Contacts of the helix formed by residues 229 - 254 (chain A) in PDB entry 5A5J
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 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ILE* 3.8 18.6 - - + +
225A TYR* 3.7 35.7 - - + +
226A PHE 3.5 21.7 + - - -
227A PRO* 4.2 8.1 - - + -
228A GLY* 1.3 89.9 - - - +
230A HIS* 1.3 68.5 + - - +
231A ASN 3.1 2.7 - - - +
232A LYS* 3.7 8.2 - - - +
233A LEU* 2.9 29.6 + - - +
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Residues in contact with HIS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 4.2 24.4 - - + +
104A GLU* 5.9 1.0 + - - -
207A ILE* 6.3 1.3 - - + -
223A ILE* 5.9 3.0 - - - +
225A TYR* 3.6 11.4 + - + -
226A PHE* 3.5 40.2 + - + +
229A THR* 1.3 86.7 + - - +
231A ASN* 1.3 62.3 + - - +
233A LEU* 3.7 13.1 - - + +
234A LEU* 3.3 30.0 + - - +
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Residues in contact with ASN 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLY* 5.5 4.5 - - - -
229A THR 3.1 4.4 - - - +
230A HIS* 1.3 81.4 - - - +
232A LYS* 1.3 61.0 + - - +
233A LEU 3.2 1.6 - - - -
234A LEU* 3.9 17.7 - - - +
235A LYS* 2.9 28.6 + - - +
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Residues in contact with LYS 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LYS* 6.1 1.3 - - - +
203A GLU* 3.1 30.5 - - + +
204A ASN* 4.4 0.2 - - - +
207A ILE* 4.7 9.0 - - + -
228A GLY 4.3 8.2 + - - +
229A THR* 3.3 18.0 + - - +
231A ASN* 1.3 74.5 - - - +
233A LEU* 1.3 61.4 + - - +
235A LYS* 3.1 45.1 - - + +
236A ASN* 3.1 36.4 + - - +
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU* 5.0 13.9 - - + +
204A ASN* 4.0 23.1 - - + +
207A ILE* 3.3 44.2 - - + -
208A LEU* 4.0 22.0 - - + -
229A THR 2.9 13.4 + - - +
230A HIS* 3.7 15.3 - - + +
232A LYS* 1.3 75.7 - - - +
234A LEU* 1.3 64.7 + - + +
236A ASN* 3.2 4.3 + - - +
237A VAL* 3.0 35.4 + - + +
1494A 6YF 4.5 11.9 - - - -
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU* 4.2 25.4 - - + +
105A ARG* 5.9 2.2 - - + +
106A ALA* 4.5 28.5 - - + +
230A HIS 3.3 18.5 + - - +
231A ASN* 3.9 18.8 - - - +
233A LEU* 1.3 81.0 - - + +
235A LYS* 1.3 70.1 + - - +
237A VAL* 3.3 9.1 + - + +
238A ALA* 3.1 21.5 + - - +
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Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LYS* 4.9 12.3 - - - +
231A ASN 2.9 21.2 + - - +
232A LYS* 3.1 40.3 - - + +
234A LEU* 1.3 78.7 - - - +
236A ASN* 1.3 72.6 + - - +
238A ALA* 3.1 15.0 + - - +
239A PHE* 3.1 15.5 + - + +
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Residues in contact with ASN 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LYS* 3.5 31.3 + - + +
203A GLU* 3.4 37.5 + - - +
204A ASN* 3.2 26.1 + - - +
232A LYS* 3.1 20.0 + - - +
233A LEU 3.2 4.0 + - - +
234A LEU 3.0 0.4 - - - -
235A LYS* 1.3 86.6 - - - +
237A VAL* 1.3 66.9 + - - +
239A PHE* 3.2 9.4 + - - +
240A MET* 3.0 27.7 + - - +
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Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ALA* 5.1 12.3 - - + +
108A ARG* 4.6 17.5 - - + +
204A ASN* 4.5 10.7 - - - +
233A LEU* 3.0 21.2 + - + +
234A LEU* 3.9 9.6 - - + +
236A ASN* 1.3 74.8 - - - +
238A ALA* 1.3 58.8 + - - +
240A MET* 3.1 9.5 + - - +
241A LYS* 2.9 54.9 + - + +
289A ASN* 5.4 0.7 - - - +
292A VAL* 4.9 12.3 - - + -
1494A 6YF 3.7 25.8 - - - +
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Residues in contact with ALA 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LEU 3.1 10.5 + - - +
235A LYS* 3.1 14.0 + - - +
237A VAL* 1.3 76.6 - - - +
239A PHE* 1.3 57.5 + - - +
241A LYS* 4.1 10.1 - - - +
242A SER* 3.0 31.4 + - - -
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Residues in contact with PHE 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ASN* 4.1 28.9 - - + -
197A LEU* 4.6 9.0 - - + -
200A LYS* 3.6 43.3 - - + -
235A LYS* 3.1 15.5 + - + +
236A ASN* 3.3 12.3 - - - +
238A ALA* 1.3 73.6 - - - +
240A MET* 1.3 69.4 + - + +
242A SER* 3.5 5.8 - - - -
243A TYR* 3.0 42.8 + + + +
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Residues in contact with MET 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 3.6 28.5 - - - -
200A LYS* 4.6 11.4 - - + -
201A LEU* 4.0 40.4 - - + +
204A ASN* 4.6 14.4 - - - +
236A ASN 3.0 15.9 + - - +
237A VAL* 3.1 9.8 + - - +
239A PHE* 1.3 83.2 - - + +
241A LYS* 1.3 66.6 + - - +
243A TYR* 3.0 13.9 + - - +
244A ILE* 3.1 21.8 + - + +
292A VAL* 3.8 24.9 - - + +
295A PHE* 5.5 7.4 - - + -
296A GLY* 6.4 0.2 - - - -
1494A 6YF 5.5 5.4 - - - +
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Residues in contact with LYS 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ALA* 4.1 18.9 + - - +
237A VAL* 2.9 38.8 + - + +
238A ALA* 4.1 8.3 - - - +
240A MET* 1.3 74.8 - - - +
242A SER* 1.3 65.1 + - - +
243A TYR 3.0 0.7 + - - -
244A ILE* 3.1 3.4 + - - +
245A LEU 3.0 15.8 + - - -
285A GLU* 3.9 16.4 + - - -
288A GLU* 2.9 53.9 + - + +
289A ASN* 3.1 28.4 + - - +
292A VAL* 4.0 12.3 - - + +
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Residues in contact with SER 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ALA 3.0 22.1 + - - -
239A PHE* 3.5 8.7 - - - -
241A LYS* 1.3 74.8 - - - +
243A TYR* 1.3 56.5 + - - -
245A LEU* 3.2 11.5 - - - +
246A GLU* 3.0 25.1 + - - +
288A GLU* 3.7 1.2 + - - -
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Residues in contact with TYR 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A PHE* 3.6 26.4 - + - -
187A PHE* 3.7 15.1 - - - -
193A GLN* 3.1 40.2 + - + +
197A LEU* 4.3 21.2 - - + +
239A PHE* 3.0 35.1 + + + +
240A MET* 3.0 6.2 + - - +
241A LYS 3.0 0.2 + - - -
242A SER* 1.3 72.4 + - - +
244A ILE* 1.3 74.2 + - + +
245A LEU 3.0 2.0 - - - -
246A GLU* 3.2 37.5 - - - +
247A LYS* 2.6 37.5 + - + +
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Residues in contact with ILE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ILE* 5.2 0.2 - - + -
183A PHE* 4.3 15.3 - - + -
197A LEU* 5.9 1.3 - - + -
240A MET* 3.1 26.9 + - + +
241A LYS* 3.6 9.0 - - - +
243A TYR* 1.3 85.0 - - + +
245A LEU* 1.3 57.1 + - - +
247A LYS* 3.4 6.9 + - - +
248A VAL* 2.9 45.2 + - + +
264A ILE* 4.6 4.1 - - + +
287A LEU* 5.0 1.6 - - + +
288A GLU* 4.0 27.6 - - + +
291A ALA* 3.9 21.5 - - + -
292A VAL* 4.1 18.6 - - + -
295A PHE* 3.9 25.4 - - + -
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Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LYS 3.0 8.6 + - - +
242A SER* 3.2 16.2 - - - +
243A TYR 3.0 0.4 - - - -
244A ILE* 1.3 75.5 - - - +
246A GLU* 1.3 62.8 + - - +
247A LYS 3.2 0.7 - - - -
248A VAL* 4.0 21.3 - - + -
249A LYS* 3.2 46.4 + - - +
284A ILE* 4.4 22.0 - - + -
288A GLU* 2.6 39.9 - - + +
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Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLN* 5.2 5.4 - - - +
242A SER* 3.0 10.8 + - - +
243A TYR* 3.2 35.7 - - + +
245A LEU* 1.3 75.2 - - - +
247A LYS* 1.3 71.1 + - + +
249A LYS* 3.5 14.3 + - - +
250A GLU* 3.5 22.2 + - - +
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Residues in contact with LYS 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A PHE* 3.9 32.8 - - + -
185A LYS* 5.5 5.4 - - - -
187A PHE* 4.6 8.7 - - - -
193A GLN* 2.3 37.3 - - - +
243A TYR* 2.6 46.3 + - + +
244A ILE 3.6 7.2 - - - +
245A LEU 3.2 0.6 - - - -
246A GLU* 1.3 81.7 + - + +
248A VAL* 1.3 59.8 + - - +
249A LYS 3.2 0.2 - - - -
250A GLU* 3.4 25.2 - - - +
251A HIS* 3.0 41.1 + - + -
264A ILE* 4.5 2.9 - - + -
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Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ILE* 2.9 39.3 + - + +
245A LEU* 3.3 18.3 + - + +
247A LYS* 1.3 76.0 - - - +
249A LYS* 1.3 60.2 + - + +
251A HIS* 3.3 7.5 + - - +
252A GLN* 3.1 34.6 + - - +
264A ILE* 4.1 16.2 - - + -
268A LEU* 4.8 6.1 - - + +
284A ILE* 4.0 27.6 - - + -
287A LEU* 4.1 25.4 - - + -
288A GLU* 5.9 0.7 - - + +
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Residues in contact with LYS 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A LEU* 3.2 35.1 + - + +
246A GLU* 3.5 10.1 - - - +
247A LYS 3.2 0.2 - - - -
248A VAL* 1.3 73.3 - - - +
250A GLU* 1.3 67.2 + - + +
252A GLN* 3.1 21.3 + - - +
253A GLU* 3.0 27.4 + - + +
284A ILE* 5.7 4.5 - - - -
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Residues in contact with GLU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A GLU* 3.5 18.1 - - - +
247A LYS* 3.4 33.8 - - - +
249A LYS* 1.3 77.5 - - + +
251A HIS* 1.3 63.3 + - + +
253A GLU* 3.3 37.6 - - - +
254A SER* 3.9 5.7 + - - -
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Residues in contact with HIS 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ILE 4.1 0.8 + - - -
183A PHE* 4.1 14.3 + - + -
247A LYS* 3.0 31.3 + - + +
248A VAL 3.5 5.2 - - - +
249A LYS 3.1 0.6 - - - -
250A GLU* 1.3 79.4 - - + +
252A GLN* 1.3 64.4 + - - +
253A GLU 3.2 2.0 - - - -
254A SER* 3.2 17.0 + - - -
255A MET* 3.6 12.6 + - - +
262A ASP* 2.8 31.5 + - - -
264A ILE* 3.2 44.6 - - + +
265A ASP* 3.7 22.0 + - - +
268A LEU* 4.2 4.2 - - + +
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Residues in contact with GLN 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A VAL* 3.1 18.5 + - - +
249A LYS* 3.5 25.1 - - - +
251A HIS* 1.3 73.3 - - - +
253A GLU* 1.3 67.9 + - - +
254A SER 3.2 0.7 - - - -
255A MET* 3.3 31.5 - - - +
268A LEU* 4.0 27.0 - - + +
271A MET* 5.5 4.0 - - - +
284A ILE* 4.2 23.0 - - - +
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Residues in contact with GLU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LYS* 3.0 17.9 + - - +
250A GLU* 3.3 33.5 - - - +
251A HIS 3.2 0.2 - - - -
252A GLN* 1.3 78.5 - - - +
254A SER* 1.3 58.0 + - - +
255A MET 3.8 0.9 + - - -
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Residues in contact with SER 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A GLU 4.7 5.1 + - - -
251A HIS* 3.2 12.6 + - - -
252A GLN 3.2 0.8 - - - -
253A GLU* 1.3 80.0 - - - +
255A MET* 1.3 62.6 + - - +
256A ASP* 4.0 7.1 - - - +
265A ASP* 5.1 4.2 + - - +
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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