Contacts of the helix formed by residues 226 - 252 (chain C) in PDB entry 5M73
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 226 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225C PHE* 1.3 78.3 - - + +
227C GLU* 1.3 53.5 + - - +
228C GLU* 3.8 14.8 + - - +
229C GLN* 3.1 22.7 + - - +
230C ALA* 2.6 35.0 + - - +
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Residues in contact with GLU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C PHE 3.7 2.7 + - - +
226C THR* 1.3 72.9 - - - +
228C GLU* 1.3 61.5 + - - +
230C ALA* 3.4 11.8 - - + +
231C VAL* 3.0 28.8 + - - +
234C ASN* 5.9 3.8 + - - +
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Residues in contact with GLU 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C THR* 3.1 12.3 + - - +
227C GLU* 1.3 79.1 - - - +
229C GLN* 1.3 61.0 + - - +
231C VAL* 3.6 19.6 + - - +
232C LEU 4.8 0.3 + - - -
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Residues in contact with GLN 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLU* 3.0 33.3 + - - +
64C GLN* 4.1 17.0 - - - +
181C LYS* 5.9 3.1 - - - +
225C PHE* 4.9 16.4 - - + -
226C THR* 3.1 21.1 + - - +
228C GLU* 1.3 76.2 - - - +
230C ALA* 1.3 65.5 + - - +
231C VAL 3.1 3.2 + - - -
232C LEU* 3.4 21.0 + - - +
233C TYR* 4.1 18.0 + - + -
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Residues in contact with ALA 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C ALA* 3.8 30.3 - - + +
225C PHE* 5.7 0.8 - - - +
226C THR 2.6 22.9 + - - +
227C GLU* 3.1 17.4 + - + +
229C GLN* 1.3 71.1 - - - +
231C VAL* 1.3 65.6 + - - +
232C LEU 3.2 0.2 - - - -
233C TYR* 3.1 7.8 + - - +
234C ASN* 2.9 35.5 + - - +
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Residues in contact with VAL 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C GLU 3.0 17.8 + - - +
228C GLU* 3.6 14.8 - - - +
229C GLN 3.1 0.8 - - - -
230C ALA* 1.3 76.2 - - - +
232C LEU* 1.3 64.4 + - - +
234C ASN* 3.4 8.1 + - - +
235C GLN* 2.9 43.6 + - + +
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Residues in contact with LEU 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU* 3.7 24.0 - - + +
64C GLN* 3.7 47.3 - - + +
67C LYS* 4.0 27.1 - - + -
228C GLU 4.8 0.6 + - - -
229C GLN* 3.4 13.5 + - - +
230C ALA 3.2 1.0 - - - -
231C VAL* 1.3 79.6 - - - +
233C TYR* 1.3 70.1 + - + +
235C GLN* 3.0 32.9 + - + +
236C ARG* 3.0 10.9 + - - -
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Residues in contact with TYR 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLU* 5.3 1.7 - - - +
63C LEU* 3.5 30.5 - - + -
64C GLN* 5.4 1.3 - - + -
181C LYS* 3.6 15.2 + - - -
185C GLU* 2.2 34.0 + - - -
218C TYR* 4.0 15.6 - + + +
221C LEU* 3.2 45.3 - - + +
222C ALA* 3.6 23.6 - - + -
225C PHE* 5.0 9.4 - + - -
229C GLN* 4.6 20.1 - - + +
230C ALA* 3.1 7.9 + - - +
232C LEU* 1.3 86.4 - - + +
234C ASN* 1.3 64.5 + - - +
236C ARG* 2.9 13.6 + - - +
237C VAL* 3.1 16.2 + - - +
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Residues in contact with ASN 234 (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 GLU* 5.7 4.7 - - - +
222C ALA* 4.0 15.2 - - - +
227C GLU* 5.9 4.0 + - - +
230C ALA* 2.9 28.9 + - - +
231C VAL* 3.8 6.7 - - - +
233C TYR* 1.3 75.6 - - - +
235C GLN* 1.3 57.7 + - + +
237C VAL* 3.4 6.0 + - - +
238C GLU* 3.0 29.7 + - - +
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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
----------------------------------------------------------
67C LYS* 5.2 7.7 + - - +
231C VAL* 2.9 33.8 + - + +
232C LEU* 3.0 28.4 + - + +
234C ASN* 1.3 75.0 - - + +
236C ARG* 1.3 58.1 + - - +
238C GLU* 3.8 6.0 - - - +
239C GLU* 2.9 33.3 + - - +
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Residues in contact with ARG 236 (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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63C LEU* 3.8 33.6 - - + +
66C ILE* 3.6 23.0 - - - +
67C LYS* 4.3 11.9 - - - +
70C GLN* 5.8 1.8 + - - -
135C TRP* 6.1 1.0 - - - -
189C TYR* 5.4 3.2 - - - -
192C TYR* 3.4 48.4 + - - -
214C CYS* 5.4 3.4 - - - -
218C TYR* 3.5 31.5 + - + -
232C LEU 3.0 4.8 + - - -
233C TYR 2.9 9.1 + - - +
235C GLN* 1.3 73.6 - - - +
237C VAL* 1.3 66.0 + - - +
239C GLU* 2.8 53.7 + - - +
240C ILE* 3.0 18.3 + - + +
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Residues in contact with VAL 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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215C LYS* 3.4 61.7 - - + +
218C TYR* 4.1 19.1 - - + -
219C GLU* 4.4 14.4 - - + +
233C TYR 3.1 12.4 + - - +
234C ASN* 4.0 7.2 - - - +
236C ARG* 1.3 76.8 - - - +
238C GLU* 1.3 64.3 + - - +
239C GLU 3.1 0.2 + - - -
240C ILE* 3.2 10.1 + - + +
241C SER* 3.0 23.4 + - - -
244C ILE* 6.0 1.1 - - + -
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Residues in contact with GLU 238 (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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234C ASN 3.0 17.8 + - - +
235C GLN* 4.0 6.3 - - - +
237C VAL* 1.3 77.9 - - - +
239C GLU* 1.3 62.6 + - - +
241C SER* 3.5 16.8 + - - -
242C PRO* 3.7 9.4 - - - +
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Residues in contact with GLU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LYS* 3.5 23.8 + - - +
192C TYR* 5.0 2.1 + - - -
235C GLN* 2.9 21.6 + - - +
236C ARG* 2.8 50.8 + - - +
238C GLU* 1.3 80.2 - - - +
240C ILE* 1.3 59.1 + - + +
242C PRO* 3.8 8.5 - - - +
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Residues in contact with ILE 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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192C TYR* 3.5 30.7 - - + +
196C MET* 4.6 10.3 - - + -
211C PHE* 4.2 37.6 - - + +
214C CYS* 4.0 26.9 - - - -
215C LYS* 5.0 4.3 - - + +
236C ARG* 3.0 18.4 + - + +
237C VAL* 3.8 11.7 - - + +
239C GLU* 1.3 79.7 - - + +
241C SER* 1.3 69.1 + - - +
242C PRO* 3.3 3.4 - - - -
243C ASN* 3.3 17.7 + - + +
244C ILE* 3.4 17.6 + - + +
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Residues in contact with SER 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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215C LYS* 5.6 4.1 + - - -
237C VAL* 3.0 19.1 + - - -
238C GLU* 3.9 16.2 - - - -
239C GLU 3.5 0.2 - - - -
240C ILE* 1.3 75.8 - - - +
242C PRO* 1.3 61.8 - - - +
244C ILE* 2.7 38.4 + - - +
245C ARG* 3.0 12.2 + - - +
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Residues in contact with PRO 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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238C GLU 3.7 10.5 - - - +
239C GLU 3.8 8.1 - - - +
240C ILE 3.5 3.6 - - - -
241C SER* 1.3 90.7 - - - +
243C ASN* 1.3 67.2 + - - +
245C ARG* 3.2 9.6 + - + +
246C TYR* 2.9 23.1 + - - +
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Residues in contact with ASN 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C MET* 3.5 35.2 - - - +
199C PHE* 4.3 24.9 - - + -
211C PHE* 3.3 24.8 - - + -
240C ILE* 3.3 10.1 + - - +
241C SER 3.2 0.6 - - - -
242C PRO* 1.3 81.2 - - - +
244C ILE* 1.3 59.3 + - - +
246C TYR* 3.2 7.4 + - - +
247C CYS* 2.8 33.9 + - - -
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Residues in contact with ILE 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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208C ILE* 4.4 12.4 - - + +
211C PHE* 3.7 39.3 - - + +
212C ASN* 4.6 16.2 - - - +
215C LYS* 4.7 18.4 - - + +
237C VAL* 5.5 1.3 - - + +
240C ILE* 3.4 23.9 + - + +
241C SER* 2.7 25.9 + - - +
243C ASN* 1.3 72.2 - - - +
245C ARG* 1.3 61.6 + - - +
247C CYS* 3.0 9.4 + - - +
248C ALA* 2.9 22.7 + - + +
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Residues in contact with ARG 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 SER* 3.0 11.3 + - - +
242C PRO* 3.2 9.4 + - + +
244C ILE* 1.3 78.0 - - - +
246C TYR* 1.3 62.4 + - - +
248C ALA* 3.2 8.3 + - + +
249C TYR* 3.0 24.8 + - + +
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Residues in contact with TYR 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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199C PHE* 4.2 20.0 - + + -
204C TRP* 4.3 11.7 - + - -
242C PRO 2.9 16.5 + - - +
243C ASN* 3.6 9.4 - - - +
245C ARG* 1.3 74.1 - - - +
247C CYS* 1.3 64.7 + - - +
249C TYR* 3.1 17.5 + + - +
250C ASN* 3.0 48.9 + - - -
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Residues in contact with CYS 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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199C PHE* 4.1 15.7 - - - -
204C TRP* 4.0 19.6 - - + +
207C ALA* 3.7 30.5 - - - -
208C ILE* 3.9 26.5 - - + -
211C PHE* 4.9 3.8 - - - -
243C ASN 2.8 19.5 + - - -
244C ILE* 3.0 8.9 + - - +
246C TYR* 1.3 75.9 - - - +
248C ALA* 1.3 64.1 + - - +
250C ASN* 3.0 4.5 + - - +
251C ILE* 3.0 26.7 + - - +
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Residues in contact with ALA 248 (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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208C ILE* 4.1 14.1 - - + +
244C ILE* 2.9 14.1 + - + +
245C ARG* 3.2 11.4 + - + +
247C CYS* 1.3 75.6 - - - +
249C TYR* 1.3 56.9 + - - +
251C ILE* 2.8 23.1 + - - +
252C GLY* 2.9 13.0 + - - -
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Residues in contact with TYR 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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245C ARG* 3.0 16.2 + - + +
246C TYR* 3.1 22.0 + + - +
248C ALA* 1.3 76.2 - - - +
250C ASN* 1.3 88.2 + - - +
252C GLY* 4.3 2.2 - - - +
253C ASP* 3.8 42.5 + - - +
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Residues in contact with ASN 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C TRP* 2.9 70.2 - - + +
246C TYR* 3.0 25.8 + - - +
247C CYS 3.0 3.3 + - - +
249C TYR* 1.3 107.8 - - - +
251C ILE* 1.3 62.3 + - - +
253C ASP* 4.0 7.4 - - - +
254C GLN* 3.7 14.6 + - - +
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Residues in contact with ILE 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C TRP* 4.2 14.1 - - + +
205C LYS* 4.3 20.6 - - + +
208C ILE* 4.1 33.0 - - + -
247C CYS 3.0 13.4 + - - +
248C ALA* 2.8 8.8 + - - +
250C ASN* 1.3 78.3 - - - +
252C GLY* 1.3 57.7 + - - +
253C ASP 3.0 9.9 + - - -
254C GLN* 3.4 24.3 - - - +
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Residues in contact with GLY 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C ALA 2.9 13.4 + - - -
249C TYR* 3.9 4.0 + - - -
250C ASN 3.6 0.2 - - - -
251C ILE* 1.3 76.5 - - - +
253C ASP* 1.3 60.6 + - - +
254C GLN* 3.5 3.6 - - - -
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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
------------------------------------------------------------
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