Contacts of the helix formed by residues 353 - 390 (chain A) in PDB entry 4DYL
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 LEU 353 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 4.4 7.8 - - + +
341A GLU* 3.8 28.0 - - + -
342A GLU* 3.7 29.2 - - + +
345A THR* 3.7 39.5 - - + +
349A GLU 5.0 0.4 - - - +
350A ARG* 2.9 28.9 + - + +
352A GLN* 1.3 79.4 - - + +
354A LEU* 1.3 63.8 + - - +
355A GLY 3.3 2.2 - - - -
356A LYS* 3.3 10.4 + - + +
357A ARG* 3.0 40.2 + - - +
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ARG 4.5 2.5 - - - +
351A VAL* 3.3 37.1 + - + +
352A GLN 3.3 0.6 - - - -
353A LEU* 1.3 77.8 - - - +
355A GLY* 1.3 62.8 + - - +
357A ARG* 3.4 24.4 + - + +
358A GLN* 3.0 34.0 + - + +
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Residues in contact with GLY 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A VAL 5.0 0.4 + - - -
352A GLN 4.6 3.0 + - - -
353A LEU 3.3 0.6 - - - -
354A LEU* 1.3 78.0 - - - +
356A LYS* 1.3 55.6 + - - +
358A GLN* 3.1 16.3 + - - +
359A VAL* 2.9 31.4 + - - +
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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
----------------------------------------------------------
334A LEU* 5.0 13.9 - - + +
337A GLU* 4.5 14.8 - - + +
338A LEU* 3.9 33.2 - - + +
341A GLU* 3.4 31.6 - - - -
352A GLN 5.4 1.5 + - - +
353A LEU* 3.3 10.8 + - + +
355A GLY* 1.3 72.1 - - - +
357A ARG* 1.3 60.8 + - - +
359A VAL* 3.2 9.3 + - + +
360A LEU* 2.9 29.0 + - + +
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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
----------------------------------------------------------
338A LEU* 3.9 30.0 - - + +
342A GLU* 2.6 40.2 + - - +
350A ARG* 3.2 22.1 + - - +
353A LEU* 3.0 29.6 + - - +
354A LEU* 3.4 31.2 - - + +
356A LYS* 1.3 75.9 - - - +
358A GLN* 1.3 57.6 + - + +
360A LEU* 3.2 6.3 + - - +
361A GLN* 3.0 26.0 + - - +
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Residues in contact with GLN 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LEU* 3.0 27.3 + - + +
355A GLY* 3.1 15.3 + - - +
357A ARG* 1.3 74.6 - - + +
359A VAL* 1.3 64.4 + - + +
361A GLN* 3.2 12.0 + - + +
362A GLU* 3.2 32.9 + - - +
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Residues in contact with VAL 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LEU* 3.9 27.6 - - + -
355A GLY 2.9 19.7 + - - +
356A LYS* 3.2 10.5 + - + +
358A GLN* 1.3 75.6 - - + +
360A LEU* 1.3 63.2 + - - +
362A GLU* 3.2 13.7 + - + +
363A ALA* 3.1 20.3 + - - +
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Residues in contact with LEU 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A VAL* 3.9 19.7 - - + +
334A LEU* 3.8 31.4 - - + +
335A GLN* 3.9 26.0 - - + +
338A LEU* 3.7 26.0 - - + -
356A LYS* 2.9 13.4 + - + +
357A ARG* 3.2 10.3 + - + +
359A VAL* 1.3 78.6 - - - +
361A GLN* 1.3 60.6 + - - +
363A ALA* 3.3 1.4 + - - +
364A LEU* 2.9 42.7 + - + +
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Residues in contact with GLN 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ARG 3.0 13.0 + - - +
358A GLN* 3.2 15.9 + - + +
360A LEU* 1.3 74.7 - - - +
362A GLU* 1.3 69.9 + - + +
364A LEU* 3.1 11.8 + - - +
365A GLN* 2.9 38.7 + - - +
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Residues in contact with GLU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A GLN* 3.2 19.1 + - - +
359A VAL* 3.2 12.0 + - + +
361A GLN* 1.3 88.9 - - + +
363A ALA* 1.3 57.1 + - - +
365A GLN* 3.5 7.4 + - - +
366A GLY* 2.9 24.4 + - - -
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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
----------------------------------------------------------
327A ARG* 4.8 2.6 - - - +
330A MET* 5.1 6.1 - - + -
331A VAL* 3.7 20.1 - - + +
334A LEU* 3.7 27.8 - - + -
359A VAL 3.1 7.1 + - - +
360A LEU* 3.7 7.4 - - - +
362A GLU* 1.3 74.6 - - - +
364A LEU* 1.3 59.7 + - - +
366A GLY* 3.3 2.2 + - - +
367A LEU* 2.9 28.2 + - - +
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Residues in contact with LEU 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A VAL* 3.6 32.8 - - + -
335A GLN* 4.4 8.7 - - - +
360A LEU* 2.9 38.8 + - + +
361A GLN* 3.1 9.2 + - - +
363A ALA* 1.3 72.1 - - - +
365A GLN* 1.3 66.5 + - - +
367A LEU* 3.3 12.0 + - + +
368A GLN* 3.0 27.2 + - - +
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Residues in contact with GLN 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A GLN* 2.9 26.9 + - - +
362A GLU* 3.7 9.0 - - - +
364A LEU* 1.3 73.2 - - - +
366A GLY* 1.3 65.8 + - - +
368A GLN* 3.0 10.4 + - - +
369A VAL* 3.0 28.2 + - + +
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Residues in contact with GLY 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ARG* 3.6 26.6 - - - -
362A GLU 2.9 15.8 + - - -
363A ALA* 3.6 4.5 - - - -
364A LEU 3.3 0.2 - - - -
365A GLN* 1.3 75.8 - - - +
367A LEU* 1.3 61.6 + - - +
369A VAL* 3.2 9.0 + - - +
370A ALA 3.1 17.3 + - - -
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Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A VAL* 3.4 41.3 - - + +
327A ARG* 3.9 15.8 - - + +
328A GLN* 3.6 35.9 - - + +
331A VAL* 4.1 19.1 - - + -
363A ALA 2.9 13.5 + - - +
364A LEU* 3.5 16.6 - - + +
366A GLY* 1.3 73.0 - - - +
368A GLN* 1.3 60.1 + - - +
370A ALA* 3.2 3.9 + - - +
371A LEU* 2.8 42.5 + - + +
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Residues in contact with GLN 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LEU* 3.0 15.0 + - - +
365A GLN* 3.0 11.0 + - - +
367A LEU* 1.3 80.3 - - - +
369A VAL* 1.3 61.9 + - + +
371A LEU* 3.2 24.2 + - - +
372A CYS* 3.0 22.5 + - - +
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Residues in contact with VAL 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ARG* 5.8 5.2 - - - -
365A GLN* 3.0 19.6 + - + +
366A GLY* 3.6 9.4 - - - +
368A GLN* 1.3 75.8 - - + +
370A ALA* 1.3 64.0 + - - +
372A CYS* 3.2 9.0 + - + +
373A SER* 3.1 27.1 + - - +
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Residues in contact with ALA 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ALA 4.6 1.4 - - - +
323A MET* 4.5 10.1 - - + -
324A VAL* 3.4 31.4 - - + +
327A ARG* 4.0 20.4 - - - -
366A GLY 3.1 12.7 + - - +
367A LEU 3.6 7.9 - - - +
369A VAL* 1.3 76.0 - - - +
371A LEU* 1.3 59.3 + - - +
373A SER* 3.3 7.7 + - - -
374A GLN* 2.9 24.6 + - - +
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Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A VAL* 3.4 29.2 - - + -
367A LEU* 2.8 39.8 + - + +
368A GLN* 3.2 27.8 + - - +
370A ALA* 1.3 73.5 - - - +
372A CYS* 1.3 56.9 + - - +
374A GLN* 3.5 16.9 - - - +
375A ALA* 2.9 31.7 + - - +
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Residues in contact with CYS 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A GLN 3.0 13.6 + - - +
369A VAL* 3.3 13.0 - - - +
371A LEU* 1.3 77.3 - - - +
373A SER* 1.3 56.1 + - - +
375A ALA* 3.3 7.4 + - - +
376A LYS* 2.9 53.3 + - - +
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Residues in contact with SER 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ALA* 4.6 9.9 - - - -
369A VAL* 3.1 19.7 + - - +
370A ALA* 3.3 10.3 + - - -
372A CYS* 1.3 74.0 - - - +
374A GLN* 1.3 63.9 - - - +
376A LYS* 3.4 16.4 + - - +
377A LEU* 3.2 30.6 + - - +
----------------------------------------------------------
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Residues in contact with GLN 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU* 3.5 15.0 - - + +
320A ALA* 4.0 13.8 - - + +
321A THR* 3.1 43.9 + - - +
324A VAL* 4.0 14.6 - - + +
370A ALA 2.9 16.8 + - - +
371A LEU* 3.5 26.8 - - - +
373A SER* 1.3 74.8 - - - +
375A ALA* 1.3 58.7 + - - +
377A LEU 3.2 2.4 + - - -
378A GLN* 2.9 32.5 + - + +
----------------------------------------------------------
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Residues in contact with ALA 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LEU 2.9 19.6 + - - +
372A CYS* 3.5 6.7 - - - +
374A GLN* 1.3 77.4 + - - +
376A LYS* 1.3 62.4 + - + +
378A GLN* 3.2 7.6 + - - +
379A ALA* 3.0 24.8 + - - +
----------------------------------------------------------
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Residues in contact with LYS 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A CYS* 2.9 41.3 + - - +
373A SER* 3.7 15.3 - - - +
374A GLN 3.3 0.2 - - - -
375A ALA* 1.3 76.7 - - + +
377A LEU* 1.3 63.3 + - + +
379A ALA* 3.6 6.0 + - - +
380A GLN* 3.3 31.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A VAL* 3.4 19.8 - - + +
316A GLU* 3.5 56.5 - - + +
317A LEU* 3.7 13.3 - - + +
320A ALA* 3.7 19.7 - - + -
373A SER* 3.2 15.4 + - - +
374A GLN 3.8 3.4 - - - +
376A LYS* 1.3 78.0 - - + +
378A GLN* 1.3 60.8 + - - +
380A GLN* 3.4 18.1 + - - +
381A GLN* 3.1 22.9 + - - +
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Residues in contact with GLN 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU* 4.0 23.6 - - + +
374A GLN* 2.9 19.7 + - + +
375A ALA* 3.5 9.2 - - - +
376A LYS 3.2 0.2 - - - -
377A LEU* 1.3 75.1 - - - +
379A ALA* 1.3 59.6 + - - +
381A GLN* 3.3 13.5 + - - +
382A GLU* 2.9 41.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ALA 3.0 15.5 + - - +
376A LYS* 3.8 6.7 - - - +
377A LEU 3.4 0.2 - - - -
378A GLN* 1.3 79.1 + - - +
380A GLN* 1.3 60.6 + - + +
382A GLU* 3.6 9.8 + - - +
383A LEU* 3.3 28.3 + - + +
----------------------------------------------------------
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Residues in contact with GLN 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A VAL* 4.3 15.7 - - + +
376A LYS* 3.3 20.7 + - - +
377A LEU* 3.7 28.1 - - - +
378A GLN 3.2 0.6 - - - -
379A ALA* 1.3 75.9 - - + +
381A GLN* 1.3 64.3 + - - +
383A LEU* 3.3 12.1 + - + +
384A LEU* 3.1 31.4 + - + +
----------------------------------------------------------
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Residues in contact with GLN 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 3.5 23.6 - - + -
313A VAL* 3.7 12.0 - - + +
314A THR* 3.0 36.5 + - - +
317A LEU* 3.3 25.6 - - + +
377A LEU 3.1 14.3 + - - +
378A GLN* 3.5 16.9 + - - +
380A GLN* 1.3 73.9 - - - +
382A GLU* 1.3 56.5 + - - +
384A LEU* 3.1 3.2 + - - +
385A GLN* 2.7 53.3 + - - +
----------------------------------------------------------
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Residues in contact with GLU 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLN* 2.9 28.7 + - - +
379A ALA* 3.8 8.8 - - - +
381A GLN* 1.3 75.8 + - - +
383A LEU* 1.3 58.8 + - + +
385A GLN* 4.4 5.6 - - - -
386A THR* 2.9 49.7 + - + +
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Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A PHE* 5.5 14.6 - - + -
294A GLY 5.6 4.9 - - - +
296A LEU* 3.8 20.0 - - + +
379A ALA* 3.3 16.4 + - + +
380A GLN* 3.7 12.8 - - + +
381A GLN 3.1 1.0 - - - -
382A GLU* 1.3 79.6 - - + +
384A LEU* 1.3 63.5 + - - +
386A THR* 3.1 16.6 + - - +
387A LYS* 3.2 15.9 + - - +
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU* 3.8 26.2 - - + -
306A VAL* 3.9 27.2 - - + +
309A THR* 3.7 31.9 - - + -
310A LEU* 3.7 28.3 - - + -
313A VAL* 3.8 15.9 - - + -
380A GLN* 3.3 16.4 - - + +
381A GLN 3.1 6.6 + - - +
383A LEU* 1.3 80.2 - - - +
385A GLN* 1.3 60.8 - - - +
387A LYS* 3.4 2.8 + - - +
388A LEU* 3.2 31.1 + - - +
----------------------------------------------------------
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Residues in contact with GLN 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 4.2 21.1 - - + +
381A GLN* 2.7 46.7 + - - +
382A GLU* 3.9 5.4 + - - +
384A LEU* 1.3 70.7 - - - +
386A THR* 1.3 61.7 + - + +
388A LEU* 3.5 3.0 + - - +
389A GLU* 2.9 32.8 + - + +
----------------------------------------------------------
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Residues in contact with THR 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLU* 2.9 40.1 + - + +
383A LEU* 3.1 10.6 + - - +
385A GLN* 1.3 77.5 - - + +
387A LYS* 1.3 59.5 + - - +
389A GLU* 3.4 6.5 + - - +
390A HIS* 3.0 31.2 + - - +
----------------------------------------------------------
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Residues in contact with LYS 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLU* 3.0 32.9 + - + +
296A LEU* 3.1 44.0 + - + -
298A LEU* 3.1 41.4 - - + +
306A VAL* 5.4 3.8 - - + -
383A LEU 3.2 15.5 + - - +
384A LEU 3.7 4.9 - - - +
385A GLN 3.2 0.2 - - - -
386A THR* 1.3 80.9 + - - +
388A LEU* 1.3 61.4 + - + +
390A HIS* 3.5 7.5 + - + +
391A LEU 3.4 11.4 + - - -
----------------------------------------------------------
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Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 4.1 17.5 - - + -
303A VAL* 4.5 7.2 - - + +
306A VAL* 3.7 32.5 - - + +
307A GLN* 4.0 27.8 - - + +
310A LEU* 3.8 31.4 - - + -
384A LEU 3.2 18.3 + - - +
385A GLN 4.2 2.2 - - - +
387A LYS* 1.3 73.5 - - - +
389A GLU* 1.3 64.9 + - - +
391A LEU* 3.3 7.3 + - + +
392A GLY* 3.1 19.6 + - - -
----------------------------------------------------------
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Residues in contact with GLU 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLN* 2.9 20.5 + - + +
386A THR* 3.7 8.1 - - - +
388A LEU* 1.3 77.6 - - - +
390A HIS* 1.3 57.4 + - - +
391A LEU 3.2 0.2 - - - -
392A GLY* 3.2 20.9 + - - -
----------------------------------------------------------
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Residues in contact with HIS 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A THR 3.0 16.8 + - - +
387A LYS* 3.9 8.7 - - + +
388A LEU 3.3 0.4 - - - -
389A GLU* 1.3 73.5 - - - +
391A LEU* 1.3 59.5 + - - +
----------------------------------------------------------
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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