Contacts of the helix formed by residues 329 - 353 (chain B) in PDB entry 4OG2
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 PRO 329 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 3.3 37.0 - - - +
283B ASN 5.5 2.7 - - - +
284B THR* 5.8 1.1 - - - -
285B SER* 5.6 4.7 - - - +
304B TYR* 4.2 1.1 - - - -
320B TYR* 3.2 31.0 - - + +
327B GLU 3.4 6.5 - - - +
328B PRO* 1.3 86.9 - - + +
330B GLN* 1.3 67.0 + - - +
331B PHE 4.2 0.2 - - - +
332B SER* 3.0 27.5 + - - +
333B ALA* 3.1 12.3 + - - +
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Residues in contact with GLN 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B VAL* 5.5 1.7 - - - +
280B ASP* 2.9 26.9 + - - +
283B ASN* 3.2 28.1 + - - +
301B ALA 4.1 0.7 - - - +
302B GLN* 3.5 12.9 + - - +
303B ALA* 2.9 27.7 + - - +
304B TYR* 3.9 29.0 - - + +
328B PRO 4.0 0.2 + - - -
329B PRO* 1.3 71.7 - - - +
331B PHE* 1.3 80.2 + - + +
333B ALA* 3.1 3.6 + - - +
334B GLN* 2.9 51.0 + - - +
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Residues in contact with PHE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 3.6 23.3 - - + -
73B GLU* 3.6 21.5 - - + +
74B GLN* 3.9 21.5 + - + +
153B SER* 4.1 15.3 - - - -
280B ASP* 3.3 45.5 - - - -
283B ASN* 3.2 28.9 + - + -
329B PRO* 3.2 2.2 - - - +
330B GLN* 1.3 92.8 - - - +
332B SER* 1.3 57.3 + - - +
334B GLN* 3.5 16.1 - - - +
335B ALA* 3.1 28.4 + - - +
501B LEU* 3.5 22.4 - - + -
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Residues in contact with SER 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 2.7 33.5 + - - +
77B GLY* 3.4 17.0 - - - -
316B PHE* 3.8 7.9 - - - -
320B TYR* 3.5 18.0 - - - -
329B PRO* 3.0 31.2 + - - +
331B PHE* 1.3 76.8 - - - +
333B ALA* 1.3 59.3 + - - +
335B ALA 3.4 0.9 + - - -
336B PHE* 3.0 26.2 + - - +
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Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B TYR* 3.5 46.2 - - + -
316B PHE* 3.6 18.3 - - + -
329B PRO 3.1 6.0 + - - +
330B GLN 3.5 7.4 - - - +
332B SER* 1.3 76.3 - - - +
334B GLN* 1.3 58.5 + - - +
336B PHE* 3.4 3.8 + - - +
337B ALA* 2.9 28.1 + - - +
379B PRO* 4.1 6.3 - - + +
380B LEU* 3.9 7.4 - - + +
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Residues in contact with GLN 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B PRO* 3.1 26.7 - - - +
153B SER* 4.5 0.3 - - - -
155B THR* 5.6 1.6 - - - +
169B VAL* 3.5 15.0 + - + +
170B SER* 3.7 25.7 - - - +
171B ALA 4.3 1.8 + - - +
280B ASP* 5.3 0.2 - - - +
303B ALA* 3.7 25.9 - - - +
330B GLN* 2.9 42.3 + - + +
331B PHE* 3.5 16.7 - - - +
333B ALA* 1.3 74.1 - - - +
335B ALA* 1.3 60.1 + - - +
337B ALA* 3.3 3.6 + - - +
338B ALA* 3.0 23.7 + - - +
380B LEU* 3.7 24.7 - - + +
393B GLN* 5.5 0.2 + - - -
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Residues in contact with ALA 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 5.5 2.0 - - + -
74B GLN* 3.2 36.1 - - + +
78B ALA* 4.0 8.5 - - + +
127B VAL* 4.8 4.4 - - + +
152B PRO* 4.1 16.0 - - + +
331B PHE 3.1 18.1 + - - +
332B SER 3.7 4.3 - - - +
334B GLN* 1.3 73.9 - - - +
336B PHE* 1.3 65.4 + - - +
338B ALA* 3.2 4.0 + - - +
339B VAL* 3.1 26.2 + - - +
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Residues in contact with PHE 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLY 3.8 11.1 + - - +
80B ILE* 4.2 3.8 - - + -
81B ALA* 3.5 36.9 - - + +
84B TYR* 3.9 19.3 - + + -
85B PHE* 3.7 18.6 - + - -
312B ILE* 3.7 22.0 - - + -
316B PHE* 3.4 37.5 - + + -
332B SER 3.0 14.0 + - - +
333B ALA* 3.5 8.7 - - - +
335B ALA* 1.3 75.5 - - - +
337B ALA* 1.3 57.8 + - - +
339B VAL* 3.2 4.9 + - - +
340B GLN* 2.8 42.8 + - - -
379B PRO* 3.5 23.3 - - + -
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Residues in contact with ALA 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B VAL* 4.4 7.4 - - + -
333B ALA 2.9 18.0 + - - +
334B GLN 3.5 5.6 - - - +
335B ALA 3.2 0.2 - - - -
336B PHE* 1.3 78.9 - - - +
338B ALA* 1.3 57.7 + - - +
340B GLN* 3.3 10.8 + - - +
341B VAL* 2.9 34.1 + - - +
378B THR* 4.0 16.4 - - + +
379B PRO* 4.6 0.9 - - + -
380B LEU* 3.7 27.4 - - + -
383B ILE* 4.8 0.4 - - + -
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Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 3.7 28.3 - - + -
150B VAL* 3.8 25.1 - - + +
152B PRO* 4.4 4.9 - - + -
169B VAL* 4.0 9.1 - - + +
334B GLN 3.0 12.9 + - - +
335B ALA 3.6 8.5 - - - +
336B PHE 3.2 0.2 - - - -
337B ALA* 1.3 76.7 - - - +
339B VAL* 1.3 61.8 + - - +
341B VAL* 3.3 5.1 + - - +
342B TYR* 3.3 25.3 + - - -
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Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 5.3 3.1 - - + -
59B ILE* 4.2 25.6 - - + -
78B ALA* 4.2 14.6 - - + -
81B ALA* 3.7 23.1 - - + -
82B GLU 4.7 0.7 - - - +
85B PHE* 4.4 2.5 - - + -
96B ILE* 4.1 25.1 - - + -
98B LEU* 4.3 10.1 - - + -
127B VAL* 4.4 7.6 - - + -
335B ALA 3.1 13.4 + - - +
336B PHE 3.6 6.1 - - - +
338B ALA* 1.3 75.0 - - - +
340B GLN* 1.3 57.8 + - - +
342B TYR* 3.1 7.2 + - - +
343B VAL* 2.9 30.4 + - + +
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Residues in contact with GLN 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 3.4 25.3 - - + -
312B ILE* 3.5 14.7 - - - +
336B PHE* 2.8 16.1 + - + +
337B ALA 3.4 8.3 - - - +
339B VAL* 1.3 76.5 - - - +
341B VAL* 1.3 57.2 + - - +
343B VAL* 4.4 0.9 - - - +
344B GLU* 2.9 62.5 + - - +
376B TYR* 5.1 1.3 - - + -
377B ASN 2.9 28.2 + - - +
378B THR* 3.3 30.8 - - + +
379B PRO* 3.5 10.4 - - - +
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Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B VAL* 4.5 9.9 - - + -
169B VAL* 3.9 19.7 - - + -
337B ALA 2.9 18.6 + - - +
338B ALA* 3.6 9.4 - - - +
339B VAL 3.3 0.4 - - - -
340B GLN* 1.3 74.1 - - + +
342B TYR* 1.3 59.0 + - - +
345B SER* 2.8 35.7 + - - -
371B LEU* 4.0 16.8 - - + -
376B TYR* 3.8 46.8 - - + +
378B THR* 5.3 0.7 - - + -
383B ILE* 4.7 3.6 - - + -
385B PHE* 4.0 17.3 - - + -
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Residues in contact with TYR 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 4.0 25.6 - - + -
124B VAL* 5.4 1.1 - - + -
125B GLY* 3.9 8.7 - - - -
126B ILE 2.9 36.3 + - - -
127B VAL* 3.6 20.4 - - + -
148B PRO* 3.0 27.9 + - + +
150B VAL* 3.5 19.4 + - + +
338B ALA 3.3 16.2 + - - -
339B VAL* 3.1 8.9 + - - +
341B VAL* 1.3 78.8 - - - +
343B VAL* 1.3 56.9 + - - +
345B SER* 3.8 1.9 - - - -
346B LEU* 2.8 37.6 + - + +
367B LEU* 3.8 29.8 - - + +
371B LEU* 3.8 22.7 - - + -
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 4.9 1.6 - - + -
85B PHE* 3.8 41.3 - - + -
90B GLY 4.0 23.8 - - - +
91B VAL* 4.3 2.6 - - + +
96B ILE* 3.8 35.7 - - + -
339B VAL* 2.9 23.6 + - + +
340B GLN 3.9 3.1 - - - +
342B TYR* 1.3 72.9 - - - +
344B GLU* 1.3 60.6 + - + +
346B LEU* 3.3 7.5 + - - +
347B LYS* 2.9 37.0 + - + +
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 4.3 13.1 - - + -
312B ILE* 5.0 1.4 - - - +
340B GLN* 2.9 53.7 + - + +
343B VAL* 1.3 74.6 - - + +
345B SER* 1.3 57.3 + - - +
347B LYS* 3.4 17.5 + - + +
348B ALA* 3.0 28.1 + - - +
375B LYS 4.5 2.8 - - - +
376B TYR* 3.5 32.1 - - + +
377B ASN 4.7 1.2 + - - -
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Residues in contact with SER 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B VAL 2.8 19.2 + - - -
342B TYR* 3.9 0.4 - - - -
344B GLU* 1.3 73.0 - - - +
346B LEU* 1.3 61.0 + - - +
348B ALA* 3.3 1.7 + - - -
349B LEU* 2.8 31.7 + - - +
367B LEU* 3.8 14.1 - - - -
370B GLN* 3.4 14.1 + - - +
371B LEU* 3.1 25.9 - - - +
376B TYR* 2.8 28.5 + - - -
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ILE* 4.0 34.3 - - + -
57B ILE* 4.1 17.0 - - + -
91B VAL* 3.7 23.9 - - + +
124B VAL* 4.4 7.2 - - + -
342B TYR* 2.8 27.7 + - + +
343B VAL* 3.6 4.5 - - - +
345B SER* 1.3 78.0 - - - +
347B LYS* 1.3 56.4 + - - +
349B LEU* 3.8 3.4 - - + +
350B ASP* 2.8 33.1 + - - +
355B VAL* 4.5 8.5 - - + +
363B LEU* 4.5 20.2 - - + -
367B LEU* 3.8 25.8 - - + -
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Residues in contact with LYS 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 6.3 0.2 - - + -
90B GLY 3.8 14.1 - - - +
91B VAL* 3.8 17.9 - - - -
92B ASN* 3.2 30.5 + - - +
343B VAL* 2.9 30.2 + - + +
344B GLU* 3.6 17.8 - - + +
345B SER 3.2 0.2 - - - -
346B LEU* 1.3 77.3 - - - +
348B ALA* 1.3 56.5 + - - +
351B THR* 2.8 34.7 + - - +
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Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B GLU 3.0 17.4 + - - +
345B SER* 3.3 1.5 + - - +
347B LYS* 1.3 73.1 - - - +
349B LEU* 1.3 65.5 + - - +
351B THR* 3.4 7.3 + - - -
352B LYS* 3.4 30.1 + - - +
370B GLN* 3.4 27.6 - - - +
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B SER 2.8 18.1 + - - +
346B LEU* 3.8 3.6 - - + +
348B ALA* 1.3 76.4 - - - +
350B ASP* 1.3 52.8 + - - +
352B LYS* 3.0 9.0 + - + +
353B ASN* 2.8 48.1 + - + +
355B VAL* 3.9 9.4 - - + -
358B ILE* 4.6 7.4 - - + -
363B LEU* 3.6 30.5 - - + -
366B GLU* 4.0 28.3 - - + +
367B LEU* 3.9 27.6 - - + +
370B GLN* 4.1 16.0 + - + +
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Residues in contact with ASP 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B VAL* 4.1 9.7 - - + +
92B ASN* 2.9 33.2 + - - +
346B LEU 2.8 19.5 + - - +
349B LEU* 1.3 77.3 - - - +
351B THR* 1.3 61.3 + - - +
352B LYS 3.4 0.2 + - - -
353B ASN 3.4 6.7 - - - -
354B LYS* 3.4 31.6 + - - +
355B VAL* 2.9 41.8 + - + +
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Residues in contact with THR 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ASN* 3.6 11.7 + - - +
347B LYS 2.8 21.7 + - - -
348B ALA* 3.6 9.4 - - - -
349B LEU 3.2 0.2 - - - -
350B ASP* 1.3 77.5 - - - +
352B LYS* 1.3 64.3 + - + +
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Residues in contact with LYS 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ALA* 3.5 16.6 - - - +
349B LEU* 3.0 10.2 + - + +
351B THR* 1.3 84.0 - - + +
353B ASN* 1.3 79.0 + - - +
370B GLN* 2.8 33.9 + - - +
373B THR* 5.4 1.2 + - - -
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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
----------------------------------------------------------
349B LEU* 2.8 25.9 + - + +
350B ASP* 3.4 4.9 - - - -
352B LYS* 1.3 98.6 + - - +
354B LYS* 1.3 67.9 + - - +
355B VAL* 3.1 3.1 + - - -
358B ILE* 3.9 18.9 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
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