Contacts of the helix formed by residues 337 - 360 (chain A) in PDB entry 4JYH
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 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A LEU* 5.4 1.3 - - + -
246A THR* 2.8 33.5 + - + +
249A ASP* 2.8 18.3 + - - +
336A GLU* 1.3 84.3 - - + +
338A PRO* 1.3 65.9 - - - +
339A THR 3.2 2.9 - - - +
340A LYS* 2.7 51.8 + - + +
341A VAL* 3.2 23.6 + - + +
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Residues in contact with PRO 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A GLY* 3.8 23.9 - - - +
332A ARG 5.7 0.4 - - - +
335A LEU* 3.5 28.2 - - + +
336A GLU 3.4 9.4 - - - +
337A GLU* 1.3 88.7 - - - +
339A THR* 1.3 54.0 + - - +
341A VAL* 3.3 4.0 + - + +
342A ASP* 2.8 36.2 + - - +
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Residues in contact with THR 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A GLU* 3.2 1.2 - - - -
338A PRO* 1.3 78.0 - - - +
340A LYS* 1.3 61.3 - - - +
342A ASP* 3.1 8.2 + - + +
343A LYS* 2.9 31.4 + - + +
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Residues in contact with LYS 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A GLY 3.8 19.3 + - - +
245A LEU* 3.7 21.5 - - + -
337A GLU* 2.7 46.3 + - + +
339A THR* 1.3 80.6 - - - +
341A VAL* 1.3 63.3 + - - +
343A LYS* 3.4 6.3 + - - +
344A LEU* 3.1 25.7 + - + +
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Residues in contact with VAL 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A LEU* 3.7 32.5 - - + -
249A ASP* 4.5 10.5 - - + +
253A LEU* 4.1 12.8 - - + -
328A ILE* 3.3 10.5 - - + +
329A CYS 3.5 40.2 - - - +
330A GLY* 3.6 2.7 - - - +
335A LEU* 4.5 8.1 - - + -
337A GLU 3.2 13.3 + - - +
338A PRO* 3.5 8.1 - - + +
340A LYS* 1.3 75.5 - - - +
342A ASP* 1.3 62.3 + - - +
344A LEU* 3.3 9.9 - - - +
345A GLN* 3.2 16.8 + - - +
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Residues in contact with ASP 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A GLY* 4.2 17.8 + - - +
331A ASP* 4.3 10.9 - - - +
338A PRO 2.8 17.5 + - - +
339A THR* 3.4 11.2 - - + +
340A LYS 3.1 0.4 - - - -
341A VAL* 1.3 73.3 - - - +
343A LYS* 1.3 59.8 - - - +
344A LEU 3.0 4.7 - - - -
345A GLN* 3.1 24.9 + - - +
346A GLU* 3.4 20.6 + - - +
373B LYS* 5.7 1.2 + - - -
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Residues in contact with LYS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A THR* 2.9 19.0 + - + +
340A LYS* 3.9 6.5 - - - +
342A ASP* 1.3 76.0 - - - +
344A LEU* 1.3 56.8 + - - +
345A GLN 3.3 0.2 - - - -
346A GLU* 3.5 20.7 + - - +
347A PRO* 3.1 23.6 - - - +
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A PRO* 3.7 18.8 - - + +
241A GLY* 3.7 33.4 - - - +
242A PHE* 4.3 2.2 - - - +
245A LEU* 4.0 23.3 - - + -
328A ILE* 3.8 17.7 - - + -
340A LYS* 3.1 12.7 + - + +
341A VAL 3.3 11.9 - - - +
342A ASP 3.0 0.2 - - - -
343A LYS* 1.3 77.7 - - - +
345A GLN* 1.3 62.5 + - - +
346A GLU 3.3 0.2 - - - -
347A PRO* 3.4 14.7 - - + +
348A LEU* 3.9 12.5 - - - +
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Residues in contact with GLN 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ILE* 3.3 31.0 + - + +
328A ILE* 3.1 32.0 + - - +
329A CYS* 3.9 15.1 - - - +
330A GLY 4.8 2.4 + - - +
341A VAL 3.2 5.4 + - - +
342A ASP* 3.1 19.5 + - - +
344A LEU* 1.3 79.3 - - - +
346A GLU* 1.3 63.4 + - - +
348A LEU* 3.0 20.8 + - + +
349A LEU* 3.2 34.8 + - + +
369B LYS* 5.9 1.2 - - - -
372B MET* 4.4 12.3 - - - +
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Residues in contact with GLU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A ASP* 3.4 21.3 + - - +
343A LYS* 3.6 18.5 - - - +
345A GLN* 1.3 77.5 - - + +
347A PRO* 1.3 70.7 - - + +
349A LEU* 3.1 17.3 + - + +
350A GLU* 3.1 20.3 + - - +
365B HIS* 4.6 25.2 - - + +
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Residues in contact with PRO 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A MET* 5.2 11.7 - - + -
177A LEU* 4.2 13.8 - - + +
180A LEU* 3.7 18.9 - - + +
343A LYS 3.1 18.4 - - - +
344A LEU* 3.4 17.3 - - + +
346A GLU* 1.3 92.4 - - + +
348A LEU* 1.3 54.7 + - + +
350A GLU* 3.2 9.2 + - + +
351A ALA* 2.9 29.1 + - - +
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Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 3.8 18.8 - - + -
184A ILE* 3.3 34.8 - - + -
239A LEU* 5.9 0.7 - - + -
240A PRO* 6.0 0.4 - - + -
321A LEU* 4.2 6.5 - - + +
324A ALA* 3.5 36.1 - - + +
325A ILE* 3.9 17.7 - - + +
328A ILE* 3.9 20.2 - - + -
344A LEU 3.9 13.0 - - - +
345A GLN* 3.0 11.1 + - - +
347A PRO* 1.3 77.6 - - + +
349A LEU* 1.3 57.4 + - - +
351A ALA* 3.1 4.9 + - - +
352A LEU* 2.9 31.4 + - - +
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ILE* 3.7 26.7 - - + -
345A GLN* 3.2 34.3 + - + +
346A GLU* 3.1 16.9 + - + +
348A LEU* 1.3 79.2 - - - +
350A GLU* 1.3 62.8 + - - +
352A LEU* 3.7 1.5 + - - -
353A LYS* 3.2 22.0 + - - +
367A PHE* 3.7 10.1 - - + -
371A LEU* 3.9 11.0 - - + -
365B HIS* 5.6 5.6 - - + +
368B PRO* 4.0 31.1 - - + +
369B LYS* 4.7 9.4 - - + +
372B MET* 3.8 26.2 - - - -
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Residues in contact with GLU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A MET* 6.0 1.1 - - + -
177A LEU* 3.4 24.2 - - + -
346A GLU 3.1 10.7 + - - +
347A PRO* 3.5 10.3 - - + +
348A LEU 3.1 0.6 - - - -
349A LEU* 1.3 76.2 - - - +
351A ALA* 1.3 60.1 + - - +
353A LYS* 2.9 42.8 + - - +
354A ILE* 2.9 44.2 + - + +
357A ARG* 5.5 0.7 + - - -
364B PRO 5.6 0.7 - - - +
365B HIS* 5.6 6.8 - - - +
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Residues in contact with ALA 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LEU* 4.5 12.7 - - + +
180A LEU* 4.1 11.7 - - + -
181A THR* 3.5 22.1 + - - +
321A LEU* 3.9 17.5 - - + -
347A PRO 2.9 14.0 + - - +
348A LEU 3.1 7.4 + - - +
350A GLU* 1.3 77.0 - - - +
352A LEU* 1.3 57.7 + - - +
354A ILE* 3.3 5.4 + - - +
355A TYR* 2.8 33.4 + - - +
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A GLU* 4.1 22.0 - - + +
321A LEU* 3.7 29.3 - - + +
322A LEU* 4.0 13.0 - - + +
325A ILE* 3.6 25.4 - - + -
348A LEU 2.9 16.0 + - - +
349A LEU* 3.9 5.8 - - - +
351A ALA* 1.3 76.3 - - - +
353A LYS* 1.3 57.2 + - - +
355A TYR* 3.9 1.1 - - + +
356A ILE* 2.8 60.5 + - + +
367A PHE* 4.2 6.1 - - + -
370A ILE* 4.7 3.8 - - + -
371A LEU* 3.8 22.2 - - + -
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Residues in contact with LYS 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A LEU 3.2 12.1 + - - +
350A GLU* 2.9 44.3 + - - +
352A LEU* 1.3 79.2 - - - +
354A ILE* 1.3 62.2 + - - +
356A ILE* 3.9 2.1 - - - +
357A ARG* 3.2 47.9 + - - +
367A PHE* 3.4 42.4 - - + +
353B LYS* 4.4 21.6 - - - +
364B PRO 5.0 8.5 + - - -
365B HIS* 6.2 0.4 - - - +
368B PRO* 5.6 7.7 - - + +
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Residues in contact with ILE 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A THR* 5.9 4.5 - - - -
177A LEU* 3.4 37.5 - - + -
178A ASP* 5.4 7.9 - - - +
350A GLU* 2.9 34.5 + - + +
351A ALA* 3.8 4.5 - - - +
353A LYS* 1.3 72.6 - - - +
355A TYR* 1.3 58.8 + - - +
357A ARG* 3.3 27.3 + - - +
358A LYS* 2.9 31.8 + - + +
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Residues in contact with TYR 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A THR* 4.0 14.6 - - + +
315A ASP* 2.5 32.6 + - - -
317A THR* 3.6 32.5 + - + -
318A GLU* 3.8 16.2 - - + -
321A LEU* 4.6 7.2 - - + -
351A ALA 2.8 22.4 + - - +
352A LEU 3.9 2.2 - - - +
354A ILE* 1.3 72.4 - - - +
356A ILE* 1.3 67.4 + - - +
358A LYS* 2.9 11.0 + - + +
359A ARG* 2.8 54.6 + - + +
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Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A GLU* 4.3 14.1 - - + +
352A LEU* 2.8 54.7 + - + +
353A LYS 3.9 3.6 - - - +
355A TYR* 1.3 73.1 - - - +
357A ARG* 1.3 57.7 + - - +
359A ARG* 4.0 1.3 - - - +
360A ARG* 3.1 44.7 + - - +
363A LYS 5.6 0.2 - - - +
366A MET* 3.8 6.5 - - + -
367A PHE* 3.7 43.1 - - + +
370A ILE* 3.6 32.5 - - + -
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Residues in contact with ARG 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A GLU* 5.5 0.6 + - - -
353A LYS* 3.2 40.5 + - - +
354A ILE* 3.6 31.3 + - - +
355A TYR 3.0 0.4 - - - -
356A ILE* 1.3 78.4 - - + +
358A LYS* 1.3 64.7 + - - +
359A ARG 3.3 0.2 - - - -
360A ARG 4.4 3.6 - - - +
361A PRO* 3.3 30.3 - - + +
364A PRO* 6.4 2.2 - - + -
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Residues in contact with LYS 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A ILE* 2.9 19.3 + - + +
355A TYR* 2.9 17.2 + - + +
357A ARG* 1.3 78.9 - - - +
359A ARG* 1.3 63.3 + - + +
361A PRO* 3.7 7.1 - - - +
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Residues in contact with ARG 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A GLU* 3.5 30.3 + - - +
315A ASP* 3.7 21.9 + - - +
318A GLU* 3.4 15.2 + - - +
355A TYR* 2.8 56.3 + - + +
356A ILE 4.0 3.6 - - - +
358A LYS* 1.3 79.4 - - + +
360A ARG* 1.3 75.9 + - + +
361A PRO* 3.0 10.5 - - - +
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Residues in contact with ARG 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A LEU 3.6 20.0 + - - -
313A GLU* 4.7 11.9 + - - +
318A GLU* 3.4 20.6 + - - -
356A ILE* 3.1 20.9 + - - +
357A ARG* 3.7 6.5 - - - +
359A ARG* 1.3 96.8 - - + +
361A PRO* 1.3 55.7 - - - +
362A SER* 2.9 19.3 + - - +
363A LYS* 3.0 39.4 - - - +
364A PRO* 4.9 0.9 - - - +
366A MET* 3.6 38.1 - - - +
370A ILE* 2.9 32.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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