Contacts of the helix formed by residues 229 - 259 (chain C) in PDB entry 5LN3
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 LYS 229 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C PHE* 4.0 15.9 - - + -
227C VAL 3.7 2.9 + - - +
228C LEU* 1.4 71.9 - - - +
230C GLN* 1.4 56.5 + - - +
231C LYS* 4.1 28.9 - - + +
232C GLU* 3.2 42.7 + - + +
233C VAL* 3.0 28.5 + - - +
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Residues in contact with GLN 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ARG* 4.4 13.8 + - - +
61C PHE* 4.2 17.8 - - + -
208C ALA* 3.4 37.5 + - + +
209C GLU* 3.7 9.9 + - - +
211C VAL 4.6 6.1 + - - -
212C GLU* 5.8 2.0 - - - +
228C LEU 4.0 12.7 + - - -
229C LYS* 1.4 69.9 + - - +
231C LYS* 1.4 59.4 + - - +
233C VAL* 3.3 8.1 + - - +
234C GLU* 2.9 31.4 + - - +
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Residues in contact with LYS 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C LYS* 3.4 24.3 - - + +
230C GLN* 1.4 75.8 - - - +
232C GLU* 1.3 63.8 + - - +
234C GLU* 3.0 30.8 + - - +
235C GLN* 3.0 11.4 + - + +
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Residues in contact with GLU 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LEU* 4.4 22.0 - - + -
229C LYS* 3.2 45.1 + - + +
231C LYS* 1.3 81.3 - - - +
233C VAL* 1.3 61.7 + - - +
235C GLN* 3.0 31.4 + - - +
236C LEU* 3.1 39.7 + - + +
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Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ALA* 3.6 16.2 - - + +
211C VAL* 3.4 33.7 - - + +
212C GLU* 6.0 0.2 - - - -
213C ILE* 4.1 23.3 - - + +
228C LEU* 3.8 27.6 - - + +
229C LYS 3.0 21.7 + - - +
230C GLN* 3.6 11.4 - - - +
232C GLU* 1.3 74.8 - - - +
234C GLU* 1.4 56.7 + - - +
236C LEU* 3.3 12.1 + - - +
237C ILE* 3.0 34.4 + - + +
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Residues in contact with GLU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ALA* 3.7 16.1 - - + +
230C GLN 2.9 16.5 + - - +
231C LYS* 3.0 27.2 - - - +
233C VAL* 1.4 73.9 - - - +
235C GLN* 1.4 65.2 + - - +
237C ILE* 3.1 9.5 + - - +
238C LYS* 3.0 37.6 + - + +
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Residues in contact with GLN 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C LYS* 3.0 15.0 + - + +
232C GLU* 3.0 35.8 + - - +
234C GLU* 1.4 84.6 - - - +
236C LEU* 1.3 71.3 + - - +
238C LYS* 3.6 4.7 + - - +
239C LYS* 3.0 41.5 + - - +
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Residues in contact with LEU 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C LEU* 3.7 46.0 - - + -
194C ILE* 4.0 16.0 - - + +
213C ILE* 5.0 11.0 - - + -
228C LEU* 4.8 15.7 - - + -
232C GLU* 3.1 35.0 + - + +
233C VAL* 3.6 12.1 - - - +
235C GLN* 1.3 85.4 - - - +
237C ILE* 1.4 63.6 + - - +
239C LYS* 3.4 3.8 + - - +
240C HIS* 3.0 24.9 + - - +
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Residues in contact with ILE 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C ILE* 4.2 19.5 - - + +
206C LEU* 4.3 39.9 - - + +
207C SER* 3.7 7.6 - - - +
208C ALA* 3.5 36.6 - - + +
211C VAL* 4.3 6.1 - - + -
213C ILE* 5.8 1.6 - - + -
233C VAL* 3.0 25.8 + - + +
234C GLU* 3.1 9.2 + - - +
236C LEU* 1.4 76.6 - - - +
238C LYS* 1.3 55.5 + - - +
240C HIS* 3.4 5.0 + - - +
241C GLU* 2.9 30.5 + - + +
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Residues in contact with LYS 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C GLU* 3.0 27.8 + - - +
235C GLN* 4.0 4.5 - - - +
237C ILE* 1.3 73.4 - - - +
239C LYS* 1.3 73.8 + - - +
241C GLU* 3.6 13.1 - - + +
242C GLU* 3.1 48.6 + - - +
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Residues in contact with LYS 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C GLN* 3.0 36.3 + - - +
236C LEU* 3.7 4.9 - - - +
237C ILE 3.3 0.2 - - - -
238C LYS* 1.3 85.8 - - + +
240C HIS* 1.3 60.3 + - - +
242C GLU* 3.3 30.1 - - - +
243C GLU* 3.1 37.5 + - + +
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Residues in contact with HIS 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C ALA* 3.5 37.0 + - + +
194C ILE* 3.6 31.2 - - + -
195C LYS* 3.5 27.0 - - + -
198C ASN* 4.3 4.1 + - - -
236C LEU 3.0 17.2 + - - +
237C ILE* 3.4 6.5 - - - +
239C LYS* 1.3 76.1 - - - +
241C GLU* 1.4 56.4 + - - +
243C GLU* 3.0 27.4 + - + +
244C GLU* 3.0 57.8 + - + +
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Residues in contact with GLU 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C ILE* 2.9 20.6 + - + +
238C LYS* 3.6 15.4 - - - +
240C HIS* 1.4 72.8 - - - +
242C GLU* 1.3 68.9 + - - +
244C GLU* 3.2 11.8 + - + +
245C ALA* 2.9 32.5 + - - +
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Residues in contact with GLU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C LYS* 3.1 38.3 + - - +
239C LYS* 3.3 32.5 - - - +
241C GLU* 1.3 86.0 - - - +
243C GLU* 1.3 55.9 + - - +
245C ALA* 3.4 8.0 + - + +
246C LYS* 2.9 48.2 + - - +
249C ARG* 5.0 1.8 + - - +
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Residues in contact with GLU 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C ALA* 4.9 11.8 - - - +
239C LYS* 3.1 40.0 + - + +
240C HIS* 3.0 27.4 + - - +
242C GLU* 1.3 72.9 - - - +
244C GLU* 1.4 59.3 + - - +
246C LYS* 3.2 19.9 + - - +
247C ALA* 2.8 32.7 + - - +
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Residues in contact with GLU 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C LYS* 3.3 27.9 + - - +
198C ASN* 4.8 8.2 + - - +
240C HIS* 3.0 52.3 + - + +
241C GLU* 3.2 11.0 + - + +
243C GLU* 1.4 75.9 - - - +
245C ALA* 1.4 64.0 + - - +
247C ALA* 3.3 7.8 + - - +
248C GLU* 3.2 25.4 + - - +
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Residues in contact with ALA 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C GLU* 2.9 21.3 + - - +
242C GLU* 3.5 12.1 - - - +
244C GLU* 1.4 75.5 - - - +
246C LYS* 1.3 57.1 + - - +
248C GLU* 3.4 8.6 + - - +
249C ARG* 3.0 43.5 + - - +
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Residues in contact with LYS 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C GLU* 2.9 34.8 + - - +
243C GLU* 3.4 25.8 - - - +
245C ALA* 1.3 77.1 - - - +
247C ALA* 1.4 61.2 + - - +
249C ARG* 3.4 29.4 + - - +
250C GLU* 3.2 38.3 + - + +
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Residues in contact with ALA 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C GLU 2.8 18.6 + - - +
244C GLU* 3.3 10.1 + - - +
246C LYS* 1.4 69.6 - - - +
248C GLU* 1.3 59.9 + - - +
250C GLU* 3.3 14.6 + - - +
251C LYS* 3.1 26.5 + - - +
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Residues in contact with GLU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C GLU 3.2 15.3 + - - +
245C ALA* 3.6 8.0 - - - +
247C ALA* 1.3 77.6 - - - +
249C ARG* 1.4 58.3 + - - +
251C LYS* 3.3 9.8 + - + +
252C LYS* 3.0 55.1 + - + +
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Residues in contact with ARG 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C GLU* 5.0 1.8 + - - +
245C ALA* 3.0 46.3 + - - +
246C LYS* 3.4 39.7 + - - +
248C GLU* 1.4 77.5 - - - +
250C GLU* 1.4 62.1 + - + +
252C LYS* 3.4 13.9 + - + +
253C GLU* 3.1 39.9 + - + +
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Residues in contact with GLU 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C LYS* 3.2 36.0 + - + +
247C ALA* 3.3 11.1 + - - +
249C ARG* 1.4 75.9 - - + +
251C LYS* 1.3 57.3 + - - +
253C GLU* 3.2 20.0 + - - +
254C LYS* 3.0 26.9 + - - +
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Residues in contact with LYS 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ALA 3.1 10.5 + - - +
248C GLU* 3.5 13.2 - - + +
250C GLU* 1.3 77.0 - - - +
252C LYS* 1.3 63.8 + - + +
254C LYS* 3.2 21.8 + - - +
255C GLU* 3.0 39.6 + - + +
258C GLU* 4.9 5.6 + - - -
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Residues in contact with LYS 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C GLU* 3.0 51.2 + - + +
249C ARG* 3.6 12.5 - - + +
251C LYS* 1.3 75.2 - - + +
253C GLU* 1.4 62.4 + - + +
255C GLU* 3.3 18.7 + - - +
256C GLN* 3.1 25.1 + - - +
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Residues in contact with GLU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ARG* 3.1 30.0 + - + +
250C GLU* 3.2 22.5 + - - +
252C LYS* 1.4 76.4 - - + +
254C LYS* 1.4 56.2 + - - +
256C GLN* 3.5 14.3 + - - +
257C LYS* 3.0 49.2 + - - +
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Residues in contact with LYS 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C GLU 3.0 13.2 + - - +
251C LYS* 3.2 23.7 + - - +
253C GLU* 1.4 74.6 - - - +
255C GLU* 1.4 49.3 + - - +
257C LYS* 3.1 25.5 + - + +
258C GLU* 3.0 49.4 + - + +
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Residues in contact with GLU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C LYS* 3.0 31.1 + - + +
252C LYS* 3.3 28.5 + - - +
254C LYS* 1.4 69.8 - - - +
256C GLN* 1.4 64.3 + - - +
258C GLU* 3.4 20.4 + - - +
259C LYS 3.1 22.0 - - - +
260C ASP* 3.9 3.1 + - - -
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Residues in contact with GLN 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C LYS 3.1 14.1 + - - +
253C GLU* 3.5 14.7 - - - +
255C GLU* 1.4 77.6 - - - +
257C LYS* 1.4 66.1 + - - +
259C LYS* 3.5 9.7 + - - -
260C ASP* 3.3 41.4 + - - +
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Residues in contact with LYS 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C GLU* 3.0 38.4 + - - +
254C LYS* 3.1 34.5 + - - +
256C GLN* 1.4 80.6 - - - +
258C GLU* 1.4 60.7 + - - +
259C LYS* 3.4 0.9 + - - -
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Residues in contact with GLU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C LYS* 4.9 5.7 + - - -
254C LYS* 3.0 38.9 + - + +
255C GLU* 3.4 20.1 + - - +
257C LYS* 1.4 74.8 - - - +
259C LYS* 1.4 66.1 + - - +
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Residues in contact with LYS 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C GLU 3.1 10.9 - - - +
256C GLN 3.8 4.7 - - - -
257C LYS 3.3 3.8 - - - -
258C GLU* 1.4 81.8 - - - +
260C ASP* 1.3 76.3 + - - +
261C LYS* 3.8 1.1 + - - -
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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