Contacts of the helix formed by residues 236 - 258 (chain C) in PDB entry 3OX4
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 236 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229C THR* 3.0 17.3 - - + +
233C ASN* 2.8 32.0 + - + +
234C GLY 3.4 0.2 - - - -
235C LYS* 1.3 72.2 - - - +
237C MET* 1.3 63.5 + - - +
238C PRO* 3.6 17.9 - - - +
239C ALA* 2.9 40.1 + - + +
240C ARG* 3.1 14.2 + - - +
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Residues in contact with MET 237 (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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16C GLU* 3.0 36.8 - - + +
177C PRO* 3.5 23.8 - - + +
178C LEU* 3.4 27.8 - - + -
181C VAL* 3.5 29.2 - - - -
235C LYS 2.8 13.1 + - - +
236C ASP* 1.3 67.7 - - - +
238C PRO* 1.3 76.1 - - + +
240C ARG* 3.0 5.1 + - - +
241C GLU* 2.8 27.8 + - - +
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Residues in contact with PRO 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C ASN* 4.9 1.3 - - - -
236C ASP* 3.5 19.1 - - - +
237C MET* 1.3 94.1 - - + +
239C ALA* 1.3 56.1 + - - +
241C GLU* 4.0 4.6 - - + +
242C ALA* 3.0 29.2 + - - +
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Residues in contact with ALA 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C ASN* 4.0 18.6 - - - +
229C THR* 3.7 16.8 - - + -
230C ALA* 3.9 20.4 - - + +
236C ASP* 2.9 27.3 + - - +
238C PRO* 1.3 77.5 - - - +
240C ARG* 1.3 59.7 + - - +
242C ALA* 3.3 1.9 + - - +
243C MET* 2.9 34.8 + - - +
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Residues in contact with ARG 240 (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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177C PRO* 4.0 17.8 - - + +
180C MET* 3.3 27.0 + - + +
181C VAL* 3.4 21.3 + - + +
183C MET* 2.8 44.8 + - - +
188C THR* 2.9 29.8 - - - +
230C ALA* 4.1 14.9 + - + +
233C ASN 5.3 0.4 - - - +
234C GLY* 2.8 44.7 + - - +
236C ASP 3.1 15.8 + - - +
237C MET* 3.0 12.0 + - - +
239C ALA* 1.3 76.8 - - + +
241C GLU* 1.3 57.5 + - - +
243C MET* 3.4 5.8 + - - +
244C ALA* 3.0 26.2 + - - +
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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
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15C GLY* 3.7 8.0 - - - -
16C GLU* 3.6 31.6 + - - +
177C PRO* 3.7 21.0 - - + +
237C MET* 2.8 19.7 + - + +
238C PRO* 4.1 4.7 - - + +
240C ARG* 1.3 71.7 - - - +
242C ALA* 1.3 65.6 + - - +
244C ALA* 3.0 13.4 + - + +
245C TYR* 3.1 40.7 + - + -
2D ALA 4.3 20.3 + - - +
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Residues in contact with ALA 242 (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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222C MET* 3.5 20.5 - - + +
226C ASN* 3.2 37.7 - - - +
238C PRO 3.0 19.9 + - - +
239C ALA 3.3 2.4 + - - +
241C GLU* 1.3 78.4 - - - +
243C MET* 1.3 56.5 + - - +
245C TYR* 3.3 2.0 + - - -
246C ALA* 2.9 28.7 + - - +
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Residues in contact with MET 243 (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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140C ALA* 3.8 23.6 - - + +
188C THR 5.3 0.2 - - - +
192C GLY* 3.7 18.6 - - - +
195C ALA* 5.4 1.6 - - + -
222C MET 4.5 0.7 - - - +
223C ILE* 4.0 33.0 - - + -
226C ASN* 4.1 6.3 - - + -
227C LEU* 3.6 44.9 - - + -
230C ALA* 4.2 18.8 - - + -
239C ALA 2.9 20.3 + - - +
240C ARG* 3.8 6.7 - - - +
242C ALA* 1.3 74.4 - - - +
244C ALA* 1.3 65.9 + - - +
246C ALA* 3.8 2.6 - - + +
247C GLN* 2.9 27.2 + - - +
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Residues in contact with ALA 244 (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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14C MET* 4.5 4.6 - - + +
15C GLY 6.0 0.7 - - - +
140C ALA* 4.7 0.4 - - - +
175C ASN* 4.5 15.2 - - + +
177C PRO* 4.7 3.6 - - + -
180C MET* 4.0 27.1 - - + -
240C ARG 3.0 15.4 + - - +
241C GLU* 3.0 16.1 + - + +
243C MET* 1.3 75.8 - - - +
245C TYR* 1.3 64.2 + - + +
247C GLN* 3.0 30.4 + - - +
248C PHE* 3.2 6.2 + - - +
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Residues in contact with TYR 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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14C MET* 3.5 46.6 + - + +
15C GLY* 4.8 2.1 + - - -
222C MET* 3.9 14.6 - - + -
241C GLU* 3.1 47.4 + - + -
242C ALA* 3.7 5.8 - - - +
244C ALA* 1.3 79.0 - - + +
246C ALA* 1.3 58.2 + - - +
248C PHE* 3.1 3.5 + - - +
249C LEU* 2.8 35.1 + - + +
2D ALA 4.2 8.3 + - - -
4D SER* 2.7 29.8 + - - -
209D THR* 4.2 9.3 - - - +
210D PRO* 3.9 33.2 - - + -
211D ILE* 3.8 13.9 - - + -
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Residues in contact with ALA 246 (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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219C ALA* 3.5 12.3 - - - +
222C MET* 3.7 28.9 - - + -
223C ILE* 3.9 24.2 - - + +
242C ALA 2.9 17.2 + - - +
243C MET* 3.8 8.3 - - - +
245C TYR* 1.3 77.4 - - - +
247C GLN* 1.3 57.3 + - - +
249C LEU* 3.2 4.2 + - - -
250C ALA* 2.9 27.5 + - - +
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Residues in contact with GLN 247 (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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137C ASN* 3.5 12.4 + - - +
140C ALA* 3.7 15.0 - - - +
141C GLY* 3.6 25.8 + - - +
143C ALA* 2.9 40.4 + - - +
145C GLU* 2.9 15.3 + - - -
175C ASN* 2.9 29.1 + - - +
195C ALA* 4.1 15.0 - - + +
198C HIS* 5.4 0.3 + - - -
243C MET* 2.9 16.7 + - + +
244C ALA* 3.0 19.9 + - - +
246C ALA* 1.3 78.3 - - - +
248C PHE* 1.3 67.8 + - - +
250C ALA* 3.6 2.6 + - - +
251C GLY 3.1 19.2 + - - -
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Residues in contact with PHE 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 4.1 13.2 - - + -
12C ASN* 3.3 40.4 - - + -
14C MET* 3.2 34.1 - - + -
143C ALA* 4.6 2.7 - - - -
145C GLU* 4.2 2.5 - - - -
146C MET* 3.7 30.2 - - + +
173C SER* 3.8 9.2 - - - -
175C ASN* 3.7 13.2 - - - -
244C ALA 3.7 3.6 - - - +
245C TYR 3.1 5.3 + - - +
246C ALA 3.1 0.6 - - - -
247C GLN* 1.3 85.9 - - - +
249C LEU* 1.3 60.0 + - - +
251C GLY* 2.9 4.0 + - - -
252C MET* 2.8 54.8 + - + +
6D PHE* 4.8 3.8 - + - -
211D ILE* 3.8 12.3 - - + -
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Residues in contact with LEU 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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215C CYS* 3.4 45.1 - - + +
218C LYS* 3.5 29.8 - - + -
219C ALA* 4.0 3.1 - - + +
222C MET* 3.8 16.8 - - - -
245C TYR 2.8 20.5 + - - +
246C ALA* 3.6 5.4 - - - +
248C PHE* 1.3 76.7 - - - +
250C ALA* 1.3 61.1 + - - +
252C MET* 3.2 26.2 + - - -
253C ALA* 3.2 9.2 + - - +
210D PRO* 4.4 4.5 - - + +
211D ILE* 3.8 37.7 - - + -
214D ALA* 4.9 3.1 - - + -
215D CYS* 6.0 0.2 - - - -
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Residues in contact with ALA 250 (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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195C ALA* 3.4 29.4 - - + +
198C HIS* 3.9 10.8 - - + +
199C ALA* 4.1 5.4 - - - +
219C ALA* 3.6 14.7 - - + +
223C ILE* 5.4 0.2 - - + -
246C ALA 2.9 17.4 + - - +
247C GLN* 3.8 7.2 - - - +
249C LEU* 1.3 78.3 - - - +
251C GLY* 1.3 57.0 + - - +
253C ALA* 3.3 6.9 + - - +
254C PHE* 3.0 32.6 + - - +
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Residues in contact with GLY 251 (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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143C ALA* 3.4 26.9 - - - +
146C MET* 3.7 7.4 - - - -
247C GLN 3.1 6.3 + - - -
248C PHE 2.9 8.3 + - - -
250C ALA* 1.3 74.8 - - - +
252C MET* 1.3 63.7 + - - +
253C ALA 3.0 2.0 - - - -
254C PHE* 3.5 7.9 - - - -
255C ASN* 3.0 31.2 + - - +
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Residues in contact with MET 252 (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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6C PHE* 3.4 19.7 - - + -
8C ILE* 4.2 9.0 - - + -
146C MET* 3.7 9.8 - - + +
212C THR* 4.0 0.9 - - - +
215C CYS* 3.8 17.7 - - - -
248C PHE* 2.8 45.4 + - + +
249C LEU* 3.2 30.0 + - - +
251C GLY* 1.3 74.8 - - - +
253C ALA* 1.3 58.6 + - - +
256C ASN* 3.0 24.7 + - - +
6D PHE* 4.1 13.2 - - + -
211D ILE* 4.0 16.6 - - + -
252D MET* 3.4 33.4 - - + -
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Residues in contact with ALA 253 (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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198C HIS 5.2 0.2 - - - +
199C ALA* 5.4 0.2 - - - -
202C ALA* 3.5 20.2 - - + -
212C THR* 3.4 31.4 - - - +
215C CYS* 4.2 0.6 - - + +
216C ALA* 3.9 12.1 - - + +
249C LEU 3.2 10.8 + - - +
250C ALA* 3.5 8.1 - - - +
251C GLY 3.0 1.4 - - - -
252C MET* 1.3 77.3 - - - +
254C PHE* 1.3 59.9 + - - +
256C ASN 3.3 1.7 + - - -
257C ALA* 2.8 30.5 + - - +
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Residues in contact with PHE 254 (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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142C THR 3.2 22.0 - - - -
143C ALA* 4.0 0.2 - - + -
147C THR* 4.0 19.7 - - + -
149C PHE* 3.9 11.0 - + - -
198C HIS* 3.1 36.8 - + - +
202C ALA* 3.7 6.9 - - + +
250C ALA 3.0 24.3 + - - +
251C GLY* 3.5 19.5 - - - -
253C ALA* 1.3 74.9 - - - +
255C ASN* 1.3 62.1 + - - +
256C ASN 3.0 2.7 - - - -
258C SER* 2.8 36.9 + - - +
259C LEU* 3.2 39.9 - - + -
1385C NAD 4.2 28.0 - + - -
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Residues in contact with ASN 255 (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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7C TYR* 2.8 41.4 + - - +
146C MET* 3.7 15.8 + - - +
147C THR* 3.2 22.4 - - + +
148C ARG* 2.9 61.5 + - - +
149C PHE* 3.5 11.9 - - - -
169C THR* 5.5 0.2 + - - -
251C GLY 3.0 19.9 + - - +
254C PHE* 1.3 81.1 - - - +
256C ASN* 1.3 61.8 + - - +
258C SER 4.8 0.2 + - - -
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Residues in contact with ASN 256 (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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5C THR 3.6 11.9 - - - +
6C PHE* 3.1 23.0 - - + -
7C TYR* 2.5 60.9 + - - +
148C ARG* 4.2 8.8 + - - +
207C ALA* 4.5 7.0 - - - +
209C THR* 5.8 2.0 - - + +
212C THR* 3.8 18.2 - - + -
252C MET* 3.0 21.4 + - - +
253C ALA 3.3 1.4 + - - -
255C ASN* 1.3 83.9 - - - +
257C ALA* 1.3 59.6 + - - +
258C SER* 3.3 1.5 - - - -
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Residues in contact with ALA 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ALA* 3.7 21.8 - - - +
205C SER* 2.5 26.6 + - - -
207C ALA* 3.5 15.5 - - - +
208C ALA* 3.9 12.1 - - - +
212C THR* 3.7 22.0 - - + +
253C ALA 2.8 19.2 + - - +
256C ASN* 1.3 74.1 - - - +
258C SER* 1.3 68.5 + - - +
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Residues in contact with SER 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ARG* 6.0 0.9 - - - +
149C PHE* 5.2 10.1 - - - -
201C GLU 4.1 0.3 - - - +
202C ALA* 3.7 12.5 - - - -
207C ALA* 5.3 0.4 - - - -
254C PHE* 2.8 30.7 + - - +
255C ASN 4.5 0.4 - - - -
256C ASN 3.3 1.6 - - - -
257C ALA* 1.3 87.8 - - - +
259C LEU* 1.3 70.2 + - - +
361C ALA 4.7 3.8 + - - -
362C CYS* 4.6 11.3 - - - +
365C THR* 3.5 20.4 + - - +
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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