Contacts of the helix formed by residues 244 - 270 (chain M) in PDB entry 2QJK
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 PHE 244 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M THR 4.6 4.0 - - - -
33M ILE* 3.4 32.1 - - + +
34M MET 3.5 1.8 + - - -
35M ILE* 3.0 33.1 + - + +
37M THR* 4.0 7.0 - - - -
217M HIS* 6.4 0.2 - + - -
242M VAL 3.5 0.6 + - - -
243M PRO* 1.3 71.3 - - - +
245M TRP* 1.3 58.3 + - - +
247M TYR 3.2 0.7 + - - -
248M PHE* 2.7 72.7 + + + -
249M ILE* 3.4 23.1 + - + -
252M ASP* 4.5 3.1 - - - -
505M ANJ 3.4 77.2 - + + -
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Residues in contact with TRP 245 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M ILE* 3.2 27.8 + - + +
34M MET* 3.5 24.5 - - + +
243M PRO* 3.4 22.2 - - - +
244M PHE* 1.3 78.4 - - - +
246M PRO* 1.3 87.4 - - + +
247M TYR 3.4 0.7 - - - -
249M ILE* 3.7 41.3 - - + -
250M ILE* 5.7 3.4 - - + -
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Residues in contact with PRO 246 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243M PRO* 4.8 0.7 - - + -
244M PHE 3.4 1.6 - - - -
245M TRP* 1.3 123.1 - - + +
247M TYR* 1.3 82.1 + - + +
248M PHE 3.4 2.2 - - - -
249M ILE* 4.1 1.1 - - + -
250M ILE* 3.0 33.4 + - + +
251N LEU* 3.7 25.6 - - + -
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Residues in contact with TYR 247 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242M VAL* 3.7 22.0 - - + -
243M PRO* 3.2 52.5 - - + +
244M PHE 3.2 1.2 + - - -
246M PRO* 1.3 88.5 - - + +
248M PHE* 1.3 61.6 + - - +
250M ILE* 3.8 3.1 + - - +
251M LYS 3.6 7.4 + - - -
251N LEU* 3.3 40.8 + - + +
252N TRP* 3.2 38.7 + + + -
254N GLY 5.2 1.6 + - - -
255N VAL* 3.8 30.9 - - + +
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Residues in contact with PHE 248 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M THR* 3.2 34.8 - - + -
38M PRO 3.2 21.8 - - - -
39M ARG 4.6 1.1 - - - -
41M LEU* 3.7 24.9 - - + -
242M VAL* 4.1 11.0 - - + -
244M PHE* 2.7 51.7 + + + -
247M TYR* 1.3 71.9 - - - +
249M ILE* 1.3 65.7 + - - +
250M ILE 2.6 7.4 + - - -
251M LYS* 2.8 24.8 + - + +
252M ASP* 2.7 30.6 + - - +
505M ANJ 4.0 12.1 - + - +
252N TRP* 3.7 24.0 - + - -
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Residues in contact with ILE 249 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M ILE* 3.3 29.4 - - + -
244M PHE* 3.4 24.0 + - + -
245M TRP* 3.7 42.8 - - + -
246M PRO 3.5 7.4 + - - +
248M PHE* 1.3 76.8 - - - +
250M ILE* 1.3 61.6 + - + +
252M ASP* 3.5 8.2 - - + +
253M VAL* 3.0 40.7 + - + +
505M ANJ 4.2 9.9 - - + -
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Residues in contact with ILE 250 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245M TRP* 5.7 2.5 - - + -
246M PRO* 3.0 24.7 + - + +
247M TYR 3.9 3.6 - - - +
248M PHE 2.6 5.3 + - - -
249M ILE* 1.3 76.5 - - + +
251M LYS* 1.3 56.9 + - - +
252M ASP 3.0 1.1 - - - -
253M VAL* 2.9 8.6 + - + +
254M PHE* 2.5 34.5 + - + +
244N LEU* 4.7 11.1 - - + +
247N THR* 4.3 20.6 - - + -
248N ASN* 3.3 33.4 - - + +
251N LEU* 3.6 24.5 - - + -
16O TYR* 6.3 2.7 - - + -
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Residues in contact with LYS 251 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41M LEU 3.5 22.8 + - - -
42M ASN* 4.4 7.4 + - - +
43M TRP* 3.1 41.3 - - + -
46M ILE* 5.3 5.2 - - + -
247M TYR 3.6 6.8 + - - +
248M PHE* 2.8 40.8 + - + +
250M ILE* 1.3 76.4 - - - +
252M ASP* 1.3 56.8 + - - +
254M PHE* 3.2 7.2 - - - +
255M ALA* 2.5 38.5 + - - +
505M ANJ 5.3 3.8 + - - -
248N ASN* 3.4 21.4 + - - +
252N TRP* 3.7 21.7 - - + +
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Residues in contact with ASP 252 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M ILE* 5.6 5.6 - - - -
49M VAL* 2.8 31.8 - - + +
244M PHE* 4.7 2.9 - - - -
248M PHE* 2.7 31.5 + - - +
249M ILE* 3.5 9.9 - - + +
251M LYS* 1.3 76.5 - - - +
253M VAL* 1.3 53.8 + - + +
255M ALA* 3.6 5.1 - - - +
256M LEU* 2.7 40.0 + - - +
505M ANJ 2.6 53.1 + - + +
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Residues in contact with VAL 253 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249M ILE* 3.0 28.5 + - + +
250M ILE* 2.9 8.9 + - + +
252M ASP* 1.3 80.8 - - + +
254M PHE* 1.3 65.0 + - - +
256M LEU* 3.3 15.0 + - + +
257M ALA* 3.0 21.7 + - + +
244N LEU* 3.7 27.8 - - + -
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Residues in contact with PHE 254 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M TRP* 3.7 35.7 - + - -
250M ILE 2.5 17.5 + - - +
251M LYS* 2.8 11.2 + - - +
253M VAL* 1.3 71.8 - - - +
255M ALA* 1.3 67.5 + - - +
257M ALA* 3.1 16.8 + - - +
258M VAL* 3.3 29.6 + - + +
241N SER* 3.8 21.3 - - - -
244N LEU* 4.1 24.8 - - + +
245N TYR* 3.9 39.5 - + + -
248N ASN* 4.4 14.1 - - + -
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Residues in contact with ALA 255 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M TRP* 4.9 7.6 - - + -
46M ILE* 3.7 42.2 - - + -
50M VAL* 5.9 0.4 - - + -
251M LYS 2.5 18.0 + - - +
252M ASP 3.6 2.9 - - - +
254M PHE* 1.3 75.7 - - - +
256M LEU* 1.3 65.2 + - - +
258M VAL* 2.7 23.6 + - - +
259M VAL* 2.9 15.7 + - - +
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Residues in contact with LEU 256 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49M VAL* 3.3 31.9 - - + -
50M VAL* 4.0 22.6 - - + +
53M PHE* 4.1 34.5 - - + -
252M ASP 2.7 20.4 + - - +
253M VAL* 3.4 16.6 - - + +
255M ALA* 1.3 71.5 - - - +
257M ALA* 1.3 57.3 + - - +
259M VAL* 3.5 7.3 - - + +
260M LEU* 3.0 42.0 + - + +
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Residues in contact with ALA 257 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253M VAL 3.0 11.3 + - - +
254M PHE 3.1 11.2 - - - +
255M ALA 2.8 1.0 + - - -
256M LEU* 1.3 73.6 - - - +
258M VAL* 1.3 55.5 + - - +
260M LEU* 3.1 6.2 + - - +
261M LEU* 2.8 34.8 + - - +
237N LEU* 4.0 18.0 - - + +
240N LEU* 4.8 3.8 - - + -
241N SER* 4.0 18.6 - - - +
244N LEU* 4.0 19.1 - - + -
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Residues in contact with VAL 258 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254M PHE* 3.3 45.3 - - + +
255M ALA* 2.7 14.9 + - - +
257M ALA* 1.3 71.5 - - - +
259M VAL* 1.3 64.1 + - + +
261M LEU* 3.1 27.4 - - + +
262M VAL* 3.2 18.7 + - + +
241N SER* 4.1 11.4 + - - +
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Residues in contact with VAL 259 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M ILE* 4.7 9.9 - - + -
47M TRP* 5.1 9.0 - - + -
50M VAL* 3.9 36.1 - - + -
103M LEU* 4.1 22.2 - - + -
255M ALA* 2.9 20.8 + - - +
256M LEU* 3.5 11.0 - - + +
258M VAL* 1.3 77.6 - - + +
260M LEU* 1.3 55.5 + - + +
262M VAL* 3.0 11.5 + - - +
263M PHE* 2.7 30.8 + - - +
504M LOP 5.1 10.2 - - + +
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Residues in contact with LEU 260 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M PHE* 3.3 54.7 - - + -
103M LEU* 4.9 4.7 - - + -
256M LEU* 3.0 26.5 + - + +
257M ALA* 3.5 5.6 - - - +
259M VAL* 1.3 79.0 - - + +
261M LEU* 1.3 59.1 + - - +
263M PHE* 3.7 21.3 - - + -
264M PHE* 2.7 54.0 + - + -
237N LEU* 4.2 11.9 - - + -
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Residues in contact with LEU 261 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257M ALA 2.8 16.7 + - - +
258M VAL* 3.1 19.3 - - + +
259M VAL 3.1 0.2 - - - -
260M LEU* 1.3 72.9 - - - +
262M VAL* 1.3 62.6 + - + +
264M PHE* 3.9 2.4 - - - +
265M ALA* 3.0 27.2 + - - +
431M BGL 4.6 17.7 - - + -
234N VAL* 3.5 42.4 - - + +
237N LEU* 4.1 15.0 - - + +
238N THR* 3.7 21.1 - - + +
241N SER* 4.1 16.4 - - - +
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Residues in contact with VAL 262 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258M VAL* 3.3 21.1 - - + +
259M VAL* 3.0 7.1 + - - +
261M LEU* 1.3 77.6 - - + +
263M PHE* 1.3 69.4 + - - +
265M ALA* 3.0 22.9 - - + +
266M ILE* 3.0 24.3 + - + +
431M BGL 5.8 4.9 - - + -
504M LOP 4.4 24.7 - - + -
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Residues in contact with PHE 263 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M PHE* 5.2 0.7 - + - -
57M LEU* 3.8 20.0 - - + -
96M LEU* 3.4 47.8 - - + -
99M ASN* 3.6 26.7 - - + -
100M GLY* 4.1 3.8 - - - -
103M LEU* 4.1 15.5 - - + -
259M VAL 2.7 18.4 + - - +
260M LEU* 3.4 27.6 - - + +
262M VAL* 1.3 72.4 - - - +
264M PHE* 1.3 74.6 + + - +
266M ILE* 2.9 15.7 + - + +
267M VAL* 2.9 28.6 + - + +
504M LOP 4.0 28.2 - - + +
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Residues in contact with PHE 264 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M PHE* 5.6 3.8 - + - -
57M LEU* 6.5 0.2 - - + -
92M MET* 5.5 9.0 - - - -
96M LEU* 4.2 32.8 - - + -
260M LEU* 2.7 50.4 + - + +
261M LEU 3.9 2.7 - - - +
263M PHE* 1.3 79.1 - + - +
265M ALA* 1.3 57.4 + - - +
267M VAL* 3.7 8.5 - - + +
268M GLY* 2.5 36.7 + - - -
230N GLY* 5.4 2.4 - - - -
233N ALA* 3.8 31.6 - - + -
234N VAL* 5.3 2.7 - - + +
237N LEU* 3.7 17.5 - - + -
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Residues in contact with ALA 265 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261M LEU* 3.0 15.6 + - + +
262M VAL* 3.0 20.4 - - + +
264M PHE* 1.3 75.8 - - - +
266M ILE* 1.3 51.7 + - + +
269M PHE* 2.7 51.3 + - + +
270M MET* 4.7 0.6 - - - +
431M BGL 4.1 32.7 - - + +
234N VAL* 4.6 9.1 - - + +
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Residues in contact with ILE 266 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99M ASN* 4.1 17.0 - - - +
262M VAL* 3.1 27.4 - - + +
263M PHE* 2.9 9.4 + - + +
265M ALA* 1.3 72.5 - - + +
267M VAL* 1.3 62.3 + - + +
268M GLY 3.0 1.6 - - - -
270M MET* 2.6 80.4 + - + +
271M PRO 2.9 0.9 - - - -
273M TYR* 5.4 0.9 - - + -
274M LEU* 5.1 13.0 - - + -
504M LOP 4.5 17.0 - - + -
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Residues in contact with VAL 267 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92M MET* 4.4 13.1 - - - +
95M TYR* 3.9 25.4 - - + +
96M LEU* 4.0 26.2 - - + +
99M ASN* 4.3 7.4 - - + +
263M PHE* 2.9 52.7 - - + +
264M PHE* 3.7 10.3 - - + +
266M ILE* 1.3 74.9 - - + +
268M GLY* 1.3 62.7 + - - +
271M PRO* 3.8 18.7 - - - +
226N ARG* 4.1 10.4 - - - +
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Residues in contact with GLY 268 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92M MET* 5.3 3.8 - - - -
264M PHE 2.5 21.8 + - - -
265M ALA 3.8 0.4 - - - -
267M VAL* 1.3 75.2 - - - +
269M PHE* 1.3 65.2 + - - +
226N ARG* 3.1 44.4 + - - +
227N LYS* 4.4 4.0 - - - +
230N GLY* 4.5 12.6 - - - -
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Residues in contact with PHE 269 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265M ALA* 2.7 34.1 + - - +
268M GLY* 1.3 76.4 - - - +
270M MET* 1.3 59.3 + - + +
271M PRO* 3.6 4.9 - - - +
431M BGL 3.3 75.5 + - + +
16N PRO* 3.5 33.9 - - + -
226N ARG* 4.1 7.8 + - - +
227N LYS* 4.0 20.6 - - + -
230N GLY* 4.2 5.4 - - - -
231N PHE* 3.8 34.5 - + - -
234N VAL* 4.1 23.8 - - + -
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Residues in contact with MET 270 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99M ASN* 4.7 0.2 - - - +
265M ALA 4.7 0.4 - - - +
266M ILE* 2.6 55.1 + - + +
269M PHE* 1.3 79.4 - - + +
271M PRO* 1.3 65.4 - - - +
272M ASN 3.3 1.8 - - - -
273M TYR* 3.3 44.7 + - + +
431M BGL 4.6 32.1 - - + +
121N LEU* 3.6 37.5 - - + +
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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