Contacts of the helix formed by residues 308 - 334 (chain B) in PDB entry 4DJH
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 308 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B PHE* 4.2 14.7 - - + -
305B SER* 4.4 16.5 - - - +
306B THR 3.3 1.6 - - - +
307B ALA* 1.3 73.8 - - - +
309B LEU* 1.3 55.2 + - - +
310B SER 2.9 3.6 - - - -
311B SER* 2.7 43.4 + - - +
312B TYR 3.4 3.1 + - - -
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ASN* 6.1 2.5 - - - +
293B PHE* 5.8 0.2 - - - -
305B SER 5.4 0.2 + - - -
306B THR* 3.8 19.0 + - + +
307B ALA* 3.0 1.9 - - - -
308B ALA* 1.3 77.7 - - - +
310B SER* 1.3 60.4 + - - +
312B TYR* 3.5 17.3 + - + +
313B TYR* 3.0 57.1 + - + +
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Residues in contact with SER 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ALA 3.6 12.1 + - - -
308B ALA 2.9 0.6 + - - -
309B LEU* 1.3 77.5 - - - +
311B SER* 1.3 63.6 + - - +
313B TYR* 3.5 9.0 + - - +
314B PHE* 3.1 21.7 + - - +
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Residues in contact with SER 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B PHE* 3.7 17.3 - - - -
308B ALA* 2.7 26.5 + - - +
310B SER* 1.3 69.6 - - - +
312B TYR* 1.3 54.6 + - - -
313B TYR 3.1 1.6 - - - -
314B PHE* 2.9 10.3 + - - +
315B CYS* 2.8 42.1 + - - -
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Residues in contact with TYR 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLN* 4.4 4.0 + - - -
290B ILE* 4.5 5.6 - - + -
293B PHE* 3.7 35.2 - + + -
294B ILE* 4.5 15.9 - - + -
297B GLU* 5.7 0.9 - - - -
308B ALA 3.4 2.0 + - - -
309B LEU* 3.6 18.4 - - + +
311B SER* 1.3 78.0 - - - +
313B TYR* 1.3 98.4 + + - +
315B CYS* 3.3 5.6 + - - +
316B ILE* 3.1 46.9 + - + +
1300B JDC 3.9 33.6 + - + +
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Residues in contact with TYR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLN* 3.7 21.1 + - + -
119B TYR* 3.4 50.0 - + + +
309B LEU* 3.0 51.0 + - + +
310B SER* 3.8 10.3 - - - +
311B SER 3.1 0.8 - - - -
312B TYR* 1.3 94.1 - + - +
314B PHE* 1.3 63.1 + - - +
316B ILE* 3.2 20.1 - - + +
317B ALA* 3.1 21.7 + - - +
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Residues in contact with PHE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PRO* 5.4 7.0 - - + -
310B SER 3.1 12.9 + - - +
311B SER* 2.9 11.3 + - - +
313B TYR* 1.3 76.0 - - - +
315B CYS* 1.3 75.1 + - - +
317B ALA* 3.1 16.6 + - + +
318B LEU* 3.2 43.7 + - + +
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Residues in contact with CYS 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B CYS 4.3 2.1 - - - +
289B PRO* 3.7 34.5 - - - -
290B ILE* 3.7 32.9 + - + +
293B PHE* 4.1 15.5 - - + -
311B SER* 2.8 23.1 + - - +
312B TYR* 3.7 6.1 - - - +
313B TYR 3.3 0.2 - - - -
314B PHE* 1.3 87.1 - - - +
316B ILE* 1.3 60.6 + - - +
318B LEU* 3.3 14.4 + - - +
319B GLY* 3.5 7.3 + - - -
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Residues in contact with ILE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLN* 2.6 35.7 - - + +
290B ILE* 3.5 21.3 - - + -
312B TYR* 3.1 29.3 + - + +
313B TYR* 3.2 30.5 - - + +
315B CYS* 1.3 74.8 - - - +
317B ALA* 1.3 60.8 + - - +
318B LEU 3.2 0.2 - - - -
319B GLY* 3.4 2.1 + - - +
320B TYR* 3.0 44.2 + - + -
1300B JDC 3.6 29.1 - - + +
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B TYR 3.1 15.1 + - - +
314B PHE* 3.1 17.7 + - + +
316B ILE* 1.3 79.3 - - - +
318B LEU* 1.3 57.7 + - + +
320B TYR* 3.8 7.3 - - - +
321B THR* 2.6 40.8 + - - +
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Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL* 5.1 4.9 - - + +
286B CYS* 3.2 56.0 - - - +
289B PRO* 4.7 9.0 - - + -
314B PHE* 3.2 50.8 + - + +
315B CYS* 3.5 7.6 - - - +
317B ALA* 1.3 77.5 - - + +
319B GLY* 1.3 59.5 + - - +
321B THR* 3.6 9.1 - - + +
322B ASN 3.0 23.0 + - - -
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Residues in contact with GLY 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B CYS 4.1 2.4 + - - -
287B TRP* 4.1 21.3 + - - -
290B ILE* 5.9 0.7 - - - -
315B CYS 3.5 6.0 + - - -
316B ILE 3.4 4.8 + - - -
317B ALA 3.3 0.4 - - - -
318B LEU* 1.3 75.6 - - - +
320B TYR* 1.3 66.1 + - - +
322B ASN* 3.3 12.0 + - - +
323B SER* 3.4 14.4 + - - -
1300B JDC 3.8 24.8 - - - +
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Residues in contact with TYR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B VAL* 3.7 11.0 - - + +
108B VAL* 3.3 24.2 - - + -
109B THR* 4.8 2.8 + - - -
111B THR* 2.7 23.4 + - - -
112B MET* 3.2 52.1 - - + +
115B GLN* 4.0 14.8 - - + +
316B ILE* 3.0 34.9 + - + +
317B ALA* 3.9 6.7 - - - +
319B GLY* 1.3 74.2 - - - +
321B THR* 1.3 62.8 + - - +
323B SER* 3.1 21.5 + - - -
324B SER 3.5 4.2 + - - -
1300B JDC 3.4 51.1 + - + +
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Residues in contact with THR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 5.5 2.4 - - - +
69B VAL* 3.9 19.4 - - + +
286B CYS* 5.5 0.7 - - - -
317B ALA* 2.6 27.1 + - - +
318B LEU* 3.6 14.4 - - + +
319B GLY 3.2 0.2 - - - -
320B TYR* 1.3 78.7 - - - +
322B ASN* 1.3 62.4 + - - +
324B SER* 2.9 24.7 + - - +
325B LEU* 3.0 30.9 + - + +
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Residues in contact with ASN 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASP* 4.5 4.4 + - - -
282B VAL* 3.7 9.0 - - - +
283B PHE* 3.1 54.7 + - - +
286B CYS* 3.7 11.9 - - + -
287B TRP* 4.2 8.7 - - - +
318B LEU 3.0 18.1 + - - +
319B GLY 3.6 5.8 + - - +
320B TYR 3.2 0.4 - - - -
321B THR* 1.3 76.4 - - - +
323B SER* 1.3 65.9 + - - +
325B LEU* 3.2 18.7 + - - +
326B ASN* 3.3 31.9 + - - +
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Residues in contact with SER 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLY* 4.5 0.7 - - - -
77B ASN* 2.8 24.6 + - - -
105B ASP* 3.5 41.3 + - - +
108B VAL* 3.3 20.2 - - - +
109B THR* 3.9 9.2 - - - -
141B ASN* 4.7 0.9 + - - -
287B TRP* 5.7 1.7 + - - -
319B GLY 3.4 11.1 + - - -
320B TYR* 3.1 11.8 + - - -
322B ASN* 1.3 79.5 + - - +
324B SER* 1.3 58.8 + - - +
327B PRO* 3.3 9.2 - - - +
1300B JDC 5.5 0.2 - - - +
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Residues in contact with SER 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B VAL* 3.2 47.7 + - - +
72B VAL* 3.4 24.0 - - - +
73B GLY* 3.4 18.2 - - - -
320B TYR 3.5 0.8 + - - -
321B THR* 2.9 15.9 + - - +
323B SER* 1.3 77.7 - - - +
325B LEU* 1.3 64.4 + - - +
327B PRO* 3.5 6.5 - - - +
328B ILE* 3.9 6.2 - - - +
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Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B VAL* 3.7 30.5 - - + -
286B CYS* 4.6 4.3 - - - -
321B THR* 3.0 36.3 + - + +
322B ASN* 3.2 10.7 + - - +
324B SER* 1.3 79.3 - - - +
326B ASN* 1.3 68.0 + - - +
328B ILE* 2.9 27.6 + - + +
329B LEU* 2.9 25.0 + - + +
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Residues in contact with ASN 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN* 4.7 0.2 - - - +
101B LEU* 3.8 16.2 - - - +
105B ASP* 2.5 31.0 + - - +
279B VAL* 3.9 19.6 - - - +
282B VAL* 5.6 0.5 - - - +
283B PHE* 5.6 1.6 - - - +
322B ASN* 3.3 28.9 + - - +
325B LEU* 1.3 75.2 - - - +
327B PRO* 1.3 72.3 - - + +
329B LEU* 2.8 26.4 + - - +
330B TYR* 2.9 38.3 + - + +
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Residues in contact with PRO 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 4.2 7.0 - - + +
76B GLY* 3.6 31.9 - - - +
77B ASN* 3.3 30.7 - - - +
80B VAL* 4.6 1.6 - - + -
323B SER 3.3 12.8 - - - +
324B SER 3.5 8.5 - - - +
325B LEU 3.5 3.1 - - - -
326B ASN* 1.3 95.7 - - + +
328B ILE* 1.3 60.2 + - + +
330B TYR* 3.5 16.4 + - + +
331B ALA* 3.4 19.1 + - - +
341B PHE* 4.0 7.6 - - + -
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Residues in contact with ILE 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 4.0 24.9 - - + -
324B SER 3.9 11.9 - - - +
325B LEU* 2.9 21.5 + - + +
327B PRO* 1.3 73.9 - - + +
329B LEU* 1.3 69.1 + - + +
331B ALA* 3.3 8.1 + - - +
332B PHE* 3.2 39.5 + - + +
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Residues in contact with LEU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LEU* 4.3 2.0 - - - -
278B VAL* 4.2 19.3 - - + -
279B VAL* 4.2 26.7 - - + -
282B VAL* 4.1 27.1 - - + -
325B LEU* 2.9 26.6 + - + +
326B ASN* 2.8 23.1 + - - +
328B ILE* 1.3 72.1 - - + +
330B TYR* 1.3 65.7 + - - +
332B PHE* 3.2 5.2 + - + +
333B LEU* 2.9 41.4 + - + +
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Residues in contact with TYR 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN* 4.6 5.2 - - - -
80B VAL* 3.6 21.1 - - + -
98B ILE* 3.8 43.6 + - + +
101B LEU* 3.2 31.9 - - + +
102B ALA* 4.6 2.6 + - + -
105B ASP* 4.6 0.2 + - - -
152B MET* 5.3 0.9 - - + -
275B LEU* 4.1 16.6 - - + -
279B VAL* 4.1 20.4 - - + -
326B ASN* 2.9 39.8 + - + +
327B PRO* 3.5 17.7 - - + +
328B ILE 3.3 0.2 - - - -
329B LEU* 1.3 74.8 - - - +
331B ALA* 1.3 56.9 + - - +
334B ASP* 3.0 35.5 + - - +
337B PHE* 3.6 25.0 - + + +
341B PHE* 4.6 2.5 - - + -
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Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A PHE* 4.6 13.5 - - + -
327B PRO 3.4 5.4 + - - +
328B ILE* 3.3 11.4 + - + +
329B LEU 3.1 0.4 - - - -
330B TYR* 1.3 79.7 - - - +
332B PHE* 1.3 70.0 + - + +
334B ASP 3.4 4.5 + - - +
338B LYS* 3.2 35.9 - - - +
341B PHE* 3.7 29.6 - - + -
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Residues in contact with PHE 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A CYS 5.4 7.6 - - - -
346A PHE* 6.3 1.6 - + - -
274B ARG* 4.8 3.6 + - - -
328B ILE* 3.2 30.3 + - + +
329B LEU* 3.2 7.4 + - + +
331B ALA* 1.3 89.1 - - + +
333B LEU* 1.3 68.7 + - + +
334B ASP 3.5 0.6 - - - -
338B LYS* 4.5 18.3 + - - +
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ARG* 3.7 30.2 - - - +
274B ARG* 3.9 36.9 + - + +
275B LEU* 3.4 30.8 - - + +
278B VAL* 3.7 39.0 - - + -
329B LEU* 2.9 27.2 + - + +
332B PHE* 1.3 87.4 - - + +
334B ASP* 1.3 60.4 + - - +
335B GLU 4.3 0.4 - - - -
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Residues in contact with ASP 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B MET* 4.9 1.0 - - - +
95B ASN* 4.9 3.3 + - - +
271B ARG* 4.6 6.2 - - - +
272B ILE* 4.3 19.3 - - - +
275B LEU* 4.3 13.0 - - + -
330B TYR 3.0 14.6 + - - +
331B ALA 3.4 9.0 - - - +
332B PHE 3.5 1.2 - - - -
333B LEU* 1.3 81.7 - - - +
335B GLU* 1.3 69.3 + - - +
336B ASN* 3.6 17.5 + - - +
337B PHE* 3.0 37.9 + - + -
338B LYS* 3.1 18.3 + - - -
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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