Contacts of the helix formed by residues 335 - 367 (chain G) in PDB entry 1R4N
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 ASP 335 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208G ASP* 3.5 17.2 - - - +
211G HIS* 3.4 31.0 + - + +
334G ALA* 1.3 78.4 - - - +
336G SER* 1.3 87.1 + - - +
337G GLY* 3.2 12.1 + - - -
338G LYS* 3.4 35.0 + - + +
339G TYR* 3.1 16.5 + - - +
221H MET* 4.3 3.8 - - - -
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Residues in contact with SER 336 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334G ALA 3.5 1.7 + - - -
335G ASP* 1.3 83.6 + - - +
337G GLY* 1.3 63.2 + - - -
339G TYR* 3.8 2.1 - - - +
340G ILE* 3.4 23.7 + - - +
220H SER 4.7 1.6 - - - -
221H MET* 3.8 9.2 - - - +
222H PRO* 3.2 28.2 + - - +
223H ARG* 5.2 0.6 - - - +
271H TYR* 2.8 47.5 + - - +
273H ILE* 5.1 0.2 - - - +
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Residues in contact with GLY 337 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335G ASP* 3.2 6.5 + - - -
336G SER* 1.3 79.8 + - - +
338G LYS* 1.3 56.2 + - - +
340G ILE* 3.5 10.0 + - - +
341G LYS* 3.0 29.6 + - - +
271H TYR 5.9 0.2 - - - -
272H ASN* 5.8 2.5 - - - -
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Residues in contact with LYS 338 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G HIS* 5.0 0.2 + - - -
199G TYR* 4.2 30.7 + - + +
208G ASP* 2.7 34.3 + - - -
211G HIS 3.0 19.9 + - - +
212G THR* 4.0 8.6 + - - -
213G PRO* 4.2 12.4 - - + +
335G ASP* 3.4 25.2 + - + +
336G SER 3.2 1.0 - - - -
337G GLY* 1.3 74.3 - - - +
339G TYR* 1.3 66.2 + - - +
341G LYS* 3.5 7.1 + - - +
342G LEU* 3.2 21.7 + - - +
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Residues in contact with TYR 339 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213G PRO* 4.3 8.4 - - - +
329G ILE* 2.8 26.6 + - + +
330G PRO 2.8 21.0 + - - -
331G ASP* 3.5 7.1 - - - -
332G MET* 3.2 49.6 - - + -
334G ALA* 4.0 4.9 - - + -
335G ASP 3.1 16.2 + - - +
336G SER 3.8 2.7 - - - +
338G LYS* 1.3 77.9 - - - +
340G ILE* 1.3 64.4 + - + +
342G LEU* 3.2 6.2 + - - +
343G GLN* 2.8 49.5 + - + +
223H ARG* 3.6 44.9 - - + -
224H LEU* 4.4 6.6 - - + +
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Residues in contact with ILE 340 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336G SER* 3.4 14.8 + - - +
337G GLY* 3.7 10.1 - - - +
338G LYS 3.3 0.2 - - - -
339G TYR* 1.3 83.1 - - + +
341G LYS* 1.3 60.1 + - - +
343G GLN* 2.6 37.0 + - + +
344G ASN* 2.7 29.0 + - - +
223H ARG* 4.9 4.7 - - - +
271H TYR 3.1 28.0 - - - +
272H ASN* 3.3 31.9 - - - +
273H ILE* 3.7 17.7 - - + -
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Residues in contact with LYS 341 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G HIS* 3.9 25.1 - - + +
198G SER* 4.6 13.7 + - - -
199G TYR* 6.0 1.9 - - + +
337G GLY 3.0 19.1 + - - +
338G LYS* 3.8 6.5 - - - +
340G ILE* 1.3 78.4 - - - +
342G LEU* 1.3 62.8 + - - +
344G ASN* 3.2 8.3 + - - +
345G VAL* 3.0 26.4 + - + +
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Residues in contact with LEU 342 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G LEU* 4.4 6.1 - - + -
195G HIS* 3.7 30.9 + - + +
196G PHE* 4.8 4.5 - - + -
213G PRO* 3.7 14.6 - - + -
215G ILE* 3.9 15.0 - - + -
216G VAL* 4.8 2.5 - - + -
329G ILE* 3.7 10.8 - - + -
332G MET* 3.2 35.2 - - + -
338G LYS 3.2 11.0 + - - +
339G TYR* 3.3 9.0 - - - +
340G ILE 3.1 0.8 - - - -
341G LYS* 1.3 75.0 - - - +
343G GLN* 1.3 69.3 + - - +
345G VAL* 3.2 9.1 + - + +
346G TYR* 3.2 42.6 - - + -
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Residues in contact with GLN 343 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327G GLY 4.8 7.1 - - - +
328G THR* 6.0 1.2 - - - +
329G ILE* 3.5 25.9 + - + +
339G TYR* 2.8 41.8 + - + +
340G ILE* 2.6 25.9 + - - +
342G LEU* 1.3 70.5 - - - +
344G ASN* 1.3 66.9 + - - +
346G TYR* 2.9 8.9 + - + +
347G ARG* 2.9 24.3 + - + -
223H ARG 4.8 5.0 + - - +
224H LEU* 5.1 7.1 - - - +
273H ILE* 5.8 2.1 - - - +
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Residues in contact with ASN 344 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ASN* 4.8 14.6 - - - +
340G ILE* 2.7 33.0 + - - +
341G LYS* 3.5 11.4 - - + +
343G GLN* 1.3 76.2 - - - +
345G VAL* 1.3 55.7 + - - +
347G ARG* 3.4 29.6 + - - +
348G GLU* 2.6 46.1 + - + +
274H ARG* 5.6 3.4 - - - +
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Residues in contact with VAL 345 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G PHE* 4.1 6.1 - - + -
191G GLU* 4.0 12.5 - - + +
192G LEU* 3.6 42.0 - - + +
195G HIS* 3.7 30.1 - - + +
341G LYS* 3.0 19.5 + - + +
342G LEU* 3.2 11.7 - - + +
343G GLN 3.1 0.2 + - - -
344G ASN* 1.3 76.5 - - - +
346G TYR* 1.3 63.6 + - + +
348G GLU* 3.6 4.3 + - - +
349G LYS* 3.1 21.1 + - - +
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Residues in contact with TYR 346 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G ASP 3.7 9.2 - - - -
183G LEU* 2.9 44.7 + - - +
184G ARG* 4.9 0.2 - - + -
185G LEU* 5.3 0.3 - - - +
189G PHE* 4.3 18.8 - + - -
192G LEU* 3.5 21.5 - - + +
196G PHE* 4.8 0.2 - - - -
215G ILE* 3.7 17.9 - - + +
325G VAL* 4.4 9.8 - - + +
327G GLY* 3.8 19.7 - - - +
328G THR 5.3 0.2 - - - -
329G ILE* 3.7 26.9 - - + -
342G LEU* 3.2 44.2 - - + -
343G GLN 2.9 6.7 + - - +
345G VAL* 1.3 81.0 - - + +
347G ARG* 1.3 66.8 + - - +
349G LYS* 3.2 1.9 + - - +
350G ALA* 2.8 25.6 + - - +
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Residues in contact with ARG 347 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327G GLY 4.0 13.4 + - - +
343G GLN* 2.9 18.1 + - + +
344G ASN* 3.4 31.6 + - - +
346G TYR* 1.3 77.1 - - - +
348G GLU* 1.3 72.9 + - + +
350G ALA* 3.2 5.7 + - - +
351G LYS* 2.9 23.6 + - + +
274H ARG* 2.8 55.2 - - - +
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Residues in contact with GLU 348 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C GLU* 4.3 6.7 - - - +
111C ASN* 3.5 17.3 + - - +
115C ASN* 3.5 40.4 + - - +
191G GLU* 6.4 1.8 - - + -
344G ASN* 2.6 31.6 + - + +
345G VAL* 3.9 4.5 - - - +
347G ARG* 1.3 79.5 + - + +
349G LYS* 1.3 66.8 + - - +
351G LYS* 3.0 23.0 + - - +
352G LYS* 3.0 39.1 + - - +
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Residues in contact with LYS 349 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184G ARG* 5.8 0.4 - - - +
189G PHE* 3.4 56.0 - - + +
190G PRO* 5.3 3.2 - - - +
191G GLU* 4.2 15.2 + - + +
318G GLU 5.4 4.9 + - - -
325G VAL* 3.4 26.7 - - + -
345G VAL 3.1 9.3 + - - +
346G TYR 3.6 2.9 - - - +
348G GLU* 1.3 77.0 - - - +
350G ALA* 1.3 57.7 + - - +
352G LYS* 2.8 30.1 + - + +
353G ASP* 2.9 48.6 + - - +
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Residues in contact with ALA 350 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324G PRO* 5.5 0.7 - - - +
325G VAL* 3.1 31.3 - - - +
326G ARG 3.5 15.7 - - - +
327G GLY* 3.7 5.2 - - - -
346G TYR 2.8 17.1 + - - +
347G ARG* 3.4 5.6 - - - +
349G LYS* 1.3 77.5 - - - +
351G LYS* 1.3 57.5 + - - +
353G ASP* 3.8 3.1 - - - +
354G ALA* 2.8 28.6 + - - +
384G CYS* 5.7 1.4 - - - +
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Residues in contact with LYS 351 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C GLU* 2.5 39.2 + - - -
347G ARG* 2.9 15.2 + - + +
348G GLU* 3.0 26.8 + - - +
350G ALA* 1.3 74.6 - - - +
352G LYS* 1.3 61.1 + - + +
354G ALA* 2.8 22.6 - - - +
355G ALA* 3.2 8.3 + - - +
381G LYS* 4.3 29.6 - - - +
----------------------------------------------------------
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Residues in contact with LYS 352 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ASN* 5.0 13.3 + - - +
191G GLU* 3.3 34.1 + - - +
348G GLU* 3.0 33.6 + - - +
349G LYS* 2.8 16.6 + - + +
351G LYS* 1.3 73.6 - - + +
353G ASP* 1.3 66.3 + - - +
354G ALA 2.8 5.4 + - - -
355G ALA* 2.8 18.1 + - - +
356G ALA* 3.0 11.1 + - - +
----------------------------------------------------------
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Residues in contact with ASP 353 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184G ARG* 5.6 0.5 + - - -
314G PHE* 3.0 34.3 - - + -
318G GLU 5.2 1.1 - - - +
323G LEU 4.5 1.2 - - - +
324G PRO* 3.7 14.7 - - + +
325G VAL* 3.6 18.6 + - - +
349G LYS* 2.9 49.1 + - - +
350G ALA 3.9 3.4 - - - +
352G LYS* 1.3 75.3 - - - +
354G ALA* 1.3 63.0 + - - +
356G ALA* 3.2 4.4 - - - +
357G VAL* 3.0 29.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA 354 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324G PRO* 5.6 0.2 - - - -
350G ALA 2.8 16.8 + - - +
351G LYS* 2.8 24.5 - - + +
352G LYS 2.8 0.4 + - - -
353G ASP* 1.3 78.1 - - - +
355G ALA* 1.3 59.9 + - - +
357G VAL* 3.2 5.2 + - - +
358G GLY* 2.9 17.2 + - - -
380G LEU* 3.8 11.1 - - + +
381G LYS* 4.9 20.0 - - + -
384G CYS* 4.1 20.6 - - + -
----------------------------------------------------------
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Residues in contact with ALA 355 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351G LYS 3.2 5.5 + - - +
352G LYS* 2.8 13.9 + - - +
354G ALA* 1.3 72.2 - - - +
356G ALA* 1.3 54.0 + - - +
358G GLY* 2.5 24.5 + - - +
359G ASN* 2.7 26.4 + - - +
380G LEU* 5.0 2.9 - - - -
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Residues in contact with ALA 356 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G PHE* 3.2 21.5 - - + -
318G GLU* 3.7 20.1 - - + +
352G LYS 3.0 8.1 + - - +
353G ASP* 3.2 15.7 - - - +
355G ALA* 1.3 74.6 - - - +
357G VAL* 1.3 62.8 + - - +
359G ASN* 3.0 21.2 + - - +
360G HIS* 3.2 19.4 + - - -
----------------------------------------------------------
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Residues in contact with VAL 357 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310G ALA* 3.6 16.4 - - + +
311G LEU* 3.3 24.7 - - + -
314G PHE* 3.4 18.8 - - + -
324G PRO* 3.5 22.9 - - + -
353G ASP 3.0 16.2 + - - +
354G ALA 3.5 5.2 - - - +
356G ALA* 1.3 74.4 - - - +
358G GLY* 1.3 63.2 + - - +
360G HIS* 3.4 11.2 + - - +
361G VAL* 3.1 26.8 + - + +
380G LEU* 4.2 12.8 - - + -
383G LEU* 4.9 2.9 - - + -
384G CYS* 4.0 10.3 - - - -
----------------------------------------------------------
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Residues in contact with GLY 358 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354G ALA 2.9 6.7 + - - -
355G ALA* 2.5 17.7 + - - -
357G VAL* 1.3 72.2 - - - +
359G ASN* 1.3 63.8 + - - +
361G VAL* 3.3 5.7 - - - +
362G ALA* 3.2 18.0 + - - +
380G LEU* 3.4 29.2 - - - -
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Residues in contact with ASN 359 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318G GLU* 5.7 1.9 - - - +
355G ALA* 2.7 20.5 + - - +
356G ALA* 3.0 13.3 + - - +
358G GLY* 1.3 70.7 - - - +
360G HIS* 1.3 69.7 + - + +
361G VAL 3.0 1.3 - - - -
362G ALA* 2.8 21.1 + - - +
363G LYS* 2.9 32.2 + - - +
----------------------------------------------------------
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Residues in contact with HIS 360 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310G ALA* 3.6 23.1 - - - +
313G GLU* 3.9 25.2 + - + +
314G PHE* 3.6 27.4 - - + -
317G LYS* 3.8 17.7 - - + -
318G GLU* 2.6 35.1 + - - -
356G ALA 3.2 19.9 + - - -
357G VAL 3.4 1.5 + - - +
359G ASN* 1.3 76.3 - - + +
361G VAL* 1.3 63.9 + - - +
363G LYS* 3.4 23.9 + - - +
364G LEU* 2.9 30.0 + - + +
----------------------------------------------------------
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Residues in contact with VAL 361 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306G ILE* 4.4 3.1 - - + -
307G LEU* 3.7 19.1 - - + -
310G ALA* 3.3 22.9 - - + -
357G VAL* 3.1 20.6 + - + +
358G GLY* 3.3 9.6 - - - +
359G ASN 2.9 1.0 + - - -
360G HIS* 1.3 74.8 - - - +
362G ALA* 1.3 65.7 + - - +
364G LEU* 2.8 8.3 + - - +
365G LEU* 2.8 45.5 + - + +
372G PRO 5.7 0.4 - - - +
375G ILE* 4.1 22.9 - - + -
380G LEU* 4.3 9.4 - - + -
----------------------------------------------------------
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Residues in contact with ALA 362 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358G GLY 3.2 8.1 + - - +
359G ASN* 2.8 15.7 + - - +
361G VAL* 1.3 75.5 - - - +
363G LYS* 1.3 66.4 + - + +
365G LEU* 2.9 14.7 + - - +
366G GLN* 2.7 29.9 + - + +
372G PRO* 4.0 23.6 - - + +
----------------------------------------------------------
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Residues in contact with LYS 363 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G LYS* 4.0 21.4 - - - +
359G ASN* 2.9 27.8 + - - +
360G HIS* 3.6 27.5 + - - +
362G ALA* 1.3 75.6 - - + +
364G LEU* 1.3 68.0 + - + +
366G GLN* 3.1 17.7 + - - +
367G SER* 3.0 22.4 + - - -
----------------------------------------------------------
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Residues in contact with LEU 364 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297G ILE* 4.2 14.1 - - + -
306G ILE* 3.7 20.0 - - + +
309G ARG* 3.2 38.6 - - + +
310G ALA* 3.6 20.0 - - + +
313G GLU* 4.8 10.8 - - + -
360G HIS* 2.9 17.6 + - + +
361G VAL* 2.8 13.9 + - - +
363G LYS* 1.3 74.5 - - + +
365G LEU* 1.3 69.2 + - - +
366G GLN 2.9 1.4 + - - -
367G SER* 2.9 25.3 + - - +
368G ILE* 3.4 13.6 + - + +
----------------------------------------------------------
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Residues in contact with LEU 365 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306G ILE* 3.6 27.1 - - + -
361G VAL* 2.8 39.4 + - + +
362G ALA* 3.4 6.7 - - - +
364G LEU* 1.3 72.7 - - - +
366G GLN* 1.3 57.2 + - - +
368G ILE* 3.3 6.8 + - - +
369G GLY 3.0 19.1 + - - -
370G GLN* 3.0 33.5 + - + +
371G ALA 4.1 3.6 - - - +
372G PRO* 3.7 34.3 - - + +
374G SER* 4.6 10.3 - - - +
375G ILE* 4.1 26.5 - - + +
----------------------------------------------------------
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Residues in contact with GLN 366 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362G ALA* 2.7 20.9 + - - +
363G LYS* 3.2 20.4 - - - +
364G LEU 2.9 0.8 + - - -
365G LEU* 1.3 67.7 - - - +
367G SER* 1.3 53.1 + - - +
368G ILE 2.4 18.3 + - - -
369G GLY* 2.9 13.9 + - - +
370G GLN 4.5 2.5 - - - -
372G PRO* 3.7 26.0 - - + +
----------------------------------------------------------
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Residues in contact with SER 367 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363G LYS 3.0 11.2 + - - -
364G LEU* 2.9 21.7 + - - +
366G GLN* 1.3 72.7 - - - +
368G ILE* 1.3 66.4 + - - +
----------------------------------------------------------
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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