Contacts of the helix formed by residues 329 - 360 (chain B) in PDB entry 5NC5
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 329 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN* 3.6 33.4 + - + +
136B PHE 4.0 6.1 - - - +
137B LEU* 3.4 24.1 + - - +
299B ALA* 5.4 1.9 - - - +
327B TYR* 3.8 33.1 - - + +
328B ASP* 1.4 70.3 + - - +
330B THR* 1.4 64.7 + - - +
331B PRO* 3.5 0.7 - - - -
332B PHE* 3.3 11.4 + - - +
333B VAL* 3.2 24.7 + - - +
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Residues in contact with THR 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 4.1 8.0 - - - +
299B ALA* 3.4 15.0 + - - +
300B LEU* 4.0 20.9 - - + +
303B ALA* 3.3 28.0 - - + +
307B ARG* 5.7 1.1 - - - +
328B ASP* 2.8 25.2 + - - +
329B THR* 1.4 69.1 + - - +
331B PRO* 1.3 70.5 - - + +
333B VAL* 3.0 8.4 + - - +
334B LYS* 2.8 26.3 + - + +
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Residues in contact with PRO 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ARG* 5.9 0.9 - - - +
328B ASP* 3.1 31.0 - - + +
329B THR 3.5 0.4 - - - -
330B THR* 1.3 96.8 - - + +
332B PHE* 1.3 61.9 + - - +
334B LYS* 3.2 10.2 + - + +
335B ILE* 3.1 28.8 + - + +
634B TRP* 4.1 19.1 - - + -
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Residues in contact with PHE 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN* 3.4 28.0 - - + +
35B TYR* 5.8 4.0 - - - -
328B ASP 4.9 0.6 + - - +
329B THR* 3.3 14.1 + - - +
330B THR 3.2 0.4 - - - -
331B PRO* 1.3 81.0 - - - +
333B VAL* 1.3 61.7 + - - +
335B ILE* 3.2 7.1 + - - +
336B SER* 3.0 37.0 + - - -
392B THR* 5.4 4.9 - - + -
567B GLU* 4.2 20.4 - - + -
568B ASP 3.9 16.4 - - - -
569B GLN* 4.5 13.7 - - + +
634B TRP* 4.0 25.7 - + + -
995B ALA* 3.9 7.0 - - + -
996B GLY* 3.6 37.7 - - - -
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Residues in contact with VAL 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL* 4.0 28.0 - - + -
33B ALA* 4.7 6.7 - - - +
34B GLN* 3.8 39.5 - - + +
299B ALA* 5.5 6.3 - - + -
300B LEU* 4.0 11.4 - - + -
329B THR* 3.2 17.9 + - - +
330B THR* 3.0 8.6 + - - +
332B PHE* 1.3 74.8 - - - +
334B LYS* 1.3 66.6 + - - +
336B SER* 3.6 7.6 - - - +
337B ILE* 3.0 26.7 + - + +
392B THR* 5.8 0.4 - - - +
395B MET* 5.2 6.5 - - + -
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Residues in contact with LYS 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 4.1 14.1 - - + +
330B THR* 2.8 15.4 + - + +
331B PRO* 3.4 13.9 - - + +
332B PHE 3.2 0.2 - - - -
333B VAL* 1.3 76.6 - - - +
335B ILE* 1.3 63.8 + - + +
337B ILE* 3.1 9.9 + - - +
338B HIS* 3.0 24.0 + - + +
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Residues in contact with ILE 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B PRO 3.1 18.5 + - - +
332B PHE* 3.2 6.9 + - + +
334B LYS* 1.3 72.6 - - + +
336B SER* 1.3 62.0 + - - +
338B HIS* 3.1 6.1 + - - +
339B GLU* 2.8 46.3 + - + +
634B TRP* 3.7 33.4 - - + -
995B ALA* 4.0 29.4 - - + +
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Residues in contact with SER 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B PHE* 3.0 33.0 + - - -
333B VAL* 3.6 8.8 - - - -
334B LYS 3.3 0.2 - - - -
335B ILE* 1.3 78.2 - - - +
337B ILE* 1.3 63.9 + - - +
339B GLU* 3.4 5.4 + - - +
340B VAL* 3.1 28.6 + - - +
392B THR* 4.6 7.3 + - - +
395B MET* 3.4 26.0 - - - -
996B GLY* 5.9 0.7 - - - -
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Residues in contact with ILE 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL* 4.1 17.3 - - + -
300B LEU* 4.6 11.9 - - + -
333B VAL* 3.0 33.3 + - + +
334B LYS* 3.1 9.2 + - + +
336B SER* 1.3 77.0 - - - +
338B HIS* 1.3 62.8 + - - +
340B VAL* 3.0 5.2 + - - +
341B VAL* 3.0 25.7 + - + +
390B ILE* 3.8 29.4 - - + -
395B MET* 3.9 11.9 - - + -
1117B D10 3.7 33.0 - - + -
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Residues in contact with HIS 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LYS* 3.0 14.2 + - + +
335B ILE* 3.5 11.9 - - + +
337B ILE* 1.3 76.9 - - - +
339B GLU* 1.3 65.2 + - - +
341B VAL* 3.3 6.1 + - + +
342B LYS* 2.9 35.1 + - + +
3H GLU* 3.6 31.8 + - - -
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Residues in contact with GLU 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ILE* 2.8 34.7 + - + +
336B SER* 3.7 6.3 - - - +
338B HIS* 1.3 82.5 + - + +
340B VAL* 1.3 59.9 + - + +
342B LYS* 3.3 36.0 + - - +
343B THR* 2.8 33.5 + - - -
988B PRO* 6.1 0.7 - - - +
989B LEU* 5.0 2.9 - - - +
992B SER* 5.1 3.1 + - - -
995B ALA 5.3 1.8 - - - +
1000B GLN* 2.8 37.8 + - - +
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B SER* 3.1 16.2 + - - +
337B ILE 3.0 6.0 + - - +
339B GLU* 1.3 80.3 - - + +
341B VAL* 1.3 64.3 + - - +
343B THR* 3.6 4.9 + - - -
344B LEU* 3.1 39.2 + - + +
395B MET* 3.9 39.0 - - + +
396B PHE* 5.0 10.3 - - + +
398B MET* 5.1 1.6 - - + -
399B VAL* 4.2 13.0 - - + -
1117B D10 4.1 23.8 - - + -
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Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ILE* 3.0 18.8 + - + +
338B HIS* 3.3 7.6 + - + +
340B VAL* 1.3 75.5 - - + +
342B LYS* 1.3 61.8 + - - +
344B LEU* 3.3 8.4 + - + +
345B VAL* 2.9 40.4 + - + +
1117B D10 4.2 28.9 - - + -
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Residues in contact with LYS 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B HIS* 2.9 22.1 + - + +
339B GLU* 3.3 35.1 + - - +
341B VAL* 1.3 79.5 - - - +
343B THR* 1.3 57.3 + - - +
345B VAL* 3.8 6.5 - - + +
346B GLU* 2.9 65.6 + - + +
988B PRO* 5.4 9.6 - - + +
3H GLU* 2.9 35.2 - - + +
7H SER* 4.7 4.3 - - - +
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Residues in contact with THR 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLU* 2.8 23.2 + - - -
340B VAL* 3.7 7.7 - - - +
342B LYS* 1.3 77.5 - - - +
344B LEU* 1.3 64.2 + - - +
346B GLU* 3.9 10.5 + - - +
347B ALA* 3.0 23.1 + - + +
399B VAL* 4.2 17.0 - - + +
402B ILE* 3.7 22.0 - - + -
985B GLY 4.6 15.8 - - - +
986B VAL* 6.3 1.6 - - + -
988B PRO* 5.9 1.2 - - - +
989B LEU* 3.9 24.1 - - + +
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B VAL* 3.1 36.7 + - + +
341B VAL* 3.3 8.9 + - + +
343B THR* 1.3 77.0 - - - +
345B VAL* 1.3 62.7 + - + +
347B ALA* 3.3 6.9 + - + +
348B ILE* 3.1 28.5 + - + +
372B VAL* 6.4 0.2 - - + -
376B LEU* 3.7 45.3 - - + -
380B PHE* 5.1 10.1 - - + -
398B MET* 4.8 12.8 - - + +
399B VAL* 5.5 1.1 - - + -
402B ILE* 3.5 32.1 - - + -
405B LEU* 6.0 0.2 - - + -
1117B D10 5.3 2.5 - - + -
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Residues in contact with VAL 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B VAL* 2.9 29.6 + - + +
342B LYS* 3.8 6.3 - - + +
344B LEU* 1.3 75.0 - - + +
346B GLU* 1.3 70.9 + - + +
348B ILE* 3.1 13.7 + - + +
349B ILE* 3.0 38.1 + - + +
4H LEU* 5.0 14.8 - - + -
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Residues in contact with GLU 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B LYS* 2.9 47.0 + - + +
343B THR* 3.9 9.4 + - - +
345B VAL* 1.3 76.5 - - + +
347B ALA* 1.3 57.2 + - - +
349B ILE* 3.0 12.1 + - + +
350B LEU* 2.8 40.1 + - + +
985B GLY* 4.7 5.6 - - - +
988B PRO* 3.5 28.3 - - - +
7H SER* 2.6 36.5 + - - +
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Residues in contact with ALA 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B THR* 3.0 19.0 + - + +
344B LEU* 3.5 9.0 - - + +
345B VAL 3.2 0.2 - - - -
346B GLU* 1.3 77.5 - - - +
348B ILE* 1.3 62.1 + - + +
350B LEU* 3.4 10.3 + - - +
351B VAL* 3.1 28.4 + - - +
402B ILE* 4.1 28.7 - - + -
406B VAL* 5.0 6.4 - - + +
981B ALA* 5.6 0.8 - - - +
985B GLY* 5.3 8.4 - - - -
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Residues in contact with ILE 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 3.1 18.0 + - + +
345B VAL* 3.1 14.6 + - + +
347B ALA* 1.3 78.2 - - + +
349B ILE* 1.3 64.5 + - + +
351B VAL* 3.7 5.5 + - - +
352B PHE* 3.1 20.3 + - - +
369B THR* 3.9 35.2 + - + +
372B VAL* 3.6 35.0 - - + -
373B PRO* 3.7 18.2 - - + -
376B LEU* 4.6 9.2 - - + -
406B VAL* 6.3 0.9 - - + -
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Residues in contact with ILE 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B VAL* 3.0 31.8 + - + +
346B GLU* 3.0 15.1 + - + +
348B ILE* 1.3 76.3 - - + +
350B LEU* 1.3 59.7 + - + +
352B PHE* 3.0 14.6 + - + +
353B LEU* 2.8 45.8 + - + +
4H LEU* 4.9 9.2 - - + -
7H SER* 5.5 5.6 - - - -
8H LEU* 4.1 34.5 - - + -
11H ALA* 5.1 4.9 - - + -
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Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B GLU* 2.8 28.3 + - + +
347B ALA* 3.7 5.6 - - - +
349B ILE* 1.3 73.4 - - + +
351B VAL* 1.3 57.6 + - - +
353B LEU* 3.0 8.9 + - + +
354B VAL* 2.8 35.4 + - + +
981B ALA* 3.6 15.5 - - + +
984B LEU* 3.4 30.5 - - + +
985B GLY* 3.3 39.3 - - - +
11H ALA* 3.8 29.8 - - + -
15H VAL* 4.6 3.1 - - + -
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Residues in contact with VAL 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B ALA 3.1 17.0 + - - +
348B ILE* 4.0 5.8 - - - +
350B LEU* 1.3 76.0 - - - +
352B PHE* 1.3 58.3 + - - +
354B VAL* 4.1 5.1 - - - +
355B MET* 2.9 40.0 + - + +
365B THR 5.6 0.2 - - - +
368B PRO* 3.6 32.8 - - + -
369B THR* 5.4 2.0 - - - +
372B VAL* 6.0 1.8 - - + -
406B VAL* 3.7 41.5 - - + +
410B ILE* 4.5 9.6 - - + -
981B ALA* 4.0 11.9 - - + -
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Residues in contact with PHE 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ILE 3.1 14.0 + - - +
349B ILE* 3.0 16.4 + - + +
351B VAL* 1.3 77.6 - - - +
353B LEU* 1.3 85.0 + - + +
355B MET* 4.6 0.4 - - - -
356B TYR* 3.1 28.2 + + + +
362B PHE* 4.3 22.2 - + - -
365B THR* 3.0 55.6 + - + -
366B LEU* 5.1 4.7 - - + -
369B THR* 4.2 12.5 + - + +
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Residues in contact with LEU 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B ILE* 2.8 35.4 + - + +
350B LEU* 3.0 8.7 + - + +
352B PHE* 1.3 95.8 - - + +
354B VAL* 1.3 59.0 + - - +
356B TYR* 3.2 7.1 + - + +
357B LEU* 2.9 29.1 + - - +
8H LEU* 4.7 5.8 - - + -
11H ALA* 3.6 35.9 - - + -
12H VAL* 4.4 20.9 - - + +
15H VAL* 3.9 19.0 - - + +
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Residues in contact with VAL 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU* 2.8 23.6 + - + +
351B VAL* 4.1 4.5 - - - +
353B LEU* 1.3 70.1 - - - +
355B MET* 1.3 67.8 + - + +
357B LEU* 3.3 7.2 + - - +
358B PHE* 3.1 29.4 + - + +
410B ILE* 5.2 4.5 - - + -
977B MET* 3.9 42.6 - - + +
980B LEU* 4.0 33.4 - - + -
981B ALA* 4.4 11.0 - - + +
984B LEU* 5.9 0.2 - - + -
15H VAL* 4.3 11.7 - - + -
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Residues in contact with MET 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B VAL* 2.9 39.6 + - + +
354B VAL* 1.3 77.3 - - + +
356B TYR* 1.3 58.4 + - - +
359B LEU* 2.7 52.2 + - + +
361B ASN 5.7 0.7 - - - -
364B ALA 3.8 6.3 - - - +
365B THR* 3.6 21.1 - - - +
368B PRO* 3.7 22.0 - - + -
410B ILE* 4.4 18.4 - - + -
413B VAL* 3.2 38.6 - - + -
414B GLU 5.2 0.9 - - - +
977B MET* 4.2 17.9 - - - +
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Residues in contact with TYR 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B PHE* 3.1 24.4 + + + +
353B LEU* 3.7 6.3 - - + +
355B MET* 1.3 73.5 - - - +
357B LEU* 1.3 64.4 + - - +
360B GLN* 2.7 50.9 + - - +
361B ASN* 3.7 15.5 - - - +
362B PHE* 3.3 50.0 - + + -
365B THR* 3.7 6.9 + - - +
513B PHE* 3.8 30.1 - + - -
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Residues in contact with LEU 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU 2.9 17.8 + - - +
354B VAL* 3.3 6.5 + - - +
356B TYR* 1.3 80.4 - - - +
358B PHE* 1.3 60.4 + - + +
360B GLN* 3.2 21.5 + - - +
512B PHE* 3.9 28.7 - - + -
513B PHE* 4.5 9.6 - - + -
516B PHE* 3.8 36.4 - - + -
980B LEU* 5.2 0.4 - - + -
15H VAL* 4.0 26.2 - - + +
16H PRO* 5.8 2.5 - - + -
19H MET* 4.1 17.3 - - + -
----------------------------------------------------------
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Residues in contact with PHE 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B VAL* 3.1 22.7 + - + +
357B LEU* 1.3 85.5 - - + +
359B LEU* 1.3 66.9 + - + +
360B GLN* 3.6 13.7 + - - +
516B PHE* 4.2 18.6 - + - -
517B ASN* 4.6 3.1 - - - +
520B PHE* 4.2 27.1 - + - -
973B ARG* 3.6 42.7 + - + -
976B LEU* 4.8 10.3 - - + -
977B MET* 3.7 37.7 - - + -
980B LEU* 4.9 0.2 - - + -
19H MET* 3.1 37.9 - - + -
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Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B MET* 2.7 47.2 + - + +
358B PHE* 1.3 77.1 - - + +
360B GLN* 1.3 70.2 + - - +
361B ASN* 3.2 15.3 + - - +
364B ALA* 3.7 23.8 - - + -
413B VAL* 4.1 2.9 - - + -
414B GLU* 5.0 5.2 - - + -
417B GLU* 3.8 35.0 - - + +
500B ILE* 5.9 1.9 - - - +
509B LYS* 4.7 2.6 + - - -
973B ARG* 3.4 32.5 - - - +
977B MET* 4.9 6.5 - - + -
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Residues in contact with GLN 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B MET 3.6 0.4 + - - -
356B TYR* 2.7 44.3 + - - +
357B LEU 3.2 18.9 + - - +
358B PHE 3.6 8.9 + - - -
359B LEU* 1.3 73.4 - - - +
361B ASN* 1.3 60.7 + - - +
509B LYS* 2.8 33.4 + - - +
513B PHE* 3.4 39.4 + - + +
516B PHE* 4.3 4.0 - - - -
517B ASN* 3.0 38.0 + - - +
----------------------------------------------------------
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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