Contacts of the helix formed by residues 342 - 369 (chain O) in PDB entry 5L4K
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 342 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218O MET* 5.7 6.5 - - + -
341O LEU* 1.3 77.3 - - - +
343O LEU* 1.3 65.6 + - - +
344O GLN* 2.9 36.4 + - - +
345O GLN* 3.0 35.6 + - - +
346O ILE* 3.3 18.0 + - - +
222U ILE* 5.1 3.8 - - - -
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Residues in contact with LEU 343 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342O ASP* 1.3 75.7 - - - +
344O GLN* 1.3 58.0 + - - +
346O ILE* 4.2 7.8 - - + +
347O LYS* 3.2 40.6 + - - +
215U VAL* 4.0 21.8 - - + +
216U ALA* 4.3 16.3 - - - +
219U LYS* 4.4 18.4 - - + -
222U ILE* 3.7 28.7 - - + +
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Residues in contact with GLN 344 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342O ASP* 2.9 14.7 + - - +
343O LEU* 1.3 78.8 - - - +
345O GLN* 1.3 64.4 + - + +
347O LYS* 3.7 33.5 + - - +
348O GLY* 3.8 5.9 + - - +
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Residues in contact with GLN 345 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282O PHE* 4.1 23.0 - - - -
339O ARG* 5.3 0.6 - - - +
340O VAL 4.6 1.2 - - - +
341O LEU* 3.4 37.4 - - + +
342O ASP* 3.0 39.1 + - - +
344O GLN* 1.3 77.0 - - + +
346O ILE* 1.3 67.8 + - - +
347O LYS 3.2 0.2 - - - -
348O GLY* 3.0 11.8 + - - -
349O MET* 3.1 12.2 + - - +
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Residues in contact with ILE 346 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341O LEU* 4.8 9.9 - - + +
342O ASP 3.3 14.2 + - - +
343O LEU* 4.2 6.3 - - + +
345O GLN* 1.3 78.3 - - - +
347O LYS* 1.3 58.0 + - - +
349O MET* 2.8 26.2 + - + +
350O LYS* 2.9 13.0 + - + +
212U LEU* 4.5 17.9 - - + +
215U VAL* 4.4 15.3 - - + -
216U ALA* 4.3 21.5 - - + -
222U ILE* 4.2 24.7 - - + -
227U ILE* 3.9 43.5 - - + -
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Residues in contact with LYS 347 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343O LEU* 3.2 30.4 + - - +
344O GLN* 3.7 33.1 + - - +
345O GLN 3.2 0.8 - - - -
346O ILE* 1.3 79.4 - - - +
348O GLY* 1.3 57.7 + - - +
350O LYS* 3.8 13.0 - - - +
351O ASP* 3.1 22.2 - - - +
216U ALA* 4.0 33.2 - - + -
217U THR* 4.9 5.4 - - - +
219U LYS* 6.3 0.4 - - - +
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Residues in contact with GLY 348 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344O GLN* 3.8 5.3 + - - +
345O GLN* 3.0 9.4 + - - -
347O LYS* 1.3 76.7 - - - +
349O MET* 1.3 64.4 + - - +
350O LYS 3.2 0.2 - - - -
351O ASP* 3.3 6.6 + - - +
352O ARG* 3.0 21.9 + - - +
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Residues in contact with MET 349 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341O LEU* 4.1 26.0 - - + -
345O GLN 3.1 10.5 + - - +
346O ILE* 2.8 13.5 + - - +
348O GLY* 1.3 73.2 - - - +
350O LYS* 1.3 67.5 + - - +
352O ARG* 4.1 7.9 - - + -
353O LEU* 2.8 24.1 + - - +
212U LEU* 4.2 20.2 - - + -
227U ILE* 5.0 8.3 - - + -
230U LEU* 4.4 19.1 - - - +
231U GLN* 4.3 16.2 - - + -
234U PHE* 4.1 32.5 - - + -
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Residues in contact with LYS 350 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346O ILE* 2.9 11.2 + - + +
347O LYS* 3.8 13.9 - - - +
348O GLY 3.2 0.4 - - - -
349O MET* 1.3 77.0 - - - +
351O ASP* 1.3 87.4 + - - +
353O LEU* 3.3 3.0 + - - +
354O GLU* 2.9 37.4 + - - +
209U ARG* 3.8 33.8 - - + +
212U LEU* 4.4 18.3 - - + +
213U GLU* 4.0 39.2 + - + +
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Residues in contact with ASP 351 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347O LYS 3.1 19.1 - - - +
348O GLY* 3.3 7.4 + - - +
349O MET 3.2 0.2 - - - -
350O LYS* 1.3 102.6 + - - +
352O ARG* 1.3 61.0 + - - +
354O GLU* 3.7 8.6 - - + +
355O PHE* 3.0 29.3 + - - +
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Residues in contact with ARG 352 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348O GLY 3.0 14.9 + - - +
349O MET* 3.1 12.5 + - + +
351O ASP* 1.3 78.0 - - - +
353O LEU* 1.3 58.5 + - - +
355O PHE* 3.6 23.9 - - - +
356O TRP* 3.6 15.7 + - - +
234U PHE* 3.7 31.5 + - + +
237U LEU* 3.4 27.1 - - - +
239U ASP* 5.2 4.6 + - - -
310V LYS 5.5 4.4 + - - -
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Residues in contact with LEU 353 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349O MET 2.8 15.7 + - - +
350O LYS 3.7 2.5 - - - +
352O ARG* 1.3 74.1 - - - +
354O GLU* 1.3 66.0 + - - +
355O PHE 3.1 1.1 - - - -
356O TRP* 2.9 41.9 + - + +
357O CYS* 2.9 12.6 + - + +
205U LEU* 4.4 13.2 - - + +
208U ILE* 3.5 32.3 - - + -
209U ARG* 3.8 27.6 - - + +
212U LEU* 4.3 10.5 - - + -
230U LEU* 5.1 3.6 - - + -
233U VAL* 5.7 0.7 - - + -
234U PHE* 3.3 33.2 - - + -
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Residues in contact with GLU 354 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350O LYS* 2.9 32.0 + - - +
351O ASP* 3.7 11.7 - - - +
353O LEU* 1.3 74.9 - - - +
355O PHE* 1.3 66.3 + - - +
357O CYS* 2.8 25.1 + - - +
358O THR* 3.1 40.8 + - - +
209U ARG* 3.4 38.4 + - + +
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Residues in contact with PHE 355 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351O ASP 3.0 18.9 + - - +
352O ARG* 3.6 20.2 - - - +
353O LEU 3.1 0.2 - - - -
354O GLU* 1.3 78.7 - - - +
356O TRP* 1.3 61.7 + - - +
358O THR* 3.2 20.4 + - - -
359O ASP* 3.4 24.9 + - - +
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Residues in contact with TRP 356 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352O ARG* 3.6 18.0 + - - +
353O LEU* 2.9 32.4 + - + +
355O PHE* 1.3 77.5 - - - +
357O CYS* 1.3 68.8 - - - +
359O ASP* 3.0 22.4 + - + +
360O VAL* 3.1 12.6 + - + +
435P LEU* 4.7 4.5 - - + -
439P VAL* 4.8 8.3 - - + -
201U LEU* 4.6 2.7 - - + -
205U LEU* 3.3 42.6 - - + -
233U VAL* 4.4 22.7 - - + -
234U PHE* 4.6 9.0 - + - -
237U LEU* 4.5 20.0 - - + -
308V VAL 3.1 26.7 + - - -
309V PHE* 3.9 33.7 - + - +
310V LYS 5.4 3.8 - - - -
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Residues in contact with CYS 357 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353O LEU* 2.9 10.8 + - + +
354O GLU* 2.8 24.7 + - - +
356O TRP* 1.3 76.4 - - - +
358O THR* 1.3 63.1 + - - +
360O VAL* 2.8 26.5 + - - +
361O LYS* 2.9 12.9 + - - -
202U ASN* 4.4 22.7 - - - +
205U LEU* 4.8 14.1 - - + +
206U LEU* 4.7 22.9 - - - +
209U ARG* 5.8 4.9 - - + -
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Residues in contact with THR 358 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354O GLU* 3.1 26.8 + - - +
355O PHE* 3.2 20.1 + - - -
357O CYS* 1.3 80.5 - - + +
359O ASP* 1.3 61.5 + - - +
361O LYS* 3.7 10.7 - - + +
362O SER* 3.0 25.8 + - - -
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Residues in contact with ASP 359 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355O PHE* 3.4 27.4 + - - +
356O TRP* 3.0 20.9 + - + +
358O THR* 1.3 75.1 + - - +
360O VAL* 1.3 66.4 + - - +
362O SER* 3.0 21.1 + - - -
363O MET* 3.0 15.5 + - + +
307V VAL* 4.3 21.6 - - + +
308V VAL 4.9 0.4 - - - +
310V LYS* 5.2 15.9 - - - +
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Residues in contact with VAL 360 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356O TRP* 3.1 17.7 + - + +
357O CYS* 2.8 13.7 + - - +
359O ASP* 1.3 72.2 - - - +
361O LYS* 1.3 66.1 + - - +
363O MET* 2.9 16.5 + - - +
364O GLU* 3.0 13.6 + - + +
198U LEU* 4.3 13.9 - - + +
201U LEU* 4.0 17.0 - - + -
202U ASN* 4.0 33.7 - - + +
205U LEU* 4.4 8.5 - - + -
308V VAL* 3.7 33.9 - - + +
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Residues in contact with LYS 361 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357O CYS* 2.9 12.7 + - - +
358O THR* 3.7 14.6 - - + +
360O VAL* 1.3 77.6 - - - +
362O SER* 1.3 66.0 + - - +
364O GLU* 3.4 19.4 + - - +
365O MET* 2.9 54.9 + - + +
202U ASN* 3.7 25.4 + - - +
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Residues in contact with SER 362 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358O THR 3.0 16.1 + - - -
359O ASP* 3.0 13.9 + - - -
360O VAL 3.2 0.2 - - - -
361O LYS* 1.3 77.8 - - - +
363O MET* 1.3 65.9 + - - +
365O MET* 3.3 10.3 + - - +
366O LEU* 2.9 24.8 + - - +
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Residues in contact with MET 363 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359O ASP* 3.0 14.3 + - + +
360O VAL 2.9 3.4 + - - +
362O SER* 1.3 82.7 + - - +
364O GLU* 1.3 58.6 + - - +
366O LEU* 2.7 49.2 + - + +
367O VAL* 3.1 10.8 + - + +
333T THR* 3.7 22.4 - - + -
336T ALA* 5.3 3.8 - - + -
198U LEU* 4.3 2.9 - - + -
304V LEU* 4.0 27.1 - - + +
307V VAL* 3.7 40.2 - - + -
308V VAL* 3.6 26.2 - - + +
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Residues in contact with GLU 364 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360O VAL* 3.0 11.5 + - + +
361O LYS* 3.6 27.4 + - - +
363O MET* 1.3 75.6 - - - +
365O MET* 1.3 58.1 + - + +
366O LEU 3.1 0.3 + - - -
367O VAL* 3.2 5.6 + - - +
368O GLU* 2.9 53.2 + - + +
195U VAL* 4.5 7.2 - - + -
198U LEU* 3.4 26.3 - - + +
199U LYS* 3.1 47.1 + - + +
202U ASN* 4.3 9.4 + - - +
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Residues in contact with MET 365 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361O LYS* 2.9 49.7 + - + +
362O SER* 3.4 14.6 - - - +
363O MET 3.1 0.2 - - - -
364O GLU* 1.3 77.1 - - - +
366O LEU* 1.3 58.7 + - - +
367O VAL 3.5 0.2 - - - -
368O GLU* 3.4 25.4 - - - +
369O HIS* 3.7 19.5 + - - +
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Residues in contact with LEU 366 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362O SER 2.9 11.2 + - - +
363O MET* 2.7 46.1 + - + +
365O MET* 1.3 75.0 - - - +
367O VAL* 1.3 60.7 + - + +
368O GLU 3.4 0.4 - - - -
369O HIS* 2.9 23.8 - - + +
370O GLN* 4.0 9.9 - - - +
333T THR* 3.9 34.5 - - + +
336T ALA* 5.2 4.0 - - + -
337T LYS* 3.6 32.3 - - + +
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Residues in contact with VAL 367 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363O MET 3.1 13.3 + - - +
364O GLU* 3.6 8.3 - - - +
366O LEU* 1.3 84.5 - - + +
368O GLU* 1.3 59.6 + - - +
369O HIS 3.3 4.9 - - - -
370O GLN* 5.6 1.6 - - - +
371O ALA* 3.4 8.3 - - + +
372O HIS* 3.2 21.3 + - - +
336T ALA* 5.6 4.0 - - + +
337T LYS* 6.4 0.2 - - - -
340T ILE* 4.1 26.9 - - + -
194U GLN 5.4 0.7 - - - +
195U VAL* 3.5 32.2 - - + +
198U LEU* 4.6 3.8 - - + -
300V LEU* 4.9 6.1 - - + -
304V LEU* 4.2 27.6 - - + -
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Residues in contact with GLU 368 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364O GLU* 2.9 40.9 + - - +
365O MET* 3.4 32.9 - - - +
366O LEU 3.4 0.4 - - - -
367O VAL* 1.3 75.2 - - - +
369O HIS* 1.3 65.7 + - - +
370O GLN 3.7 0.2 + - - -
372O HIS* 3.2 21.4 - - + +
373O ASP* 3.2 24.9 + - - +
195U VAL* 4.0 13.9 - - + -
199U LYS* 3.5 18.7 - - - +
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Residues in contact with HIS 369 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365O MET* 3.7 17.1 + - - +
366O LEU* 2.9 22.1 - - + +
367O VAL* 3.3 3.1 - - - -
368O GLU* 1.3 80.1 - - - +
370O GLN* 1.3 81.7 + - + +
371O ALA 2.8 15.9 + - - -
373O ASP* 5.0 5.1 + - - -
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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