Contacts of the helix formed by residues 356 - 386 (chain A) in PDB entry 3IO6
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 356 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ALA* 5.0 0.7 - - - -
355A GLN* 1.3 75.0 - - - +
357A VAL* 1.3 59.8 + - + +
358A ASP* 4.2 7.7 - - - +
359A ALA* 3.1 18.9 + - - +
360A ALA* 2.8 32.9 + - - +
51C ALA 4.3 5.7 + - - -
52C ALA 3.3 7.7 + - - -
53C THR 4.6 1.8 - - - +
54C GLY* 3.8 26.9 - - - +
75C LEU* 5.7 0.2 - - - +
269C ALA* 4.2 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LYS* 3.4 24.2 - - + +
192A LEU* 3.8 24.9 - - + +
193A THR* 3.4 42.0 - - + +
196A VAL* 4.3 23.6 - - + -
350A ALA* 4.7 3.7 - - + +
355A GLN 4.1 0.2 + - - -
356A THR* 1.3 72.4 - - - +
358A ASP* 1.3 62.7 + - - +
360A ALA* 5.0 0.2 - - - -
361A LEU* 3.4 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ASP 5.7 0.5 - - - +
189A LYS* 3.3 34.9 + - - +
356A THR* 3.1 7.2 - - - +
357A VAL* 1.3 80.7 - - - +
359A ALA* 1.3 60.6 + - - +
361A LEU* 4.5 1.5 - - - +
362A ALA* 3.5 22.2 + - - +
73C SER 4.0 2.0 - - - +
74C GLY* 3.9 21.3 - - - +
268C ALA* 4.1 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A GLN* 4.7 6.7 - - + +
356A THR* 3.1 19.5 + - - +
358A ASP* 1.3 78.2 - - - +
360A ALA* 1.3 60.6 + - - +
362A ALA* 3.2 2.6 + - - +
363A ALA* 2.9 33.5 + - - +
52C ALA* 4.3 15.3 - - + +
73C SER* 3.2 22.5 - - - +
74C GLY 4.5 2.0 + - - +
75C LEU* 4.4 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 5.3 1.1 - - + -
346A ALA* 3.6 32.5 - - - +
349A ASN* 4.6 1.1 - - + -
350A ALA* 4.5 10.1 - - + +
355A GLN* 3.7 28.4 + - + +
356A THR 2.8 21.1 + - - +
357A VAL* 4.5 1.6 - - - +
359A ALA* 1.3 72.9 - - - +
361A LEU* 1.3 56.5 + - - +
363A ALA* 3.6 2.8 + - - +
364A ALA* 3.2 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TRP* 6.0 1.8 - - + -
161A ILE* 5.0 10.8 - - + -
183A VAL* 3.5 37.6 - - + +
184A ASP* 3.6 17.0 - - + +
188A ALA 3.8 10.5 - - - +
189A LYS* 3.7 32.8 - - + +
192A LEU* 3.8 25.1 - - + -
343A VAL* 6.1 3.6 - - + -
346A ALA* 4.5 12.3 - - + -
347A VAL* 6.2 1.6 - - + -
357A VAL* 3.4 21.4 + - + +
358A ASP* 4.5 1.8 - - - +
359A ALA 3.2 0.4 - - - -
360A ALA* 1.3 78.5 - - - +
362A ALA* 1.3 64.0 + - - +
364A ALA* 3.5 11.2 + - - +
365A GLN 3.6 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ASP* 4.0 19.8 - - + +
358A ASP 3.5 18.3 + - - +
359A ALA 3.2 3.9 + - - +
361A LEU* 1.3 78.3 - - - +
363A ALA* 1.3 61.8 + - - +
365A GLN* 3.2 18.0 + - - +
366A THR* 3.6 10.7 + - - +
72C GLN 3.7 21.6 - - - +
73C SER 3.9 11.4 - - - -
74C GLY* 4.2 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A GLN* 4.9 11.2 - - - +
359A ALA 2.9 18.0 + - - +
360A ALA* 4.0 6.1 - - - +
362A ALA* 1.3 76.4 - - - +
364A ALA* 1.3 59.0 + - - +
365A GLN 3.2 0.2 - - - -
366A THR* 2.6 26.8 + - - +
367A ASN* 3.0 21.9 + - - +
72C GLN 5.1 0.6 + - - -
73C SER* 5.4 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A VAL* 4.4 13.2 - - + -
342A ALA* 3.1 42.8 - - + +
343A VAL* 4.4 0.9 - - - +
346A ALA* 3.8 8.5 - - + -
360A ALA 3.2 17.7 + - - +
361A LEU 3.7 7.4 - - - +
362A ALA 3.3 0.6 - - - -
363A ALA* 1.3 76.4 - - - +
365A GLN* 1.3 58.6 + - - +
367A ASN* 4.1 4.5 - - - +
368A ALA* 2.8 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A VAL* 2.6 49.9 + - + +
183A VAL* 3.4 24.2 - - + +
184A ASP* 3.0 36.0 + - - +
361A LEU 3.6 3.1 + - - +
362A ALA 3.2 11.3 + - - +
363A ALA 3.2 0.4 - - - -
364A ALA* 1.3 77.4 - - - +
366A THR* 1.3 63.4 + - + +
368A ALA* 3.9 6.1 - - - +
369A ALA* 3.4 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ALA 3.6 10.7 + - - +
363A ALA* 2.6 28.7 + - - +
365A GLN* 1.3 76.3 - - + +
367A ASN* 1.3 63.3 + - - +
369A ALA* 3.7 4.3 + - - +
370A ALA* 3.1 29.6 + - - +
72C GLN* 3.9 26.9 - - + +
379C LYS* 5.6 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ALA 5.4 0.2 - - - -
341A TYR* 5.1 5.6 - - + -
342A ALA* 3.9 17.9 + - + +
345A THR* 5.1 12.7 - - - +
363A ALA* 3.0 20.3 + - - +
364A ALA* 3.5 11.7 - - - +
365A GLN 3.3 0.2 - - - -
366A THR* 1.3 80.4 + - - +
368A ALA* 1.3 58.7 + - - +
370A ALA* 4.6 3.7 - - - +
371A MET* 2.8 36.5 + - - +
379C LYS 5.2 1.9 - - - +
383C SER* 3.3 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PHE* 6.1 3.8 - - + -
181A VAL* 5.3 15.3 - - + -
183A VAL* 6.4 1.1 - - + -
338A ALA* 3.5 21.8 - - + +
339A PHE* 4.6 7.0 - - + +
342A ALA* 3.9 12.1 - - + +
364A ALA 2.8 19.7 + - - +
365A GLN* 4.2 7.9 - - - +
366A THR 3.5 0.2 - - - -
367A ASN* 1.3 72.7 - - - +
369A ALA* 1.3 59.4 + - - +
372A ALA* 3.1 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LYS* 5.7 7.4 - - - +
365A GLN 3.4 15.8 + - - +
366A THR* 4.1 4.7 - - - +
367A ASN 3.2 0.6 - - - -
368A ALA* 1.3 78.1 - - - +
370A ALA* 1.3 64.0 + - - +
372A ALA* 3.5 3.3 + - - +
373A THR* 3.3 30.6 + - + +
376C LYS* 4.9 18.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A THR 3.1 20.2 + - - +
367A ASN* 3.4 4.5 + - - +
369A ALA* 1.3 74.5 - - - +
371A MET* 1.3 58.9 + - - +
373A THR* 3.4 7.5 + - - -
374A LEU* 3.0 31.2 + - - +
376C LYS* 4.2 19.9 - - + +
377C LEU* 4.0 4.0 - - - +
379C LYS* 4.6 4.3 - - + -
380C ALA* 3.7 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A SER* 5.8 4.0 - - - +
338A ALA* 4.1 24.0 - - + +
341A TYR* 4.8 23.3 - - + -
367A ASN 2.8 21.9 + - - +
370A ALA* 1.3 74.9 - - - +
372A ALA* 1.3 56.2 + - - +
374A LEU* 3.6 12.4 + - - +
375A GLU* 3.2 40.0 + - + +
380C ALA* 4.2 5.3 - - + +
383C SER* 5.1 9.4 + - - +
384C LEU* 4.6 20.6 - - + -
387C PHE* 5.5 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLN* 4.5 23.1 - - + -
338A ALA* 3.9 13.2 - - + +
368A ALA 3.1 21.6 + - - +
369A ALA* 3.8 5.2 - - - +
370A ALA 3.2 0.8 - - - -
371A MET* 1.3 77.7 - - - +
373A THR* 1.3 63.9 + - + +
375A GLU* 3.5 18.8 + - - +
376A LYS* 3.8 12.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ALA 3.3 14.4 + - - +
370A ALA* 3.4 7.1 + - - -
372A ALA* 1.3 75.5 - - + +
374A LEU* 1.3 64.8 + - - +
375A GLU 3.2 1.8 - - - -
376A LYS* 3.2 45.9 + - - +
377A LEU* 3.5 5.5 + - - +
374B LEU* 4.6 7.4 - - - +
376C LYS* 5.6 10.4 - - - +
377C LEU* 3.3 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ALA 3.0 19.6 + - - +
371A MET* 3.8 13.0 - - - +
373A THR* 1.3 75.6 + - - +
375A GLU* 1.3 59.1 + - - +
376A LYS 3.3 0.2 - - - -
377A LEU* 3.4 19.4 - - + +
378A MET* 3.2 27.7 + - + +
377C LEU* 3.5 41.3 - - + +
378C MET* 6.2 1.8 - - - -
380C ALA* 4.1 17.9 - - + +
381C PHE* 6.4 2.5 - - + -
384C LEU* 4.4 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A PRO* 4.2 22.9 - - - +
337A SER* 4.0 23.7 + - - -
338A ALA* 5.4 0.5 + - - +
371A MET* 3.2 26.3 + - + +
372A ALA* 3.6 14.5 - - - +
373A THR 3.2 0.6 - - - -
374A LEU* 1.3 75.1 - - - +
376A LYS* 1.3 61.7 + - - +
378A MET* 3.6 9.0 + - + +
379A LYS* 3.0 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLN* 6.3 0.9 - - - +
372A ALA 3.8 6.9 + - - +
373A THR* 3.2 48.0 + - - +
374A LEU 3.3 0.2 - - - -
375A GLU* 1.3 78.6 - - + +
377A LEU* 1.3 52.1 + - - +
379A LYS* 3.1 6.7 + - - +
380A ALA* 2.6 37.8 + - - +
369B ALA* 6.4 1.1 - - + -
370B ALA* 4.8 12.2 - - + +
373B THR* 5.9 2.7 - - - +
374B LEU* 3.4 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A THR 3.5 3.8 + - - +
374A LEU* 3.4 30.0 + - + +
375A GLU 3.3 0.2 - - - -
376A LYS* 1.3 75.5 - - - +
378A MET* 1.3 69.0 + - + +
380A ALA* 3.9 1.0 - - + +
381A PHE* 2.9 60.8 + - + +
405A PRO* 5.9 4.7 - - + +
374B LEU* 3.5 27.2 - - + +
378B MET* 5.5 8.7 - - + -
377C LEU* 4.5 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LEU* 3.2 14.4 + - + +
375A GLU* 3.8 12.8 - - + +
377A LEU* 1.3 86.7 - - + +
379A LYS* 1.3 56.8 + - - +
381A PHE* 3.9 4.5 - - - +
382A GLU* 2.9 41.9 + - + +
404A GLN* 6.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLU* 3.0 21.4 + - + +
376A LYS* 3.1 6.9 + - - +
378A MET* 1.3 74.6 - - - +
380A ALA* 1.3 54.0 + - - +
382A GLU* 3.7 28.9 + - - +
383A SER* 2.7 48.6 + - - +
370B ALA* 5.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LYS 2.6 20.2 + - - +
377A LEU* 3.9 2.9 - - + +
379A LYS* 1.3 72.3 - - - +
381A PHE* 1.3 56.7 + - + +
382A GLU 3.2 0.2 - - - -
383A SER* 3.7 4.6 + - - -
384A LEU* 2.7 41.5 + - + +
370B ALA* 3.7 34.0 - - + +
371B MET* 4.8 8.4 - - + +
374B LEU* 3.8 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 2.9 45.1 + - + +
378A MET* 4.0 5.6 - - - +
380A ALA* 1.3 77.8 - - + +
382A GLU* 1.3 58.2 + - - +
384A LEU* 4.3 17.2 - - + +
385A LYS* 3.1 31.5 + - + +
404A GLN* 4.6 26.2 - - + -
405A PRO 6.2 1.1 - - - -
406A PRO* 5.0 18.6 - - + -
378B MET* 5.1 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A MET* 2.9 29.6 + - + +
379A LYS* 3.7 35.9 + - - +
380A ALA 3.2 0.2 - - - -
381A PHE* 1.3 77.6 - - - +
383A SER* 1.3 57.5 + - - +
385A LYS* 3.4 20.4 + - - +
386A SER* 3.1 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LYS* 2.7 35.5 + - - +
380A ALA* 3.8 4.7 + - - -
382A GLU* 1.3 77.5 - - - +
384A LEU* 1.3 52.7 + - - +
386A SER* 3.3 14.6 + - - -
387A PHE* 2.3 48.6 - - - -
367B ASN* 4.0 17.6 + - - -
370B ALA* 5.5 2.3 - - - +
371B MET* 5.4 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ALA 2.7 20.9 + - - +
381A PHE* 4.3 20.2 - - + +
383A SER* 1.3 76.4 - - - +
385A LYS* 1.3 61.4 + - - +
386A SER 3.3 0.2 - - - -
387A PHE* 3.0 26.2 + - - +
388A GLN* 3.3 31.6 + - + +
341B TYR* 4.6 11.7 - - + +
371B MET* 3.6 35.6 - - + +
375B GLU* 4.8 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A PHE* 3.1 23.5 + - + +
382A GLU* 3.4 25.4 + - - +
384A LEU* 1.3 74.1 - - - +
386A SER* 1.3 58.7 + - - +
387A PHE 3.0 8.6 + - - -
388A GLN* 3.2 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLU* 3.1 9.0 + - - -
383A SER* 3.3 23.9 + - - -
384A LEU 3.3 0.2 - - - -
385A LYS* 1.3 77.8 - - - +
387A PHE* 1.3 66.1 + - - +
388A GLN 3.6 3.5 - - - +
354B ARG* 5.5 8.6 + - - -
----------------------------------------------------------
Back to top of page
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