Contacts of the helix formed by residues 325 - 355 (chain B) in PDB entry 1IVH
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 ALA 325 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ASP* 3.8 29.0 + - - +
255B ARG* 5.4 1.1 + - - +
324B THR* 1.3 73.1 - - - +
326B LYS* 1.3 57.8 + - - +
328B CYS* 3.4 1.7 + - - +
329B ALA* 3.0 30.7 + - - +
384B VAL* 3.9 15.7 - - + +
388B ALA* 6.3 1.3 - - + -
400B COS 4.0 16.2 - - - +
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Residues in contact with LYS 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B THR* 3.9 12.3 - - - +
325B ALA* 1.3 79.3 - - - +
327B ASP* 1.3 57.9 + - - +
329B ALA 3.7 0.5 - - - -
330B GLY* 2.7 31.4 + - - -
384B VAL* 4.3 4.4 - - - +
385B ILE* 3.7 27.2 - - + +
388B ALA* 3.7 31.8 - - + +
389B PHE* 2.9 40.7 - - + -
392B ASP* 3.6 12.5 + - - -
301C TYR* 3.6 36.0 + - + +
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Residues in contact with ASP 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B TYR* 4.3 11.3 + - - -
314B VAL* 4.0 17.8 - - + +
324B THR* 3.1 27.8 + - + +
326B LYS* 1.3 77.7 - - - +
328B CYS* 1.3 64.4 + - - +
330B GLY* 3.9 1.3 - - - +
331B VAL* 3.2 28.2 + - - +
8C ASP* 3.7 18.4 - - - +
10C ILE* 3.8 15.1 - - + +
301C TYR* 3.0 31.7 + - - -
305C MET* 4.1 9.6 - - - +
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Residues in contact with CYS 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ASP* 3.3 46.9 - - + +
255B ARG* 3.6 18.0 - - + +
256B LEU* 4.1 19.1 - - - +
314B VAL* 5.0 2.7 - - - -
318B CYS* 4.7 3.4 - - - -
323B CYS* 4.4 22.0 - - - -
324B THR 3.0 21.0 + - - +
325B ALA 3.9 3.1 - - - +
327B ASP* 1.3 76.6 - - - +
329B ALA* 1.3 62.8 + - - +
330B GLY 3.6 0.2 + - - -
331B VAL* 3.7 6.0 + - - +
332B ILE 3.6 13.0 + - - -
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Residues in contact with ALA 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ARG* 4.0 25.3 - - - +
325B ALA 3.0 17.8 + - - +
326B LYS 3.9 2.9 - - - +
328B CYS* 1.3 77.9 - - - +
330B GLY* 1.3 59.4 + - - +
332B ILE* 3.6 2.5 + - - +
333B LEU* 2.9 32.9 + - - +
381B ARG* 4.2 20.4 - - + +
384B VAL* 4.1 17.5 - - + -
385B ILE* 4.5 2.2 - - + -
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Residues in contact with GLY 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B TYR* 3.5 18.2 - - - -
326B LYS 2.7 19.9 + - - -
327B ASP 3.9 0.4 - - - -
328B CYS 3.3 0.4 - - - -
329B ALA* 1.3 78.7 - - - +
331B VAL* 1.3 61.2 + - - +
333B LEU* 3.7 1.5 - - - +
334B TYR* 3.1 27.0 + - - +
385B ILE* 3.8 6.5 - - - -
301C TYR* 6.0 0.2 - - - -
302C THR* 3.7 15.6 - - - +
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ARG 4.3 2.9 - - - +
256B LEU* 4.4 7.0 - - + +
259B ALA* 3.4 27.1 - - + -
310B TYR* 3.7 16.7 + - + +
311B VAL* 3.5 25.6 - - + +
314B VAL* 3.4 39.7 - - + -
327B ASP 3.2 13.9 + - - +
328B CYS* 3.9 7.9 - - - +
330B GLY* 1.3 76.2 - - - +
332B ILE* 1.3 60.1 + - - +
334B TYR* 4.1 1.4 - - - +
335B SER* 3.0 32.4 + - - -
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Residues in contact with ILE 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ARG* 3.4 41.7 - - + +
258B LEU* 4.0 26.7 - - + +
259B ALA* 4.2 9.6 - - + -
262B PRO* 4.9 4.3 - - + -
328B CYS 3.6 1.2 + - - +
329B ALA 3.6 7.6 + - - +
331B VAL* 1.3 79.5 - - - +
333B LEU* 1.3 64.4 + - - +
335B SER* 4.4 3.1 - - - -
336B ALA* 2.9 39.9 + - + +
371B TYR* 4.5 9.6 - - + -
375B ALA* 4.2 9.0 - - + -
381B ARG* 3.3 39.0 - - - +
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ALA 2.9 19.7 + - - +
330B GLY 3.4 2.4 + - - +
332B ILE* 1.3 78.7 - - - +
334B TYR* 1.3 66.6 + - - +
336B ALA* 4.0 1.0 - - - +
337B GLU* 3.4 28.2 + - - +
378B SER* 3.7 41.3 - - - +
381B ARG* 3.8 14.3 + - + +
382B ARG* 4.0 37.9 - - + +
385B ILE* 3.9 24.0 - - + -
298C ALA* 4.4 5.8 - - + -
299C ASP* 4.9 3.6 - - - +
302C THR* 4.6 10.3 - - + +
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Residues in contact with TYR 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ALA* 5.0 1.3 - - + -
307B CYS* 3.8 25.4 - - - -
310B TYR* 4.0 13.9 - + + -
330B GLY 3.1 14.4 + - - +
331B VAL 4.1 0.2 - - - +
333B LEU* 1.3 81.8 - - + +
335B SER* 1.3 65.6 + - - +
337B GLU* 3.4 5.6 + - - +
338B CYS* 3.1 32.6 + - - -
302C THR* 3.8 20.2 - - - -
303C ARG* 3.9 33.0 - - + +
306C ALA* 3.5 28.7 - - + -
334C TYR* 2.7 38.1 + + - -
338C CYS* 4.1 4.3 - - - -
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Residues in contact with SER 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ALA* 4.5 5.8 - - - -
262B PRO* 3.7 17.2 - - - +
263B LEU* 4.0 5.7 - - - +
266B MET* 4.3 1.4 - - - +
307B CYS* 3.4 31.2 + - - +
310B TYR* 5.4 0.5 - - - -
311B VAL* 3.4 15.1 - - - +
331B VAL 3.0 19.6 + - - -
332B ILE* 4.2 4.5 - - - -
334B TYR* 1.3 78.0 - - - +
336B ALA* 1.3 58.4 + - - +
338B CYS* 3.1 2.8 + - - +
339B ALA* 2.9 31.0 + - - +
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Residues in contact with ALA 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B PRO* 4.0 13.5 - - + +
332B ILE* 2.9 25.1 + - + +
333B LEU 4.0 1.8 - - - +
335B SER* 1.3 72.9 - - - +
337B GLU* 1.3 61.8 + - + +
339B ALA* 3.5 3.3 - - - +
340B THR* 3.4 24.9 + - - -
368B ALA 4.5 1.7 - - - +
371B TYR* 3.3 39.0 - - + +
372B GLU* 3.5 8.5 - - + +
381B ARG* 3.6 5.2 - - - +
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Residues in contact with GLU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU* 3.4 21.0 + - - +
334B TYR* 3.4 6.4 + - - +
335B SER 3.3 0.6 - - - -
336B ALA* 1.3 76.3 - - + +
338B CYS* 1.3 66.7 + - - +
340B THR* 3.7 2.4 + - - -
341B GLN* 3.5 25.1 + - - +
372B GLU* 3.2 22.8 - - + +
378B SER* 3.7 18.7 + - - +
382B ARG* 3.1 34.9 + - - -
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Residues in contact with CYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B MET* 3.9 9.0 - - - -
303B ARG* 4.2 20.6 - - + +
307B CYS* 3.7 24.9 - - - -
334B TYR* 3.1 24.6 + - - +
335B SER 3.1 8.3 + - - +
337B GLU* 1.3 75.6 - - - +
339B ALA* 1.3 66.2 + - - +
341B GLN* 3.2 5.9 + - - +
342B VAL* 2.9 29.4 + - - +
334C TYR* 4.2 17.0 - - - -
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Residues in contact with ALA 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B PRO* 3.6 31.4 - - + +
265B LEU* 5.1 3.2 - - + +
266B MET* 3.5 15.6 - - + +
269B VAL* 5.6 0.2 - - - +
335B SER 2.9 16.4 + - - +
336B ALA* 3.5 7.2 - - - +
338B CYS* 1.3 76.8 - - - +
340B THR* 1.3 57.6 + - - +
342B VAL* 3.3 2.3 + - - +
343B ALA* 2.9 29.8 + - - +
368B ALA* 4.1 17.2 - - + +
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Residues in contact with THR 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 4.1 31.4 - - + -
336B ALA 3.4 7.2 + - - -
337B GLU 4.1 1.8 - - - -
338B CYS 3.3 0.6 - - - -
339B ALA* 1.3 78.1 - - - +
341B GLN* 1.3 64.8 + - - +
343B ALA* 3.3 3.0 + - - +
344B LEU* 3.0 21.6 + - + +
365B LEU* 4.1 19.1 - - + +
368B ALA* 3.7 8.6 - - - -
369B LYS* 3.7 24.3 + - + +
372B GLU* 3.3 28.4 + - - +
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Residues in contact with GLN 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A GLN* 3.2 31.4 + - - +
344A LEU* 3.7 18.2 - - - +
303B ARG* 3.4 24.9 - - - +
337B GLU 3.5 13.1 + - - +
338B CYS* 3.2 6.0 + - - +
340B THR* 1.3 78.3 - - - +
342B VAL* 1.3 64.4 + - - +
344B LEU* 3.1 15.4 + - - +
345B ASP* 3.0 24.1 + - - +
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Residues in contact with VAL 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B MET* 3.7 37.5 - - + +
269B VAL* 3.9 15.2 - - + +
270B LEU* 5.4 0.9 - - + -
300B MET* 3.5 32.1 - - + +
303B ARG* 3.8 34.1 - - + +
338B CYS 2.9 20.9 + - - +
339B ALA 3.5 3.6 - - - +
341B GLN* 1.3 73.6 - - - +
343B ALA* 1.3 58.4 + - - +
345B ASP* 2.8 22.3 + - - +
346B GLY 3.0 10.0 + - - -
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Residues in contact with ALA 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LEU* 6.4 0.9 - - + -
269B VAL* 3.9 15.2 - - + +
339B ALA 2.9 18.0 + - - +
340B THR* 3.4 8.7 - - - +
342B VAL* 1.3 76.8 - - - +
344B LEU* 1.3 61.1 + - - +
346B GLY* 3.4 8.3 + - - -
347B ILE* 3.4 19.3 + - - +
361B MET* 4.4 4.3 - - - +
364B PHE* 3.9 10.5 - - + +
365B LEU* 3.7 33.2 - - - +
368B ALA* 4.3 1.6 - - + -
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A THR* 4.0 26.0 - - + -
341A GLN* 4.1 17.3 - - - +
344A LEU* 4.2 16.4 - - + -
365A LEU* 5.0 2.7 - - + -
369A LYS* 3.2 49.1 + - + +
372A GLU* 5.3 1.8 - - - +
340B THR 3.0 11.5 + - - +
341B GLN* 3.1 21.3 + - - +
343B ALA* 1.3 74.2 - - - +
345B ASP* 1.3 66.7 + - - +
347B ILE* 3.7 2.5 + - + +
348B GLN 3.4 6.2 + - - -
365B LEU* 3.6 33.2 - - + -
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Residues in contact with ASP 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LYS* 2.7 41.0 + - + +
299B ASP* 5.0 1.7 - - - +
300B MET* 3.8 20.1 - - + +
303B ARG* 2.8 28.6 + - - -
341B GLN 3.0 8.1 + - - +
342B VAL 2.8 10.4 + - - +
344B LEU* 1.3 78.3 - - - +
346B GLY* 1.3 58.5 + - - +
348B GLN* 3.1 7.1 + - - +
349B CYS* 2.9 32.7 + - - -
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Residues in contact with GLY 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B VAL* 3.9 3.4 - - - -
273B THR* 3.6 18.8 - - - -
300B MET* 3.6 8.0 - - - +
342B VAL 3.0 9.7 + - - -
343B ALA 3.4 4.9 + - - -
344B LEU 3.3 0.4 - - - -
345B ASP* 1.3 73.2 - - - +
347B ILE* 1.3 65.5 + - - +
349B CYS* 3.2 10.2 + - - +
350B PHE* 3.3 19.6 - - - -
361B MET* 3.7 15.3 - - - -
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Residues in contact with ILE 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 3.9 16.8 - - + -
369A LYS* 3.8 24.0 - - + -
373A ILE* 4.1 12.1 - - + +
343B ALA 3.4 11.3 + - - +
344B LEU* 3.9 8.3 - - + +
345B ASP 3.3 0.2 - - - -
346B GLY* 1.3 73.3 - - - +
348B GLN* 1.3 64.9 + - - +
350B PHE* 3.0 14.9 + - - +
351B GLY* 3.3 9.9 + - - +
354B GLY* 3.6 21.8 - - - +
355B TYR* 4.1 4.0 - - + +
361B MET* 3.8 26.9 - - + +
365B LEU* 3.5 39.7 - - + -
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Residues in contact with GLN 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LYS* 2.6 36.8 + - - +
372A GLU* 3.0 36.6 + - - +
373A ILE* 3.9 8.3 - - - +
377A THR* 4.0 6.1 - - - +
378A SER* 3.5 13.0 + - - +
379A GLU* 3.0 34.9 + - - +
399A FAD 2.7 24.6 + - - +
293B MET* 5.9 0.7 - - + -
296B LYS* 4.1 14.1 - - - +
344B LEU 3.4 5.3 + - - +
345B ASP* 3.1 14.2 + - - +
347B ILE* 1.3 80.6 - - - +
349B CYS* 1.3 56.7 + - - +
351B GLY* 3.2 10.6 + - - -
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Residues in contact with CYS 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A FAD 3.3 24.1 - - - +
273B THR* 3.5 34.1 - - + -
276B TYR* 3.9 3.8 - - - -
277B LEU* 3.6 18.8 - - + -
287B ILE* 3.8 12.1 - - - +
293B MET* 4.4 8.3 - - - -
296B LYS* 4.3 24.2 - - - -
300B MET* 4.5 3.6 - - - -
345B ASP 2.9 17.1 + - - -
346B GLY 3.2 7.2 + - - +
348B GLN* 1.3 75.8 - - - +
350B PHE* 1.3 61.2 + - + +
351B GLY 3.3 0.2 - - - -
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Residues in contact with PHE 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A FAD 4.3 7.5 + - - +
272B HIS* 3.3 33.9 - - + -
273B THR* 3.5 26.0 - - + -
276B TYR* 3.5 44.1 + + + -
346B GLY 3.3 13.5 - - - +
347B ILE 3.0 3.7 + - - +
349B CYS* 1.3 79.7 - - + +
351B GLY* 1.3 64.6 + - - +
352B GLY 3.5 0.3 + - - -
353B ASN* 3.1 17.7 + - + +
354B GLY* 3.2 22.0 - - - +
359B PHE* 3.9 33.2 - + - -
361B MET* 3.6 22.2 - - + -
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Residues in contact with GLY 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ILE* 3.9 21.2 - - - +
377A THR* 4.9 0.4 - - - -
399A FAD 3.9 23.0 - - - -
347B ILE 3.3 5.1 + - - +
348B GLN 3.2 14.8 + - - -
349B CYS 3.3 1.0 + - - -
350B PHE* 1.3 76.8 - - - +
352B GLY* 1.3 53.9 + - - -
354B GLY* 2.7 26.5 + - - -
355B TYR 3.5 2.9 + - - -
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Residues in contact with GLY 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A TRP* 3.1 28.3 - - - -
373A ILE* 3.7 8.1 - - - +
399A FAD 2.9 41.5 + - - -
351B GLY* 1.3 70.1 - - - -
353B ASN* 1.3 60.0 + - - +
355B TYR* 3.1 18.7 + - - +
356B ILE 3.6 2.6 + - - -
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Residues in contact with ASN 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PHE* 5.5 1.6 - - - -
166A TRP* 3.5 21.6 - - - -
399A FAD 4.6 1.0 + - - -
276B TYR* 2.9 26.4 + - - +
280B ARG* 4.9 9.1 - - - +
350B PHE* 3.1 16.2 + - + +
351B GLY 2.8 0.8 + - - -
352B GLY* 1.3 72.1 - - - +
354B GLY* 1.3 64.9 + - - +
356B ILE* 3.1 13.6 + - - +
359B PHE* 3.1 55.7 - - + +
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Residues in contact with GLY 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 4.5 1.7 - - - +
347B ILE* 3.6 23.6 - - - +
350B PHE* 3.2 21.3 - - - +
351B GLY 2.7 13.0 + - - -
353B ASN* 1.3 75.2 - - - +
355B TYR* 1.3 57.9 + - - +
356B ILE 3.4 3.7 + - - +
359B PHE* 5.3 0.2 - - - +
361B MET* 3.9 22.8 - - - +
362B GLY* 3.9 10.9 + - - -
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Residues in contact with TYR 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LYS* 3.5 10.2 - - + -
214A LEU* 2.8 40.3 + - + -
215A GLY 3.0 42.7 - - - -
216A MET* 3.4 13.2 + - + +
366A ARG 2.7 29.2 + - - -
367A ASP 3.6 0.3 + - - -
369A LYS* 4.4 8.3 - - + -
370A LEU* 3.5 44.8 - - + +
373A ILE* 4.4 19.3 - - + -
399A FAD 4.2 15.0 - - + -
347B ILE* 4.1 1.3 - - + +
351B GLY 3.5 1.8 + - - -
352B GLY* 3.1 15.0 + - - +
353B ASN 3.1 1.0 - - - -
354B GLY* 1.3 78.8 - - - +
356B ILE* 1.3 59.3 + - - +
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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