Contacts of the helix formed by residues 232 - 255 (chain C) in PDB entry 5Y1Z
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 HIS 232 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228C ASN* 3.3 42.7 + - + +
229C GLY 3.1 10.7 + - - +
230C GLY 3.3 0.8 - - - +
231C ASN* 1.3 80.7 - - - +
233C LYS* 1.3 83.1 + - + +
234C LEU* 2.9 40.5 + - + +
235C THR* 3.3 11.0 + - - +
236C GLN* 3.2 22.7 + - - +
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Residues in contact with LYS 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASP* 4.9 10.3 - - + +
201A SO4 3.0 28.9 - - - +
231C ASN 3.9 0.8 + - - -
232C HIS* 1.3 82.1 + - + +
234C LEU* 1.3 62.8 + - + +
236C GLN* 2.8 39.0 + - - +
237C ILE* 3.1 16.1 + - + +
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Residues in contact with LEU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C ALA* 3.9 26.9 - - + -
173C PHE* 3.3 15.9 - - + -
224C CYS* 3.6 15.0 - - - -
228C ASN* 3.6 19.5 - - - +
232C HIS* 2.9 29.5 + - + +
233C LYS* 1.3 75.6 - - + +
235C THR* 1.3 59.8 + - - +
237C ILE* 2.9 11.1 + - + +
238C ALA 2.8 24.6 + - - -
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Residues in contact with THR 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C LEU* 4.2 5.6 - - + -
224C CYS* 3.3 26.8 + - - -
225C ILE* 3.7 24.5 - - + -
229C GLY 2.8 21.2 + - - -
230C GLY* 3.3 20.2 - - - +
232C HIS* 3.3 14.4 + - - +
233C LYS 3.2 0.6 - - - -
234C LEU* 1.3 78.9 - - - +
236C GLN* 1.3 56.0 + - + +
238C ALA* 3.3 2.7 + - - +
239C LYS* 2.9 39.7 + - - +
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Residues in contact with GLN 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PRO* 5.2 8.9 - - - +
93A ALA* 3.6 29.7 - - + +
201A SO4 5.8 1.0 + - - -
230C GLY 5.8 1.6 - - - +
231C ASN 4.4 6.2 - - - +
232C HIS 3.2 9.8 + - - +
233C LYS* 2.8 33.8 + - - +
235C THR* 1.3 76.2 - - - +
237C ILE* 1.3 60.8 + - - +
239C LYS* 3.3 17.4 + - + +
240C VAL* 3.1 24.1 + - - +
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Residues in contact with ILE 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ASP* 4.1 8.3 - - + +
93A ALA* 3.7 30.1 - - - +
96A CYS* 3.9 16.8 - - + -
169C GLY* 3.6 25.8 - - - +
170C THR* 3.9 19.7 - - + -
173C PHE* 3.6 19.1 - - + -
233C LYS 3.1 11.9 + - - +
234C LEU* 2.9 15.1 + - + +
236C GLN* 1.3 76.4 - - - +
238C ALA* 1.3 57.1 + - - +
240C VAL* 2.8 21.0 + - - +
241C VAL* 3.0 12.0 + - - +
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Residues in contact with ALA 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C PHE* 3.7 22.4 - - + -
220C ILE* 4.7 3.4 - - + -
221C LEU* 3.8 31.3 - - + +
224C CYS* 4.2 6.1 - - + -
234C LEU 2.8 14.7 + - - +
235C THR 3.3 4.7 + - - +
237C ILE* 1.3 75.6 - - - +
239C LYS* 1.3 58.2 + - - +
241C VAL* 3.4 10.1 + - - +
242C ILE* 3.0 31.5 + - - +
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Residues in contact with LYS 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C LEU* 4.1 24.5 - - + -
225C ILE* 5.5 5.1 - - - +
230C GLY* 3.7 22.8 + - - -
231C ASN* 5.6 0.6 + - - -
235C THR* 2.9 24.9 + - - +
236C GLN* 3.4 18.7 - - + +
237C ILE 3.1 0.2 - - - -
238C ALA* 1.3 75.1 - - - +
240C VAL* 1.3 66.4 + - + +
242C ILE* 3.4 2.5 + - - +
243C LYS* 3.0 40.6 + - - +
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Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ALA* 3.6 25.8 - - + +
96A CYS* 4.1 13.7 - - + -
97A ALA* 3.5 35.4 - - + +
236C GLN 3.1 15.1 + - - +
237C ILE* 2.8 18.0 + - - +
239C LYS* 1.3 72.7 - - + +
241C VAL* 1.3 57.7 + - + +
243C LYS* 3.0 7.8 + - + +
244C ILE* 2.9 42.2 + - + +
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Residues in contact with VAL 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A CYS* 5.4 0.2 - - - -
165C MET* 3.8 30.6 - - + +
170C THR* 3.6 33.0 - - + -
173C PHE* 4.8 5.6 - - + -
195C LEU* 4.7 12.1 - - + -
220C ILE* 4.8 9.6 - - + -
237C ILE* 3.0 16.8 + - + +
238C ALA* 3.6 10.5 - - - +
240C VAL* 1.3 77.8 - - + +
242C ILE* 1.3 83.2 + - + +
244C ILE* 3.9 10.1 - - + +
245C CYS* 2.9 23.6 + - - +
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Residues in contact with ILE 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C MET* 5.1 0.9 - - + -
214C LEU* 4.1 3.7 - - + +
217C ALA* 3.5 31.2 - - + +
218C LYS* 3.9 33.0 - - + +
220C ILE* 4.4 2.5 - - + -
221C LEU* 4.1 30.1 - - + +
238C ALA 3.0 18.0 + - - +
239C LYS 4.1 2.7 - - - +
241C VAL* 1.3 96.8 - - + +
243C LYS* 1.3 60.8 + - - +
245C CYS* 3.3 4.4 + - - +
246C GLU* 2.9 45.2 + - - +
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Residues in contact with LYS 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.6 39.6 + - + +
239C LYS* 3.0 31.8 + - - +
240C VAL* 3.5 6.5 - - + +
242C ILE* 1.3 78.2 - - - +
244C ILE* 1.3 66.7 + - + +
246C GLU* 3.4 18.4 + - - +
247C HIS* 3.0 23.4 + - - +
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Residues in contact with ILE 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A SER* 3.9 22.0 - - - +
164C LYS* 3.6 28.5 - - + +
165C MET* 3.9 11.4 - - + +
167C GLN* 3.8 29.2 - - + -
240C VAL* 2.9 36.9 + - + +
241C VAL* 3.9 7.9 - - + +
243C LYS* 1.3 75.1 - - + +
245C CYS* 1.3 65.0 + - - +
247C HIS* 3.1 8.0 + - - +
248C GLU* 2.9 34.9 + - + +
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Residues in contact with CYS 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C MET* 3.6 22.6 - - + +
213C PHE* 3.7 36.3 - - - -
214C LEU* 3.9 15.7 - - + -
217C ALA* 3.9 13.5 - - + -
241C VAL 2.9 17.7 + - - +
242C ILE* 3.4 7.4 - - - +
244C ILE* 1.3 77.5 - - - +
246C GLU* 1.3 63.8 + - - +
248C GLU* 3.2 5.4 + - - -
249C MET* 2.9 30.2 + - - +
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Residues in contact with GLU 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET 4.6 7.1 + - - +
214C LEU* 3.7 29.1 - - + +
218C LYS* 3.9 14.6 + - - -
242C ILE* 2.9 31.2 + - - +
243C LYS* 3.6 26.5 - - - +
245C CYS* 1.3 72.7 - - - +
247C HIS* 1.3 64.2 + - - +
249C MET* 3.2 5.8 + - - +
250C ASN* 3.0 23.4 + - - +
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Residues in contact with HIS 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET 3.1 31.1 - - - +
2A ALA* 3.6 20.0 + - - -
3A GLY* 5.4 0.6 - - - -
104A LYS* 4.2 13.4 + - + -
243C LYS 3.0 14.3 + - - +
244C ILE* 3.1 11.9 + - - +
246C GLU* 1.3 74.8 - - - +
248C GLU* 1.3 89.8 + - - +
250C ASN* 3.2 8.7 + - + +
251C GLU* 3.0 47.4 + - + +
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Residues in contact with GLU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C ALA* 3.9 17.9 - - + +
164C LYS* 3.0 35.6 - - + +
244C ILE* 2.9 31.2 + - + +
245C CYS* 3.9 3.6 - - - +
247C HIS* 1.3 98.9 + - - +
249C MET* 1.3 69.9 + - + +
251C GLU* 3.1 6.0 + - - +
252C ILE* 2.9 26.7 + - - +
259C TYR* 2.7 39.7 + - - +
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Residues in contact with MET 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C LEU* 3.8 14.1 - - + -
161C ALA* 3.7 27.1 - - + -
210C THR* 3.7 44.3 + - - +
213C PHE* 3.6 28.3 - - + -
214C LEU* 4.1 17.0 - - + -
245C CYS* 2.9 25.2 + - - +
246C GLU* 3.5 7.4 - - - +
248C GLU* 1.3 77.4 - - - +
250C ASN* 1.3 61.7 + - - +
252C ILE* 3.3 7.8 + - + +
253C GLU* 3.0 29.6 + - - +
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Residues in contact with ASN 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C GLU 3.0 13.4 + - - +
247C HIS* 3.5 11.4 - - + +
249C MET* 1.3 77.8 - - - +
251C GLU* 1.3 61.1 + - - +
253C GLU* 3.1 9.1 + - - +
254C VAL* 2.8 34.2 + - - +
297C ARG* 4.0 25.0 + - - +
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Residues in contact with GLU 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LYS* 6.2 0.3 - - - -
247C HIS* 3.0 45.8 + - + +
248C GLU* 3.1 8.9 + - - +
250C ASN* 1.3 78.5 - - - +
252C ILE* 1.3 63.9 + - - +
254C VAL* 3.1 20.8 + - - +
255C CYS 3.2 15.8 + - - +
259C TYR* 3.6 23.9 - - + +
306C ARG* 3.9 27.1 + - - -
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Residues in contact with ILE 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ALA* 3.7 3.3 - - + +
146C MET* 6.1 0.4 - - - -
149C LEU* 4.7 6.1 - - + -
154C LEU* 4.4 7.4 - - + -
157C LEU* 3.8 37.5 - - + +
158C LEU* 4.4 7.2 - - + -
161C ALA* 4.8 0.2 - - + -
210C THR* 3.9 17.9 - - + -
248C GLU 2.9 16.9 + - - +
249C MET* 3.6 26.9 - - + +
251C GLU* 1.3 75.0 - - - +
253C GLU* 1.3 62.5 + - - +
255C CYS 4.6 0.2 - - - -
256C PRO* 3.1 28.6 - - + +
259C TYR* 3.5 45.1 - - + +
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Residues in contact with GLU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C SER* 2.7 35.8 + - - -
144C LYS* 5.9 0.9 - - - +
145C ALA* 3.4 24.0 + - - +
146C MET* 4.3 6.6 - - - +
210C THR* 2.8 36.7 + - + +
211C GLU* 4.2 11.0 - - - +
249C MET 3.0 21.3 + - - +
250C ASN* 3.1 9.8 + - - +
252C ILE* 1.3 76.0 - - - +
254C VAL* 1.3 64.6 + - - +
255C CYS 3.6 0.2 + - - -
256C PRO* 4.8 0.2 - - - +
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Residues in contact with VAL 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C ASN* 2.8 24.7 + - - +
251C GLU* 3.1 15.2 + - - +
253C GLU* 1.3 78.9 - - - +
255C CYS* 1.3 65.4 + - + +
256C PRO* 4.8 0.5 - - - +
278C HIS* 5.3 2.1 - - - -
296C LEU* 4.2 34.3 - - + +
297C ARG* 3.5 43.5 - - - +
304C ASP* 4.6 1.3 - - - +
306C ARG* 4.3 16.6 - - - +
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Residues in contact with CYS 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C MET* 5.8 1.6 - - - -
251C GLU 3.2 4.5 + - - +
252C ILE 3.4 3.1 - - - -
253C GLU 3.4 0.4 - - - -
254C VAL* 1.3 87.7 - - + +
256C PRO* 1.3 74.0 - - - +
257C GLU* 3.5 12.6 - - - -
258C CYS* 3.3 19.5 - - + +
259C TYR* 3.0 21.7 + - - +
274C CYS* 3.9 7.2 - - - -
278C HIS* 3.7 12.6 - - + -
296C LEU* 5.1 0.2 - - + -
306C ARG* 5.0 0.4 - - - +
502C ZN 2.3 36.1 - - - -
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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) + - + + + + + -
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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