Contacts of the helix formed by residues 245 - 272 (chain C) in PDB entry 6D6Q
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 GLY 245 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C THR* 1.3 77.3 - - - +
246C ALA* 1.3 56.0 + - - +
248C LEU* 3.4 13.9 - - - +
249C GLN* 2.9 32.7 + - - +
207D GLN* 3.9 26.4 + - - -
210D LEU* 4.8 11.0 - - - +
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Residues in contact with ALA 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C THR* 2.7 15.8 + - + +
245C GLY* 1.3 74.9 - - - +
247C LYS* 1.3 62.5 + - + +
248C LEU 3.1 2.3 + - - -
249C GLN* 4.2 7.3 + - - +
250C ASP* 4.2 12.1 + - - +
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Residues in contact with LYS 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C ASP 5.7 0.4 - - - +
204C THR* 2.4 51.8 + - + +
206C LEU* 3.1 38.9 - - + +
243C LEU* 4.0 26.7 - - + +
244C THR* 2.8 19.3 + - - +
246C ALA* 1.3 77.4 - - + +
248C LEU* 1.3 56.6 + - - +
250C ASP* 4.7 5.8 - - - +
251C CYS* 3.4 8.3 - - - -
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Residues in contact with LEU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C LEU* 4.4 17.5 - - + -
224C ILE* 5.2 4.5 - - + -
235C LEU* 4.2 28.7 - - + -
243C LEU* 5.0 9.2 - - + -
244C THR 3.9 3.4 - - - +
245C GLY* 3.4 19.1 - - - +
246C ALA 3.1 0.2 - - - -
247C LYS* 1.3 79.2 - - - +
249C GLN* 1.3 66.8 + - - +
250C ASP 3.2 1.6 - - - -
251C CYS* 3.1 11.1 + - + +
252C MET* 3.0 34.3 + - - +
192D LEU* 5.2 10.3 - - + -
206D LEU* 4.2 16.8 - - + -
207D GLN* 4.2 17.3 - - - +
210D LEU* 5.0 9.6 - - + -
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Residues in contact with GLN 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C GLY 2.9 15.4 + - - +
246C ALA* 4.8 4.5 - - - +
248C LEU* 1.3 76.0 - - - +
250C ASP* 1.3 57.7 + - - +
252C MET* 3.2 14.4 + - - +
253C SER* 3.0 29.8 + - - +
203D ASP* 2.5 39.8 + - - +
207D GLN* 4.4 8.7 + - - +
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Residues in contact with ASP 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C LEU* 6.4 0.4 - - + -
246C ALA 4.2 12.1 + - - +
247C LYS* 5.1 4.3 - - - -
248C LEU 3.2 1.0 - - - -
249C GLN* 1.3 78.9 - - - +
251C CYS* 1.3 61.7 + - - +
253C SER* 2.4 33.9 + - - -
254C ARG* 3.0 10.9 + - - +
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Residues in contact with CYS 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C PHE* 3.3 51.9 - - + -
206C LEU* 3.5 19.1 - - - -
222C LEU* 5.3 8.7 - - + -
224C ILE* 5.2 3.6 - - + -
243C LEU* 6.2 0.2 - - - -
247C LYS 3.4 21.1 - - - -
248C LEU* 3.1 14.8 + - + +
250C ASP* 1.3 80.4 - - - +
252C MET* 1.3 58.9 + - + +
254C ARG* 3.3 1.0 + - - -
255C ALA* 2.9 29.9 + - - +
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Residues in contact with MET 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ILE* 3.7 20.0 - - + -
226C MET* 4.8 7.4 - - + +
232C LEU* 3.5 33.2 - - + -
248C LEU* 3.0 20.5 + - + +
249C GLN* 3.2 17.7 + - - +
251C CYS* 1.3 76.0 - - - +
253C SER* 1.3 62.9 + - - +
255C ALA* 3.2 8.6 + - - +
256C VAL* 3.0 28.0 + - + +
203D ASP* 3.3 50.5 - - + +
206D LEU* 4.5 13.2 - - + -
207D GLN* 5.1 1.3 - - - -
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Residues in contact with SER 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C GLN* 3.0 14.6 + - - +
250C ASP* 2.4 38.5 + - - -
252C MET* 1.3 75.4 - - - +
254C ARG* 1.3 64.6 + - - +
256C VAL* 3.0 20.2 + - - +
257C THR* 3.0 15.7 + - - -
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Residues in contact with ARG 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C GLY* 2.7 30.1 + - - -
31C GLU* 3.7 13.9 - - - +
32C PHE* 3.7 24.9 - - - +
196C THR* 4.8 4.3 - - + -
198C PHE* 4.6 7.0 - - + -
208C VAL* 4.6 16.8 - - + +
250C ASP* 3.0 14.2 + - - +
251C CYS* 3.7 7.0 - - - +
253C SER* 1.3 81.8 + - - +
255C ALA* 1.3 56.9 + - - +
257C THR* 3.2 17.9 + - - +
258C ARG* 3.0 51.3 + - - +
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Residues in contact with ALA 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C VAL* 5.6 0.7 - - - +
196C THR* 3.5 24.8 + - - +
224C ILE* 3.9 20.9 - - + +
226C MET* 4.1 19.7 - - + +
251C CYS 2.9 14.7 + - - +
252C MET* 3.4 11.9 - - - +
253C SER 3.1 0.2 - - - -
254C ARG* 1.3 74.5 - - - +
256C VAL* 1.3 60.2 + - - +
258C ARG* 3.3 2.1 + - - +
259C HIS* 2.9 28.6 + - - +
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Residues in contact with VAL 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C MET* 3.9 29.2 - - + -
230C GLY* 6.0 0.4 - - - -
252C MET 3.0 16.8 + - - +
253C SER* 3.0 10.5 + - - +
255C ALA* 1.3 75.7 - - - +
257C THR* 1.3 63.6 + - - +
259C HIS* 3.2 10.0 + - + +
260C LYS* 3.0 45.2 + - + +
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Residues in contact with THR 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C SER 3.0 13.9 + - - -
254C ARG* 3.5 25.9 - - - +
255C ALA 3.2 0.2 - - - -
256C VAL* 1.3 76.1 - - - +
258C ARG* 1.3 61.7 + - - +
260C LYS* 3.2 15.6 + - + +
261C GLU* 3.0 23.0 + - + +
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Residues in contact with ARG 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C PHE* 3.1 45.7 - - + +
33C ARG 5.3 0.2 + - - -
35C THR* 2.9 40.2 + - - +
53C LEU* 3.8 10.3 - - - +
150C ASP* 6.3 1.2 - - - +
154C PHE* 5.9 1.4 - - - -
194C VAL* 4.3 9.7 - - + +
195C ALA 4.7 2.3 + - - +
196C THR* 3.7 19.1 - - - +
254C ARG* 3.0 29.4 + - - +
255C ALA 3.3 0.8 + - - +
257C THR* 1.3 73.7 - - - +
259C HIS* 1.3 66.5 + - - +
261C GLU* 2.8 32.8 + - - +
262C VAL* 3.0 42.0 + - + +
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Residues in contact with HIS 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C HIS* 3.0 27.0 + - - +
194C VAL* 3.8 14.7 - - + +
226C MET* 3.0 28.0 - - + +
227C ASP 4.8 1.3 - - - -
228C GLU* 3.3 40.1 + - + +
255C ALA 2.9 14.4 + - - +
256C VAL* 3.2 14.5 + - + +
258C ARG* 1.3 75.5 - - - +
260C LYS* 1.3 69.5 + - - +
262C VAL* 3.4 7.7 - - - +
263C LYS* 3.0 49.2 + - + +
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Residues in contact with LYS 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C VAL* 3.0 31.4 + - + +
257C THR* 3.2 13.8 + - + +
259C HIS* 1.3 85.5 + - - +
261C GLU* 1.3 64.9 + - - +
263C LYS* 3.9 3.0 - - - +
264C LYS* 3.0 44.0 + - - +
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Residues in contact with GLU 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C THR* 5.2 2.0 - - - -
257C THR* 3.0 14.7 + - + +
258C ARG* 2.8 38.9 + - - +
260C LYS* 1.3 78.2 - - - +
262C VAL* 1.3 77.4 + - - +
264C LYS* 3.2 10.8 + - - +
265C LEU* 3.0 37.9 + - - +
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Residues in contact with VAL 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C THR* 5.2 1.8 - - + -
154C PHE* 3.8 29.0 - - + -
194C VAL* 3.2 40.6 - - + -
258C ARG* 3.0 47.7 + - + +
259C HIS 3.4 1.3 - - - +
261C GLU* 1.3 92.4 - - - +
263C LYS* 1.3 60.2 + - - +
265C LEU* 3.3 7.4 + - - +
266C MET* 2.9 29.9 + - + +
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Residues in contact with LYS 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C LYS* 5.9 1.1 - - - +
192C HIS* 4.1 32.0 + - + -
194C VAL* 5.8 1.6 - - + -
228C GLU* 2.6 28.6 + - - +
259C HIS* 3.0 38.9 + - + +
260C LYS* 3.9 3.4 - - - +
262C VAL* 1.3 76.9 - - + +
264C LYS* 1.3 67.3 + - - +
266C MET* 3.3 8.7 + - + +
267C ASP* 2.9 47.6 + - - +
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Residues in contact with LYS 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C LYS* 3.0 31.9 + - - +
261C GLU* 3.4 10.7 - - - +
263C LYS* 1.3 77.3 - - - +
265C LEU* 1.3 62.8 + - - +
267C ASP* 3.3 8.2 + - - +
268C GLU* 2.9 35.8 + - + +
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Residues in contact with LEU 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C THR* 3.7 34.5 - - + +
36C THR* 5.1 0.7 - - - -
37C VAL* 3.7 33.0 - - + +
154C PHE* 4.1 13.5 - - + -
261C GLU* 3.0 32.2 + - - +
262C VAL* 3.5 9.9 - - - +
263C LYS 3.2 0.2 - - - -
264C LYS* 1.3 77.0 - - - +
266C MET* 1.3 63.5 + - - +
268C GLU* 3.1 15.2 + - - +
269C VAL* 3.0 30.4 + - + +
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Residues in contact with MET 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C VAL* 5.7 1.8 - - + -
39C ILE* 6.2 1.6 - - + -
154C PHE* 3.3 36.1 - - + +
157C LEU* 3.8 24.7 - - + -
158C ALA* 4.0 26.5 - - + +
161C LYS* 3.5 41.1 - - + +
192C HIS* 5.1 1.8 - - - -
194C VAL* 6.4 0.2 - - + -
262C VAL* 2.9 15.4 + - + +
263C LYS* 3.8 8.5 - - + +
265C LEU* 1.3 81.7 - - - +
267C ASP* 1.3 57.3 + - - +
269C VAL* 3.2 6.3 + - + +
270C ILE* 2.9 38.1 + - + +
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Residues in contact with ASP 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C LYS* 3.8 18.0 + - - -
263C LYS* 2.9 43.5 + - - +
264C LYS* 3.6 7.1 - - - +
266C MET* 1.3 73.7 - - - +
268C GLU* 1.3 66.7 + - + +
270C ILE* 3.1 16.4 - - + +
271C LYS* 2.9 26.6 + - - +
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Residues in contact with GLU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C LYS* 2.9 27.7 + - + +
265C LEU* 3.4 13.5 - - - +
267C ASP* 1.3 75.1 - - - +
269C VAL* 1.3 58.9 + - + +
271C LYS* 3.4 20.4 + - - +
272C SER* 2.9 29.5 + - - -
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Residues in contact with VAL 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C VAL* 3.5 29.2 - - + +
38C ASN* 5.7 0.4 - - - -
39C ILE* 3.6 34.5 - - + +
265C LEU* 3.0 19.6 + - + +
266C MET* 3.6 7.9 - - + +
267C ASP 3.1 0.2 - - - -
268C GLU* 1.3 74.5 - - + +
270C ILE* 1.3 60.9 + - + +
271C LYS 3.0 4.3 - - - -
272C SER* 2.8 26.4 + - - -
273C MET* 3.5 12.9 - - + +
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Residues in contact with ILE 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ILE* 5.4 8.3 - - + -
158C ALA 6.0 0.7 - - - +
161C LYS* 4.8 23.3 - - + +
162C ASN* 6.1 1.8 - - - +
266C MET* 2.9 29.7 + - + +
267C ASP* 3.1 30.5 - - + +
269C VAL* 1.3 77.3 - - + +
271C LYS* 1.3 63.0 + - + +
273C MET* 4.0 25.9 + - - +
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Residues in contact with LYS 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C ASP* 2.9 20.0 + - - +
268C GLU* 3.7 25.0 + - - +
270C ILE* 1.3 81.9 - - + +
272C SER* 1.3 55.0 + - - +
273C MET 3.1 11.7 + - - -
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Residues in contact with SER 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C GLU 2.9 15.8 + - - -
269C VAL* 2.8 11.3 + - - -
271C LYS* 1.3 75.0 - - - +
273C MET* 1.3 59.4 + - - +
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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