Contacts of the helix formed by residues 210 - 237 (chain D) in PDB entry 4BPW
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 210 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D ILE* 5.0 4.7 - - + -
170D SER* 4.3 17.7 - - - +
172D SER* 4.7 8.1 - - - +
181D GLU* 3.9 16.8 - - - +
182D SER 4.0 2.9 - - - +
183D ILE* 3.9 19.0 - - + -
184D TYR* 4.4 1.4 - - - -
200D VAL* 4.6 3.6 - - + -
208D TYR 3.9 5.8 - - - +
209D VAL* 1.3 96.8 - - + +
211D LEU* 1.3 63.5 + - - +
212D LYS* 4.1 9.9 - - + +
213D ASP* 3.6 23.3 - - - +
214D ILE* 3.4 21.7 + - - +
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Residues in contact with LEU 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D PHE* 5.0 4.5 - - + -
137D LYS* 4.2 28.5 - - + +
140D ILE* 4.1 35.9 - - + -
181D GLU* 4.6 11.2 + - + +
182D SER* 3.8 19.7 + - - +
184D TYR* 3.9 22.7 - - + +
210D PRO* 1.3 72.7 - - - +
212D LYS* 1.3 66.1 + - + +
213D ASP 3.2 2.2 - - - -
214D ILE* 3.3 30.0 - - + +
215D VAL* 3.4 12.0 - - + +
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Residues in contact with LYS 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D SER* 4.6 25.8 + - - +
173D LEU* 5.3 5.8 - - + +
181D GLU* 3.2 29.4 + - - +
210D PRO* 3.4 4.7 - - + +
211D LEU* 1.3 80.3 - - + +
213D ASP* 1.3 67.7 + - - +
215D VAL* 4.0 14.8 - - - +
216D ALA* 4.9 1.0 + - - +
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Residues in contact with ASP 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D SER* 4.9 1.6 + - - -
172D SER* 4.0 18.4 + - - -
194D LEU* 4.1 23.5 - - + +
199D LYS 4.7 8.9 - - - +
209D VAL* 3.8 18.6 - - + +
210D PRO* 3.6 24.5 + - + +
211D LEU 3.2 0.6 - - - -
212D LYS* 1.3 85.1 - - - +
214D ILE* 1.3 62.2 + - - +
215D VAL 3.1 6.1 + - - -
216D ALA* 3.5 15.8 + - - +
217D ILE* 3.7 12.0 + - - +
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Residues in contact with ILE 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D PHE* 5.6 3.8 - - + -
144D LEU* 3.9 18.4 - - + -
151D PHE* 3.5 39.9 - - + -
184D TYR* 3.5 29.4 - - + -
186D ILE* 4.2 3.8 - - + -
209D VAL* 4.0 1.8 - - + +
210D PRO 3.4 11.5 + - - +
211D LEU* 3.3 35.7 - - + +
213D ASP* 1.3 74.9 - - - +
215D VAL* 1.3 69.8 + - + +
217D ILE* 3.4 28.0 - - + +
218D ILE* 3.6 10.6 + - + +
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Residues in contact with VAL 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ARG* 5.2 15.3 - - + +
132D PHE* 3.7 37.2 - - + -
211D LEU* 3.4 18.2 - - + +
212D LYS* 4.0 12.3 - - - +
213D ASP 3.1 0.6 - - - -
214D ILE* 1.3 74.6 - - + +
216D ALA* 1.3 59.0 + - - +
217D ILE 3.0 5.0 + - - -
218D ILE* 3.2 6.1 + - - +
219D LEU* 2.8 39.2 + - + +
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Residues in contact with ALA 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D LEU* 6.6 0.4 - - + -
212D LYS 4.9 1.1 + - - +
213D ASP* 3.5 10.7 + - - +
214D ILE 3.5 0.6 - - - -
215D VAL* 1.3 79.8 - - - +
217D ILE* 1.3 57.4 + - - +
219D LEU* 3.7 16.4 - - + +
220D ASN* 2.9 30.0 + - - +
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Residues in contact with ILE 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D LEU* 3.7 29.4 - - + -
151D PHE* 4.4 7.2 - - + -
186D ILE* 3.8 27.8 - - + -
190D ASP* 4.0 20.2 - - + +
191D ALA* 5.0 4.7 - - - -
194D LEU* 4.8 9.6 - - + -
209D VAL* 4.4 11.4 - - + -
213D ASP 3.7 12.6 - - - +
214D ILE* 3.4 21.5 - - + +
215D VAL 3.0 0.4 - - - -
216D ALA* 1.3 78.2 - - + +
218D ILE* 1.3 58.9 + - - +
220D ASN* 3.1 6.1 + - - +
221D GLU* 2.8 26.3 + - + +
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Residues in contact with ILE 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D LEU* 5.2 5.4 - - + -
132D PHE* 6.3 0.7 - - + -
143D PHE* 4.3 33.2 - - + -
144D LEU* 3.6 32.1 - - + -
147D SER* 3.9 28.0 - - - +
151D PHE* 4.0 14.1 - - + -
214D ILE 3.6 9.1 + - - +
215D VAL* 3.2 6.5 + - - +
217D ILE* 1.3 72.9 - - - +
219D LEU* 1.3 58.1 + - - +
221D GLU* 4.0 15.5 - - - +
222D PHE* 2.7 38.2 + - + +
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Residues in contact with LEU 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D MET* 3.8 54.9 - - + +
128D LEU* 4.9 11.0 - - + -
129D ARG* 4.1 44.2 - - + +
215D VAL* 2.8 24.2 + - + +
216D ALA* 3.7 15.0 - - + +
218D ILE* 1.3 77.1 - - - +
220D ASN* 1.3 57.1 + - - +
222D PHE* 4.1 4.1 - - + +
223D ARG* 3.4 23.2 + - - +
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Residues in contact with ASN 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D ASP* 3.3 24.4 + - - +
216D ALA 2.9 17.8 + - - +
217D ILE* 3.5 3.8 - - - +
219D LEU* 1.3 77.1 - - - +
221D GLU* 1.3 59.6 + - - +
222D PHE 3.2 1.3 - - - -
223D ARG* 2.6 41.3 + - - +
224D ALA* 2.9 29.8 + - - +
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Residues in contact with GLU 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D SER* 3.1 33.4 + - - +
148D GLN 4.8 0.5 - - - -
149D LEU* 3.4 43.4 + - + +
217D ILE* 2.8 15.6 + - + +
218D ILE* 3.2 12.7 + - + +
220D ASN* 1.3 77.0 - - - +
222D PHE* 1.3 61.5 + - - +
224D ALA* 3.8 5.4 - - - +
225D LYS* 3.1 47.4 + - + +
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Residues in contact with PHE 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D TYR* 3.5 46.2 - + + -
30D LEU* 5.9 6.3 - - + -
124D GLU* 4.2 31.9 - - + -
125D MET* 4.4 12.1 - - + -
128D LEU* 3.6 27.8 - - + -
218D ILE* 2.7 25.2 + - + +
219D LEU* 4.1 3.1 - - + +
221D GLU* 1.3 71.2 - - - +
223D ARG* 1.3 63.2 + - - +
225D LYS* 3.2 5.7 + - + +
226D LEU* 2.8 65.4 + - + +
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Residues in contact with ARG 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D ILE* 4.0 18.4 - - + +
125D MET* 3.7 29.9 - - - +
219D LEU 3.4 16.7 + - - +
220D ASN* 2.6 42.3 + - - +
222D PHE* 1.3 84.7 - - - +
224D ALA* 1.3 59.9 + - - +
226D LEU* 3.7 4.2 - - - +
227D SER* 2.8 34.9 + - - +
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Residues in contact with ALA 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D ASN* 2.9 20.9 + - - +
221D GLU* 3.8 6.7 - - - +
222D PHE 3.1 0.2 - - - -
223D ARG* 1.3 79.6 - - - +
225D LYS* 1.3 65.8 + - + +
227D SER* 2.7 21.4 + - - -
228D LYS* 3.0 25.4 + - - +
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Residues in contact with LYS 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D TYR 6.1 0.9 - - - -
30D LEU* 3.6 33.2 - - + +
107D ARG* 5.8 0.2 + - - -
147D SER 3.9 7.1 + - - -
148D GLN* 3.6 23.6 + - - +
221D GLU* 3.1 43.5 + - + +
222D PHE* 3.9 6.1 - - + +
224D ALA* 1.3 80.8 - - + +
226D LEU* 1.3 57.3 + - - +
228D LYS* 3.9 10.7 - - + +
229D ALA* 3.1 26.9 + - - +
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Residues in contact with LEU 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D TYR 5.4 0.7 - - - +
103D HIS* 3.5 30.7 - - + +
107D ARG* 4.0 17.7 - - - +
120D PHE* 4.5 9.9 - - + -
121D ILE* 3.9 35.7 - - + -
124D GLU* 4.4 8.7 - - + -
222D PHE* 2.8 47.6 + - + +
223D ARG* 3.7 4.3 - - - +
225D LYS* 1.3 77.1 - - - +
227D SER* 1.3 59.9 + - - +
228D LYS 3.1 0.2 - - - -
229D ALA* 3.1 4.5 + - - +
230D LEU* 2.9 38.8 + - + +
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Residues in contact with SER 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ARG* 5.3 3.7 - - - +
121D ILE* 3.8 23.1 - - - +
223D ARG* 2.8 20.7 + - - +
224D ALA* 2.7 24.3 + - - -
226D LEU* 1.3 76.6 - - - +
228D LYS* 1.3 58.4 + - - +
230D LEU* 3.8 6.3 + - - +
231D ALA* 3.3 23.2 + - - +
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Residues in contact with LYS 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D ALA* 3.0 27.5 + - - +
225D LYS* 3.9 9.6 - - + +
227D SER* 1.3 78.9 - - - +
229D ALA* 1.3 64.1 + - - +
230D LEU 3.3 0.2 - - - -
231D ALA* 3.4 6.2 + - - +
232D LEU* 3.1 32.9 + - + +
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Residues in contact with ALA 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D LEU 6.0 0.7 - - - +
107D ARG* 3.5 33.9 - - - +
225D LYS 3.1 18.5 + - - +
226D LEU* 3.1 5.3 + - - +
228D LYS* 1.3 74.0 - - - +
230D LEU* 1.3 55.7 + - - +
232D LEU* 3.4 6.9 + - - +
233D THR* 2.6 37.2 + - - -
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Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D ARG* 4.0 44.2 - - + +
110D TYR 4.5 0.9 - - - +
111D CYS* 3.6 13.0 - - + +
117D ARG* 4.0 33.4 - - + -
120D PHE* 4.2 20.4 - - + -
121D ILE* 3.9 30.3 - - + -
226D LEU* 2.9 21.8 + - + +
227D SER* 4.0 5.4 - - - +
228D LYS 3.3 0.2 - - - -
229D ALA* 1.3 74.9 - - - +
231D ALA* 1.3 60.4 + - - +
233D THR* 3.1 5.6 + - - -
234D ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ARG* 5.7 6.5 - - - +
117D ARG* 4.9 8.5 - - - +
227D SER 3.3 13.3 + - - +
228D LYS* 3.6 11.2 - - - +
229D ALA 3.3 0.2 - - - -
230D LEU* 1.3 78.5 - - - +
232D LEU* 1.3 68.0 + - + +
234D ALA* 3.3 19.2 + - - +
235D ARG* 3.4 22.8 + - - +
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Residues in contact with LEU 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D LYS* 3.1 25.3 + - + +
229D ALA* 3.7 7.4 - - - +
231D ALA* 1.3 75.8 - - + +
233D THR* 1.3 65.5 + - - +
234D ALA 3.0 1.8 - - - -
235D ARG* 3.1 49.6 + - + +
236D SER* 3.0 20.0 + - - +
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Residues in contact with THR 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D ARG* 4.0 24.3 + - + +
108D LEU* 3.8 28.5 - - + -
111D CYS* 3.8 16.2 - - - -
229D ALA* 2.6 23.5 + - - +
230D LEU* 3.1 9.4 + - - -
232D LEU* 1.3 77.3 - - - +
234D ALA* 1.3 57.9 + - - +
236D SER* 3.3 8.1 + - - -
237D LEU* 2.9 28.2 + - - +
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Residues in contact with ALA 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ARG* 5.7 7.9 - - + -
111D CYS* 4.0 25.6 - - - +
112D GLN* 5.8 0.4 - - - -
117D ARG* 4.3 13.0 - - - +
230D LEU 2.9 11.3 + - - +
231D ALA* 3.4 12.8 - - - +
232D LEU 3.0 0.6 - - - -
233D THR* 1.3 79.5 - - - +
235D ARG* 1.3 56.8 + - + +
237D LEU* 3.7 4.0 + - - +
238D PRO* 3.0 23.0 - - - +
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Residues in contact with ARG 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ARG* 3.1 44.2 + - + +
236B SER* 4.6 10.9 + - - +
237B LEU 5.1 4.6 + - - -
238B PRO* 6.1 1.6 - - - +
231D ALA* 3.4 24.1 + - - +
232D LEU* 3.1 39.7 + - + +
234D ALA* 1.3 77.4 - - + +
236D SER* 1.3 58.6 + - - +
238D PRO* 3.2 17.6 - - - +
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Residues in contact with SER 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D LEU* 6.2 1.3 - - - -
232D LEU* 3.0 15.6 + - - +
233D THR* 3.5 12.9 - - - -
234D ALA 3.2 0.2 - - - -
235D ARG* 1.3 78.9 - - - +
237D LEU* 1.3 63.1 + - - +
238D PRO* 3.3 3.0 - - - +
239D ALA* 3.8 16.6 + - - +
240D VAL* 4.7 3.3 + - - +
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Residues in contact with LEU 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D LEU* 3.7 25.1 - - + +
111D CYS* 3.8 9.0 - - - -
112D GLN* 3.6 32.3 - - + +
233D THR 2.9 17.7 + - - +
234D ALA* 4.0 4.0 - - - +
236D SER* 1.3 72.1 - - - +
238D PRO* 1.3 57.0 - - + +
239D ALA 2.6 19.9 + - - -
240D VAL* 3.3 23.0 + - + -
241D GLN* 3.2 46.5 + - + +
246D LEU* 5.5 0.2 - - + -
250D LEU* 3.9 21.1 - - + -
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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