + - - +
386G TYR* 3.4 4.7 - - - +
388G THR* 1.3 86.5 - - - +
390G ASP* 1.3 63.7 + - - +
392G LEU* 3.2 1.5 + - - +
393G GLU* 3.1 47.7 + - + +
422G GLN* 4.7 0.9 - - - +
425G ILE* 2.8 39.6 + - + +
426G LEU* 4.0 26.7 + - + +
479G ARG* 3.9 13.7 - - - +
480G ASN* 3.3 30.1 + - - +
483G TYR* 3.6 49.1 - - + +
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Residues in contact with ASP 390 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353G ALA 5.2 1.1 - - - +
354G PRO* 4.1 19.8 - - + +
355G TYR* 2.6 37.2 + - + +
386G TYR 2.8 8.6 + - - -
387G GLN* 2.7 16.1 + - - +
389G ARG* 1.3 74.8 - - - +
391G VAL* 1.3 65.9 + - + +
393G GLU* 3.4 9.2 + - - +
394G ALA* 3.4 10.9 + - - +
483G TYR* 2.5 41.5 + - - +
486G TRP* 3.0 22.1 + - - -
487G LYS* 3.6 4.9 + - - +
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Residues in contact with VAL 391 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263G ASN* 5.1 1.1 - - - +
271G MET* 3.6 35.0 - - + -
286G LEU* 3.7 13.0 - - + +
304G GLY* 3.5 30.7 - - - +
306G VAL* 4.7 10.1 - - + -
353G ALA* 3.9 18.4 - - + +
354G PRO* 4.8 2.2 - - + -
387G GLN 2.9 8.4 + - - +
388G THR* 3.7 10.5 - - - +
390G ASP* 1.3 80.5 - - + +
392G LEU* 1.3 67.5 + - - +
394G ALA* 3.1 8.4 - - + +
395G MET* 3.0 20.1 + - + +
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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
----------------------------------------------------------
271G MET* 3.4 28.9 - - + -
388G THR* 2.9 12.6 + - + +
389G ARG* 3.6 7.2 - - - +
390G ASP 3.1 0.4 - - - -
391G VAL* 1.3 82.5 - - - +
393G GLU* 1.3 78.1 + - + +
395G MET* 3.0 6.0 + - + +
396G GLN* 2.9 50.3 + - + +
403G LEU* 4.9 11.4 - - + -
406G LEU* 4.7 13.7 - - + -
426G LEU* 4.2 24.9 - - + -
428G THR* 5.9 4.5 - - + +
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Residues in contact with GLU 393 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389G ARG* 3.1 54.7 + - + +
390G ASP 4.0 4.0 - - - +
392G LEU* 1.3 87.3 - - + +
394G ALA* 1.3 64.5 + - - +
396G GLN* 3.1 6.4 + - - +
397G ALA* 3.0 22.9 + - - +
483G TYR* 4.1 16.2 + - - +
487G LYS* 4.9 3.1 + - - -
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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
----------------------------------------------------------
284G ASN* 3.6 26.1 - - - +
286G LEU* 3.5 20.0 - - + -
354G PRO* 5.0 7.0 - - + -
390G ASP 3.4 8.9 + - - +
391G VAL* 3.1 14.4 - - + +
393G GLU* 1.3 79.6 - - - +
395G MET* 1.3 63.3 + - - +
396G GLN 3.0 0.3 + - - -
397G ALA* 3.1 5.0 + - - +
398G ASP* 2.9 27.2 + - - +
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Residues in contact with MET 395 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261G ALA* 5.4 0.9 - - + -
271G MET* 3.2 61.2 - - + +
272G LEU* 3.8 10.8 - - - +
273G MET* 4.1 26.7 - - + +
286G LEU* 3.4 12.3 - - + +
302G LEU* 3.9 27.3 - - - +
303G GLU 5.1 0.2 - - - -
304G GLY 4.7 3.4 - - - +
391G VAL* 3.0 9.5 + - + +
392G LEU* 3.3 14.1 - - + +
394G ALA* 1.3 80.6 - - - +
396G GLN* 1.3 62.6 + - + +
398G ASP* 3.8 2.5 - - - +
399G SER* 2.9 28.6 + - - +
403G LEU* 5.0 7.9 - - + -
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Residues in contact with GLN 396 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392G LEU* 2.9 38.0 + - + +
393G GLU* 3.6 8.3 - - - +
394G ALA 3.0 0.4 - - - -
395G MET* 1.3 77.3 - - + +
397G ALA* 1.3 56.6 + - - +
399G SER* 3.1 2.8 + - - -
400G GLY* 2.7 36.9 + - - -
401G ILE 3.1 22.0 + - - +
402G ARG* 3.6 17.2 - - - +
403G LEU* 2.8 49.3 + - + +
428G THR* 6.0 0.2 + - - -
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Residues in contact with ALA 397 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284G ASN* 3.4 24.0 - - - +
393G GLU 3.0 12.6 + - - +
394G ALA* 3.5 6.5 - - - +
396G GLN* 1.3 76.1 - - - +
398G ASP* 1.3 64.4 + - - +
400G GLY* 3.4 8.2 + - - -
----------------------------------------------------------
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Residues in contact with ASP 398 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G VAL* 4.4 11.0 - - - +
281G LYS 4.2 2.9 - - - +
282G SER* 2.3 37.4 + - - -
283G GLU* 2.9 19.9 + - - +
284G ASN* 2.7 26.3 + - - +
286G LEU* 3.9 8.1 - - + +
302G LEU* 4.1 16.0 - - + +
394G ALA 2.9 12.8 + - - +
395G MET* 3.8 4.9 - - - +
397G ALA* 1.3 81.3 - - - +
399G SER* 1.3 57.1 + - - +
400G GLY 3.3 0.6 + - - -
----------------------------------------------------------
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Residues in contact with SER 399 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273G MET* 4.1 24.4 - - - +
275G THR* 6.1 1.1 - - - -
280G VAL* 5.5 3.6 - - - -
302G LEU* 4.6 10.8 - - - -
395G MET* 2.9 20.2 + - - +
396G GLN* 3.1 2.3 + - - -
398G ASP* 1.3 77.6 - - - +
400G GLY* 1.3 53.0 + - - +
401G ILE* 2.5 48.1 + - - +
----------------------------------------------------------
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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