Contacts of the helix formed by residues 318 - 346 (chain A) in PDB entry 6EBT
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 HIS 318 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A PRO* 3.7 11.1 - - + +
195A MET* 3.3 28.8 - - + +
196A HIS* 4.9 10.0 + - - +
314A ALA 3.5 13.9 + - - -
315A LEU 4.2 0.6 + - - -
317A ALA* 1.3 85.4 + - - +
319A ASP* 1.3 67.1 + - - +
320A ALA* 3.1 4.0 - - - +
321A LEU* 3.1 24.6 + - + +
322A VAL* 3.3 13.9 + - - +
398A GLY* 5.1 1.8 + - - -
406A ASN* 3.9 25.4 - - - +
409A LYS* 2.8 40.2 + - + +
412A MET* 3.7 23.3 - - + +
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A GLU* 4.7 8.5 + - - +
317A ALA* 3.6 14.2 - - - +
318A HIS* 1.3 78.6 + - - +
320A ALA* 1.3 56.6 + - - +
321A LEU 3.3 0.2 - - - -
322A VAL* 3.3 7.7 + - - +
323A GLU* 2.8 28.8 + - - +
398A GLY 4.2 10.9 - - - +
254B GLN* 3.1 27.5 + - - +
261B ARG* 3.4 23.2 + - - +
330B THR* 3.4 12.2 - - + +
333B CYS* 4.3 4.7 - - - +
334B SER* 2.7 31.8 + - - -
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A HIS* 4.1 11.9 - - + +
265A ALA 4.6 0.3 - - - +
268A ARG* 3.9 26.0 - - + +
269A ILE* 3.6 21.3 - - + +
313A GLU* 5.4 2.7 + - - +
318A HIS* 3.1 1.4 - - - +
319A ASP* 1.3 74.6 - - - +
321A LEU* 1.3 60.0 + - - +
323A GLU* 3.2 7.3 + - - +
324A LEU* 2.8 30.1 + - - +
261B ARG* 3.3 17.3 - - - +
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A MET* 3.9 36.6 - - + -
196A HIS* 4.1 17.0 - - + +
199A ALA* 4.4 4.7 - - + -
269A ILE* 4.0 17.7 - - + -
318A HIS* 3.1 19.9 + - + +
320A ALA* 1.3 74.7 - - - +
322A VAL* 1.3 59.6 + - - +
324A LEU* 3.7 2.5 - - + +
325A SER* 2.8 31.9 + - - -
394A VAL* 4.1 2.5 - - - -
412A MET* 4.3 20.4 - - + -
413A ILE* 4.3 21.3 - - + +
416A VAL* 3.9 27.4 - - + +
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A HIS 3.3 13.6 + - - +
319A ASP* 3.5 13.0 - - - +
321A LEU* 1.3 76.6 - - - +
323A GLU* 1.3 58.2 + - - +
325A SER* 3.7 1.4 - - - -
326A GLY* 2.9 26.7 + - - -
391A HIS* 3.7 2.6 - - + -
394A VAL* 3.9 19.3 - - + +
395A THR* 4.4 5.2 - - - +
398A GLY* 4.1 10.8 - - - -
412A MET* 3.9 16.8 - - + -
329B ASN* 3.8 19.1 - - - +
330B THR* 3.5 29.3 + - + +
333B CYS* 3.9 14.1 - - + -
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Residues in contact with GLU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ALA 3.5 2.1 - - - +
265A ALA* 3.4 29.4 - - + +
268A ARG* 2.6 38.5 + - - +
319A ASP 2.8 13.5 + - - +
320A ALA* 3.2 9.7 + - - +
322A VAL* 1.3 76.7 - - - +
324A LEU* 1.3 62.3 + - - +
326A GLY* 3.1 3.5 + - - -
327A ALA* 3.1 20.3 + - - +
261B ARG* 2.7 47.4 + - + +
264B ALA* 5.6 1.4 - - - +
330B THR* 3.6 9.6 + - - +
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Residues in contact with LEU 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ALA* 4.1 14.1 - - + -
203A VAL* 4.0 25.8 - - + -
262A ILE* 4.3 15.3 - - + -
265A ALA* 4.0 17.2 - - + +
266A MET* 4.1 17.3 - - - -
269A ILE* 4.2 16.6 - - + -
320A ALA 2.8 19.8 + - - +
321A LEU* 3.9 4.0 - - + +
323A GLU* 1.3 72.5 - - - +
325A SER* 1.3 66.0 + - - +
327A ALA* 3.1 4.3 + - + +
328A MET* 3.1 33.4 + - + +
416A VAL* 4.0 21.8 - - + -
420A ALA* 6.4 0.2 - - + -
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Residues in contact with SER 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU 2.8 22.3 + - - -
322A VAL 3.7 2.5 - - - -
324A LEU* 1.3 72.2 - - - +
326A GLY* 1.3 57.3 - - - +
328A MET* 3.2 17.0 + - - +
329A ASN* 2.7 28.2 + - - +
387A VAL* 5.2 1.2 - - - +
390A ASN 4.7 0.2 - - - -
391A HIS* 2.9 39.6 + - - +
394A VAL* 3.9 20.5 - - - +
416A VAL* 4.3 6.5 - - - +
419A SER* 5.4 3.1 + - - -
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Residues in contact with GLY 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL 2.9 13.1 + - - -
323A GLU* 3.1 4.9 + - - -
325A SER* 1.3 77.9 - - - +
327A ALA* 1.3 55.4 + - - +
329A ASN* 3.2 6.4 + - - +
330A THR* 3.0 30.7 + - - -
391A HIS* 3.4 19.3 - - - -
322B VAL 5.5 0.2 - - - +
323B GLU* 5.7 0.2 - - - -
326B GLY* 5.1 16.1 - - - -
391B HIS* 5.2 0.4 + - - -
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Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ARG* 3.6 36.6 - - + +
262A ILE* 4.0 11.6 - - + +
265A ALA* 4.0 7.6 - - + -
323A GLU 3.1 12.0 + - - +
324A LEU* 3.1 8.7 + - + +
326A GLY* 1.3 76.6 - - - +
328A MET* 1.3 57.5 + - - +
330A THR* 3.3 10.0 + - - -
331A THR* 3.0 29.6 + - - -
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Residues in contact with MET 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 3.9 20.4 - - + -
262A ILE* 4.8 2.9 - - + -
324A LEU* 3.1 19.1 + - + +
325A SER* 3.6 26.2 - - - +
327A ALA* 1.3 73.7 - - - +
329A ASN* 1.3 59.5 + - - +
331A THR* 3.3 9.2 + - - -
332A ALA* 2.9 23.7 + - - +
387A VAL* 3.5 14.7 - - + +
416A VAL* 3.5 35.0 - - + +
419A SER* 3.8 11.7 - - - -
420A ALA* 3.5 35.9 - - - -
423A LEU* 3.7 12.8 - - + +
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Residues in contact with ASN 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A SER 2.7 18.7 + - - +
326A GLY* 3.2 10.7 + - - +
328A MET* 1.3 72.8 - - - +
330A THR* 1.3 60.1 + - - +
332A ALA* 3.3 4.0 + - - +
333A CYS* 3.2 22.9 + - - -
387A VAL* 4.1 8.9 - - - +
388A MET* 3.5 27.5 - - - +
391A HIS* 3.9 23.2 - - + +
322B VAL* 3.9 6.3 - - - +
391B HIS* 3.3 16.6 + - - -
395B THR* 2.9 36.5 + - - +
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Residues in contact with THR 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ALA* 6.1 0.4 - - + -
261A ARG* 3.6 32.0 - - - +
326A GLY 3.0 14.0 + - - -
327A ALA* 3.5 9.3 - - - -
328A MET 3.3 0.2 - - - -
329A ASN* 1.3 74.5 - - - +
331A THR* 1.3 66.7 + - - +
333A CYS* 3.0 13.3 + - - +
334A SER* 3.0 13.4 + - - +
319B ASP* 3.6 31.9 - - + +
322B VAL* 3.6 15.0 + - + +
323B GLU* 3.6 22.3 + - - +
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Residues in contact with THR 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 4.0 22.7 - - + -
258A ALA* 3.6 25.0 + - + +
261A ARG* 5.6 0.2 - - - +
262A ILE* 3.7 14.1 - - + +
327A ALA 3.0 15.1 + - - -
328A MET* 3.4 11.9 - - - -
330A THR* 1.3 75.9 - - - +
332A ALA* 1.3 57.8 + - - +
334A SER* 3.1 7.8 + - - -
335A LEU* 2.8 50.3 + - + +
423A LEU* 4.3 11.0 - - + -
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Residues in contact with ALA 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A MET 2.9 14.0 + - - +
329A ASN* 3.5 9.6 - - - +
330A THR 3.1 0.2 - - - -
331A THR* 1.3 76.0 - - - +
333A CYS* 1.3 57.4 - - - +
335A LEU* 4.5 3.6 - - - +
336A MET* 2.8 32.1 + - - +
384A ALA* 3.5 37.3 - - + +
387A VAL* 3.9 14.6 - - + -
388A MET* 4.0 7.9 - - + -
423A LEU* 4.6 5.6 - - + +
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Residues in contact with CYS 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ASN 3.2 18.0 + - - -
330A THR* 3.0 9.9 + - - +
332A ALA* 1.3 77.7 - - - +
334A SER* 1.3 60.8 + - - +
336A MET* 3.4 2.1 + - - +
337A LYS* 3.2 22.0 + - - +
388A MET* 4.0 8.7 - - - -
319B ASP* 4.4 9.1 - - - +
322B VAL* 3.9 19.5 - - + -
395B THR* 3.4 42.2 - - - -
398B GLY 4.2 6.5 - - - +
399B SER* 3.9 18.3 - - - +
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Residues in contact with SER 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A GLN* 3.7 36.3 + - - +
255A VAL* 5.8 0.2 - - - -
258A ALA* 5.1 2.8 - - - +
261A ARG* 4.7 2.1 + - - -
330A THR* 3.0 12.7 + - - +
331A THR* 3.4 11.4 - - - -
333A CYS* 1.3 77.2 - - - +
335A LEU* 1.3 59.1 + - - +
337A LYS* 3.2 4.7 + - - +
338A ILE* 3.0 34.2 + - - +
319B ASP* 2.7 29.5 + - - +
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Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 4.3 7.0 - - + -
214A LEU* 3.4 31.2 - - + -
255A VAL* 4.4 5.8 - - + -
331A THR* 2.8 39.4 + - + +
332A ALA* 4.1 4.0 - - - +
334A SER* 1.3 70.8 - - - +
336A MET* 1.3 60.3 + - - +
338A ILE* 4.0 17.3 - - + +
339A ALA* 2.9 33.1 + - - +
380A MET* 3.8 35.2 - - + +
384A ALA* 5.0 1.8 - - + -
423A LEU* 3.8 17.0 - - + -
427A SER* 4.2 10.3 - - - +
430A PHE* 6.1 0.7 - - + -
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Residues in contact with MET 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ALA 2.8 19.3 + - - +
333A CYS 3.7 5.2 - - - +
334A SER 3.3 0.2 - - - -
335A LEU* 1.3 77.2 - - - +
337A LYS* 1.3 57.0 + - - +
339A ALA* 4.2 0.2 - - - +
340A ASN* 3.0 37.8 + - + +
343A ARG* 5.5 1.3 - - - -
381A THR* 3.5 48.2 - - - +
384A ALA* 3.9 12.7 - - + +
385A ALA* 3.9 14.8 - - + +
388A MET* 4.2 12.6 - - + -
399B SER* 3.4 28.0 - - - +
400B ASN* 5.6 2.5 - - - +
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Residues in contact with LYS 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A TYR* 4.0 9.2 - - + -
254A GLN* 4.1 21.0 + - - +
333A CYS 3.2 9.2 + - - +
334A SER 3.2 8.8 + - - +
336A MET* 1.3 79.5 - - - +
338A ILE* 1.3 63.6 + - - +
340A ASN* 4.0 2.3 - - - +
341A ASP* 2.6 53.0 + - - +
316B ALA* 3.4 30.7 - - - +
317B ALA* 5.1 1.8 - - + -
398B GLY 5.2 2.9 - - - +
399B SER 4.0 9.3 + - - +
401B GLY* 3.2 39.3 - - - +
402B HIS 3.5 1.6 - - - +
403B PHE 2.8 24.8 + - - +
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Residues in contact with ILE 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 5.8 0.4 - - + -
218A LEU* 4.5 9.0 - - + -
251A TYR* 3.7 51.1 - - + +
254A GLN* 3.8 14.6 - - + +
255A VAL* 3.6 31.0 - - + -
334A SER* 3.0 20.0 + - - +
335A LEU* 4.0 12.3 - - + +
337A LYS* 1.3 75.1 - - - +
339A ALA* 1.3 63.4 + - - +
341A ASP* 3.5 1.9 + - - +
342A ILE* 3.1 39.2 + - + +
430A PHE* 4.4 12.1 - - + -
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Residues in contact with ALA 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU 2.9 19.0 + - - +
338A ILE* 1.3 77.5 - - - +
340A ASN* 1.3 59.5 + - - +
342A ILE 3.4 0.5 + - - -
343A ARG* 2.8 28.8 + - - +
377A CYS* 3.5 17.5 - - - +
380A MET* 3.8 19.1 - - + -
381A THR* 3.6 20.6 - - + -
430A PHE* 4.2 15.3 - - + -
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Residues in contact with ASN 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A MET* 3.0 23.3 + - + +
337A LYS* 4.1 2.5 - - - +
339A ALA* 1.3 73.8 - - - +
341A ASP* 1.3 69.6 + - - +
343A ARG* 2.9 42.6 + - - +
344A PHE* 2.9 46.7 + - - -
381A THR* 4.1 2.2 - - + +
399B SER 6.0 0.7 - - - +
401B GLY 4.8 4.7 + - - +
402B HIS* 4.3 21.2 + - - -
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Residues in contact with ASP 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLU* 5.2 0.2 - - - +
251A TYR* 2.7 28.3 + - + +
337A LYS* 2.6 50.2 + - - +
338A ILE 3.6 3.4 - - - +
340A ASN* 1.3 78.4 + - - +
342A ILE* 1.3 53.8 + - - +
344A PHE* 3.1 3.5 + - - +
345A LEU* 2.7 40.6 + - + +
401B GLY 4.2 1.4 - - - +
402B HIS* 3.9 3.5 - - - -
403B PHE* 2.9 44.8 + - + -
----------------------------------------------------------
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Residues in contact with ILE 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LEU* 4.6 5.4 - - + -
248A PHE* 4.5 13.2 - - + -
251A TYR* 4.5 12.3 - - + +
338A ILE* 3.1 29.8 + - + +
339A ALA 3.8 3.1 - - - +
341A ASP* 1.3 75.3 - - - +
343A ARG* 1.3 64.1 + - - +
345A LEU* 3.9 7.7 - - + +
346A GLY* 3.0 19.9 + - - -
356A LEU* 4.3 10.9 - - + +
358A LEU* 4.0 24.6 - - + +
377A CYS* 3.9 16.8 - - - -
430A PHE* 3.9 19.7 - - + -
434A CYS* 4.4 3.1 - - - -
435A VAL* 4.8 0.4 - - + -
438A ILE* 4.0 23.1 - - + -
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Residues in contact with ARG 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A MET* 5.5 1.2 - - - -
339A ALA 2.8 14.8 + - - +
340A ASN* 2.9 35.4 + - - +
341A ASP 3.1 0.2 - - - -
342A ILE* 1.3 79.0 - - - +
344A PHE* 1.3 74.9 + - - +
346A GLY* 3.3 2.6 + - - -
347A SER* 3.3 16.8 + - - -
374A PRO* 3.5 33.9 - - + +
377A CYS* 3.8 12.5 - - + -
378A GLU* 3.6 30.3 + - - +
381A THR* 3.4 37.1 + - - +
----------------------------------------------------------
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Residues in contact with PHE 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ASN* 2.9 52.6 + - - +
341A ASP* 3.8 2.5 - - - +
343A ARG* 1.3 87.5 - - - +
345A LEU* 1.3 64.0 + - - +
347A SER* 2.6 33.5 + - - -
353A LEU* 3.5 15.4 - - + +
402B HIS* 6.3 0.9 - + - -
403B PHE* 3.9 24.9 - + + -
----------------------------------------------------------
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Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ARG* 3.7 20.0 - - - +
244A LEU* 4.8 3.4 - - + -
247A GLU* 3.3 26.9 - - - +
248A PHE* 5.0 3.6 - - + -
251A TYR* 4.0 14.4 - - + +
341A ASP* 2.7 26.4 + - + +
342A ILE* 4.0 1.1 - - - +
344A PHE* 1.3 73.6 - - - +
346A GLY* 1.3 58.3 + - - +
353A LEU* 4.3 4.3 - - + -
354A GLY 3.5 2.1 + - - -
355A GLU* 2.9 54.2 + - + +
356A LEU* 3.0 34.4 + - + -
403B PHE* 3.9 17.7 - - + -
----------------------------------------------------------
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Residues in contact with GLY 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ILE 3.0 14.8 + - - -
343A ARG 3.7 6.3 - - - -
344A PHE 3.2 0.2 - - - -
345A LEU* 1.3 75.4 - - - +
347A SER* 1.3 63.8 + - - +
348A GLY* 3.6 1.9 + - - -
354A GLY* 4.7 0.7 - - - -
356A LEU* 3.4 26.7 - - - +
358A LEU* 4.5 13.5 - - - +
372A VAL 5.0 7.8 - - - +
374A PRO* 6.5 0.2 - - - -
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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