Contacts of the helix formed by residues 229 - 259 (chain C) in PDB entry 6CM1
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 ALA 229 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 5.7 0.4 - - - -
323B PX4 5.1 2.9 - - + -
225C LEU 3.7 2.6 + - - +
226C SER 3.1 8.0 + - - +
228C LYS* 1.4 78.0 - - - +
230C LYS* 1.4 63.0 + - - +
231C PRO* 3.6 1.3 - - - -
232C ALA* 4.0 4.3 + - - +
233C LEU* 3.2 25.0 + - - +
317C PX4 4.1 24.7 - - + -
333C PX4 3.8 40.8 - - + +
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Residues in contact with LYS 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C SER* 3.3 15.4 + - - +
227C GLU* 3.7 34.1 + - + +
228C LYS 3.4 0.8 - - - -
229C ALA* 1.4 76.5 - - - +
231C PRO* 1.3 67.1 - - + +
233C LEU* 3.3 17.3 + - + +
234C GLU* 2.8 42.4 + - + +
237C ARG* 5.7 5.2 - - - +
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Residues in contact with PRO 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 3.2 52.9 - - + +
74B ASN* 5.1 7.0 - - + +
75B LEU* 4.1 20.4 - - + -
78B GLU* 4.6 12.6 - - - +
227C GLU 4.2 4.9 - - - +
228C LYS 3.7 14.4 - - - +
229C ALA 3.8 0.7 - - - -
230C LYS* 1.3 93.6 - - + +
232C ALA* 1.3 53.0 - - - +
234C GLU* 3.2 1.4 + - + -
235C ASP* 2.9 29.5 + - - +
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Residues in contact with ALA 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 5.3 0.4 - - - -
72B TRP* 6.0 0.2 - - + -
75B LEU* 4.3 14.3 - - + +
305B PX4 3.8 40.0 - - + +
229C ALA* 4.0 6.2 + - - +
231C PRO* 1.3 76.8 - - - +
233C LEU* 1.4 58.5 + - - +
235C ASP* 3.8 12.3 - - - +
236C LEU* 3.1 30.6 + - - +
333C PX4 4.4 9.6 - - + -
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Residues in contact with LEU 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C SER 5.8 0.4 - - - +
229C ALA 3.2 19.9 + - - +
230C LYS* 3.3 20.2 - - + +
231C PRO 3.2 0.4 - - - -
232C ALA* 1.4 77.5 - - - +
234C GLU* 1.4 57.9 + - - +
235C ASP 3.3 0.2 - - - -
236C LEU* 3.0 19.9 + - - +
237C ARG* 3.1 48.0 + - - +
333C PX4 3.8 37.8 - - + +
346C PX4 3.4 48.9 - - + -
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Residues in contact with GLU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 3.4 31.2 - - + -
230C LYS* 2.8 31.3 + - + +
231C PRO 3.2 0.4 + - - +
233C LEU* 1.4 71.2 - - - +
235C ASP* 1.3 59.2 + - - +
237C ARG* 2.8 49.6 + - - +
238C GLN* 2.8 49.2 + - - +
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Residues in contact with ASP 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 5.2 2.1 - - - +
67B VAL* 4.7 1.9 - - - +
68B THR* 2.6 43.5 + - - +
71B PHE* 3.3 21.2 - - + +
72B TRP* 5.9 2.8 - - - -
305B PX4 6.0 1.4 - - - +
231C PRO 2.9 18.3 + - - +
232C ALA* 3.8 14.0 - - - +
234C GLU* 1.3 74.7 - - - +
236C LEU* 1.4 61.0 + - - +
238C GLN* 4.0 2.2 - - - +
239C GLY* 3.1 22.9 + - - -
328C PX4 4.3 8.2 - - - +
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Residues in contact with LEU 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B PX4 4.8 11.7 - - + -
312B PX4 3.8 33.0 - - + -
232C ALA 3.1 20.4 - - - +
233C LEU* 3.0 9.4 + - - +
235C ASP* 1.4 81.3 - - + +
237C ARG* 1.3 52.4 + - - +
239C GLY 3.5 0.3 + - - -
240C LEU* 2.8 34.3 + - - +
328C PX4 3.6 38.7 - - + +
333C PX4 3.9 21.3 - - + -
346C PX4 3.6 25.1 - - + +
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Residues in contact with ARG 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C LYS* 5.7 5.7 - - - +
233C LEU* 3.1 50.5 + - - +
234C GLU* 2.8 47.7 + - - +
235C ASP 3.4 0.2 - - - -
236C LEU* 1.3 72.2 - - - +
238C GLN* 1.3 66.0 + - - +
240C LEU* 3.3 7.6 + - + +
241C LEU* 3.3 31.8 + - + +
346C PX4 3.8 26.4 - - + +
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Residues in contact with GLN 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 3.6 9.1 - - + +
67B VAL* 4.0 23.8 - - + -
71B PHE* 4.0 19.2 - - + -
234C GLU* 2.8 41.6 + - - +
235C ASP 4.1 2.9 - - - +
237C ARG* 1.3 71.9 - - - +
239C GLY* 1.4 55.6 + - - +
241C LEU* 3.8 21.3 + - - +
242C PRO* 3.1 22.5 - - - +
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Residues in contact with GLY 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 3.6 24.9 - - - +
235C ASP 3.1 14.8 + - - -
236C LEU 3.6 2.7 - - - -
238C GLN* 1.4 73.4 - - - +
240C LEU* 1.4 61.2 + - - +
241C LEU 3.4 0.6 + - - -
242C PRO* 3.4 4.0 - - - +
243C VAL* 3.2 25.6 + - - +
328C PX4 4.0 14.1 - - - -
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C LEU 2.8 20.5 + - - +
237C ARG* 3.5 11.2 - - + +
239C GLY* 1.4 70.6 - - - +
241C LEU* 1.3 52.2 + - + +
243C VAL* 3.0 12.7 + - + +
244C LEU* 2.8 52.6 + - + +
328C PX4 3.6 56.5 - - + +
331C PX4 5.0 4.3 - - + -
346C PX4 4.1 19.3 - - + -
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Residues in contact with LEU 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C ARG* 3.3 19.2 + - + +
238C GLN* 3.8 24.7 - - - +
240C LEU* 1.3 72.4 - - + +
242C PRO* 1.4 72.1 - - + +
244C LEU* 3.4 34.4 - - + +
245C GLU* 3.6 9.1 + - - +
331C PX4 6.0 1.8 - - - -
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Residues in contact with PRO 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 4.0 28.0 - - + +
64B LEU* 4.5 7.4 - - + -
238C GLN 3.1 22.4 - - - +
239C GLY 3.4 9.4 - - - +
241C LEU* 1.4 88.8 - - + +
243C VAL* 1.4 57.3 + - - +
244C LEU 3.3 0.2 - - - -
245C GLU* 3.2 17.9 + - + +
246C SER* 2.9 28.1 + - - -
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Residues in contact with VAL 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 5.6 2.9 - - + -
60B LEU* 3.7 26.2 - - + -
64B LEU* 5.4 0.9 - - + -
239C GLY* 3.2 21.9 + - - +
240C LEU* 3.0 16.2 + - + +
242C PRO* 1.4 73.6 - - + +
244C LEU* 1.3 53.0 + - - +
246C SER* 3.5 4.5 - - - -
247C PHE* 2.7 38.7 + - - +
313C PX4 4.6 4.9 - - + +
328C PX4 4.6 2.2 - - + -
331C PX4 3.2 63.0 - - + -
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Residues in contact with LEU 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C LEU* 2.8 36.0 + - + +
241C LEU* 3.4 26.7 - - + +
243C VAL* 1.3 72.9 - - - +
245C GLU* 1.3 59.8 + - + +
247C PHE* 3.3 4.2 + - - +
248C LYS* 2.8 33.6 + - - +
328C PX4 6.2 0.2 - - + -
331C PX4 3.0 71.3 - - + +
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Residues in contact with GLU 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C LEU 3.6 11.6 + - - +
242C PRO* 3.2 17.1 + - + +
244C LEU* 1.3 75.1 - - + +
246C SER* 1.4 58.1 + - - +
248C LYS* 3.8 3.8 - - - +
249C VAL* 2.8 39.9 + - + +
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Residues in contact with SER 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR* 5.1 12.8 - - - +
57B PHE* 4.5 17.9 - - - -
60B LEU* 4.6 14.2 - - - +
242C PRO 2.9 16.2 + - - -
243C VAL* 3.7 7.6 - - - -
245C GLU* 1.4 75.7 - - - +
247C PHE* 1.3 60.9 + - - +
249C VAL* 4.1 4.2 - - - +
250C SER* 2.9 34.9 + - - -
313C PX4 5.5 2.8 - - - +
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Residues in contact with PHE 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B PX4 5.6 6.5 - - + -
243C VAL 2.7 22.5 + - - +
244C LEU* 3.9 3.6 - - - +
246C SER* 1.3 73.1 - - - +
248C LYS* 1.3 61.6 + - + +
250C SER* 3.6 4.3 - - - -
251C PHE* 2.9 42.1 + + - +
313C PX4 4.0 75.1 - - + +
331C PX4 3.8 67.8 - - + -
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Residues in contact with LYS 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C LEU 2.8 21.0 + - - +
245C GLU* 3.8 4.9 - - - +
247C PHE* 1.3 74.3 - - + +
249C VAL* 1.4 67.9 + - + +
251C PHE* 3.4 17.2 + - + +
252C LEU* 3.1 44.9 + - + +
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Residues in contact with VAL 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C GLU* 2.8 29.9 + - + +
246C SER* 4.1 4.9 - - - +
248C LYS* 1.4 71.8 - - + +
250C SER* 1.4 53.2 + - - +
252C LEU* 3.3 13.1 + - + +
253C SER* 2.8 37.5 + - - -
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Residues in contact with SER 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 5.8 0.5 - - - -
246C SER* 2.9 29.9 + - - -
247C PHE 3.6 1.8 - - - -
249C VAL* 1.4 71.9 - - - +
251C PHE* 1.3 64.1 + - - +
253C SER* 4.0 7.1 - - - -
254C ALA* 3.2 24.1 + - - +
313C PX4 3.5 38.9 - - - +
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Residues in contact with PHE 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C PHE* 2.9 31.2 + + + +
248C LYS* 3.5 20.0 - - + +
250C SER* 1.3 74.8 - - - +
252C LEU* 1.4 77.7 + - + +
254C ALA* 3.1 4.7 + - - +
255C LEU* 3.0 27.5 + - + +
313C PX4 3.6 110.6 - - + +
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Residues in contact with LEU 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C LYS* 3.1 41.0 + - + +
249C VAL* 3.7 11.7 - - + +
251C PHE* 1.4 86.9 - - + +
253C SER* 1.4 58.0 + - - +
255C LEU* 3.3 3.6 + - - +
256C GLU* 2.9 30.6 + - - +
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Residues in contact with SER 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C VAL* 2.8 25.8 + - - -
250C SER* 4.0 9.4 - - - -
251C PHE 3.2 0.2 - - - -
252C LEU* 1.4 72.7 - - - +
254C ALA* 1.3 55.7 + - - +
256C GLU* 3.3 21.0 + - - +
257C GLU* 3.0 32.7 + - - +
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Residues in contact with ALA 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C SER 3.2 16.8 + - - +
251C PHE 3.1 5.3 + - - +
253C SER* 1.3 76.8 + - - +
255C LEU* 1.3 65.5 + - - +
257C GLU* 3.7 15.9 - - - +
258C TYR* 3.4 18.5 + - - +
313C PX4 4.0 18.4 - - + -
329C PX4 4.1 31.0 - - + +
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Residues in contact with LEU 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C PHE* 3.0 20.6 + - + +
252C LEU* 4.2 3.8 - - - +
254C ALA* 1.3 78.7 - - - +
256C GLU* 1.4 60.4 + - - +
258C TYR* 3.3 25.4 - - + +
259C THR* 3.8 7.4 + - - -
313C PX4 3.5 43.1 - - + +
329C PX4 3.4 47.8 - - - -
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Residues in contact with GLU 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C LEU 2.9 18.2 + - - +
253C SER* 3.5 20.2 + - - +
255C LEU* 1.4 75.0 - - - +
257C GLU* 1.3 60.4 + - - +
258C TYR 3.5 0.2 + - - -
259C THR* 3.5 14.6 + - - -
260C LYS* 3.4 34.7 + - - +
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Residues in contact with GLU 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LYS* 2.9 33.6 + - - -
253C SER* 3.0 17.9 + - - +
254C ALA* 3.7 15.9 - - - +
256C GLU* 1.3 75.3 - - - +
258C TYR* 1.3 65.7 - - - +
260C LYS* 3.5 23.0 - - + +
261C LYS* 2.7 56.2 + - + +
329C PX4 6.0 1.2 - - - +
335C PX4 6.4 0.2 - - - -
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Residues in contact with TYR 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C ALA 3.4 5.8 + - - +
255C LEU* 3.3 23.1 + - + +
257C GLU* 1.3 80.7 - - - +
259C THR* 1.3 75.1 + - + +
261C LYS* 2.9 23.5 + - - +
262C LEU* 3.5 38.7 + - + +
265C GLN* 4.9 13.4 - - + +
319C PX4 2.6 40.5 + - - -
329C PX4 3.3 70.0 - - - +
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Residues in contact with THR 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C LEU 3.8 6.8 + - - -
256C GLU* 3.5 14.7 + - - -
257C GLU 3.5 0.4 - - - -
258C TYR* 1.3 93.8 - - + +
260C LYS* 1.4 58.6 + - - +
261C LYS 3.4 0.2 - - - -
262C LEU* 4.0 23.4 + - + +
329C PX4 6.5 0.7 - - - -
----------------------------------------------------------
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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