Contacts of the helix formed by residues 221 - 247 (chain C) in PDB entry 3L73
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 221 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.0 57.7 - - + -
20C ILE 3.8 3.8 + - - +
22C LEU* 3.0 37.4 + - + +
24C ALA* 4.8 1.8 - - + -
219C ILE 3.5 0.8 + - - -
220C PRO* 1.3 70.4 - - - +
222C HIS* 1.3 57.7 + - - +
225C TYR* 2.6 62.6 + + + -
226C SER* 3.1 25.0 + - - -
229C ASP* 3.8 15.5 - - + -
2002C UQ 3.5 43.1 - + + -
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Residues in contact with HIS 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ARG* 2.8 40.2 + - - -
2008A PEE 3.4 53.2 + - + +
19C LEU 3.9 16.2 - - - +
20C ILE* 3.5 20.9 + - + +
220C PRO* 3.4 7.4 - - - +
221C PHE* 1.3 78.6 - - - +
223C PRO* 1.3 78.4 - - + +
224C TYR 3.5 0.9 - - - -
226C SER* 2.8 27.7 + - - +
227C PHE* 4.0 8.3 - + - -
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Residues in contact with PRO 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ASP* 3.6 19.3 - - - +
435A ASN* 4.2 21.1 - - + +
436A ARG* 4.0 10.5 - - - -
439A SER* 6.1 0.4 - - - +
222C HIS* 1.3 92.5 - - + +
224C TYR* 1.3 71.9 + - + +
225C TYR 3.5 0.2 - - - -
226C SER* 3.2 9.2 - - - +
227C PHE* 2.8 51.3 + - + +
226D LYS* 4.2 22.7 - - + -
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Residues in contact with TYR 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ASP* 2.6 41.7 + - + -
435A ASN* 2.8 27.8 + - + -
219C ILE* 3.4 44.4 - - + -
220C PRO* 3.6 16.8 - - + +
221C PHE 3.4 1.2 + - - -
222C HIS 3.5 0.2 - - - -
223C PRO* 1.3 82.8 - - + +
225C TYR* 1.3 59.0 + - + +
227C PHE* 3.9 0.3 - - - +
228C LYS* 3.1 14.9 + - - +
226D LYS* 3.9 12.3 - - + -
227D TRP* 2.9 51.1 + + + +
229D VAL* 4.2 6.8 - - - +
230D LEU* 3.8 26.9 - - + +
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Residues in contact with TYR 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ALA* 3.4 33.7 - - + -
25C PRO 2.5 21.7 + - - -
26C SER 3.6 6.2 + - - -
28C ILE* 2.9 33.7 + - + +
219C ILE* 3.7 15.3 - - + -
221C PHE* 2.6 43.8 + - + +
224C TYR* 1.3 72.7 - - + +
226C SER* 1.3 64.5 + - - -
227C PHE 3.1 1.1 - - - -
228C LYS* 3.7 31.2 - - + -
229C ASP* 2.9 32.4 + - - +
2002C UQ 4.0 7.2 - - - -
227D TRP* 3.5 23.6 - + - -
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Residues in contact with SER 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2008A PEE 5.3 9.2 - - - -
19C LEU 5.4 0.4 - - - -
221C PHE* 3.1 25.5 + - - -
222C HIS* 2.8 35.3 + - - -
223C PRO* 3.0 15.1 + - - +
225C TYR* 1.3 77.6 - - - +
227C PHE* 1.3 65.3 + - - +
229C ASP* 4.0 2.7 - - - +
230C ILE* 3.2 29.6 + - - +
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Residues in contact with PHE 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2008A PEE 4.9 8.1 - - + -
222C HIS* 4.0 14.6 - + - -
223C PRO* 2.8 48.5 + - + +
224C TYR 3.9 2.0 - - - +
226C SER* 1.3 80.4 + - - +
228C LYS* 1.3 65.4 + - - +
230C ILE* 3.2 9.1 + - + +
231C LEU* 3.0 24.4 + - - +
219D LEU* 5.7 7.0 - - + +
222D MET* 4.0 41.5 - - + -
223D LYS* 4.5 15.5 - - + +
226D LYS* 4.1 25.6 - - + -
227D TRP* 5.2 2.5 - - + +
2005E PEE 3.5 32.8 - - - -
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Residues in contact with LYS 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ILE 3.7 14.4 + - - -
29C SER* 3.6 23.4 - - - +
30C ALA* 4.2 3.7 - - - +
33C ASN* 3.1 29.8 + - - +
224C TYR 3.1 16.5 + - - +
225C TYR* 3.7 29.6 - - + +
227C PHE* 1.3 79.2 - - - +
229C ASP* 1.3 59.8 + - - +
231C LEU* 3.4 4.0 + - - +
232C GLY 3.0 20.6 + - - -
223D LYS* 4.0 37.3 - - - +
227D TRP* 4.5 7.5 - - + +
2003D CDL 4.2 21.3 + - - +
72F HIS* 6.0 2.0 + - - -
2004G CDL 5.2 2.0 + - - -
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Residues in contact with ASP 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C TRP 4.9 1.0 - - - +
33C ASN* 3.5 21.2 + - - +
36C SER* 3.2 28.7 + - - +
37C LEU* 5.1 1.9 - - - +
221C PHE* 3.8 11.1 - - + -
225C TYR* 2.9 24.9 + - - +
226C SER* 4.0 3.8 - - - +
228C LYS* 1.3 79.6 - - - +
230C ILE* 1.3 55.0 + - + +
232C GLY* 2.9 1.7 + - - -
233C LEU* 2.7 34.9 + - - +
2002C UQ 3.0 27.9 - - + +
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Residues in contact with ILE 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2008A PEE 3.6 31.9 - - + -
226C SER* 3.2 17.9 + - - +
227C PHE* 3.2 8.3 + - + +
229C ASP* 1.3 77.8 - - + +
231C LEU* 1.3 63.8 + - - +
233C LEU* 3.3 13.5 + - + +
234C THR* 3.1 22.0 + - - +
219D LEU* 3.7 32.8 - - + -
2005E PEE 3.8 27.4 - - + -
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Residues in contact with LEU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C PHE 3.0 12.0 + - - +
228C LYS* 3.5 10.1 - - - +
230C ILE* 1.3 78.1 - - - +
232C GLY* 1.3 63.8 + - - +
234C THR* 2.9 26.0 + - - +
235C LEU* 2.9 33.3 + - + +
216D THR* 4.2 6.1 - - + +
219D LEU* 3.9 12.3 - - + +
220D TYR* 3.8 51.1 - - + +
223D LYS* 3.9 26.5 - - + -
2003D CDL 4.0 17.9 - - + +
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Residues in contact with GLY 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ASN* 3.6 19.7 - - - -
37C LEU* 4.3 6.7 - - - -
228C LYS 3.0 7.9 + - - -
229C ASP 2.9 7.2 + - - -
231C LEU* 1.3 78.2 - - - +
233C LEU* 1.3 60.0 + - - +
235C LEU* 3.3 2.4 + - - +
236C MET* 3.1 28.6 + - - +
2003D CDL 4.0 19.2 + - - +
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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
----------------------------------------------------------
37C LEU* 3.6 23.9 - - + +
40C VAL* 3.7 37.2 - - + -
90C PHE* 5.7 3.4 - - + -
229C ASP 2.7 16.3 + - - +
230C ILE* 3.4 16.8 - - + +
231C LEU 3.2 0.2 - - - -
232C GLY* 1.3 72.7 - - - +
234C THR* 1.3 59.4 + - - +
236C MET* 3.3 2.1 + - - +
237C LEU* 2.8 49.3 + - + +
2005E PEE 4.6 27.1 - - + -
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Residues in contact with THR 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C ILE 3.1 8.0 + - - +
231C LEU* 2.9 22.2 + - - +
233C LEU* 1.3 78.1 - - + +
235C LEU* 1.3 66.0 + - - +
237C LEU* 3.8 9.2 - - + +
238C THR* 3.1 27.7 + - - -
215D LEU* 5.1 6.5 - - + -
216D THR* 3.8 20.6 + - - -
219D LEU* 3.3 31.4 - - + +
2009D BOG 6.4 3.1 - - + -
2005E PEE 4.4 20.6 - - + -
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Residues in contact with LEU 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C LEU* 2.9 35.9 + - + +
232C GLY* 3.7 5.6 - - - +
233C LEU 3.2 0.2 - - - -
234C THR* 1.3 82.9 + - - +
236C MET* 1.3 59.7 + - + +
238C THR* 4.1 3.7 - - - +
239C PRO* 3.1 21.8 - - - +
216D THR* 3.5 30.3 - - + +
2003D CDL 4.2 62.4 - - + +
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Residues in contact with MET 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C PHE* 4.8 14.6 - - + -
37C LEU* 3.6 23.6 - - + -
90C PHE* 3.3 42.9 - - + -
93C ILE* 4.4 23.8 - - + -
94C CYS* 4.6 6.7 - - - -
97C LEU* 5.2 2.7 - - + -
232C GLY 3.1 14.7 + - - +
233C LEU 4.0 1.3 - - - +
235C LEU* 1.3 75.5 - - - +
237C LEU* 1.3 68.0 + - - +
238C THR 3.1 2.5 - - - -
239C PRO* 3.0 21.8 - - + +
240C PHE 3.4 7.8 + - - -
2003D CDL 5.2 10.3 - - + -
2004G CDL 5.5 9.4 - - + -
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Residues in contact with LEU 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C PHE* 4.2 6.5 - - + -
233C LEU* 2.8 34.9 + - + +
234C THR* 3.8 10.8 - - + +
236C MET* 1.3 78.1 - - - +
238C THR* 1.3 62.1 + - - +
240C PHE* 3.3 28.7 - - + +
241C LEU* 3.0 42.0 + - + +
2009D BOG 4.7 12.8 - - + -
2005E PEE 4.1 29.4 - - + -
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Residues in contact with THR 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C THR 3.1 15.2 + - - -
235C LEU* 4.1 3.3 - - - +
236C MET 3.0 1.2 + - - -
237C LEU* 1.3 78.8 - - - +
239C PRO* 1.3 73.5 - - + +
241C LEU* 3.9 3.5 - - - +
242C THR* 2.9 36.2 + - - +
208D MET* 4.6 2.9 - - - +
209D LEU* 4.9 8.5 - - + -
212D SER* 2.7 30.7 + - - +
216D THR* 4.1 6.4 + - - -
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Residues in contact with PRO 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C LEU 3.1 17.5 - - - +
236C MET* 3.0 25.4 - - + +
238C THR* 1.3 86.9 - - + +
240C PHE* 1.3 63.1 + - - +
242C THR* 3.3 9.0 + - + +
243C LEU* 2.9 25.6 + - - +
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Residues in contact with PHE 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C THR* 5.4 12.8 - - + -
83C LEU* 3.7 23.3 - - + -
86C ASN* 3.6 21.3 - - + -
87C GLY* 3.5 36.6 - - - -
90C PHE* 4.0 29.4 - + + -
236C MET 3.4 10.9 + - - +
237C LEU* 3.3 27.4 - - + +
239C PRO* 1.3 80.2 - - - +
241C LEU* 1.3 77.5 + - + +
243C LEU* 3.0 8.2 + - + +
244C ALA* 2.8 28.8 + - + -
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Residues in contact with LEU 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LEU* 3.9 23.3 - - + -
237C LEU* 3.0 29.9 + - + +
238C THR* 4.1 0.4 - - - +
240C PHE* 1.3 98.8 - - + +
242C THR* 1.3 53.3 + - - +
244C ALA* 4.4 2.9 - - + +
245C LEU* 2.8 45.5 + - + +
208D MET* 3.7 36.6 - - + -
2009D BOG 4.6 20.6 - - + -
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Residues in contact with THR 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C THR* 2.9 26.1 + - - +
239C PRO* 3.5 8.1 - - - +
241C LEU* 1.3 76.0 - - - +
243C LEU* 1.3 59.7 + - - +
246C PHE* 2.9 44.4 + - + +
247C SER 3.9 0.2 + - - -
208D MET* 3.5 18.7 - - - +
209D LEU* 3.9 13.4 - - + +
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Residues in contact with LEU 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ASN* 3.5 26.0 - - + +
89C SER* 6.0 0.9 - - - -
239C PRO 2.9 12.6 + - - +
240C PHE* 3.3 11.9 - - + +
242C THR* 1.3 74.9 - - - +
244C ALA* 1.3 57.7 + - - +
245C LEU 3.0 4.7 + - - -
247C SER* 2.9 58.8 + - - +
250C LEU* 3.8 27.4 - - + -
251C LEU* 3.7 23.3 - - + -
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Residues in contact with ALA 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ASN* 3.6 29.0 - - + +
83C LEU* 4.7 12.1 - - + -
86C ASN* 3.7 34.8 - - + +
240C PHE* 2.8 24.0 + - + +
241C LEU* 4.2 6.3 - - - +
243C LEU* 1.3 73.3 - - - +
245C LEU* 1.3 67.8 + - + +
248C PRO* 4.1 7.5 - - - +
201D ARG* 4.8 0.2 - - - -
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Residues in contact with LEU 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C TRP* 4.4 7.0 - - + -
79C LEU* 4.3 23.6 - - + -
83C LEU* 6.2 0.4 - - + -
241C LEU* 2.8 25.6 + - + +
242C THR 4.5 0.4 - - - +
244C ALA* 1.3 90.8 - - + +
246C PHE* 1.3 68.9 + - + +
248C PRO* 4.3 0.7 - - - -
201D ARG* 2.6 52.2 + - + +
204D MET* 4.1 16.6 - - + -
205D GLY* 3.7 34.8 - - - +
208D MET* 4.2 17.7 - - + -
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Residues in contact with PHE 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C THR* 2.9 38.2 + - + +
245C LEU* 1.3 81.3 - - - +
247C SER* 1.3 59.3 + - - +
248C PRO* 3.3 11.0 - - - +
17D PRO* 3.4 50.1 - - + +
18D LEU* 4.2 10.3 - - + -
201D ARG* 3.6 9.2 + - - +
202D LYS* 4.2 11.1 - - + -
205D GLY* 3.5 39.5 - - - -
206D LEU 4.0 0.9 - - - -
208D MET* 4.2 5.6 - - + -
209D LEU* 3.6 30.7 - - + -
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Residues in contact with SER 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ASN* 5.3 0.2 + - - -
242C THR 3.9 0.6 + - - -
243C LEU* 2.9 29.6 + - - +
246C PHE* 1.3 80.9 - - - +
248C PRO* 1.3 64.2 - - - +
249C ASN 3.1 3.2 + - - -
250C LEU* 3.1 43.1 + - - +
----------------------------------------------------------
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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