Contacts of the helix formed by residues 216 - 242 (chain C) in PDB entry 5MKE
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 TYR 216 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215C LYS* 1.3 89.5 - - + +
217C LEU* 1.3 53.6 + - + +
219C SER* 2.6 18.6 + - - -
220C VAL* 2.6 48.4 + - + +
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Residues in contact with LEU 217 (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* 3.1 34.1 - - + +
216C TYR* 1.3 76.9 - - + +
218C LYS* 1.3 57.5 + - - +
220C VAL* 4.3 9.9 - - + -
221C LEU* 3.2 34.0 - - + +
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Residues in contact with LYS 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C LYS 2.8 28.0 + - - +
217C LEU* 1.3 73.3 - - - +
219C SER* 1.3 57.2 + - - +
222C ARG* 3.1 47.3 + - + +
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Residues in contact with SER 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C LYS 3.0 6.1 + - - -
216C TYR* 2.6 34.2 + - - -
218C LYS* 1.3 75.4 - - - +
220C VAL* 1.3 65.4 + - - -
222C ARG* 3.5 4.2 - - - +
223C GLU* 3.3 19.1 + - - +
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Residues in contact with VAL 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C TYR* 2.6 39.2 + - + +
217C LEU* 4.3 11.2 - - + -
219C SER* 1.3 73.2 - - - +
221C LEU* 1.3 62.9 + - + +
223C GLU* 2.8 20.1 + - + +
224C LEU* 2.3 57.4 + - + +
579C PHE* 6.1 4.7 - - + -
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Residues in contact with LEU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C LEU* 3.2 26.3 + - + +
218C LYS* 5.3 0.2 - - - -
220C VAL* 1.3 82.2 - - + +
222C ARG* 1.3 52.5 + - - +
224C LEU* 3.2 19.4 - - + +
225C VAL* 2.3 58.0 + - + +
228C LEU* 5.6 4.5 - - + -
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Residues in contact with ARG 222 (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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218C LYS* 3.1 40.7 + - + +
219C SER* 3.5 5.6 - - - +
221C LEU* 1.3 78.4 - - - +
223C GLU* 1.3 63.6 + - + +
225C VAL* 3.1 18.8 - - - +
226C THR* 3.0 54.5 + - - +
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Residues in contact with GLU 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C SER 3.3 5.4 + - - +
220C VAL* 2.8 36.9 + - + +
222C ARG* 1.3 74.8 - - - +
224C LEU* 1.3 57.6 + - + +
226C THR* 2.1 36.9 + - + +
227C TYR* 2.6 59.0 + - + -
487C TYR* 4.7 8.0 - - + +
490C GLU* 5.4 1.6 - - - +
576C PHE* 5.5 1.4 - - - -
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Residues in contact with LEU 224 (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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220C VAL* 2.3 52.8 + - + +
221C LEU* 3.3 29.4 - - + +
223C GLU* 1.3 69.4 - - + +
225C VAL* 1.3 49.6 + - - +
227C TYR* 2.9 9.5 + - + +
228C LEU* 2.4 47.2 + - + +
576C PHE* 3.5 53.1 - - + +
579C PHE* 4.5 17.3 - - + -
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Residues in contact with VAL 225 (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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221C LEU* 2.3 55.8 + - + +
222C ARG* 3.1 22.7 - - - +
224C LEU* 1.3 68.0 - - - +
226C THR* 1.3 52.2 + - - +
228C LEU* 3.2 16.7 - - + +
229C LEU* 2.6 58.0 + - + +
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Residues in contact with THR 226 (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 ARG* 3.0 35.1 + - - +
223C GLU* 2.1 40.7 + - + +
225C VAL* 1.3 72.3 - - + +
227C TYR* 1.3 54.9 + - - -
229C LEU* 4.9 2.2 - - - -
230C PHE* 2.8 37.9 + - - +
483C PHE* 3.5 21.1 - - + -
487C TYR* 2.7 26.7 + - + -
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Residues in contact with TYR 227 (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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223C GLU* 2.6 76.6 + - + -
224C LEU* 3.2 11.9 - - + +
226C THR* 1.3 74.1 + - - +
228C LEU* 1.3 63.7 + - + +
230C PHE* 5.0 3.3 - - - -
231C LEU* 3.0 27.9 + - - +
487C TYR* 4.3 23.3 - + - -
490C GLU* 5.5 0.7 + - - -
491C GLU* 5.3 4.5 + - - -
572C LYS* 3.3 38.8 + - + -
576C PHE* 3.2 35.2 - + + -
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Residues in contact with LEU 228 (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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221C LEU* 5.6 4.5 - - + -
224C LEU* 2.4 36.9 + - + +
225C VAL* 2.9 30.6 + - + +
227C TYR* 1.3 68.8 - - + +
229C LEU* 1.3 69.2 + - + +
231C LEU* 3.0 24.4 - - + +
232C ILE* 3.0 14.0 - - + +
576C PHE* 6.4 1.8 - - + -
1006C CHS 5.2 8.2 - - + +
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Residues in contact with LEU 229 (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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225C VAL* 2.6 43.5 + - + +
226C THR* 4.4 2.5 - - - +
228C LEU* 1.3 75.5 - - + +
230C PHE* 1.3 55.1 + - - +
231C LEU 2.9 3.8 - - - -
232C ILE* 2.7 39.0 + - + +
233C VAL* 3.2 13.4 + - + +
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Residues in contact with PHE 230 (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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226C THR* 2.8 22.9 + - - +
227C TYR* 5.5 2.2 - - - -
229C LEU* 1.3 72.5 - - - +
231C LEU* 1.3 65.0 + - - +
233C VAL* 3.2 30.6 + - + +
234C LEU* 3.4 42.0 + - + +
480C PHE* 3.5 16.8 - - + -
483C PHE* 3.4 33.2 - + + -
484C ILE* 3.3 42.2 - - + -
487C TYR* 5.0 5.8 - + - -
514C ILE* 6.2 4.0 - - + -
569C VAL* 5.5 7.1 - - + +
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Residues in contact with LEU 231 (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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227C TYR 3.0 18.2 + - - +
228C LEU* 3.0 19.1 - - + +
229C LEU 2.9 0.6 + - - -
230C PHE* 1.3 81.4 - - - +
232C ILE* 1.3 64.1 + - + +
233C VAL 3.1 0.2 + - - -
234C LEU* 3.6 2.3 + - - +
235C CYS* 3.1 32.6 + - - -
569C VAL* 5.3 19.7 - - + +
570C TRP* 4.3 20.4 - - + +
572C LYS* 6.6 0.2 - - + -
573C LEU* 4.2 28.5 - - + +
1006C CHS 3.7 40.2 - - + +
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Residues in contact with ILE 232 (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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228C LEU* 3.0 29.4 - - + +
229C LEU* 2.7 24.2 + - + +
231C LEU* 1.3 72.2 - - + +
233C VAL* 1.3 49.9 + - - +
235C CYS* 3.1 0.3 + - - +
236C ILE* 2.2 67.0 + - + +
1006C CHS 3.4 63.5 - - + +
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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
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229C LEU* 3.2 8.2 + - + +
230C PHE* 3.3 44.6 - - + +
231C LEU 3.1 0.6 - - - -
232C ILE* 1.3 74.9 - - - +
234C LEU* 1.3 62.7 + - + +
236C ILE* 2.8 16.5 + - + +
237C LEU* 2.7 28.0 + - + +
476C CYS* 4.1 28.7 - - + -
479C ILE* 6.3 1.6 - - + -
480C PHE* 4.4 17.3 - - + -
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Residues in contact with LEU 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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230C PHE* 3.4 44.8 + - + +
231C LEU 4.4 4.0 - - - +
233C VAL* 1.3 77.5 - - - +
235C CYS* 1.3 56.8 + - - +
237C LEU* 3.2 26.3 + - + +
238C THR* 2.8 37.1 + - + +
480C PHE* 4.8 14.4 - - + -
484C ILE* 5.6 0.9 - - + -
514C ILE* 6.5 0.2 - - + -
565C THR* 5.8 2.0 - - - +
566C VAL* 5.7 9.9 - - + -
569C VAL* 4.7 25.1 - - + -
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Residues in contact with CYS 235 (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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231C LEU* 3.1 35.0 + - - -
232C ILE 3.1 7.6 + - - +
234C LEU* 1.3 75.6 - - - +
236C ILE* 1.3 52.4 + - - +
238C THR* 2.4 10.8 + - - -
239C TYR* 2.3 41.8 + - + +
566C VAL* 5.8 2.9 - - - -
569C VAL* 6.5 0.4 - - - -
570C TRP* 4.5 4.7 - - - -
1005C CHS 6.5 0.2 - - - -
1006C CHS 3.2 32.3 - - - +
613D GLN* 4.3 20.6 - - - -
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Residues in contact with ILE 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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232C ILE* 2.2 61.1 + - + +
233C VAL* 2.8 12.9 + - + +
235C CYS* 1.3 65.5 - - - +
237C LEU* 1.3 55.6 + - + +
239C TYR* 3.9 11.2 - - + -
240C GLY* 2.2 41.1 + - - -
472C PHE 5.7 2.5 - - - +
473C LEU* 6.0 3.4 - - + -
476C CYS* 4.5 17.5 - - + -
1006C CHS 4.1 6.7 + - - +
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Residues in contact with LEU 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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233C VAL 2.7 18.6 + - - +
234C LEU* 3.3 28.9 - - + +
236C ILE* 1.3 72.0 - - + +
238C THR* 1.3 55.9 + - - +
240C GLY* 4.7 0.2 - - - -
241C MET* 2.2 59.8 + - + +
461C LYS* 5.1 0.9 - - - +
464C ARG* 3.7 27.8 - - - +
473C LEU* 4.2 24.2 - - + +
476C CYS* 4.3 11.9 - - - -
477C GLU* 4.9 0.2 - - + -
480C PHE* 3.5 33.7 - - + -
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Residues in contact with THR 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 LEU* 2.8 21.9 + - + +
235C CYS* 2.4 27.9 + - - +
237C LEU* 1.3 71.1 - - + +
239C TYR* 1.3 58.7 + - - +
241C MET* 3.4 21.3 - - + +
242C MET* 2.7 36.3 + - - +
562C ALA* 6.5 1.3 - - + -
566C VAL* 5.0 7.9 - - + -
616D TYR* 5.6 4.7 - - - -
617D LEU* 4.6 30.2 - - + +
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Residues in contact with TYR 239 (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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235C CYS 2.3 33.4 + - - +
236C ILE* 3.6 9.4 - - + +
238C THR* 1.3 69.7 + - - +
240C GLY* 1.3 62.5 + - - +
242C MET 2.8 22.2 - - - +
243C SER* 3.6 11.7 + - - -
244C SER 6.2 1.1 - - - -
1005C CHS 3.9 31.4 - - + +
1006C CHS 3.2 43.0 + - - +
616D TYR* 6.4 0.9 - - - -
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Residues in contact with GLY 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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236C ILE* 2.2 30.1 + - - -
237C LEU* 2.9 0.6 + - - -
239C TYR* 1.3 72.8 - - - +
241C MET* 1.3 63.8 + - - +
242C MET* 3.1 3.5 + - - -
243C SER* 4.4 2.3 + - - -
473C LEU* 5.7 9.2 - - - +
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Residues in contact with MET 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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237C LEU* 2.2 64.9 + - + +
238C THR* 3.4 18.4 - - + +
240C GLY* 1.3 67.8 - - - +
242C MET* 1.3 94.3 + - + +
243C SER 4.3 0.5 + - - -
246C VAL* 5.1 0.5 - - - +
433C ILE* 6.0 0.3 - - - +
435C LEU* 4.1 8.7 - - - +
461C LYS* 3.3 59.0 - - + +
473C LEU* 5.6 8.2 - - + +
558C PHE* 5.4 12.6 - - + -
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Residues in contact with MET 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 THR* 2.7 27.2 + - - +
239C TYR* 2.8 15.9 - - - +
241C MET* 1.3 125.2 - - + +
243C SER* 1.3 64.9 + - - +
246C VAL* 4.1 15.9 - - + -
435C LEU* 3.7 22.2 - - + -
459C PRO* 5.6 8.7 - - + +
460C LEU* 5.2 2.9 - - - -
461C LYS* 4.5 18.4 - - + +
555C GLN* 5.6 7.4 - - - +
559C ASN* 5.5 9.6 - - - +
616D TYR* 4.0 15.1 + - + +
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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
------------------------------------------------------------
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