Contacts of the helix formed by residues 342 - 376 (chain A) in PDB entry 3GZN
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ASP* 5.2 1.9 - - - +
218A HIS* 3.3 29.8 + - + +
341A ALA* 1.3 75.4 - - - +
343A SER* 1.3 66.6 + - - +
344A GLY* 3.5 6.2 + - - -
345A LYS* 3.1 49.2 + - - +
346A TYR* 3.1 19.3 + - - +
242B MET* 3.8 18.2 - - + -
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Residues in contact with SER 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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341A ALA 4.0 0.8 + - - -
342A ASP* 1.3 73.8 - - - +
344A GLY* 1.3 53.8 + - - +
346A TYR* 3.2 3.9 + - - +
347A ILE* 2.8 40.4 + - - +
241B SER 4.9 0.2 + - - -
242B MET* 3.8 6.0 - - - +
243B PRO* 3.1 35.2 + - - +
244B ARG* 5.0 0.2 - - - -
292B TYR* 3.2 44.2 - - - -
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Residues in contact with GLY 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ASP* 3.4 6.6 + - - -
343A SER* 1.3 78.1 - - - +
345A LYS* 1.3 56.9 + - - +
347A ILE* 3.8 5.5 - - - +
348A LYS* 2.9 39.2 + - - +
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Residues in contact with LYS 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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202A HIS* 4.5 0.7 - - - -
206A TYR* 3.3 43.6 + - + +
211A MET* 4.2 4.7 - - - -
215A ASP* 3.3 43.6 + - - +
218A HIS 3.7 15.9 - - - +
219A THR* 4.2 2.0 - - - -
220A PRO* 3.9 14.0 - - + +
342A ASP* 3.1 34.6 + - - +
344A GLY* 1.3 75.3 - - - +
346A TYR* 1.3 60.9 + - - +
348A LYS* 4.2 4.2 - - - +
349A LEU* 3.3 22.7 + - - +
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Residues in contact with TYR 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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220A PRO* 5.2 3.1 - - + -
336A ILE* 3.3 34.4 + - + +
337A PRO 2.9 21.7 + - - -
338A ASP* 3.5 7.7 - - - -
339A MET* 3.6 36.6 - - + -
341A ALA* 4.2 8.2 - - + +
342A ASP 3.1 11.9 + - - +
343A SER 3.6 6.5 - - - +
345A LYS* 1.3 74.5 - - - +
347A ILE* 1.3 60.0 + - + +
349A LEU* 3.0 7.8 + - + +
350A GLN* 2.7 51.2 + - - +
244B ARG* 3.2 58.3 - - + -
245B LEU* 4.1 7.3 - - + +
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Residues in contact with ILE 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A SER* 2.8 25.5 + - - +
344A GLY* 3.9 4.9 - - - +
346A TYR* 1.3 74.4 - - + +
348A LYS* 1.3 60.8 + - + +
350A GLN* 3.2 27.2 + - - +
351A ASN* 2.9 44.7 + - - +
243B PRO 5.6 0.7 - - - +
244B ARG* 4.6 8.3 - - - +
292B TYR 3.3 17.7 - - - +
293B ASN* 3.4 43.3 - - + +
294B ILE* 3.9 17.9 - - + -
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Residues in contact with LYS 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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202A HIS* 3.8 18.8 - - + +
344A GLY* 2.9 22.4 + - - +
345A LYS* 4.3 3.8 - - - +
347A ILE* 1.3 79.6 - - + +
349A LEU* 1.3 59.8 + - - +
351A ASN* 3.5 7.4 + - - +
352A VAL* 3.1 29.1 + - - +
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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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199A LEU* 4.6 5.6 - - + -
202A HIS* 3.9 26.6 + - + +
203A PHE* 4.5 17.3 - - + -
220A PRO* 3.8 29.4 - - + -
222A ILE* 3.9 28.0 - - + -
223A VAL* 4.5 2.5 - - + -
336A ILE* 4.6 8.1 - - + -
339A MET* 4.5 3.6 - - - -
345A LYS 3.3 17.4 + - - +
346A TYR* 3.0 6.5 + - + +
348A LYS* 1.3 76.1 - - - +
350A GLN* 1.3 65.3 - - - +
352A VAL* 3.4 10.2 + - + +
353A TYR* 3.4 34.3 + - + -
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Residues in contact with GLN 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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334A GLY 4.6 5.0 - - - +
335A THR* 6.1 0.4 - - - -
336A ILE* 3.8 29.7 + - + +
346A TYR* 2.7 36.1 + - + +
347A ILE* 3.2 32.7 + - - +
349A LEU* 1.3 73.8 - - - +
351A ASN* 1.3 59.5 + - - +
353A TYR* 3.3 5.5 + - - +
354A ARG* 2.7 40.8 + - + +
244B ARG 4.7 3.8 + - - +
245B LEU* 5.1 5.7 - - - +
293B ASN 5.3 0.6 + - - -
294B ILE* 5.9 3.8 - - - +
295B ARG* 5.1 12.8 + - - +
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Residues in contact with ASN 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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347A ILE* 2.9 34.8 + - - +
348A LYS* 4.0 7.4 - - - +
349A LEU 3.2 0.4 - - - -
350A GLN* 1.3 82.9 + - - +
352A VAL* 1.3 60.1 + - - +
354A ARG* 3.9 6.8 - - - -
355A GLU* 3.0 45.7 + - + +
293B ASN* 5.8 1.4 + - - +
295B ARG* 3.3 27.2 + - - +
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Residues in contact with VAL 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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196A PHE* 3.5 19.6 - - + -
198A GLU* 3.4 37.2 - - + +
199A LEU* 3.8 15.3 - - + -
202A HIS* 3.9 26.7 - - + -
348A LYS 3.1 18.3 + - - +
349A LEU* 3.8 7.4 - - + +
350A GLN 3.3 0.4 - - - -
351A ASN* 1.3 78.3 - - + +
353A TYR* 1.3 60.6 + - - +
355A GLU* 4.6 1.4 - - - +
356A LYS* 3.5 13.5 + - - +
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Residues in contact with TYR 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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189A ASP 3.8 19.7 - - - -
190A LEU* 2.5 43.4 + - + +
191A ARG* 5.1 0.4 - - + -
196A PHE* 4.1 22.2 - + - -
199A LEU* 3.9 21.6 - - + +
222A ILE* 3.8 17.4 - - + +
332A VAL* 3.9 11.7 - - + +
334A GLY* 3.7 21.8 - - - +
335A THR 5.2 1.3 - - - -
336A ILE* 3.4 30.5 - - + -
349A LEU* 3.4 34.8 + - + -
350A GLN* 3.3 7.7 + - - +
351A ASN 3.3 0.4 - - - -
352A VAL* 1.3 78.0 - - - +
354A ARG* 1.3 66.0 + - - +
355A GLU 3.4 0.2 + - - -
356A LYS* 3.5 3.8 + - - +
357A ALA* 3.3 14.4 + - - +
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Residues in contact with ARG 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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334A GLY* 3.8 17.4 + - - +
350A GLN* 2.7 26.0 + - + +
351A ASN* 3.8 9.6 - - - +
353A TYR* 1.3 73.3 - - - +
355A GLU* 1.3 72.7 + - - +
357A ALA* 3.2 6.9 + - - +
358A LYS* 3.0 60.7 + - - +
388A LYS* 5.1 12.3 - - - +
295B ARG* 3.0 54.5 - - - +
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Residues in contact with GLU 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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351A ASN* 3.0 32.1 + - + +
352A VAL* 4.7 1.8 - - - +
354A ARG* 1.3 91.0 - - - +
356A LYS* 1.3 66.6 + - - +
358A LYS* 3.2 27.0 + - - +
359A LYS* 2.9 30.5 + - - +
295B ARG* 5.5 0.7 + - - -
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Residues in contact with LYS 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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196A PHE* 3.6 43.4 - - + +
197A PRO* 5.9 1.6 - - - +
198A GLU* 4.2 20.3 + - + +
325A GLU 5.1 7.9 + - - -
332A VAL* 3.7 22.7 - - + -
352A VAL 3.5 18.5 + - - +
353A TYR 3.5 3.5 + - - +
354A ARG 3.4 0.4 - - - -
355A GLU* 1.3 77.1 - - - +
357A ALA* 1.3 57.5 + - - +
359A LYS* 3.3 14.8 + - + +
360A ASP* 2.8 52.2 + - - +
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Residues in contact with ALA 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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332A VAL* 3.2 29.2 - - - +
333A ARG 4.0 3.4 - - - +
334A GLY* 3.8 13.7 - - - -
353A TYR 3.3 8.7 + - - +
354A ARG 3.2 10.4 + - - +
355A GLU 3.1 0.6 - - - -
356A LYS* 1.3 75.1 - - - +
358A LYS* 1.3 52.2 + - - +
359A LYS 2.8 5.3 + - - -
360A ASP* 2.8 7.8 + - - +
361A ALA* 2.7 36.4 + - - +
391A CYS* 5.6 2.4 - - + +
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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 ARG* 3.0 55.8 + - - +
355A GLU* 3.5 30.1 + - - +
357A ALA* 1.3 73.9 - - - +
359A LYS* 1.3 57.1 + - - +
361A ALA* 4.2 7.0 - - - +
362A ALA* 3.7 18.9 + - - +
388A LYS* 5.1 15.4 - - - +
295B ARG* 5.9 0.6 - - - +
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Residues in contact with LYS 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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198A GLU* 3.3 28.9 - - - +
355A GLU* 2.9 19.1 + - - +
356A LYS* 3.4 16.8 - - + +
357A ALA 2.8 0.6 - - - -
358A LYS* 1.3 78.5 - - - +
360A ASP* 1.3 61.5 + - - +
361A ALA 3.3 1.6 - - - -
362A ALA* 3.8 6.1 + - - +
363A ALA* 3.2 24.1 + - - +
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Residues in contact with ASP 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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191A ARG* 4.8 1.6 + - - -
321A PHE* 3.4 29.1 - - + -
325A GLU* 5.7 1.2 - - - +
331A PRO* 3.9 14.4 - - + +
332A VAL* 3.5 19.1 + - - +
356A LYS* 2.8 52.0 + - - +
357A ALA* 2.8 6.8 + - - +
359A LYS* 1.3 77.7 - - - +
361A ALA* 1.3 59.4 + - - +
363A ALA* 3.6 5.5 - - - +
364A VAL* 3.1 31.2 + - - +
391A CYS* 4.7 1.8 - - - -
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Residues in contact with ALA 361 (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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357A ALA 2.7 16.0 + - - +
358A LYS* 4.3 7.6 - - - +
360A ASP* 1.3 73.7 - - - +
362A ALA* 1.3 51.1 + - - +
363A ALA 2.9 4.0 - - - -
364A VAL* 2.7 24.6 + - - +
365A GLY 2.7 15.6 + - - -
387A LEU* 3.4 18.4 - - + +
388A LYS* 5.4 6.7 - - + +
391A CYS* 3.5 30.2 - - + +
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Residues in contact with ALA 362 (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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358A LYS 3.7 17.0 + - - +
359A LYS* 4.0 6.7 - - - +
361A ALA* 1.3 77.2 - - - +
363A ALA* 1.3 59.7 + - - +
365A GLY* 3.6 4.6 + - - +
366A ASN* 3.4 28.3 + - - +
387A LEU* 4.6 3.3 - - - +
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Residues in contact with ALA 363 (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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321A PHE* 3.7 14.1 - - + -
325A GLU* 3.6 23.2 - - + +
359A LYS 3.2 19.4 + - - +
360A ASP* 3.4 9.6 - - - +
361A ALA 2.9 0.6 - - - -
362A ALA* 1.3 76.1 - - - +
364A VAL* 1.3 62.3 + - - +
366A ASN* 3.4 13.7 + - - +
367A HIS* 3.0 24.7 + - - -
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Residues in contact with VAL 364 (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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317A ALA* 3.3 34.3 - - + +
318A LEU* 4.3 5.2 - - + -
321A PHE* 3.5 21.3 - - + -
331A PRO* 4.2 9.0 - - + -
360A ASP 3.1 15.1 + - - +
361A ALA 2.7 12.8 + - - +
363A ALA* 1.3 67.6 - - - +
365A GLY* 1.3 52.8 + - - +
366A ASN 3.1 4.3 - - - -
367A HIS* 2.8 26.7 + - - +
368A VAL* 2.9 11.5 + - - +
387A LEU* 4.0 17.3 - - + -
390A LEU* 4.5 8.5 - - + -
391A CYS* 4.0 18.6 - - - -
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Residues in contact with GLY 365 (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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361A ALA 2.7 15.5 + - - -
362A ALA* 3.9 3.8 - - - -
363A ALA 3.3 0.2 - - - -
364A VAL* 1.3 72.4 - - - +
366A ASN* 1.3 62.8 + - - +
368A VAL* 3.4 23.0 - - - +
369A ALA* 3.6 8.8 + - - +
379A PRO 5.8 0.2 - - - +
387A LEU* 3.6 21.6 - - - +
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Residues in contact with ASN 366 (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 GLU* 5.5 2.0 - - - +
362A ALA 3.4 16.0 + - - +
363A ALA* 3.5 12.2 - - - +
364A VAL 3.1 0.6 - - - -
365A GLY* 1.3 77.4 + - - +
367A HIS* 1.3 65.6 + - + +
368A VAL 3.1 2.0 + - - -
369A ALA* 3.5 6.5 + - - +
370A LYS* 3.3 22.3 + - - +
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Residues in contact with HIS 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ALA* 4.0 22.4 - - - +
320A GLU* 3.2 45.0 + - + +
321A PHE* 4.5 7.3 - + - -
324A LYS* 4.3 6.3 - - + -
325A GLU* 3.0 29.1 + - - -
363A ALA 3.0 25.8 - - - -
364A VAL* 2.8 10.1 + - - +
366A ASN* 1.3 76.4 - - + +
368A VAL* 1.3 64.8 + - - +
370A LYS* 3.7 8.7 + - - +
371A LEU* 3.3 27.0 + - - +
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Residues in contact with VAL 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ILE* 4.8 6.4 - - + +
314A LEU* 4.3 10.1 - - + -
317A ALA* 3.9 17.3 - - + -
364A VAL 2.9 15.8 + - - +
365A GLY* 3.4 18.4 - - - +
367A HIS* 1.3 75.8 - - - +
369A ALA* 1.3 65.0 + - - +
371A LEU* 3.1 8.3 + - - +
372A LEU* 3.1 42.7 + - + +
379A PRO 4.7 8.3 - - - +
382A ILE* 4.6 19.7 - - + +
387A LEU* 4.0 19.1 - - + -
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Residues in contact with ALA 369 (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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365A GLY 3.6 8.1 + - - +
366A ASN* 3.5 9.3 + - - +
368A VAL* 1.3 80.7 - - + +
370A LYS* 1.3 57.1 + - - +
371A LEU 3.2 0.2 - - - -
372A LEU* 3.2 9.0 + - - +
373A GLN* 3.0 28.1 + - - +
379A PRO* 3.8 26.8 - - + +
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Residues in contact with LYS 370 (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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366A ASN 3.3 15.7 + - - +
367A HIS* 4.1 9.6 - - - +
368A VAL 3.2 1.0 - - - -
369A ALA* 1.3 76.6 - - - +
371A LEU* 1.3 62.2 + - + +
373A GLN* 4.0 14.4 - - - +
374A SER* 4.4 4.9 + - - -
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Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ILE* 4.6 20.6 - - + +
313A ILE* 3.9 25.6 - - + +
316A ARG* 3.7 46.0 - - + +
317A ALA* 3.9 9.9 - - + +
320A GLU* 5.0 9.2 - - + -
367A HIS 3.3 17.7 + - - +
368A VAL 3.1 4.9 + - - +
370A LYS* 1.3 77.3 - - + +
372A LEU* 1.3 59.1 + - - +
373A GLN 3.1 4.9 - - - -
374A SER* 3.2 10.5 + - - +
375A ILE* 2.9 27.3 + - - +
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Residues in contact with LEU 372 (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 ILE* 4.1 31.4 - - + -
368A VAL* 3.1 31.9 + - + +
369A ALA* 3.2 8.5 + - - +
371A LEU* 1.3 73.8 - - - +
373A GLN* 1.3 55.0 + - - +
375A ILE* 4.0 4.7 - - + -
376A GLY* 2.8 24.6 + - - -
377A GLN* 2.9 43.3 + - + +
378A ALA 3.5 23.1 - - - +
379A PRO* 3.6 16.2 - - + -
381A SER* 3.9 9.2 - - - +
382A ILE* 4.2 12.3 - - + -
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Residues in contact with GLN 373 (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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369A ALA 3.0 14.1 + - - +
370A LYS* 4.0 11.2 - - - +
371A LEU 3.1 0.2 - - - -
372A LEU* 1.3 75.0 - - - +
374A SER* 1.3 66.0 + - - +
376A GLY* 3.0 14.3 + - - -
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Residues in contact with SER 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ILE* 5.5 8.3 - - - -
306A LYS* 5.6 1.6 - - - +
370A LYS 4.4 3.6 + - - -
371A LEU* 3.2 14.1 + - - -
373A GLN* 1.3 78.2 - - - +
375A ILE* 1.3 60.5 + - - +
376A GLY* 3.4 0.7 + - - -
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Residues in contact with ILE 375 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ILE* 5.2 3.3 - - + +
305A THR 4.4 15.3 - - - +
306A LYS* 4.2 20.5 - - - +
313A ILE* 5.0 8.5 - - + -
371A LEU 2.9 15.9 + - - +
372A LEU* 4.0 12.1 - - + -
374A SER* 1.3 76.2 - - - +
376A GLY* 1.3 62.2 + - - +
377A GLN* 3.7 32.2 + - - +
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Residues in contact with GLY 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LEU 2.8 10.8 + - - -
373A GLN* 3.0 12.5 + - - -
374A SER 3.2 0.9 - - - -
375A ILE* 1.3 79.5 - - - +
377A GLN* 1.3 59.6 + - - +
----------------------------------------------------------
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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