Contacts of the helix formed by residues 209 - 233 (chain A) in PDB entry 3OX4
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 THR 209 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA* 5.9 3.4 - - + -
4A SER* 3.7 32.3 - - - +
6A PHE* 5.6 0.7 - - - -
207A ALA 3.8 9.0 - - - +
208A ALA* 1.3 80.1 - - - +
210A PRO* 1.3 77.5 - - - +
211A ILE* 3.2 10.4 + - - +
212A THR* 2.9 32.4 + - + +
213A ASP* 2.9 27.9 + - - -
256A ASN 5.8 1.6 - - - +
245B TYR* 3.9 9.8 - - + +
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Residues in contact with PRO 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A THR* 1.3 89.3 - - - +
211A ILE* 1.3 59.6 + - - +
213A ASP* 3.7 6.9 - - + +
214A ALA* 3.2 19.1 + - - +
218B LYS* 3.4 20.8 - - - +
222B MET* 3.7 39.7 - - + -
245B TYR* 4.0 31.6 - - + -
249B LEU* 4.5 2.2 - - + -
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Residues in contact with ILE 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 3.6 33.2 - - + -
209A THR* 3.1 5.9 + - - +
210A PRO* 1.3 74.9 - - - +
212A THR* 1.3 65.0 + - - +
214A ALA* 3.1 4.3 + - - +
215A CYS* 3.1 25.6 + - - -
14B MET* 3.4 42.2 - - + -
245B TYR* 3.9 15.5 - - + -
248B PHE* 3.7 17.3 - - + -
249B LEU* 3.9 23.3 - - + -
252B MET* 3.9 20.4 - - + -
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Residues in contact with THR 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 4.8 5.4 - - + -
202A ALA 4.5 2.6 + - - -
208A ALA* 3.5 10.4 - - - +
209A THR* 2.9 39.2 + - + +
211A ILE* 1.3 75.7 - - - +
213A ASP* 1.3 57.9 + - - +
215A CYS* 3.3 1.9 + - - +
216A ALA* 2.8 33.1 + - - +
252A MET 4.4 2.5 - - - +
253A ALA* 3.5 36.4 - - - +
256A ASN* 3.8 22.7 - - + -
257A ALA* 3.7 11.5 - - + +
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Residues in contact with ASP 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A TYR* 3.4 23.2 + - + +
208A ALA* 3.6 12.5 - - - +
209A THR 2.9 23.5 + - - +
210A PRO* 3.7 8.9 - - + +
212A THR* 1.3 78.1 + - - +
214A ALA* 1.3 62.2 + - - +
216A ALA* 3.4 1.2 + - - +
217A LEU* 3.0 32.0 + - + +
299A ARG* 2.7 37.8 + - - -
218B LYS* 4.5 11.9 + - - +
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Residues in contact with ALA 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A PRO 3.2 11.5 + - - +
211A ILE 3.1 9.5 + - - +
213A ASP* 1.3 79.5 - - - +
215A CYS* 1.3 64.2 + - - +
217A LEU* 3.7 4.3 + - - +
218A LYS* 3.2 24.3 + - - +
214B ALA* 4.2 14.3 - - + +
215B CYS* 5.3 0.7 - - - -
218B LYS* 3.7 32.1 - - + -
249B LEU* 4.5 8.5 - - + -
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Residues in contact with CYS 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ILE* 3.1 29.2 + - - +
212A THR* 3.8 4.5 - - - +
214A ALA* 1.3 79.6 - - - +
216A ALA* 1.3 60.2 + - - +
218A LYS* 3.5 0.5 + - - +
219A ALA* 3.0 29.6 + - - +
249A LEU* 3.5 37.6 - - + +
252A MET* 3.9 37.7 - - + -
253A ALA* 4.3 3.6 - - + +
214B ALA* 5.5 1.3 - - - -
215B CYS* 5.0 7.6 - - - -
249B LEU* 6.0 0.2 - - - -
252B MET* 4.9 2.7 - - - -
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Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ALA* 3.5 33.0 - - - +
203A TYR* 4.0 18.2 - - + +
212A THR 2.8 19.4 + - - +
213A ASP 3.7 2.9 - - - +
215A CYS* 1.3 77.7 - - - +
217A LEU* 1.3 58.1 + - - +
219A ALA* 3.2 8.0 + - - +
220A ALA* 3.0 25.2 + - - +
250A ALA* 5.4 0.4 - - - +
253A ALA* 3.9 15.0 - - + +
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Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A TYR* 3.5 40.6 - - + +
213A ASP* 3.0 15.1 + - + +
214A ALA* 4.2 3.8 - - - +
216A ALA* 1.3 73.3 - - - +
218A LYS* 1.3 66.4 + - - +
220A ALA* 3.4 2.2 + - - +
221A SER* 3.0 24.0 + - - -
302A ASP* 4.0 9.9 - - + +
303A VAL* 3.7 39.9 - - + +
306A ALA* 3.6 17.3 - - + +
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Residues in contact with LYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ALA 3.2 16.6 + - - +
215A CYS* 3.9 4.3 - - - +
216A ALA 3.3 0.2 - - - -
217A LEU* 1.3 78.2 - - - +
219A ALA* 1.3 63.4 + - - +
221A SER* 3.3 11.7 + - - -
222A MET* 3.0 46.7 + - + +
249A LEU* 3.5 21.1 - - + -
210B PRO* 3.5 24.3 - - - +
213B ASP* 4.7 12.3 + - - +
214B ALA* 3.7 23.8 - - + +
217B LEU* 6.2 2.0 - - - +
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Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ALA* 4.3 4.9 - - + -
215A CYS 3.0 19.4 + - - +
216A ALA 3.5 5.2 - - - +
218A LYS* 1.3 74.3 - - - +
220A ALA* 1.3 66.4 + - - +
222A MET* 3.2 2.1 + - - +
223A ILE* 2.9 32.4 + - + +
246A ALA* 3.5 29.6 - - - +
249A LEU* 3.8 4.7 - - + +
250A ALA* 3.7 21.1 - - + +
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Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU* 4.0 21.1 - - + +
199A ALA* 4.2 7.3 - - + +
216A ALA 3.0 16.4 + - - +
217A LEU* 3.9 5.8 - - - +
219A ALA* 1.3 74.8 - - - +
221A SER* 1.3 57.3 + - - +
223A ILE* 3.8 0.9 - - - +
224A ALA* 2.8 33.1 + - - +
303A VAL* 3.8 30.1 - - + +
306A ALA* 5.0 0.4 - - + -
307A MET* 3.8 11.3 - - + +
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Residues in contact with SER 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A LEU 3.0 16.8 + - - -
218A LYS* 3.4 15.6 + - - +
220A ALA* 1.3 78.1 - - - +
222A MET* 1.3 65.4 + - - +
224A ALA* 3.2 1.2 + - - +
225A LYS* 3.0 48.2 + - - +
306A ALA* 3.2 25.2 + - - -
307A MET* 4.3 1.1 - - - +
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Residues in contact with MET 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A LYS* 3.0 27.3 + - + +
221A SER* 1.3 77.0 - - - +
223A ILE* 1.3 58.2 + - - +
225A LYS* 3.1 3.6 + - - -
226A ASN* 2.9 45.0 + - - +
242A ALA* 3.4 33.0 - - + +
243A MET* 5.1 0.2 - - - -
245A TYR* 3.7 13.9 - - + -
246A ALA* 3.8 16.4 - - + -
249A LEU* 3.7 29.6 - - - -
210B PRO* 3.7 26.0 - - + -
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Residues in contact with ILE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A GLY 4.1 5.4 - - - +
195A ALA* 3.6 17.7 - - + +
196A LEU* 3.5 49.1 - - + +
219A ALA* 2.9 30.9 + - + +
220A ALA* 3.8 3.4 - - - +
222A MET* 1.3 76.5 - - - +
224A ALA* 1.3 60.4 + - - +
227A LEU* 3.0 52.7 + - + +
243A MET* 4.0 16.6 - - + -
246A ALA* 3.8 17.5 - - + +
330A LEU* 4.8 4.1 - - + +
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Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU* 6.1 0.2 - - - -
220A ALA 2.8 19.1 + - - +
221A SER 3.4 5.4 - - - +
222A MET 3.2 0.2 - - - -
223A ILE* 1.3 78.7 - - - +
225A LYS* 1.3 61.3 + - + +
227A LEU 5.2 0.3 + - - -
228A LYS* 5.8 2.3 + - - +
307A MET* 3.5 50.4 - - + +
330A LEU* 5.4 10.2 - - - +
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Residues in contact with LYS 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A SER* 3.0 36.3 + - - +
222A MET* 3.1 3.6 + - - -
224A ALA* 1.3 82.3 - - + +
226A ASN* 1.3 73.4 + - - +
228A LYS* 5.7 0.7 - - - -
229A THR* 4.5 6.8 + - - -
306A ALA 3.3 16.0 + - - -
307A MET 4.0 12.0 + - - +
308A GLY* 4.0 7.3 - - - +
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Residues in contact with ASN 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A MET* 2.9 32.1 + - - +
223A ILE 3.3 0.4 + - - -
224A ALA 3.5 0.2 - - - -
225A LYS* 1.3 94.6 - - - +
227A LEU* 1.3 63.7 + - - +
228A LYS 3.4 2.9 - - - -
229A THR* 3.3 10.8 + - - -
230A ALA* 3.2 22.3 + - - +
238A PRO 4.4 1.2 - - - +
239A ALA* 3.8 20.8 + - - +
242A ALA* 3.4 32.8 - - + +
243A MET* 4.2 7.1 - - - +
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A THR* 3.6 28.9 - - + +
189A ALA* 4.5 0.4 - - - -
192A GLY* 3.8 32.1 - - - -
193A MET* 4.0 10.8 - - - +
223A ILE* 3.0 31.9 + - + +
226A ASN* 1.3 73.9 - - - +
228A LYS* 1.3 66.0 + - - +
230A ALA* 3.4 1.8 + - - +
231A CYS* 3.1 35.2 + - - -
243A MET* 3.9 15.5 - - + -
330A LEU* 4.3 9.9 - - + -
334A ILE* 3.8 27.6 - - + -
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Residues in contact with LYS 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ILE 4.9 0.2 + - - -
224A ALA 5.8 2.4 + - - +
225A LYS 6.5 0.4 - - - -
226A ASN 3.4 0.8 - - - +
227A LEU* 1.3 76.9 - - - +
229A THR* 1.3 59.9 + - - +
231A CYS* 3.2 2.6 + - - +
232A ASP* 2.9 62.6 + - - +
330A LEU* 4.8 11.2 - - + +
333A SER* 2.7 49.1 + - - +
334A ILE* 4.0 13.0 - - + -
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Residues in contact with THR 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A LYS 4.5 9.7 + - - -
226A ASN* 3.3 11.3 + - - -
227A LEU 3.3 0.4 - - - -
228A LYS* 1.3 80.6 - - - +
230A ALA* 1.3 58.6 + - - +
232A ASP* 3.2 5.2 + - - +
233A ASN* 2.8 32.3 + - + +
236A ASP* 3.7 32.8 - - + +
239A ALA* 3.7 7.2 - - + -
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Residues in contact with ALA 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LYS* 5.7 0.5 - - - -
188A THR* 3.9 24.2 - - + +
226A ASN 3.2 12.8 + - - +
227A LEU* 3.9 3.4 - - - +
228A LYS 3.4 0.2 - - - -
229A THR* 1.3 78.5 - - - +
231A CYS* 1.3 59.6 + - - +
233A ASN 4.0 7.0 - - - -
234A GLY* 3.3 23.2 + - - -
239A ALA* 3.9 10.9 - - + +
240A ARG* 4.1 22.0 + - - +
243A MET* 4.4 13.2 - - + -
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Residues in contact with CYS 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LYS* 3.2 44.1 + - - +
188A THR* 3.8 9.9 - - - -
189A ALA* 3.7 42.0 - - - -
227A LEU* 3.1 24.3 + - - +
228A LYS 3.5 7.9 - - - +
229A THR 3.1 0.4 - - - -
230A ALA* 1.3 79.1 - - - +
232A ASP* 1.3 62.4 + - - +
233A ASN 3.6 0.5 + - - -
234A GLY 4.8 1.0 + - - -
334A ILE* 3.8 16.2 - - + -
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Residues in contact with ASP 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LYS* 4.2 10.7 + - - -
228A LYS* 2.9 56.8 + - - +
229A THR* 4.1 3.7 - - - +
231A CYS* 1.3 79.6 - - - +
233A ASN* 1.3 62.9 + - + +
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Residues in contact with ASN 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A THR* 2.8 14.6 + - + +
230A ALA* 3.6 5.5 - - - +
231A CYS 3.3 0.6 - - - -
232A ASP* 1.3 83.6 - - + +
234A GLY* 1.3 59.0 + - - +
235A LYS* 2.8 32.7 + - - +
236A ASP* 2.8 42.3 + - + +
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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
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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