Contacts of the helix formed by residues 216 - 242 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B LYS* 1.3 88.5 - - + +
217B LEU* 1.3 53.8 + - + +
219B SER* 2.6 19.2 + - - -
220B VAL* 2.6 47.5 + - + +
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B LYS* 3.1 34.1 - - + +
216B TYR* 1.3 77.9 - - + +
218B LYS* 1.3 56.1 + - - +
220B VAL* 4.3 9.2 - - + -
221B LEU* 3.2 34.6 - - + +
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Residues in contact with LYS 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LYS 2.8 27.1 + - - +
217B LEU* 1.3 73.9 - - - +
219B SER* 1.3 57.9 + - - +
222B ARG* 3.1 46.7 + - + +
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Residues in contact with SER 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LYS 3.0 6.0 + - - -
216B TYR* 2.6 34.6 + - - -
218B LYS* 1.3 75.1 - - - +
220B VAL* 1.3 64.3 + - - -
222B ARG* 3.5 4.1 - - - +
223B GLU* 3.3 19.4 + - - +
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Residues in contact with VAL 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TYR* 2.6 38.5 + - + +
217B LEU* 4.3 11.9 - - + -
219B SER* 1.3 72.0 - - - +
221B LEU* 1.3 63.8 + - + +
223B GLU* 2.8 21.0 + - + +
224B LEU* 2.3 57.0 + - + +
579B PHE* 6.1 4.9 - - + -
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LEU* 3.2 26.3 + - + +
219B SER 3.6 0.2 - - - -
220B VAL* 1.3 82.4 - - + +
222B ARG* 1.3 52.9 + - - +
224B LEU* 3.3 19.0 - - + +
225B VAL* 2.3 58.7 + - + +
228B LEU* 5.6 4.5 - - + -
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Residues in contact with ARG 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B LYS* 3.1 40.9 + - + +
219B SER* 3.5 5.8 - - - +
220B VAL 3.1 0.2 - - - -
221B LEU* 1.3 76.7 - - - +
223B GLU* 1.3 63.6 + - + +
225B VAL* 3.1 19.0 - - - +
226B THR* 3.0 53.8 + - - +
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Residues in contact with GLU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B SER 3.3 5.6 + - - +
220B VAL* 2.8 36.7 + - + +
222B ARG* 1.3 75.8 - - - +
224B LEU* 1.3 56.2 + - + +
226B THR* 2.1 36.3 + - + +
227B TYR* 2.6 61.3 + - + -
487B TYR* 4.7 7.6 - - + +
490B GLU* 5.4 1.6 - - - +
576B PHE* 5.5 1.7 - - - -
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Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B VAL* 2.3 51.5 + - + +
221B LEU* 3.3 29.4 - - + +
223B GLU* 1.3 68.9 - - + +
225B VAL* 1.3 50.6 + - - +
227B TYR* 2.9 10.0 + - + +
228B LEU* 2.4 46.8 + - + +
576B PHE* 3.5 52.7 - - + -
579B PHE* 4.5 17.5 - - + -
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Residues in contact with VAL 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 2.3 54.5 + - + +
222B ARG* 3.1 23.1 - - - +
224B LEU* 1.3 67.9 - - - +
226B THR* 1.3 53.4 + - + +
228B LEU* 2.9 16.7 + - + +
229B LEU* 2.6 58.4 + - + +
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Residues in contact with THR 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ARG* 3.0 34.7 + - - +
223B GLU* 2.1 40.2 + - + +
225B VAL* 1.3 72.5 - - + +
227B TYR* 1.3 54.5 + - - -
229B LEU* 4.9 2.5 - - - -
230B PHE* 2.8 38.5 + - - +
483B PHE* 3.5 21.1 - - + -
487B TYR* 2.7 27.1 + - - +
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Residues in contact with TYR 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B GLU* 2.6 77.3 + - + -
224B LEU* 3.2 11.7 - - + +
226B THR* 1.3 73.8 + - - +
228B LEU* 1.3 64.6 + - + +
230B PHE* 5.0 3.3 - - - -
231B LEU* 3.0 27.9 + - - +
487B TYR* 4.3 22.7 - + - -
490B GLU* 5.5 0.3 + - - -
491B GLU* 5.3 4.5 + - - -
572B LYS* 3.3 38.4 + - + -
576B PHE* 3.2 34.8 - + + -
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B LEU* 5.6 4.5 - - + -
224B LEU* 2.4 37.0 + - + +
225B VAL* 2.9 30.4 + - + +
227B TYR* 1.3 68.8 - - + +
229B LEU* 1.3 70.1 + - + +
231B LEU* 3.0 23.4 - - + +
232B ILE* 3.0 15.0 - - + +
576B PHE* 6.4 2.2 - - + -
1006B CHS 5.1 8.4 - - + +
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B VAL* 2.6 42.5 + - + +
226B THR* 4.4 2.7 - - - +
228B LEU* 1.3 77.4 - - + +
230B PHE* 1.3 56.0 + - - +
231B LEU 2.9 4.0 - - - -
232B ILE* 2.7 38.5 + - + +
233B VAL* 3.2 13.0 + - + +
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Residues in contact with PHE 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR* 2.8 22.6 + - - +
227B TYR* 5.5 2.5 - - - -
229B LEU* 1.3 73.9 - - - +
231B LEU* 1.3 63.8 + - - +
233B VAL* 3.2 31.1 + - + +
234B LEU* 3.4 43.4 + - + +
480B PHE* 3.5 16.2 - - + -
483B PHE* 3.4 33.4 - + + -
484B ILE* 3.3 42.6 - - + -
487B TYR* 5.0 5.8 - + - -
514B ILE* 6.2 4.0 - - + -
569B VAL* 5.5 7.1 - - + +
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Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B TYR 3.0 18.4 + - - +
228B LEU* 3.0 20.0 - - + +
229B LEU 2.9 0.8 + - - -
230B PHE* 1.3 81.1 - - - +
232B ILE* 1.3 64.1 + - + +
233B VAL 3.1 0.2 + - - -
234B LEU* 3.6 2.8 + - - +
235B CYS* 3.1 31.5 + - - -
569B VAL* 5.3 19.3 - - + +
570B TRP* 4.3 20.6 - - + +
573B LEU* 4.2 29.2 - - + +
1006B CHS 3.6 41.3 - - + +
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Residues in contact with ILE 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B LEU* 3.0 29.4 - - + +
229B LEU* 2.7 24.0 + - + +
231B LEU* 1.3 72.6 - - + +
233B VAL* 1.3 49.3 + - - +
235B CYS 3.1 0.2 + - - -
236B ILE* 2.2 66.3 + - + +
1006B CHS 3.4 64.6 - - + +
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B LEU* 3.2 8.0 + - + +
230B PHE* 3.3 44.6 - - + +
231B LEU 3.1 0.6 - - - -
232B ILE* 1.3 74.0 - - + +
234B LEU* 1.3 61.9 + - + +
236B ILE* 2.8 16.3 + - + +
237B LEU* 2.7 28.8 + - + +
476B CYS* 4.1 29.3 - - + +
479B ILE* 6.3 1.6 - - + -
480B PHE* 4.4 16.4 - - + -
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PHE* 3.4 44.8 + - + +
231B LEU 4.4 4.3 - - - +
233B VAL* 1.3 77.8 - - - +
235B CYS* 1.3 58.3 + - - +
237B LEU* 3.2 26.0 + - + +
238B THR* 2.8 37.5 + - + +
480B PHE* 4.8 13.5 - - + -
484B ILE* 5.6 0.4 - - + -
565B THR* 5.8 2.2 - - - +
566B VAL* 5.7 9.0 - - + -
569B VAL* 4.7 24.5 - - + -
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Residues in contact with CYS 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B LEU* 3.1 34.3 + - - -
232B ILE 3.1 8.2 + - - +
234B LEU* 1.3 75.9 - - - +
236B ILE* 1.3 51.4 + - - +
238B THR* 2.4 10.5 + - - -
239B TYR* 2.3 41.8 + - + +
566B VAL* 5.8 2.5 - - - -
569B VAL* 6.5 0.4 - - - -
570B TRP* 4.5 4.5 - - - -
1005B CHS 6.5 0.4 - - - -
1006B CHS 3.2 32.5 - - - +
613C GLN* 4.3 20.6 - - - -
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Residues in contact with ILE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B ILE* 2.2 60.7 + - + +
233B VAL* 2.8 10.9 + - + +
235B CYS* 1.3 65.7 - - - +
237B LEU* 1.3 56.3 + - + +
239B TYR* 3.9 11.4 - - + -
240B GLY* 2.2 40.8 + - - +
472B PHE 5.7 2.9 - - - +
473B LEU* 6.0 2.9 - - + -
476B CYS* 4.5 17.5 - - - -
1006B CHS 4.4 7.0 - - - +
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Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B VAL 2.7 17.1 + - - +
234B LEU* 3.3 28.3 - - + +
236B ILE* 1.3 72.1 - - + +
238B THR* 1.3 55.6 + - - +
240B GLY* 4.7 0.4 - - - -
241B MET* 2.2 59.2 + - + +
461B LYS* 5.1 0.7 - - - +
464B ARG* 3.7 27.1 - - - +
473B LEU* 4.2 24.0 - - + +
476B CYS* 4.3 12.3 - - - -
477B GLU* 4.9 0.2 - - + -
480B PHE* 3.5 33.7 - - + -
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Residues in contact with THR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B LEU* 2.8 22.0 + - + +
235B CYS* 2.4 28.1 + - - -
237B LEU* 1.3 70.9 - - - +
239B TYR* 1.3 57.1 + - - +
241B MET* 3.4 20.8 - - + +
242B MET* 2.7 37.6 + - - +
562B ALA* 6.5 1.6 - - + -
566B VAL* 5.0 8.5 - - + -
616C TYR* 5.6 5.2 - - - -
617C LEU* 4.6 28.6 - - + +
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Residues in contact with TYR 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B CYS* 2.3 33.1 + - + +
236B ILE* 3.6 9.0 - - + +
238B THR* 1.3 68.4 + - - -
240B GLY* 1.3 62.7 + - - +
242B MET 2.8 22.1 - - - +
243B SER* 3.6 10.9 + - - -
244B SER 6.2 0.9 - - - -
1005B CHS 3.9 33.0 - - + +
1006B CHS 3.3 43.0 + - - +
616C TYR* 6.4 1.1 - - - -
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Residues in contact with GLY 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ILE* 2.2 29.7 + - - -
237B LEU* 2.9 0.6 + - - -
239B TYR* 1.3 73.3 - - - +
241B MET* 1.3 65.2 + - - +
242B MET* 3.1 3.4 + - - -
243B SER* 4.4 2.1 + - - -
473B LEU* 5.7 9.4 - - - +
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Residues in contact with MET 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B LEU* 2.2 65.5 + - + +
238B THR* 3.4 18.6 - - + +
240B GLY 1.3 67.8 - - - +
242B MET* 1.3 93.4 + - + +
243B SER 4.1 0.7 + - - -
246B VAL* 5.1 0.2 - - - +
433B ILE* 6.0 0.3 - - - +
435B LEU* 4.1 8.7 - - - +
461B LYS* 3.3 58.6 - - + +
473B LEU* 5.6 9.0 - - + +
558B PHE* 5.4 12.8 - - + -
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Residues in contact with MET 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B THR* 2.7 27.2 + - - +
239B TYR* 2.8 16.1 - - - +
241B MET* 1.3 125.5 - - + +
243B SER* 1.3 65.1 + - - +
246B VAL* 4.1 17.3 - - + -
435B LEU* 3.7 22.0 - - + -
459B PRO* 5.6 8.7 - - + +
460B LEU* 5.2 2.7 - - - -
461B LYS* 4.5 18.4 - - + +
555B GLN* 5.6 7.4 - - - +
559B ASN* 5.5 9.9 - - - +
616C TYR* 4.0 15.3 + - + +
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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) + - + + + + + -
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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