Contacts of the helix formed by residues 253 - 282 (chain D) in PDB entry 5J0Z
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 253 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D PHE* 3.5 37.2 - - + +
117D ARG* 3.8 4.0 - - - +
119D TYR* 4.9 3.1 - - + -
246D LEU* 4.4 21.8 - - + +
249D THR* 3.9 17.6 + - + +
251D TYR* 3.4 4.6 + - + -
252D MET* 1.3 83.5 - - - +
254D TYR* 1.3 60.0 + - - +
255D THR* 4.4 2.0 - - - -
256D GLY* 3.3 22.0 + - - -
257D ALA* 3.0 23.0 + - - +
314D PHE* 3.7 0.8 - - - -
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Residues in contact with TYR 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D PHE 4.5 0.2 + - - -
117D ARG 2.8 22.8 + - - +
118D ARG* 4.4 2.9 - - - -
119D TYR 3.7 14.5 + - - +
120D PRO* 5.3 0.2 - - + -
121D PHE* 3.9 29.5 - + - -
253D THR* 1.3 71.0 - - - +
255D THR* 1.3 67.9 + - - +
257D ALA* 3.3 4.3 + - - +
258D ILE* 3.1 51.4 + - + +
307D ASN* 5.2 5.0 + - - -
310D LEU* 4.7 4.5 - - + -
311D ALA* 4.3 26.5 - - - +
314D PHE* 3.7 36.8 - + + -
315D PHE* 4.1 21.1 - + + -
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Residues in contact with THR 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D TYR* 2.5 47.9 + - + -
120D PRO* 3.3 10.4 - - + +
201D ILE* 5.4 6.1 - - + -
202D ILE* 6.6 0.4 - - + -
242D VAL* 4.1 30.3 - - + -
246D LEU* 5.7 0.9 - - - -
253D THR* 5.0 1.8 - - - -
254D TYR* 1.3 79.7 - - - +
256D GLY* 1.3 58.1 + - - +
258D ILE* 3.5 10.0 + - + +
259D ILE* 2.9 37.1 + - + +
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Residues in contact with GLY 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C PRO* 5.5 0.3 - - - +
200C ASN* 5.7 7.0 + - - -
242D VAL* 5.8 3.1 - - - -
246D LEU* 6.2 0.2 - - - +
252D MET* 4.7 7.7 - - - +
253D THR* 3.3 21.7 + - - -
254D TYR 3.2 1.0 - - - -
255D THR* 1.3 75.9 - - - +
257D ALA* 1.3 56.2 + - - +
259D ILE* 3.6 8.0 + - - +
260D PHE* 2.8 35.2 + - - +
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Residues in contact with ALA 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D MET* 4.3 13.3 - - + +
253D THR 3.0 15.3 + - - +
254D TYR 3.4 8.7 - - - +
256D GLY* 1.3 73.0 - - - +
258D ILE* 1.3 57.3 + - - +
260D PHE* 3.0 8.6 + - - +
261D MET* 2.6 35.9 + - - +
310D LEU* 3.8 23.8 - - + -
314D PHE* 4.1 14.1 - - + -
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Residues in contact with ILE 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D ILE* 6.4 2.0 - - + -
205D MET* 5.4 2.9 - - - -
206D LEU* 6.6 0.2 - - + -
254D TYR* 3.1 56.1 + - + +
255D THR* 3.6 11.4 - - + +
257D ALA* 1.3 77.4 - - - +
259D ILE* 1.3 62.7 + - + +
261D MET* 3.3 7.1 + - - +
262D ILE* 3.0 45.0 + - + +
303D PHE* 5.8 1.6 - - + -
307D ASN* 4.0 27.6 - - - +
310D LEU* 4.0 13.4 - - + +
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Residues in contact with ILE 259 (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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201D ILE* 5.6 0.2 - - + -
205D MET* 3.8 37.0 - - + -
235D HIS* 3.9 2.4 + - + +
238D PHE 4.3 4.0 - - - +
239D ASN* 3.7 31.9 - - + +
242D VAL* 3.6 37.7 - - + -
255D THR* 2.9 24.8 + - + +
256D GLY* 3.8 7.0 - - - +
258D ILE* 1.3 79.6 - - + +
260D PHE* 1.3 62.9 + - - +
262D ILE* 3.2 17.6 + - - +
263D TYR* 3.2 21.7 + - + -
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Residues in contact with PHE 260 (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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199C PRO* 3.7 38.8 - - + +
203C LEU* 3.6 44.2 - - + -
204C PRO* 4.9 4.7 - - + -
207C PHE* 3.9 19.7 - + - -
252D MET* 5.7 4.3 - - + -
256D GLY 2.8 23.1 + - - +
257D ALA* 3.0 6.7 + - - +
259D ILE* 1.3 72.2 - - - +
261D MET* 1.3 71.5 + - + +
263D TYR* 3.3 22.2 + - + +
264D LEU* 3.9 19.8 + - + +
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Residues in contact with MET 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D ALA 2.6 21.4 + - - +
258D ILE* 3.6 8.3 - - + +
260D PHE* 1.3 77.4 - - + +
262D ILE* 1.3 67.0 + - - +
264D LEU* 3.0 30.8 + - + +
265D PHE* 3.5 20.5 + - + -
303D PHE* 3.3 29.6 - - + -
306D ALA* 4.0 30.1 - - + +
307D ASN* 3.3 26.5 - - - +
310D LEU* 4.4 13.2 - - + -
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Residues in contact with ILE 262 (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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205D MET* 4.1 18.6 - - + +
206D LEU* 5.3 4.7 - - + -
209D LEU* 4.5 13.5 - - + -
235D HIS* 3.2 33.4 - - + +
258D ILE* 3.0 38.0 + - + +
259D ILE* 3.2 7.6 + - - +
261D MET* 1.3 77.0 - - - +
263D TYR* 1.3 57.4 + - - +
264D LEU 2.8 6.6 + - - -
265D PHE* 2.9 18.7 + - - +
266D TYR* 3.2 31.3 + - + -
303D PHE* 4.2 26.7 - - + -
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Residues in contact with TYR 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C PRO* 3.6 35.7 - - + -
207C PHE* 3.8 24.3 - + + +
208C ILE* 5.0 4.9 - - + -
211C ILE* 5.9 0.3 - - - +
238C PHE* 3.5 7.0 - + - -
232D LEU* 4.6 12.3 - - + +
235D HIS* 3.4 26.2 - + - -
236D ILE* 3.5 28.9 - - + +
239D ASN* 2.7 45.7 + - - +
259D ILE* 3.2 25.2 + - + -
260D PHE* 3.3 16.3 + - + +
261D MET 3.2 0.8 - - - -
262D ILE* 1.3 77.0 - - - +
264D LEU* 1.3 57.9 + - - +
266D TYR* 4.2 7.9 - - - +
267D PHE* 3.4 21.5 + - - +
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Residues in contact with LEU 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C PHE* 3.4 40.8 - - + -
260D PHE* 4.0 22.7 - - + +
261D MET* 3.0 22.1 + - + +
262D ILE 2.8 1.8 + - - -
263D TYR* 1.3 71.9 - - - +
265D PHE* 1.3 64.6 + - + +
266D TYR 3.0 4.5 - - - -
267D PHE* 2.6 12.8 + - + -
268D VAL* 2.5 44.6 + - + +
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Residues in contact with PHE 265 (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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209D LEU* 4.3 13.8 - - + +
212D SER* 4.2 8.7 + - - -
213D TRP* 4.0 22.6 + + - +
261D MET* 3.5 34.8 - - + +
262D ILE* 2.9 11.0 + - - +
264D LEU* 1.3 81.6 - - + +
266D TYR* 1.3 58.6 + - - +
268D VAL* 4.7 7.0 - - + -
269D ALA* 3.3 20.8 + - - +
299D PHE* 3.9 16.7 - + - -
302D VAL* 3.9 27.1 - - + -
303D PHE* 3.3 50.3 - + + -
306D ALA* 5.0 2.2 - - + -
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Residues in contact with TYR 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C ILE* 5.0 1.3 - - + -
208D ILE* 3.2 39.0 + - - +
209D LEU* 3.3 15.9 - - + +
212D SER* 3.8 16.8 - - - -
228D VAL* 3.9 18.3 - - + +
231D THR* 3.4 26.7 + - - -
232D LEU* 3.6 38.1 - - + -
235D HIS* 3.8 11.6 + + + -
262D ILE* 3.2 47.5 + - + +
263D TYR* 4.4 4.5 - - - +
264D LEU 3.0 0.6 - - - -
265D PHE* 1.3 79.5 - - - +
267D PHE* 1.3 65.5 + - - +
269D ALA* 3.3 4.5 + - - +
270D VAL* 2.9 28.4 + - - +
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Residues in contact with PHE 267 (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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207C PHE* 4.1 25.8 - + + -
210C PHE* 3.6 41.3 - + + -
211C ILE* 3.6 31.1 - - + +
214C THR* 5.8 1.1 - - + -
263D TYR 3.4 15.2 + - - +
264D LEU* 2.6 19.0 + - + +
266D TYR* 1.3 75.7 - - - +
268D VAL* 1.3 65.0 + - + +
270D VAL* 3.4 5.2 + - - +
271D ILE* 3.1 51.1 + - + +
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Residues in contact with VAL 268 (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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264D LEU* 2.5 28.1 + - + +
265D PHE* 4.7 3.8 - - + -
267D PHE* 1.3 79.6 - - + +
269D ALA* 1.3 58.0 + - - +
271D ILE* 3.0 12.5 + - + +
272D GLU* 2.9 27.4 + - - +
299D PHE* 3.4 27.4 - - + -
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Residues in contact with ALA 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D SER* 4.5 7.4 - - - +
213D TRP* 5.2 0.4 - - + -
216D PHE* 4.5 9.9 - - + -
228D VAL* 4.3 18.4 - - + -
265D PHE 3.3 21.0 + - - +
266D TYR* 3.3 8.5 + - - +
268D VAL* 1.3 75.4 - - - +
270D VAL* 1.3 66.9 + - - +
272D GLU* 3.2 4.8 + - - +
273D VAL* 2.9 28.0 + - + +
299D PHE* 3.7 18.6 - - + -
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Residues in contact with VAL 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C ILE* 4.1 35.2 - - + -
214C THR* 3.6 33.9 - - + +
227C LEU* 5.0 2.0 - - + -
228D VAL* 3.4 27.1 - - + +
229D VAL* 4.8 5.8 - - + -
232D LEU* 6.1 0.9 - - + -
266D TYR* 2.9 13.9 + - + +
267D PHE 3.4 8.7 - - - +
269D ALA* 1.3 73.2 - - - +
271D ILE* 1.3 53.8 + - + +
273D VAL* 3.1 7.1 + - + +
274D THR* 2.6 44.6 + - - +
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Residues in contact with ILE 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C THR* 4.9 12.8 - - + -
267D PHE* 3.1 45.6 + - + +
268D VAL* 3.0 18.6 + - + +
270D VAL* 1.3 77.0 - - - +
272D GLU* 1.3 53.4 + - - +
274D THR* 3.1 5.3 + - + -
275D VAL* 2.8 45.9 + - + +
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Residues in contact with GLU 272 (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 ALA 4.4 0.5 - - - +
216D PHE* 3.2 25.9 - - + -
268D VAL 2.9 11.3 + - - +
269D ALA 3.5 5.8 - - - +
271D ILE* 1.3 76.5 - - - +
273D VAL* 1.3 87.9 + - - +
275D VAL* 3.3 7.7 + - - +
276D GLN* 2.8 32.7 + - - +
291D ILE* 4.0 13.6 - - + +
292D THR* 2.6 34.8 + - - -
295D SER* 3.5 21.3 - - - +
299D PHE* 4.5 7.6 - - + -
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Residues in contact with VAL 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D ALA* 4.2 13.0 - - + +
216D PHE* 5.1 1.8 - - + -
221D TYR* 3.6 24.9 - - + -
224D ASN* 3.7 42.8 - - + +
225D VAL* 4.6 2.9 - - + +
228D VAL* 4.6 9.2 - - + -
269D ALA 2.9 18.5 + - - +
270D VAL* 3.6 7.2 - - - +
272D GLU* 1.3 96.0 + - - +
274D THR* 1.3 66.0 + - - +
276D GLN* 3.4 5.3 + - - +
277D HIS* 3.0 24.1 + - - +
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Residues in contact with THR 274 (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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214C THR* 3.3 47.7 + - + +
217C TRP* 4.2 21.7 - - + +
221D TYR* 3.4 20.2 + - - +
225D VAL* 5.8 0.3 - - - +
270D VAL* 2.6 26.3 + - - +
271D ILE* 3.6 8.3 - - + +
273D VAL* 1.3 73.3 - - - +
275D VAL* 1.3 58.4 + - + +
277D HIS* 3.8 5.5 - - - +
278D TYR* 2.9 25.3 + - + +
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Residues in contact with VAL 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D ILE* 2.8 27.4 + - + +
272D GLU* 3.4 10.1 - - - +
274D THR* 1.3 74.9 - - + +
276D GLN* 1.3 61.9 + - - +
277D HIS 3.2 1.3 - - - -
278D TYR* 2.7 26.1 + - + +
279D LEU* 2.8 26.3 + - + +
291D ILE* 3.9 32.1 - - + -
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Residues in contact with GLN 276 (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 ALA 4.3 0.9 - - - +
218D SER 3.0 19.5 + - - -
219D THR* 3.7 20.0 - - + +
224D ASN* 3.5 20.8 + - - -
272D GLU* 2.8 28.9 + - - +
273D VAL* 3.7 9.1 - - - +
275D VAL* 1.3 76.6 - - - +
277D HIS* 1.3 62.3 + - - +
279D LEU 3.6 0.5 + - - -
280D LYS* 3.2 28.2 + - + +
288D ALA* 3.7 27.2 - - + +
289D ALA* 5.3 1.7 - - + +
291D ILE* 5.7 1.3 - - + -
292D THR* 2.7 38.5 + - - +
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Residues in contact with HIS 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C TRP 4.0 13.9 + - - -
218C SER* 4.1 14.3 + - - -
219C THR* 4.6 5.8 + - - -
220C SER* 4.9 8.7 - - - -
221D TYR* 3.4 61.8 - + + +
222D GLU* 5.1 6.8 + - - -
273D VAL 3.0 9.7 + - - +
274D THR 3.8 4.0 - - - +
276D GLN* 1.3 77.0 + - - +
278D TYR* 1.3 74.9 + + - +
280D LYS* 3.3 14.1 + - - +
281D VAL* 3.2 37.5 + - + +
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Residues in contact with TYR 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C TRP* 3.9 36.6 - + + +
293C ARG* 5.8 0.9 - - - -
296C ARG* 3.9 31.0 + - - -
274D THR 2.9 18.1 + - - +
275D VAL* 2.7 19.2 + - + +
277D HIS* 1.3 73.8 - + - +
279D LEU* 1.3 68.4 + - + +
281D VAL* 2.9 27.8 + - + +
282D GLU* 3.0 51.9 + - + +
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Residues in contact with LEU 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D VAL* 2.8 26.7 + - + +
278D TYR* 1.3 86.8 - - + +
280D LYS* 1.3 53.1 + - - +
282D GLU* 3.0 10.8 + - + +
283D SER 2.7 31.2 + - - -
284D GLN* 3.2 24.7 + - + +
287D ARG* 3.9 25.6 - - + +
288D ALA* 3.5 40.6 - - + +
291D ILE* 3.9 15.5 - - + -
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Residues in contact with LYS 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D THR* 3.8 32.6 + - + +
276D GLN* 3.2 22.3 + - + +
277D HIS* 3.8 12.3 - - - +
278D TYR 3.2 0.4 + - - -
279D LEU* 1.3 78.6 - - - +
281D VAL* 1.3 61.4 + - - +
283D SER* 3.7 9.7 + - - +
285D PRO* 4.7 24.5 - - + +
288D ALA* 4.4 6.9 - - + +
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Residues in contact with VAL 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C THR* 4.9 13.5 - - + +
277D HIS* 3.2 35.5 + - + +
278D TYR* 2.9 14.7 + - + +
280D LYS* 1.3 76.4 - - + +
282D GLU* 1.3 72.7 + - - +
283D SER* 3.2 7.4 + - - -
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Residues in contact with GLU 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D TYR* 3.0 57.3 + - + +
279D LEU* 3.0 12.8 + - + +
281D VAL* 1.3 95.0 - - - +
283D SER* 1.3 69.1 + - - +
284D GLN* 3.3 15.6 - - - +
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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).
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