Contacts of the helix formed by residues 214 - 238 (chain A) in PDB entry 4JYH
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 ASP 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A SER* 2.6 27.7 + - - -
206A SER* 3.0 26.4 + - - +
211A VAL* 4.4 2.4 - - + +
213A LEU* 1.3 73.0 - - - +
215A LEU* 1.3 64.5 + - - +
216A GLY* 2.8 18.4 + - - -
217A LEU* 2.9 26.4 + - + +
218A TRP* 2.9 13.2 + - - +
292A ASN* 3.0 28.5 + - + +
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Residues in contact with LEU 215 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A LEU* 3.6 12.9 + - + +
214A ASP* 1.3 72.2 + - - +
216A GLY* 1.3 61.4 + - - +
218A TRP* 4.4 18.8 - - + -
219A ASP* 3.2 25.0 + - + +
395A ILE* 4.6 4.7 - - + -
396A PRO* 3.9 37.2 - - + -
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Residues in contact with GLY 216 (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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205A SER* 5.1 4.3 - - - -
214A ASP* 2.8 10.7 + - - -
215A LEU* 1.3 81.4 - - - +
217A LEU* 1.3 59.7 + - - -
219A ASP* 3.6 5.4 + - - +
220A LYS* 3.5 19.2 + - - +
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Residues in contact with LEU 217 (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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203A THR* 4.2 15.0 - - + -
205A SER* 3.5 28.7 - - - +
214A ASP* 2.9 22.8 + - + +
216A GLY* 1.3 72.4 - - - +
218A TRP* 1.3 61.0 + - - +
220A LYS* 3.3 6.1 + - + +
221A PHE* 2.8 32.9 + - - +
283A LEU* 5.5 3.8 - - + -
285A LEU* 3.9 29.9 - - + +
289A GLN* 3.5 32.1 - - + +
292A ASN* 4.0 13.0 - - + -
293A ALA* 3.9 12.1 - - + -
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Residues in contact with TRP 218 (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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213A LEU* 4.0 13.0 - - + -
214A ASP 2.9 15.2 + - - +
215A LEU* 3.8 22.0 - - + +
217A LEU* 1.3 76.9 - - - +
219A ASP* 1.3 73.3 + - + +
221A PHE* 3.0 12.9 + + - -
222A SER* 2.7 57.9 + - - -
293A ALA 3.5 29.9 + - - +
294A GLY* 4.9 0.9 - - - -
391A LEU* 4.0 19.1 - - + -
395A ILE* 3.5 37.9 - - + +
398A SER 5.2 2.4 + - - -
399A MET* 3.6 38.0 - - + +
400A PRO* 3.9 10.0 - - + +
403A ILE* 5.1 0.7 - - + -
501A JYH 4.1 14.6 - + - -
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Residues in contact with ASP 219 (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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215A LEU* 3.2 14.5 + - + +
216A GLY* 3.9 6.5 - - - +
218A TRP* 1.3 86.5 - - + +
220A LYS* 1.3 58.0 + - - +
222A SER* 2.8 19.9 + - - -
223A GLU* 3.0 19.4 + - - +
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Residues in contact with LYS 220 (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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201A TYR* 4.5 5.6 + - - +
216A GLY 3.5 10.1 + - - +
217A LEU* 3.3 10.2 + - + +
218A TRP 3.1 0.6 - - - -
219A ASP* 1.3 76.4 - - - +
221A PHE* 1.3 67.0 + - - +
223A GLU* 3.0 30.6 + - - +
224A LEU* 3.1 43.1 + - + +
227A LYS* 5.8 0.8 - - - +
281A ASP* 3.5 25.8 + - - +
283A LEU* 3.9 23.3 - - + -
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Residues in contact with PHE 221 (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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217A LEU 2.8 21.9 + - - +
218A TRP* 3.5 12.1 - + - +
220A LYS* 1.3 73.6 - - - +
222A SER* 1.3 62.6 + - - +
224A LEU* 3.1 7.5 + - - +
225A ALA* 2.8 31.0 + - + +
266A ILE* 6.4 0.2 - - + -
279A PHE* 3.7 31.6 - + + -
283A LEU* 5.7 1.3 - - - +
285A LEU* 5.4 2.9 - - + -
290A MET* 4.8 2.0 - - + -
293A ALA* 3.9 32.8 - - + -
294A GLY* 5.5 1.3 - - - -
295A PHE* 3.8 26.2 - + - -
501A JYH 3.5 66.9 - + - -
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Residues in contact with SER 222 (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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218A TRP* 2.7 52.0 + - - -
219A ASP* 2.8 25.6 + - - -
221A PHE* 1.3 79.0 - - - +
223A GLU* 1.3 55.6 + - - +
225A ALA* 3.9 5.4 - - - -
226A THR* 2.9 32.6 + - - -
400A PRO* 3.7 17.5 - - - +
403A ILE* 3.7 5.2 - - - +
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Residues in contact with GLU 223 (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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219A ASP* 3.0 18.4 + - - +
220A LYS* 3.0 39.7 + - - +
221A PHE 3.2 0.2 - - - -
222A SER* 1.3 83.3 + - - +
224A LEU* 1.3 62.7 + - - +
226A THR* 3.5 6.2 + - - -
227A LYS* 3.1 59.9 + - - +
400A PRO* 5.3 2.0 - - - -
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Residues in contact with LEU 224 (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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220A LYS* 3.1 31.0 + - - +
221A PHE* 3.7 3.8 - - - +
223A GLU* 1.3 76.9 - - - +
225A ALA* 1.3 61.9 + - - +
227A LYS* 3.5 16.3 + - + +
228A CYS 3.0 21.3 + - - -
279A PHE* 3.5 41.5 - - + -
280A SER* 5.8 0.9 - - - -
281A ASP* 3.7 38.4 - - + +
283A LEU* 4.1 17.5 - - + -
501A JYH 3.4 17.5 - - - +
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Residues in contact with ALA 225 (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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221A PHE* 2.8 22.2 + - + +
222A SER* 3.9 8.5 - - - +
224A LEU* 1.3 75.6 - - - +
226A THR* 1.3 58.8 + - - +
228A CYS* 3.0 4.3 + - - +
229A ILE* 2.8 34.3 + - + +
262A LEU* 4.2 6.0 - - + +
403A ILE* 4.4 9.9 - - + -
501A JYH 3.1 37.9 - - + +
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Residues in contact with THR 226 (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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222A SER 2.9 21.7 + - - -
223A GLU* 3.6 7.6 - - - +
224A LEU 3.3 0.2 - - - -
225A ALA* 1.3 76.1 - - - +
227A LYS* 1.3 58.6 + - + +
229A ILE* 3.1 13.9 + - - +
230A ILE* 3.0 36.6 + - + +
400A PRO* 3.3 25.0 - - + +
401A PRO* 6.3 0.7 - - + -
402A LEU* 4.2 22.7 - - + -
403A ILE* 3.5 8.7 + - - +
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Residues in contact with LYS 227 (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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220A LYS* 5.8 0.6 - - - +
223A GLU* 3.1 49.3 + - + +
224A LEU* 3.8 15.5 - - + +
225A ALA 3.2 0.2 - - - -
226A THR* 1.3 79.6 - - + +
228A CYS* 1.3 58.0 + - - +
230A ILE* 3.5 17.5 - - + +
231A LYS* 2.9 30.5 + - - +
501A JYH 5.6 0.4 - - - +
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Residues in contact with CYS 228 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A PHE* 5.0 0.7 - - - -
224A LEU 3.0 14.0 + - - +
225A ALA 3.0 9.5 + - - +
227A LYS* 1.3 75.0 - - - +
229A ILE* 1.3 54.2 - - - +
231A LYS* 3.1 8.0 + - - +
232A ILE* 2.6 41.2 + - - +
262A LEU* 3.9 15.3 - - + -
265A ARG* 3.7 33.9 - - - -
501A JYH 3.6 38.1 + - + +
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Residues in contact with ILE 229 (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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225A ALA* 2.8 19.2 + - + +
226A THR* 3.3 9.2 - - - +
228A CYS* 1.3 71.9 - - - +
230A ILE* 1.3 54.8 + - - +
232A ILE* 2.8 11.7 + - + +
233A VAL* 2.7 38.9 + - + +
258A CYS* 3.7 27.1 - - - -
262A LEU* 4.1 15.0 - - + -
402A LEU* 3.5 22.9 - - + -
403A ILE* 3.8 33.7 - - + +
406A MET* 4.0 28.0 - - + -
407A MET* 5.3 1.6 - - + -
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Residues in contact with ILE 230 (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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226A THR* 3.0 25.0 + - + +
227A LYS* 3.5 20.4 - - + +
229A ILE* 1.3 73.6 - - - +
231A LYS* 1.3 68.6 + - + +
233A VAL* 3.2 10.2 + - + +
234A GLU* 3.1 21.6 + - + +
402A LEU* 3.9 14.6 - - + -
636G LEU* 4.1 27.8 - - + -
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Residues in contact with LYS 231 (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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190A GLU 4.8 4.6 + - - -
191A THR* 2.9 42.9 - - - +
193A PRO* 6.1 0.9 - - + -
227A LYS 2.9 17.1 + - - +
228A CYS* 3.1 15.5 + - - +
230A ILE* 1.3 81.7 - - + +
232A ILE* 1.3 58.9 + - - +
234A GLU* 3.2 24.4 + - - +
235A PHE* 3.1 20.8 + - - +
265A ARG* 3.7 7.9 - - - +
280A SER* 6.2 0.4 - - - +
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Residues in contact with ILE 232 (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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228A CYS* 2.6 25.5 + - - +
229A ILE* 2.8 11.9 + - + +
231A LYS* 1.3 72.9 - - - +
233A VAL* 1.3 63.2 + - + +
235A PHE* 3.2 12.6 + - + +
236A ALA* 3.1 21.0 + - - +
254A LEU* 4.7 12.3 - - + -
258A CYS* 4.0 20.0 - - + +
261A ILE* 3.8 43.3 - - + -
262A LEU* 3.9 26.9 - - + +
265A ARG* 4.1 18.4 - - - +
327A LEU* 5.3 2.7 - - + -
406A MET* 6.2 0.7 - - + -
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Residues in contact with VAL 233 (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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229A ILE* 2.7 28.0 + - + +
230A ILE* 3.5 9.6 - - - +
232A ILE* 1.3 71.7 - - + +
234A GLU* 1.3 64.4 + - - +
236A ALA* 3.4 2.9 + - - +
237A LYS* 3.2 38.3 + - + +
254A LEU* 4.2 26.9 - - + -
406A MET* 5.1 2.0 - - + -
633G LEU* 3.7 26.2 - - + -
636G LEU* 4.1 29.6 - - + +
637G LEU* 4.5 3.4 - - - +
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Residues in contact with GLU 234 (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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190A GLU 4.9 2.2 - - - +
191A THR* 4.1 14.9 - - + +
230A ILE* 3.1 12.3 + - + +
231A LYS* 3.2 28.5 + - - +
233A VAL* 1.3 75.5 - - - +
235A PHE* 1.3 64.1 + - - +
237A LYS* 3.6 15.8 + - + +
238A ARG* 3.1 52.2 + - + +
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Residues in contact with PHE 235 (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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184A ILE* 4.0 18.8 - - + -
187A ALA* 3.2 25.4 - - + -
188A HIS* 4.1 10.8 - + + -
191A THR* 3.9 16.1 - - - +
231A LYS 3.1 12.7 + - - +
232A ILE* 3.2 15.7 - - + +
234A GLU* 1.3 74.0 - - - +
236A ALA* 1.3 68.2 + - - +
238A ARG* 2.9 18.5 + - - +
239A LEU* 3.4 37.4 + - + +
261A ILE* 4.9 7.2 - - + -
265A ARG* 4.2 8.3 - - - +
320A GLY* 3.6 22.2 - - - -
323A SER* 3.9 23.8 - - - -
324A ALA 4.1 5.8 - - - -
327A LEU* 4.4 9.2 - - + -
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Residues in contact with ALA 236 (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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232A ILE 3.1 6.6 + - - +
233A VAL 3.4 8.5 + - - +
235A PHE* 1.3 75.0 - - - +
237A LYS* 1.3 54.9 + - - +
239A LEU* 2.7 34.0 + - - +
242A PHE* 3.4 33.5 - - + +
254A LEU* 3.9 13.7 - - + -
327A LEU* 3.3 32.1 - - + -
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Residues in contact with LYS 237 (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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233A VAL* 3.2 31.9 + - + +
234A GLU* 3.8 12.8 - - + +
235A PHE 3.3 0.2 - - - -
236A ALA* 1.3 75.8 - - + +
238A ARG* 1.3 59.8 + - + +
239A LEU 3.3 3.9 + - - +
242A PHE* 4.3 7.4 - - + -
243A THR* 4.4 24.7 + - + +
636G LEU 2.8 23.9 + - - +
637G LEU* 3.1 36.5 + - + +
639G GLU* 3.5 21.0 - - - +
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Residues in contact with ARG 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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183A LYS* 5.0 12.2 + - - +
184A ILE* 5.8 0.2 - - - +
186A LYS* 3.9 7.4 + - - +
187A ALA* 3.5 37.8 - - + +
190A GLU* 2.9 54.0 + - - +
191A THR* 4.5 3.2 - - - +
234A GLU* 3.1 42.2 + - + +
235A PHE* 2.9 12.3 + - - +
237A LYS* 1.3 78.7 - - + +
239A LEU* 1.3 61.6 + - - +
240A PRO* 3.4 8.1 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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