Contacts of the helix formed by residues 334 - 368 (chain A) in PDB entry 3X0Y
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 THR 334 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A SER 4.6 3.6 - - - -
332A ALA 4.0 8.7 - - - +
333A LEU* 1.3 80.7 - - - +
335A PRO* 1.3 70.7 - - + +
336A GLU* 3.7 10.4 + - - +
337A ASP* 3.0 34.1 + - - +
338A ARG* 3.0 28.4 + - - +
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Residues in contact with PRO 335 (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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243A GLN 4.3 8.7 - - - +
244A SER* 3.8 30.5 + - - +
333A LEU 4.8 0.9 - - - +
334A THR* 1.3 90.5 - - + +
336A GLU* 1.3 55.3 + - - +
338A ARG* 3.9 0.7 - - - +
339A GLY* 2.9 27.0 + - - -
410A TYR* 4.2 9.4 - - + +
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Residues in contact with GLU 336 (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 THR* 3.1 10.7 + - - +
335A PRO* 1.3 77.4 - - - +
337A ASP* 1.3 64.5 + - - +
339A GLY* 3.9 0.2 - - - -
340A GLU* 2.8 43.0 + - + +
410A TYR* 3.5 29.3 + - + +
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Residues in contact with ASP 337 (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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322A LEU* 5.9 0.2 - - - +
326A VAL* 4.0 20.5 - - + +
329A LYS* 2.7 35.8 + - + +
332A ALA 4.8 0.5 - - - +
333A LEU* 4.1 6.0 - - + -
334A THR* 3.0 38.1 + - - +
336A GLU* 1.3 81.8 - - - +
338A ARG* 1.3 58.6 + - - +
340A GLU* 3.9 4.2 - - - +
341A LEU* 2.9 30.2 + - - +
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Residues in contact with ARG 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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241A PHE* 5.1 0.2 - - - -
244A SER* 4.3 19.7 - - - +
248A SER* 2.8 48.1 + - - +
249A LEU* 4.5 12.6 - - + -
251A ALA* 3.8 2.0 - - - +
252A PRO* 3.8 16.1 - - + +
326A VAL* 5.1 3.5 - - - +
333A LEU* 4.7 6.5 - - + +
334A THR 3.0 15.1 + - - +
335A PRO 3.9 3.6 - - - +
337A ASP* 1.3 77.3 - - - +
339A GLY* 1.3 60.2 + - - +
341A LEU* 3.2 10.0 + - - +
342A MET* 2.9 38.2 + - - +
411A PRO* 4.2 5.9 + - - +
413A PRO* 3.8 25.4 - - - +
414A GLY 4.1 3.4 + - - -
417A SER* 2.7 43.4 + - - -
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Residues in contact with GLY 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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335A PRO 2.9 15.4 + - - -
338A ARG* 1.3 82.6 - - - +
340A GLU* 1.3 56.6 + - - +
342A MET* 3.4 3.5 + - - +
343A VAL* 3.0 32.9 + - - +
410A TYR* 3.3 30.9 - - - -
411A PRO* 3.9 5.8 - - - +
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Residues in contact with GLU 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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322A LEU* 4.8 4.9 - - + -
336A GLU* 2.8 38.1 + - + +
337A ASP* 3.9 4.5 - - - +
339A GLY* 1.3 69.9 - - - +
341A LEU* 1.3 65.4 + - - +
343A VAL* 3.3 7.2 + - - +
344A LYS* 3.1 33.1 + - + +
404A HIS* 3.1 28.3 + - - -
410A TYR* 2.8 23.9 + - - +
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Residues in contact with LEU 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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249A LEU* 3.7 30.3 - - + -
252A PRO* 3.9 14.4 - - + -
319A ALA 4.1 7.0 - - - +
322A LEU* 4.0 18.7 - - + +
323A LEU* 3.7 46.2 - - + +
326A VAL* 4.0 19.1 - - + -
337A ASP 2.9 19.6 + - - +
338A ARG* 3.4 4.3 - - - +
340A GLU* 1.3 76.3 - - - +
342A MET* 1.3 61.7 + - - +
344A LYS* 3.2 4.8 + - + +
345A VAL* 3.1 29.3 + - + +
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Residues in contact with MET 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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251A ALA* 3.9 7.0 - - - -
252A PRO* 3.6 33.9 - - + -
255A GLN* 4.1 18.2 - - + -
338A ARG* 2.9 25.8 + - - +
339A GLY 3.8 5.4 - - - +
340A GLU 3.3 0.4 - - - -
341A LEU* 1.3 75.1 - - - +
343A VAL* 1.3 57.3 + - - +
345A VAL* 3.4 13.2 + - + -
346A SER* 2.6 57.8 + - - +
397A LYS* 4.4 2.9 - - - -
411A PRO* 4.0 13.7 - - + -
416A THR 4.0 8.7 - - - +
417A SER* 3.5 34.8 - - - +
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Residues in contact with VAL 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 GLY 3.0 20.2 + - - +
340A GLU* 3.3 11.4 + - - +
342A MET* 1.3 76.1 - - - +
344A LYS* 1.3 68.8 + - + +
346A SER* 3.5 3.9 + - - -
347A GLY* 3.2 17.3 + - - -
400A ASP 4.8 3.4 - - - +
401A VAL* 3.5 24.5 - - + +
404A HIS* 3.5 54.5 - - + +
411A PRO* 4.1 17.0 - - + -
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Residues in contact with LYS 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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318A GLU* 4.3 30.7 + - + +
319A ALA* 4.5 12.8 - - + -
322A LEU* 3.8 24.2 - - + -
340A GLU* 3.1 19.6 + - + +
341A LEU* 3.5 8.5 - - + +
343A VAL* 1.3 84.7 - - + +
345A VAL* 1.3 57.7 + - - +
347A GLY* 3.3 3.6 + - - -
348A VAL* 3.0 30.6 + - - +
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Residues in contact with VAL 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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252A PRO* 3.6 18.4 - - + +
255A GLN* 3.5 19.0 - - + +
256A LEU* 3.5 48.0 - - + +
259A ALA* 5.4 0.2 - - - +
319A ALA* 4.4 4.0 - - + -
323A LEU* 6.0 0.2 - - + -
341A LEU* 3.1 31.1 + - + +
342A MET* 3.8 11.7 - - + +
344A LYS* 1.3 71.9 - - - +
346A SER* 1.3 61.8 + - - +
348A VAL* 3.1 8.2 + - - +
349A LYS* 2.8 27.9 + - - +
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Residues in contact with SER 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 MET* 2.6 40.7 + - - +
343A VAL* 3.7 5.7 - - - -
345A VAL* 1.3 77.8 - - - +
347A GLY* 1.3 60.9 + - - +
349A LYS* 3.5 3.3 + - - +
350A ALA* 3.2 18.9 + - - +
397A LYS* 3.6 48.0 - - - +
400A ASP* 4.6 12.0 + - - +
401A VAL* 4.0 6.3 - - - -
411A PRO* 5.0 0.3 - - - +
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Residues in contact with GLY 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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343A VAL 3.2 13.2 + - - -
344A LYS* 3.3 4.5 + - - -
345A VAL 3.2 0.2 - - - -
346A SER* 1.3 75.8 - - - +
348A VAL* 1.3 63.2 + - - +
350A ALA* 3.3 7.5 + - - +
351A LEU* 3.1 31.6 + - - +
401A VAL* 3.8 12.9 - - - +
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Residues in contact with VAL 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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256A LEU* 4.0 8.3 - - + -
259A ALA* 3.7 18.6 - - + -
263A LEU* 5.0 0.9 - - + -
312A ALA 4.8 2.9 - - - +
315A ALA* 3.5 36.1 - - + +
316A ALA* 3.8 26.0 - - + +
319A ALA* 4.0 10.1 - - + -
344A LYS 3.0 15.2 + - - +
345A VAL* 3.1 9.2 + - - +
347A GLY* 1.3 72.4 - - - +
349A LYS* 1.3 61.1 + - - +
351A LEU* 3.3 7.0 + - + +
352A ALA* 2.9 31.8 + - + +
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Residues in contact with LYS 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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255A GLN* 2.7 46.1 + - + +
258A PHE* 4.1 8.8 - - - -
259A ALA* 3.9 12.3 - - + +
262A TYR* 3.5 37.8 + - + -
345A VAL 2.8 19.7 + - - +
346A SER 3.5 6.5 - - - +
348A VAL* 1.3 73.7 - - - +
350A ALA* 1.3 53.2 + - - +
352A ALA* 3.6 1.4 + - - +
353A THR* 2.7 41.4 + - - +
389A SER 5.2 2.6 + - - -
391A HIS* 5.1 1.2 - - - +
392A ASP* 3.3 31.7 + - - +
394A VAL* 5.2 3.1 - - + -
397A LYS* 4.0 19.9 - - + +
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Residues in contact with ALA 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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346A SER 3.2 10.2 + - - +
347A GLY* 3.5 11.0 - - - +
348A VAL 3.2 0.4 - - - -
349A LYS* 1.3 78.0 - - - +
351A LEU* 1.3 65.5 + - + +
353A THR* 3.3 1.6 + - - -
354A ASN* 3.1 31.1 + - - +
394A VAL* 3.8 14.8 - - + +
397A LYS* 5.1 0.4 - - + -
398A ILE* 3.8 31.0 - - + -
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Residues in contact with LEU 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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311A GLY 4.7 2.2 - - - +
312A ALA* 4.0 21.8 - - + +
315A ALA* 3.6 30.7 - - + -
347A GLY 3.1 23.9 + - - +
348A VAL* 3.3 5.1 + - - +
350A ALA* 1.3 76.4 - - + +
352A ALA* 1.3 58.0 + - - +
354A ASN* 5.5 0.9 - - - -
355A ALA* 3.0 33.9 + - - +
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Residues in contact with ALA 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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259A ALA* 3.3 38.8 - - + +
262A TYR* 3.9 5.3 - - + +
263A LEU* 3.7 24.7 - - + +
312A ALA* 4.5 0.6 - - - +
348A VAL 2.9 17.5 + - - +
349A LYS 3.9 1.6 - - - +
351A LEU* 1.3 73.2 - - - +
353A THR* 1.3 61.5 + - - +
355A ALA* 4.0 0.2 - - - +
356A ALA* 2.9 35.2 + - - +
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Residues in contact with THR 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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262A TYR* 3.5 23.2 - - - -
349A LYS* 2.7 29.2 + - - +
350A ALA 3.3 4.7 + - - -
352A ALA* 1.3 76.8 - - - +
354A ASN* 1.3 70.3 + - - +
356A ALA* 3.8 1.8 - - - +
357A LEU* 3.0 47.3 + - + +
385A VAL* 4.4 1.6 - - - +
386A ARG* 5.5 1.1 - - - +
389A SER* 4.2 16.0 + - - +
394A VAL* 4.1 27.5 - - + +
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Residues in contact with ASN 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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350A ALA* 3.1 16.0 + - - +
351A LEU* 4.7 1.1 - - - +
353A THR* 1.3 89.9 - - - +
355A ALA* 1.3 60.5 + - - +
357A LEU* 4.1 12.0 - - - +
358A ASN* 3.0 31.4 + - - +
394A VAL* 5.2 7.6 - - - +
398A ILE* 5.0 14.3 - - - +
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Residues in contact with ALA 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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263A LEU* 4.9 0.4 - - + -
266A ALA* 4.9 0.2 - - - -
308A ALA* 4.5 22.2 - - + +
309A LEU* 4.7 6.7 - - + -
312A ALA* 4.4 15.0 - - + -
351A LEU 3.0 21.3 + - - +
352A ALA* 4.0 2.9 - - - +
354A ASN* 1.3 74.3 - - - +
356A ALA* 1.3 60.4 + - - +
358A ASN* 3.4 3.4 + - - -
359A ILE* 3.0 45.1 + - + +
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Residues in contact with ALA 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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262A TYR* 3.4 26.9 - - + +
263A LEU* 5.4 0.2 - - - -
266A ALA* 3.9 14.8 - - + +
352A ALA 2.9 20.4 + - - +
353A THR 3.8 0.2 - - - +
355A ALA* 1.3 75.8 - - - +
357A LEU* 1.3 51.5 + - - +
359A ILE* 4.2 0.2 - - - +
360A SER* 2.7 40.9 + - - -
385A VAL* 3.6 26.2 - - + -
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Residues in contact with LEU 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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353A THR* 3.0 37.5 + - + +
354A ASN* 4.1 11.7 - - - +
356A ALA* 1.3 77.1 - - - +
358A ASN* 1.3 62.8 + - - +
360A SER* 3.2 3.1 + - - -
361A SER* 3.2 27.2 + - - -
382A TRP* 4.0 16.0 + - + +
385A VAL* 3.9 19.5 - - + -
386A ARG* 3.7 59.0 - - - +
389A SER* 4.6 0.7 - - - +
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Residues in contact with ASN 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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305A PHE* 4.0 17.7 - - - -
354A ASN 3.0 20.7 + - - +
355A ALA* 3.9 4.5 - - - +
357A LEU* 1.3 77.7 - - - +
359A ILE* 1.3 61.5 + - + +
361A SER* 4.5 1.5 - - - -
362A GLY* 2.9 25.3 + - - -
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Residues in contact with ILE 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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266A ALA* 4.0 22.9 - - + +
269A ALA* 4.6 1.6 - - + -
270A LEU* 4.2 10.5 - - + +
305A PHE* 3.5 38.6 - - + +
308A ALA* 4.6 5.2 - - + -
309A LEU* 3.4 39.9 - - + -
355A ALA* 3.0 24.8 + - + +
356A ALA 4.2 1.6 - - - +
358A ASN* 1.3 78.6 - - + +
360A SER* 1.3 61.3 + - - +
363A VAL* 2.9 50.6 + - + +
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Residues in contact with SER 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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265A ILE* 5.5 1.1 - - - -
266A ALA* 5.7 0.9 - - - +
269A ALA* 4.1 13.1 - - - +
356A ALA 2.7 23.7 + - - -
357A LEU* 3.2 7.8 + - - -
359A ILE* 1.3 77.3 - - - +
361A SER* 1.3 61.0 + - - +
363A VAL* 4.3 5.1 - - - +
364A PHE* 3.7 20.1 - - - -
378A PHE 5.0 2.4 - - - +
381A PHE* 3.9 12.9 - - - +
382A TRP* 3.3 44.3 + - - +
385A VAL* 4.6 3.9 - - - +
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Residues in contact with SER 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 LEU 3.2 16.7 + - - -
358A ASN* 4.5 1.3 - - - -
360A SER* 1.3 76.9 + - - +
362A GLY* 1.3 66.6 + - - +
363A VAL 3.1 2.9 + - - -
364A PHE* 3.1 26.1 + - - +
365A GLU 4.5 0.5 + - - -
382A TRP* 3.9 19.0 - - - -
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Residues in contact with GLY 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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305A PHE* 3.5 21.3 - - - -
358A ASN 2.9 24.7 + - - -
361A SER* 1.3 75.3 - - - +
363A VAL* 1.3 63.0 + - - +
364A PHE 3.1 1.2 + - - -
365A GLU* 3.1 23.3 + - - +
366A VAL* 4.2 1.6 + - - +
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Residues in contact with VAL 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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269A ALA* 3.8 17.7 - - + +
270A LEU* 4.2 4.9 - - + -
273A ALA* 3.3 24.7 - - + +
305A PHE* 3.8 15.7 - - + -
359A ILE* 2.9 37.0 + - + +
360A SER* 4.3 8.3 - - - +
361A SER 3.1 0.4 + - - -
362A GLY* 1.3 76.1 - - - +
364A PHE* 1.3 65.7 + - + +
366A VAL* 3.0 21.1 - - + +
367A ILE* 3.2 30.7 + - + +
378A PHE* 5.9 2.5 - - + +
381A PHE* 6.4 0.9 - - + -
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Residues in contact with PHE 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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360A SER 3.7 16.6 - - - -
361A SER* 3.1 19.1 + - - +
362A GLY 3.1 1.2 + - - -
363A VAL* 1.3 80.5 - - + +
365A GLU* 1.3 59.1 + - - +
367A ILE* 4.2 12.1 - - + -
368A GLY* 2.9 32.5 + - - +
371A GLY 4.1 12.1 - - - -
372A THR* 4.5 22.0 - - + -
378A PHE* 3.6 27.1 - - + -
379A ASP* 3.6 37.9 - - + -
382A TRP* 5.6 2.7 - - + -
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Residues in contact with GLU 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A TYR* 5.7 5.0 - - - +
301A SER* 4.4 15.6 + - - +
305A PHE* 6.2 0.2 - - + -
361A SER 4.5 0.6 + - - -
362A GLY* 3.1 15.2 + - - +
364A PHE* 1.3 78.0 - - - +
366A VAL* 1.3 61.8 + - + +
368A GLY* 4.3 5.2 + - - -
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Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ALA* 4.6 2.9 - - + -
277A THR* 3.6 12.5 + - - +
281A ALA* 4.2 10.7 - - - +
298A THR* 3.8 29.3 + - + +
301A SER* 3.6 33.0 - - - +
302A TYR* 3.6 36.6 - - + +
305A PHE* 4.6 5.6 - - + -
362A GLY 5.1 0.4 - - - +
363A VAL* 3.0 25.5 - - - +
365A GLU* 1.3 79.4 - - + +
367A ILE* 1.3 63.6 + - - +
368A GLY* 4.9 0.2 - - - -
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Residues in contact with ILE 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ALA* 3.9 23.8 - - + +
276A TYR* 3.2 43.1 + - + -
277A THR* 4.8 0.2 - - - -
281A ALA* 4.2 6.8 - - - +
363A VAL* 3.2 39.1 + - + +
364A PHE* 3.1 12.0 + - + +
366A VAL* 1.3 81.2 - - - +
368A GLY* 1.3 61.9 + - - +
370A ARG* 5.1 2.9 + - - -
371A GLY* 3.6 30.3 - - - -
378A PHE* 3.9 30.1 - - + -
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Residues in contact with GLY 368 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A PHE* 2.9 16.0 + - - +
365A GLU 4.8 4.3 - - - -
366A VAL 3.7 1.0 - - - -
367A ILE* 1.3 84.4 - - - +
369A ALA* 1.3 66.0 + - - +
370A ARG 3.5 2.0 - - - -
371A GLY* 3.3 11.6 + - - -
372A THR* 4.0 6.9 + - - +
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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