Contacts of the helix formed by residues 216 - 242 (chain D) in PDB entry 5MKF
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215D LYS* 1.3 87.4 - - + +
217D LEU* 1.3 50.6 + - + +
219D SER* 2.7 20.2 + - - -
220D VAL* 2.4 48.4 + - + +
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Residues in contact with LEU 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D LYS* 3.1 35.5 - - + +
216D TYR* 1.3 78.3 - - + +
218D LYS* 1.3 56.9 + - - +
220D VAL* 3.6 19.6 - - + +
221D LEU* 2.9 39.1 + - + +
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Residues in contact with LYS 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D LYS 3.3 15.6 + - - +
216D TYR 2.9 0.8 + - - -
217D LEU* 1.3 78.8 - - - +
219D SER* 1.3 57.4 + - - +
221D LEU* 3.8 16.1 - - + +
222D ARG* 2.9 58.6 + - + +
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Residues in contact with SER 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D LYS 3.9 2.2 + - - -
216D TYR* 2.7 38.1 + - - +
218D LYS* 1.3 74.1 - - - +
220D VAL* 1.3 65.3 + - - +
222D ARG* 4.1 6.1 - - - -
223D GLU* 3.7 30.4 + - - +
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Residues in contact with VAL 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D TYR* 2.4 49.7 + - + +
217D LEU* 3.6 21.5 - - + +
219D SER* 1.3 71.5 - - - +
221D LEU* 1.3 63.5 + - + +
223D GLU* 4.1 1.6 - - - +
224D LEU* 2.9 44.2 + - + +
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Residues in contact with LEU 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D LEU* 2.9 33.4 + - + +
218D LYS* 3.8 18.2 - - + +
220D VAL* 1.3 73.4 - - + +
222D ARG* 1.3 74.9 + - + +
224D LEU* 2.8 12.8 + - + -
225D VAL* 2.2 60.2 + - + +
228D LEU* 5.9 1.8 - - + -
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Residues in contact with ARG 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D LYS* 2.9 43.2 + - - +
219D SER* 4.4 5.2 - - - -
221D LEU* 1.3 83.6 - - + +
223D GLU* 1.3 66.5 + - + +
225D VAL* 3.2 12.6 + - - +
226D THR* 3.1 59.3 + - - +
486D TYR* 5.2 14.7 + - - +
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Residues in contact with GLU 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D SER* 3.7 21.5 + - - +
220D VAL 4.2 1.3 - - - +
221D LEU 3.4 0.4 - - - -
222D ARG* 1.3 80.6 - - + +
224D LEU* 1.3 59.3 + - + +
226D THR* 2.1 29.9 + - - -
227D TYR* 3.1 16.7 - - + -
486D TYR* 6.2 0.7 - - + +
487D TYR* 3.6 17.6 - - + +
490D GLU* 4.9 11.1 - - - +
576D PHE* 6.2 0.3 - - - -
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Residues in contact with LEU 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D VAL* 2.9 42.4 + - + +
221D LEU* 2.8 12.0 + - + +
223D GLU* 1.3 75.6 - - + +
225D VAL* 1.3 56.8 + - - +
227D TYR* 2.7 10.1 + - + +
228D LEU* 2.3 55.8 + - + -
576D PHE* 3.8 32.1 - - + -
577D ILE* 3.5 36.6 - - + -
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Residues in contact with VAL 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D LEU* 2.2 62.8 + - + +
222D ARG* 3.6 14.8 - - - +
224D LEU* 1.3 65.2 - - - +
226D THR* 1.3 56.9 + - - +
228D LEU* 3.9 13.7 - - + -
229D LEU* 2.7 42.8 + - + +
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Residues in contact with THR 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D ARG* 3.1 35.4 + - - +
223D GLU* 2.1 31.3 + - - -
225D VAL* 1.3 76.4 - - - +
227D TYR* 1.3 52.8 + - - -
229D LEU* 3.3 3.2 - - - +
230D PHE* 2.4 36.2 + - - +
483D PHE* 3.5 32.5 - - + -
486D TYR* 5.0 8.3 - - + +
487D TYR* 2.6 23.8 + - + +
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Residues in contact with TYR 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D GLU* 3.1 23.8 - - + -
224D LEU* 2.7 14.5 + - + +
226D THR* 1.3 79.1 + - - +
228D LEU* 1.3 57.2 + - + +
230D PHE* 3.6 26.4 - + + -
231D LEU* 2.6 38.1 + - - +
483D PHE* 5.2 1.8 - + - -
487D TYR* 3.3 39.0 - + - +
491D GLU* 2.9 26.3 + - - -
514D ILE* 5.3 10.8 - - + -
569D VAL* 5.9 3.4 - - + -
572D LYS* 4.6 35.6 + - + -
576D PHE* 5.9 6.1 - + + -
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Residues in contact with LEU 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D LEU* 5.7 1.6 - - + -
224D LEU* 2.3 62.9 + - + +
225D VAL* 3.9 12.3 - - + +
227D TYR* 1.3 67.9 - - + +
229D LEU* 1.3 56.8 + - - +
231D LEU* 3.1 23.7 - - + +
232D ILE* 3.0 24.3 - - - +
573D LEU* 6.2 2.9 - - + -
577D ILE* 4.2 26.9 - - + -
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Residues in contact with LEU 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D VAL* 2.7 29.8 + - + +
226D THR* 3.6 2.9 - - - +
228D LEU* 1.3 71.7 - - - +
230D PHE* 1.3 63.9 + - - +
231D LEU 3.1 3.1 + - - -
232D ILE* 3.1 23.1 + - + +
233D VAL* 3.4 16.6 + - + +
483D PHE* 6.1 3.4 - - + -
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Residues in contact with PHE 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D THR 2.4 33.1 + - - +
227D TYR* 3.5 26.0 - + - +
229D LEU* 1.3 68.0 - - - +
231D LEU* 1.3 66.4 + - - +
233D VAL* 3.0 29.8 + - + +
234D LEU* 3.7 17.0 + - + +
480D PHE* 3.4 39.9 - + - -
483D PHE* 3.3 35.6 - + + -
484D ILE* 3.8 16.6 - - + -
514D ILE* 5.1 8.1 - - + -
569D VAL* 4.2 25.8 - - + -
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Residues in contact with LEU 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D TYR 2.6 13.6 + - - +
228D LEU* 3.1 45.8 - - + +
229D LEU 3.1 0.4 + - - -
230D PHE* 1.3 79.0 - - - +
232D ILE* 1.3 81.1 + - + +
233D VAL 3.3 0.5 + - - -
234D LEU* 3.6 5.7 + - - +
235D CYS* 3.4 23.2 + - - -
569D VAL* 5.1 13.0 - - + -
570D TRP* 6.1 4.3 - - + +
573D LEU* 5.3 15.7 - - + -
1011D CHS 3.5 29.4 - - + -
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Residues in contact with ILE 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D LEU 3.0 27.8 - - - +
229D LEU* 3.1 19.5 + - + +
231D LEU* 1.3 84.1 - - + +
233D VAL* 1.3 67.2 + - + +
235D CYS* 3.1 3.3 + - - +
236D ILE* 3.1 30.2 + - + +
1011D CHS 3.5 54.3 - - + +
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Residues in contact with VAL 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D LEU* 3.4 21.1 - - + +
230D PHE* 3.0 26.4 + - + +
232D ILE* 1.3 80.3 - - + +
234D LEU* 1.3 64.1 + - + +
236D ILE* 3.1 19.4 - - - +
237D LEU* 3.1 24.0 - - + +
476D CYS* 3.7 27.5 - - - -
479D ILE* 5.9 5.2 - - + -
480D PHE* 4.5 23.8 - - + -
483D PHE* 6.4 1.1 - - + -
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Residues in contact with LEU 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D PHE* 3.8 31.9 - - + +
231D LEU* 3.6 6.9 + - - +
232D ILE 3.3 0.4 - - - -
233D VAL* 1.3 71.6 - - - +
235D CYS* 1.3 61.4 + - - +
236D ILE 3.0 2.2 - - - -
237D LEU* 2.7 49.9 + - + +
238D THR* 2.9 17.3 + - + +
480D PHE* 3.4 32.5 - - + -
565D THR* 5.5 2.0 - - - +
566D VAL* 4.3 32.8 - - + -
569D VAL* 4.6 14.6 - - + -
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Residues in contact with CYS 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A GLN* 4.4 15.0 - - - +
231D LEU* 3.4 17.3 - - - -
232D ILE 3.1 7.7 + - - +
234D LEU* 1.3 76.5 - - - +
236D ILE* 1.3 58.5 + - - +
238D THR* 2.3 30.0 + - - -
239D TYR* 3.5 2.6 + - - +
566D VAL* 6.4 0.4 - - - -
570D TRP* 4.7 14.1 - - - -
1010D CHS 4.3 9.1 - - - +
1011D CHS 2.7 54.7 + - + +
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Residues in contact with ILE 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D ILE* 3.1 26.4 + - + +
233D VAL* 3.1 14.1 - - - +
234D LEU 3.0 0.6 - - - -
235D CYS* 1.3 74.5 - - - +
237D LEU* 1.3 55.0 + - + +
238D THR 3.1 0.3 + - - -
239D TYR* 3.3 3.2 + - + +
240D GLY* 2.4 37.4 + - - -
469D PHE* 4.2 23.6 - - + -
473D LEU* 4.4 15.3 - - + -
476D CYS* 5.2 12.1 - - + -
1011D CHS 3.9 20.2 - - - +
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Residues in contact with LEU 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D VAL* 3.1 37.2 - - + +
234D LEU* 2.7 35.3 + - + +
236D ILE* 1.3 74.8 - - + +
238D THR* 1.3 59.5 + - + +
241D MET* 2.4 71.1 + - + +
473D LEU* 4.1 18.4 - - + -
476D CYS* 5.3 5.2 - - - +
477D GLU* 6.0 7.2 - - + -
480D PHE* 5.3 13.7 - - + -
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Residues in contact with THR 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A GLN* 3.7 21.7 + - - +
616A TYR* 4.9 8.4 - - - -
617A LEU* 4.1 32.5 - - + -
234D LEU* 2.9 20.1 + - + +
235D CYS* 2.3 31.9 + - - -
237D LEU* 1.3 79.9 - - + +
239D TYR* 1.3 61.2 + - - -
242D MET* 2.9 27.4 + - - +
566D VAL* 5.1 6.5 - - + -
1010D CHS 3.2 16.4 + - - -
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Residues in contact with TYR 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A TYR* 5.6 3.1 - - - -
235D CYS 4.1 0.2 - - - +
236D ILE* 3.3 0.8 + - + -
238D THR* 1.3 83.1 + - - +
240D GLY* 1.3 66.2 + - - +
242D MET 2.8 21.2 - - - +
243D SER* 3.7 7.6 + - - -
244D SER* 4.8 25.1 - - - -
469D PHE* 5.6 8.3 - + - -
1010D CHS 3.8 24.1 + - + +
1011D CHS 3.4 35.4 - - - +
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Residues in contact with GLY 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D ILE* 2.4 27.7 + - - -
237D LEU* 4.1 0.9 - - - -
239D TYR* 1.3 75.3 - - - +
241D MET* 1.3 63.9 + - - +
242D MET* 3.2 2.1 + - - -
243D SER 4.5 1.0 + - - -
461D LYS* 4.8 0.7 + - - -
469D PHE* 4.0 26.9 - - - -
473D LEU* 4.4 8.9 - - - +
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Residues in contact with MET 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D LEU* 2.4 66.8 + - + +
240D GLY* 1.3 68.6 - - - -
242D MET* 1.3 78.3 + - + +
461D LYS* 3.3 45.6 + - - +
464D ARG* 4.6 16.8 - - - +
473D LEU* 3.8 15.0 - - + -
558D PHE* 4.6 24.0 - - + -
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Residues in contact with MET 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A TYR* 3.9 13.6 + - + +
621A THR* 5.5 15.7 - - + -
238D THR 2.9 18.9 + - - +
239D TYR* 2.8 20.3 - - - +
240D GLY 3.2 0.4 - - - -
241D MET* 1.3 100.7 - - + +
243D SER* 1.3 65.8 + - - +
246D VAL* 5.0 9.9 - - + -
435D LEU* 5.7 7.2 - - - -
459D PRO 5.9 1.6 - - - +
460D LEU* 5.5 2.7 - - + -
461D LYS* 4.9 22.9 - - + +
555D GLN* 4.3 23.6 - - - +
558D PHE* 6.5 0.7 - - + -
559D ASN* 4.9 13.9 - - - +
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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
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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