Contacts of the helix formed by residues 239 - 261 (chain B) in PDB entry 1TD2
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 239 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B LEU* 4.8 0.4 - - - -
237B GLY 3.5 3.3 + - - +
238B ALA* 1.3 74.8 - - - +
240B LEU* 1.3 65.8 + - - +
241B GLN* 3.6 8.1 + - - +
242B GLU* 2.9 45.0 + - - +
243B ALA* 2.8 22.6 + - - +
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Residues in contact with LEU 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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178B ILE* 4.4 16.8 - - + -
198B LEU* 3.6 34.5 - - + +
200B THR* 4.0 23.1 - - + -
203B GLU* 3.6 41.1 - - + +
205B TRP* 4.0 21.3 - - + +
234B LEU* 4.4 10.4 - - + +
238B ALA 3.9 0.2 + - - -
239B THR* 1.3 72.8 - - - +
241B GLN* 1.3 62.9 + - - +
243B ALA* 3.7 3.0 - - - +
244B LEU* 3.1 24.9 + - - +
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Residues in contact with GLN 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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205B TRP* 2.9 53.1 - - + -
239B THR* 3.2 7.0 + - - +
240B LEU* 1.3 76.7 - - - +
242B GLU* 1.3 62.6 + - + +
244B LEU* 3.3 5.3 + - - +
245B GLU* 2.9 61.2 + - - +
281B TYR* 5.7 1.6 + - - -
283B SER* 5.8 0.4 + - - -
284B ALA* 4.4 4.0 + - + +
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Residues in contact with GLU 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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233B LYS* 4.5 3.3 + - - +
237B GLY 4.5 1.4 - - - +
238B ALA* 3.5 14.1 - - + +
239B THR* 2.9 48.8 + - - +
241B GLN* 1.3 80.8 - - + +
243B ALA* 1.3 58.9 + - - +
245B GLU* 3.9 5.1 - - - +
246B HIS* 3.0 32.9 + - - +
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Residues in contact with ALA 243 (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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198B LEU* 5.1 0.4 - - + -
230B LEU* 3.8 18.4 - - + -
233B LYS* 3.8 27.8 - - + +
234B LEU* 4.1 15.7 - - + -
238B ALA* 4.0 2.6 - - + +
239B THR 2.8 17.5 + - - +
240B LEU 3.7 4.3 - - - +
242B GLU* 1.3 78.2 - - - +
244B LEU* 1.3 56.2 + - - +
246B HIS* 4.0 0.9 - - - +
247B VAL* 3.0 37.5 + - - +
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Residues in contact with LEU 244 (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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180B LEU* 4.8 5.4 - - + -
196B MET* 3.7 22.9 - - + +
198B LEU* 4.3 22.2 - - + +
205B TRP* 3.8 39.5 - - + +
207B ILE* 3.4 42.6 - - + -
230B LEU* 4.5 6.4 - - + +
240B LEU 3.1 14.5 + - - +
241B GLN* 3.7 4.3 - - - +
243B ALA* 1.3 80.3 - - - +
245B GLU* 1.3 55.7 + - - +
247B VAL* 3.9 3.2 - - + +
248B THR* 2.7 37.2 + - - -
284B ALA* 4.2 7.6 - - + -
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Residues in contact with GLU 245 (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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207B ILE* 3.5 14.6 - - + -
241B GLN* 2.9 48.0 + - - +
242B GLU* 4.1 5.0 - - - +
244B LEU* 1.3 75.4 - - - +
246B HIS* 1.3 66.2 + - - +
248B THR* 3.9 1.2 - - - -
249B ALA* 3.2 24.8 + - - +
281B TYR* 3.9 16.7 + - + -
282B PHE* 3.0 27.9 + - - +
283B SER* 3.9 3.6 + - - -
284B ALA* 2.9 25.0 + - + +
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Residues in contact with HIS 246 (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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29B LEU* 4.1 20.7 - - + +
229B LEU* 6.2 0.7 - - + -
233B LYS* 2.8 37.9 + - + +
242B GLU 3.0 18.9 + - - +
245B GLU* 1.3 77.4 - - - +
247B VAL* 1.3 59.2 + - - +
249B ALA* 3.9 2.3 - - - +
250B ALA* 2.9 29.2 + - + +
275B ILE 2.9 26.1 + - - -
276B ALA 3.6 18.5 + - - -
278B PRO* 3.9 13.5 - - + +
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Residues in contact with VAL 247 (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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29B LEU* 6.2 0.2 - - + -
196B MET* 4.6 6.7 - - + -
226B THR* 3.7 40.8 - - + +
229B LEU* 3.6 18.8 - - + +
230B LEU* 3.5 34.5 - - + +
233B LYS* 4.1 6.7 - - + -
243B ALA 3.0 22.0 + - - +
244B LEU* 3.9 3.8 - - - +
246B HIS* 1.3 77.2 - - + +
248B THR* 1.3 64.6 + - - +
250B ALA* 3.9 4.4 - - - +
251B VAL* 3.1 25.8 + - + +
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Residues in contact with THR 248 (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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194B PHE* 6.0 1.6 - - + -
196B MET* 3.7 11.2 - - + +
207B ILE* 3.3 41.2 - - + +
208B SER* 4.2 2.5 - - - +
209B ARG* 3.8 33.9 - - + +
244B LEU 2.7 22.4 + - - -
245B GLU 3.9 1.6 - - - -
247B VAL* 1.3 77.4 - - - +
249B ALA* 1.3 62.9 + - - +
251B VAL* 3.6 3.8 + - - +
252B TYR* 3.1 22.2 + - - +
282B PHE* 4.1 11.0 - - + -
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Residues in contact with ALA 249 (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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245B GLU 3.2 16.0 + - - +
246B HIS* 3.9 0.7 - - - +
248B THR* 1.3 78.1 - - - +
250B ALA* 1.3 65.2 + - - +
252B TYR* 3.2 4.2 + - - +
253B GLU* 2.9 25.3 + - - +
278B PRO* 3.8 17.9 - - + -
280B HIS* 3.5 25.7 - - + +
281B TYR* 5.2 0.4 - - - -
282B PHE* 3.8 20.2 - - + +
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Residues in contact with ALA 250 (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* 4.2 19.3 - - + -
246B HIS* 2.9 23.0 + - + +
247B VAL 3.9 2.9 - - - +
249B ALA* 1.3 75.7 - - - +
251B VAL* 1.3 62.8 + - - +
253B GLU* 3.1 5.4 + - - +
254B ILE* 3.1 26.2 + - - +
274B ARG 4.0 11.4 - - - -
275B ILE* 3.7 30.4 - - + +
278B PRO* 4.0 1.7 - - - +
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Residues in contact with VAL 251 (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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194B PHE* 6.5 0.2 - - + -
209B ARG* 4.4 10.1 - - - +
222B VAL* 3.5 32.8 - - + +
225B VAL* 3.9 25.8 - - + -
226B THR* 3.5 24.9 - - - +
229B LEU* 4.6 3.8 - - + -
247B VAL* 3.1 18.8 + - + +
248B THR* 4.0 3.6 - - - +
250B ALA* 1.3 71.0 - - - +
252B TYR* 1.3 66.4 + - - +
254B ILE* 3.1 12.3 + - + +
255B MET* 2.9 29.5 + - - +
266B LEU* 6.2 1.3 - - + -
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Residues in contact with TYR 252 (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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209B ARG* 3.9 20.8 - - - +
210B PRO* 3.3 42.6 - - + +
212B VAL* 4.0 14.5 - - + +
248B THR 3.1 14.9 + - - +
249B ALA 3.5 7.4 - - - +
251B VAL* 1.3 76.3 - - - +
253B GLU* 1.3 57.6 + - - +
255B MET* 2.8 25.8 + - + +
256B VAL* 2.8 39.0 + - + +
280B HIS* 3.7 37.7 - + + -
282B PHE* 3.6 24.9 - + + -
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Residues in contact with GLU 253 (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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249B ALA 2.9 19.1 + - - +
250B ALA 3.1 8.3 + - - +
252B TYR* 1.3 76.5 - - - +
254B ILE* 1.3 62.6 + - + +
256B VAL* 3.2 8.5 - - - +
257B THR* 3.0 27.7 + - - -
271B ALA* 4.3 2.2 - - + -
274B ARG* 2.9 66.7 + - + +
275B ILE 5.0 0.2 - - - +
278B PRO* 3.6 5.4 - - + -
279B GLU* 3.0 20.6 + - - +
280B HIS* 2.7 36.2 + - + -
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Residues in contact with ILE 254 (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* 3.9 28.5 - - + -
229B LEU* 5.4 0.2 - - + -
250B ALA 3.1 13.8 + - - +
251B VAL* 3.1 12.1 + - + +
253B GLU* 1.3 76.2 - - - +
255B MET* 1.3 54.9 + - - +
257B THR* 3.5 1.7 + - - -
258B THR* 2.6 37.8 + - - -
266B LEU* 3.4 33.2 - - + -
267B GLN* 4.0 18.7 + - - +
268B VAL* 4.1 11.7 - - + +
271B ALA* 3.8 13.2 - - + -
275B ILE* 3.7 36.6 - - + -
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Residues in contact with MET 255 (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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209B ARG* 4.4 14.8 - - - +
212B VAL* 3.3 32.8 - - + -
214B PHE* 3.5 21.3 - - + -
218B GLN* 4.9 7.0 - - - +
219B PRO* 3.2 35.2 - - + -
222B VAL* 3.7 22.2 - - + -
251B VAL* 2.9 21.9 + - - +
252B TYR* 2.8 17.2 + - - +
254B ILE* 1.3 75.9 - - - +
256B VAL* 1.3 60.8 + - - +
258B THR* 3.2 5.6 + - - -
259B LYS* 3.1 18.5 + - - +
266B LEU* 3.5 17.5 - - + -
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Residues in contact with VAL 256 (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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212B VAL* 4.9 6.3 - - + -
252B TYR* 2.8 55.1 + - + +
253B GLU* 3.2 26.7 - - - +
255B MET* 1.3 69.6 - - + +
257B THR* 1.3 66.5 + - - +
259B LYS* 3.3 6.3 + - - +
260B ALA* 2.9 31.2 + - - +
274B ARG* 4.3 2.2 - - - +
280B HIS* 4.8 9.2 - - + +
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Residues in contact with THR 257 (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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253B GLU 3.0 7.8 + - - -
254B ILE 3.8 3.6 - - - -
256B VAL* 1.3 79.0 - - - +
258B THR* 1.3 64.8 + - - +
260B ALA* 3.1 6.6 + - + +
261B MET* 2.9 47.5 + - + +
267B GLN* 4.2 4.7 - - + -
270B ALA* 3.9 16.2 - - + -
271B ALA* 3.5 7.3 - - + +
274B ARG* 2.8 42.6 + - - +
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Residues in contact with THR 258 (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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214B PHE* 3.9 13.7 - - + -
219B PRO* 4.8 2.9 - - + -
254B ILE* 2.6 24.9 + - - +
255B MET* 3.5 6.1 - - - -
257B THR* 1.3 76.7 - - - +
259B LYS* 1.3 58.5 + - - +
261B MET 3.6 0.3 + - - -
262B GLN 3.4 1.7 + - - -
263B GLU* 2.9 48.7 + - + +
264B TYR 4.5 2.2 - - - +
265B GLU 3.2 24.9 - - - +
266B LEU* 3.6 8.8 - - - +
267B GLN* 2.9 27.1 + - - -
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Residues in contact with LYS 259 (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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212B VAL* 3.8 17.9 - - + -
213B ASP* 3.2 46.0 + - - +
214B PHE* 3.8 21.5 - - + -
255B MET 3.1 8.5 + - - +
256B VAL* 3.9 4.0 - - - +
257B THR 3.2 0.2 - - - -
258B THR* 1.3 75.6 - - - +
260B ALA* 1.3 63.6 + - - +
261B MET 3.1 2.2 - - - -
262B GLN* 2.9 22.8 + - - +
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Residues in contact with ALA 260 (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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256B VAL 2.9 18.3 + - - +
257B THR* 3.6 7.4 - - + +
259B LYS* 1.3 77.0 - - - +
261B MET* 1.3 60.5 + - + +
262B GLN* 3.1 10.3 + - - +
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Residues in contact with MET 261 (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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2A MET* 4.3 15.0 - - + +
257B THR* 2.9 38.7 + - + +
258B THR 4.1 4.0 - - - +
260B ALA* 1.3 78.7 - - + +
262B GLN* 1.3 73.3 + - - +
263B GLU* 3.2 16.6 + - + +
267B GLN* 3.0 36.3 - - - +
270B ALA* 3.7 12.6 - - + -
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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
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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