Contacts of the helix formed by residues 228 - 252 (chain E) in PDB entry 5ZR1
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 228 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E CYS* 1.3 79.2 - - - +
229E ASP* 1.3 60.8 + - - +
230E ASP* 3.6 9.9 + - - +
231E GLN* 3.4 22.6 + - - +
232E PHE* 2.9 37.5 + - - -
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Residues in contact with ASP 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E MET* 4.9 11.7 - - + +
228E THR* 1.3 74.7 - - - +
230E ASP* 1.3 60.5 + - - +
232E PHE* 3.4 21.4 - - + +
233E GLN* 2.7 37.7 + - - +
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Residues in contact with ASP 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E THR* 3.2 8.9 + - - +
229E ASP* 1.3 82.7 - - - +
231E GLN* 1.3 59.6 + - - +
233E GLN* 4.1 10.4 - - - +
234E ASN* 3.3 24.9 + - - +
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Residues in contact with GLN 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E CYS* 4.9 6.5 - - + -
228E THR* 3.4 23.5 + - - +
230E ASP* 1.3 77.8 - - - +
232E PHE* 1.3 60.1 + - - +
233E GLN 3.3 0.2 - - - -
234E ASN* 3.7 16.8 + - - +
235E VAL* 2.9 34.2 + - - +
278E ILE* 3.4 44.0 + - + +
279E PHE* 4.3 23.7 + - + +
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Residues in contact with PHE 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210E MET* 4.7 19.4 - - + +
215E LEU* 4.8 10.3 - - + +
219E ILE* 3.5 36.8 - - + -
227E CYS* 3.5 34.1 - - + -
228E THR* 2.9 25.2 + - - +
229E ASP* 3.1 25.1 + - - +
231E GLN* 1.3 77.2 - - - +
233E GLN* 1.3 62.6 + - - +
235E VAL* 3.3 22.5 - - + +
236E ALA* 3.5 11.3 + - - +
278E ILE* 6.3 0.7 - - + -
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Residues in contact with GLN 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206E CYS* 4.2 15.4 - - + +
210E MET* 3.6 27.8 - - + +
229E ASP* 2.7 20.7 + - - +
230E ASP* 4.4 10.4 - - - +
232E PHE* 1.3 73.4 - - - +
234E ASN* 1.3 58.0 + - - +
236E ALA* 3.5 3.0 + - - +
237E ALA* 3.0 31.4 + - + +
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Residues in contact with ASN 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E ASP 3.3 18.1 + - - +
231E GLN* 3.3 20.0 + - - +
232E PHE 3.3 0.4 - - - -
233E GLN* 1.3 77.0 - - - +
235E VAL* 1.3 59.9 + - - +
237E ALA* 4.3 8.9 - - - +
238E ASN* 3.1 32.1 + - - +
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Residues in contact with VAL 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E LEU* 4.5 22.2 - - + -
231E GLN* 2.9 19.8 + - - +
232E PHE* 3.3 24.9 - - + +
234E ASN* 1.3 77.2 - - - +
236E ALA* 1.3 60.2 + - - +
238E ASN* 4.2 3.4 - - - +
239E PHE* 3.4 20.1 + - - +
266E TRP* 4.5 5.3 - - + -
269E TYR* 4.6 9.6 + - + +
273E ILE* 5.8 4.0 - - + -
277E ASN 5.4 0.2 - - - +
278E ILE* 4.9 29.2 - - + +
284E LEU* 4.7 18.8 - - + -
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Residues in contact with ALA 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206E CYS* 4.1 14.6 - - + +
209E LEU* 4.0 32.7 - - + +
210E MET* 5.6 1.1 - - + -
215E LEU* 5.4 0.7 - - + -
232E PHE 3.5 13.1 + - - +
233E GLN* 4.1 3.1 - - - +
234E ASN 3.3 0.2 - - - -
235E VAL* 1.3 81.4 - - - +
237E ALA* 1.3 63.6 + - - +
239E PHE* 3.4 3.1 + - - +
240E ILE* 3.2 27.4 + - - +
266E TRP* 4.2 15.0 - - + -
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Residues in contact with ALA 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E VAL* 3.7 20.9 - - + -
206E CYS* 3.8 11.1 - - - -
233E GLN* 3.0 22.0 + - + +
234E ASN* 4.1 10.3 - - - +
236E ALA* 1.3 77.9 - - - +
238E ASN* 1.3 56.9 + - - +
240E ILE* 3.3 2.8 + - - +
241E HIS* 3.1 37.2 + - + +
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Residues in contact with ASN 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E ASN* 3.1 27.3 + - - +
235E VAL* 4.3 3.8 - - - +
236E ALA 3.3 0.2 - - - -
237E ALA* 1.3 73.8 - - - +
239E PHE* 1.3 62.3 + - - +
241E HIS* 4.0 11.6 - - - +
242E LEU* 3.2 27.3 + - - +
269E TYR* 5.3 2.5 - - - +
281E PRO* 3.3 34.8 - - - +
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Residues in contact with PHE 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E LEU* 4.2 8.7 - - + -
235E VAL 3.4 14.4 + - - +
236E ALA 3.4 7.1 + - - +
237E ALA 3.2 0.6 - - - -
238E ASN* 1.3 76.5 - - - +
240E ILE* 1.3 59.1 + - + +
242E LEU* 3.1 3.9 + - - -
243E ILE* 2.7 55.4 + - + +
262E ILE* 3.9 28.7 - - + -
265E LYS 3.6 24.0 - - - -
266E TRP* 3.4 29.2 - + + -
269E TYR* 3.5 43.9 + + + -
291E LEU* 4.7 0.9 - - + -
292E PHE* 3.7 20.2 - + - -
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Residues in contact with ILE 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E SER* 4.7 4.3 - - - +
201E LEU* 3.7 54.1 - - + +
202E VAL* 4.0 11.0 - - + +
205E ARG* 4.1 14.4 - - + -
206E CYS* 3.9 22.7 - - - +
209E LEU* 4.4 8.1 - - + -
236E ALA 3.2 15.8 + - - +
237E ALA 3.3 6.5 + - - +
239E PHE* 1.3 84.2 - - + +
241E HIS* 1.3 57.1 + - + +
243E ILE* 3.3 5.9 - - - +
244E VAL* 3.0 33.4 + - + +
262E ILE* 4.2 11.9 - - + -
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Residues in contact with HIS 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E SER* 4.2 29.9 - - - -
199E THR* 5.6 1.6 - - - -
202E VAL* 4.5 20.2 - - + +
237E ALA* 3.1 33.3 + - + +
238E ASN* 4.1 13.5 - - - +
239E PHE 3.4 0.2 - - - -
240E ILE* 1.3 76.5 - - + +
242E LEU* 1.3 56.8 + - - +
244E VAL* 4.1 5.3 - - - +
245E GLN* 3.3 26.0 + - - +
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Residues in contact with LEU 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E ASN* 3.2 21.8 + - - +
239E PHE 3.1 5.4 + - - +
241E HIS* 1.3 77.2 - - - +
243E ILE* 1.3 61.8 + - - +
244E VAL 3.3 0.7 - - - -
245E GLN* 4.0 12.7 - - + +
246E ALA* 3.4 24.0 + - + +
269E TYR* 4.3 15.7 - - + +
281E PRO 5.7 1.6 - - - +
285E TYR* 3.6 47.8 - - + -
292E PHE* 3.6 26.3 - - + -
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Residues in contact with ILE 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E PHE* 2.7 36.3 + - + +
240E ILE* 3.3 15.0 - - - +
242E LEU* 1.3 72.6 - - - +
244E VAL* 1.3 69.4 + - + +
246E ALA 4.2 0.7 - - - -
247E PHE* 3.4 47.0 + - + +
258E LEU* 4.2 7.5 - - + +
261E LEU* 3.9 19.3 - - + +
262E ILE* 3.7 26.0 - - + -
265E LYS* 3.7 18.6 - - + -
292E PHE* 3.6 20.8 - - + -
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Residues in contact with VAL 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E VAL* 4.3 18.4 - - + +
197E VAL* 5.1 5.6 - - + -
198E SER* 4.7 20.4 - - - -
201E LEU* 3.7 27.1 - - + -
240E ILE* 3.0 22.7 + - + +
241E HIS* 4.3 5.4 - - - +
243E ILE* 1.3 75.9 - - + +
245E GLN* 1.3 61.5 + - + +
246E ALA 3.1 1.8 - - - -
247E PHE 3.1 0.3 + - - -
248E HIS* 2.7 51.0 + - + +
258E LEU* 3.8 17.3 - - + -
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Residues in contact with GLN 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E HIS 3.3 18.8 + - - +
242E LEU* 4.4 14.6 - - + +
243E ILE 3.6 0.2 - - - -
244E VAL* 1.3 79.9 - - - +
246E ALA* 1.3 61.3 + - - +
248E HIS* 4.9 3.5 + - - +
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Residues in contact with ALA 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449D LYS* 5.7 0.9 + - - -
451D TRP* 4.2 15.6 - - - -
242E LEU* 3.4 17.9 + - + +
244E VAL 3.1 0.4 - - - -
245E GLN* 1.3 81.6 + - - +
247E PHE* 1.3 77.8 + - + +
248E HIS 3.6 1.2 + - - -
249E SER* 4.8 2.3 + - - -
285E TYR* 6.3 0.2 - - + -
292E PHE* 3.6 30.9 - - + +
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Residues in contact with PHE 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449D LYS* 6.1 0.2 - - - -
451D TRP* 4.6 8.5 - + - -
243E ILE* 3.4 49.8 + - + +
244E VAL* 3.1 3.6 + - - -
246E ALA* 1.3 89.0 - - + +
248E HIS* 1.3 61.8 + - - +
249E SER 3.3 2.2 - - - +
250E TYR* 3.8 6.5 - - + +
251E THR* 2.9 27.8 + - + +
258E LEU* 5.1 2.7 - - + -
261E LEU* 3.8 23.3 - - + -
265E LYS* 3.7 22.9 - - + -
291E LEU 3.8 11.0 - - - -
292E PHE* 3.9 17.5 - - - -
293E LEU 4.7 2.5 - - - -
294E SER 3.9 7.9 - - - -
295E THR* 3.6 39.5 - - + -
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Residues in contact with HIS 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D LEU 5.8 0.2 - - - -
384D SER* 3.9 21.8 + - - -
194E VAL* 3.6 34.5 - - + +
197E VAL* 5.6 4.4 - - + +
244E VAL* 2.7 30.9 + - + +
245E GLN* 4.7 3.8 - - - -
246E ALA 3.6 1.6 - - - -
247E PHE* 1.3 73.4 - - - +
249E SER* 1.3 57.9 + - - +
251E THR* 3.8 4.0 + - - -
252E GLY* 2.7 57.1 + - - -
253E ASN* 3.2 28.1 + - - -
258E LEU* 5.5 3.1 - - - +
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Residues in contact with SER 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384D SER* 3.7 17.2 + - - -
385D ASP* 4.6 5.9 + - - +
386D LEU* 3.2 46.0 + - - +
387D GLU* 4.8 0.3 - - - +
451D TRP* 3.8 22.1 + - - -
459D VAL* 4.0 3.3 - - - +
246E ALA 4.8 2.4 + - - -
247E PHE* 3.3 1.2 - - - +
248E HIS* 1.3 79.9 - - - +
250E TYR* 1.3 58.4 + - - +
252E GLY 4.8 0.2 + - - -
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Residues in contact with TYR 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C GLN* 3.8 13.3 + - - +
257C ARG* 3.7 6.8 + - - -
386D LEU* 4.6 2.7 - - - -
451D TRP* 3.7 23.1 - + + -
454D LYS 5.1 1.4 + - - -
455D ASP* 3.2 44.9 - - + -
458D ASN* 3.5 35.4 + - + -
459D VAL* 3.4 21.6 - - - +
462D ASN* 4.7 0.9 + - - -
247E PHE* 3.5 8.4 + - + +
248E HIS 3.2 0.6 - - - -
249E SER* 1.3 77.8 - - - +
251E THR* 1.3 76.0 + - + +
261E LEU* 4.1 11.0 - - + -
295E THR* 3.9 26.0 + - + -
297E ASP* 3.0 32.5 + - - +
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Residues in contact with THR 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387D GLU* 3.3 9.5 - - - +
458D ASN* 4.5 4.5 - - - +
462D ASN* 3.6 6.9 + - - -
191E ARG* 5.5 0.3 + - - -
247E PHE* 2.9 18.9 + - + +
248E HIS* 3.6 2.3 + - - -
250E TYR* 1.3 94.6 - - + +
252E GLY* 1.3 64.2 + - - +
254E ASP* 3.0 23.2 - - - +
257E ALA* 3.8 24.9 - - + -
258E LEU* 3.2 30.7 - - + +
261E LEU* 3.8 16.4 - - + -
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Residues in contact with GLY 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384D SER* 4.1 6.9 + - - -
387D GLU* 3.4 22.8 + - - -
191E ARG* 4.8 0.2 - - - -
197E VAL* 5.5 0.2 - - - +
248E HIS* 2.7 44.0 + - - -
250E TYR 3.6 0.8 - - - -
251E THR* 1.3 78.0 + - - +
253E ASN* 1.3 59.7 + - - -
254E ASP 3.2 7.4 + - - -
258E LEU* 4.2 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
------------------------------------------------------------
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