Contacts of the helix formed by residues 211 - 251 (chain A) in PDB entry 1LJ2
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 ASN 211 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A HIS* 4.1 16.2 + - - +
208A SER* 2.9 27.5 + - - +
210A GLN* 1.3 75.2 - - - +
212A VAL* 1.3 62.7 + - - +
213A ILE 3.1 1.3 - - - -
214A PRO* 3.4 20.9 - - - +
215A GLN* 3.0 43.6 + - - +
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A HIS 5.6 1.3 - - - +
208A SER 4.0 8.1 - - - +
209A LEU* 3.0 29.5 + - + +
211A ASN* 1.3 78.4 - - - +
213A ILE* 1.3 61.7 + - - +
215A GLN* 3.4 14.7 + - + +
216A GLN* 3.1 40.0 + - + +
213B ILE* 4.1 19.1 - - + -
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Residues in contact with ILE 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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210A GLN* 3.5 7.2 - - + +
212A VAL* 1.3 78.0 - - - +
214A PRO* 1.3 71.4 - - + +
216A GLN* 3.2 2.9 + - - -
217A GLN* 3.0 45.6 + - - +
207B HIS 5.2 1.1 - - - +
209B LEU* 3.4 31.9 - - + -
212B VAL* 4.1 27.6 - - + -
213B ILE* 3.9 22.0 - - + -
216B GLN* 3.4 17.0 - - - +
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Residues in contact with PRO 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 GLN 3.1 20.9 - - - +
211A ASN* 3.4 22.9 - - - +
213A ILE* 1.3 92.1 - - + +
215A GLN* 1.3 61.0 + - + +
217A GLN* 3.7 13.8 + - - +
218A ALA* 3.1 23.4 + - - +
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Residues in contact with GLN 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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207A HIS* 5.6 6.1 + - - +
211A ASN* 3.0 44.0 + - - +
212A VAL* 3.4 16.0 + - + +
213A ILE 3.2 1.0 - - - -
214A PRO* 1.3 77.3 - - + +
216A GLN* 1.3 65.9 + - + +
218A ALA* 3.4 7.3 + - - +
219A HIS* 3.1 20.1 + - - +
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Residues in contact with GLN 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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212A VAL* 3.1 27.7 + - + +
213A ILE* 3.2 1.6 + - - +
215A GLN* 1.3 73.9 - - + +
217A GLN* 1.3 59.3 + - - +
219A HIS* 2.6 26.2 + - - +
220A ILE* 2.7 16.1 + - - +
213B ILE* 3.2 44.1 + - - +
216B GLN* 2.9 37.0 - - + +
217B GLN* 3.7 20.8 + - - +
220B ILE* 4.1 18.3 - - + +
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Residues in contact with GLN 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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213A ILE* 3.0 28.7 - - - +
214A PRO* 3.9 12.0 - - - +
216A GLN* 1.3 75.8 - - - +
218A ALA* 1.3 63.1 + - - +
220A ILE* 3.0 13.8 + - - +
221A ALA* 2.9 25.0 + - - +
212B VAL* 5.7 0.6 - - - +
216B GLN* 3.3 26.2 + - - +
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Residues in contact with ALA 218 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A PRO 3.1 13.0 + - - +
215A GLN* 3.5 11.2 - - - +
216A GLN 3.1 0.4 - - - -
217A GLN* 1.3 78.3 - - - +
219A HIS* 1.3 60.0 + - - +
221A ALA* 3.6 7.0 + - - +
222A GLU* 2.9 32.0 + - + +
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Residues in contact with HIS 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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215A GLN 3.1 11.4 + - - +
216A GLN* 2.6 18.5 + - - +
218A ALA* 1.3 71.5 - - - +
220A ILE* 1.3 62.5 + - - -
222A GLU* 3.3 22.0 + - + +
223A LEU* 3.2 40.1 + - + +
220B ILE* 3.8 30.3 - - + +
224B GLN* 4.2 12.1 + - - -
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Residues in contact with ILE 220 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A GLN 2.7 16.7 + - - +
217A GLN* 3.0 16.1 + - + +
219A HIS* 1.3 72.3 - - - +
221A ALA* 1.3 65.0 + - - +
222A GLU 3.2 0.3 + - - -
223A LEU 3.2 2.9 + - - -
224A GLN* 3.0 45.4 + - - +
216B GLN* 4.2 30.7 - - + +
219B HIS* 3.6 38.1 - - + +
220B ILE* 3.5 22.0 - - + -
223B LEU* 3.6 14.5 - - + +
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Residues in contact with ALA 221 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A GLN 2.9 14.3 + - - +
218A ALA* 3.7 8.3 - - - +
220A ILE* 1.3 76.7 - - - +
222A GLU* 1.3 53.3 + - + +
224A GLN* 3.0 16.2 + - - +
225A VAL* 2.7 44.2 + - + +
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Residues in contact with GLU 222 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ALA* 2.9 23.7 - - - +
219A HIS* 3.4 28.9 - - + +
220A ILE 3.2 0.4 - - - -
221A ALA* 1.3 76.8 - - + +
223A LEU* 1.3 66.2 + - + +
224A GLN 2.9 0.9 + - - -
225A VAL* 2.9 6.8 + - - +
226A TYR* 2.8 28.9 + - - +
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Residues in contact with LEU 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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219A HIS* 3.2 24.2 + - + +
220A ILE 3.7 0.9 - - - +
222A GLU* 1.3 80.2 - - + +
224A GLN* 1.3 56.7 + - - +
226A TYR* 4.5 7.4 - - + -
227A ASN* 2.9 28.8 + - - +
220B ILE* 3.6 17.7 - - + +
223B LEU* 3.4 43.5 - - + +
224B GLN* 3.5 31.2 - - + +
227B ASN* 3.5 21.6 + - + +
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Residues in contact with GLN 224 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ILE* 3.0 34.0 + - - +
221A ALA* 3.3 14.5 - - - +
222A GLU 2.9 1.4 - - - -
223A LEU* 1.3 75.9 - - - +
225A VAL* 1.3 61.1 + - + +
227A ASN* 3.3 10.2 + - - +
228A ASN* 2.8 41.4 + - - +
219B HIS* 4.2 14.3 + - - -
223B LEU* 4.0 16.7 - - + +
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Residues in contact with VAL 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ALA* 2.7 28.4 + - + +
222A GLU* 3.6 6.1 - - - +
224A GLN* 1.3 70.9 - - + +
226A TYR* 1.3 58.7 + - - +
228A ASN* 2.7 11.0 + - + +
229A LYS* 2.6 43.0 + - + +
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Residues in contact with TYR 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A GLU 2.8 19.7 + - - +
223A LEU* 4.2 6.1 - - + +
225A VAL* 1.3 75.8 - - - +
227A ASN* 1.3 58.9 + - - +
229A LYS* 3.4 18.2 + - + +
230A LEU* 2.9 40.9 + - + +
227B ASN* 3.7 29.4 - - + -
231B GLU* 3.7 16.5 + - - -
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Residues in contact with ASN 227 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A LEU 2.9 20.5 + - - +
224A GLN* 3.6 11.8 + - - +
225A VAL 3.0 0.6 - - - -
226A TYR* 1.3 82.1 - - - +
228A ASN* 1.3 66.5 + - - +
230A LEU* 3.7 4.8 + - - +
231A GLU* 3.6 22.7 + - - +
223B LEU* 5.2 7.2 - - + +
226B TYR* 3.4 37.7 + - + -
227B ASN* 3.5 20.4 - - - +
230B LEU* 3.8 9.1 - - - +
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Residues in contact with ASN 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLN* 2.8 29.9 + - - +
225A VAL* 2.7 13.1 + - - +
227A ASN* 1.3 78.8 + - - +
229A LYS* 1.3 64.7 + - - +
231A GLU* 3.5 6.9 + - - +
232A ARG* 3.1 21.3 + - - +
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Residues in contact with LYS 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 VAL* 2.6 26.9 + - + +
226A TYR* 3.6 19.7 - - + +
228A ASN* 1.3 71.2 - - - +
230A LEU* 1.3 68.4 + - - +
232A ARG* 2.8 19.1 + - - +
233A ASP* 2.9 39.7 + - - +
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Residues in contact with LEU 230 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A TYR* 2.9 32.7 + - + +
227A ASN 3.8 4.7 - - - +
229A LYS* 1.3 79.3 - - - +
231A GLU* 1.3 90.3 + - + +
233A ASP* 3.6 6.5 + - - +
234A LEU* 3.2 40.0 + - + +
227B ASN* 4.7 7.6 - - - +
230B LEU* 4.4 14.1 - - + -
231B GLU* 3.1 38.6 - - + +
234B LEU* 4.8 7.4 - - + -
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Residues in contact with GLU 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ASN* 3.6 18.6 + - - +
228A ASN* 3.5 9.3 + - - +
229A LYS 3.1 0.6 - - - -
230A LEU* 1.3 95.2 - - + +
232A ARG* 1.3 67.2 + - - +
234A LEU* 3.4 10.9 + - - +
235A GLN* 3.0 36.7 + - - +
272A ILE 4.9 1.9 - - - +
274A PRO* 3.9 22.1 - - - +
226B TYR* 5.9 1.6 - - - +
230B LEU* 4.0 17.7 - - + +
234B LEU* 5.5 1.0 - - - +
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Residues in contact with ARG 232 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ASN 3.1 13.9 + - - +
229A LYS* 2.8 17.6 + - - +
231A GLU* 1.3 71.9 - - - +
233A ASP* 1.3 59.8 + - - +
235A GLN* 3.3 13.8 + - - +
236A ASN* 2.9 42.0 + - - +
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Residues in contact with ASP 233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A LYS* 2.9 51.0 + - - +
230A LEU* 3.9 6.2 + - - +
232A ARG* 1.3 79.6 - - - +
234A LEU* 1.3 58.7 + - - +
236A ASN* 3.4 7.7 + - - +
237A LYS* 2.9 30.7 + - - +
275B LEU* 3.8 24.3 - - + +
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Residues in contact with LEU 234 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A LEU* 3.2 30.1 + - + +
231A GLU* 3.7 11.0 - - - +
232A ARG 3.2 0.2 - - - -
233A ASP* 1.3 77.8 - - - +
235A GLN* 1.3 56.4 + - - +
237A LYS* 3.2 1.7 + - - +
238A ILE* 2.9 36.8 + - - +
274A PRO* 3.8 27.6 - - + -
234B LEU* 3.6 26.5 - - + -
274B PRO* 4.1 17.5 - - + -
275B LEU* 3.6 23.8 - - + -
278B PHE* 3.8 21.8 - - + -
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Residues in contact with GLN 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A GLU* 3.0 25.0 + - + +
232A ARG* 3.7 11.6 - - - +
234A LEU* 1.3 76.8 - - - +
236A ASN* 1.3 63.0 + - - +
238A ILE* 3.5 5.7 + - - +
239A GLY* 3.1 19.8 + - - -
271A ALA* 3.6 18.8 - - - +
272A ILE* 3.1 49.1 + - - +
274A PRO* 5.0 3.4 - - + -
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Residues in contact with ASN 236 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ARG* 2.9 31.0 + - - +
233A ASP* 3.9 7.3 + - - +
235A GLN* 1.3 76.8 - - - +
237A LYS* 1.3 56.2 + - - +
239A GLY* 3.4 1.6 + - - +
240A SER* 2.8 37.2 + - - -
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Residues in contact with LYS 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ASP 2.9 17.7 + - - +
234A LEU* 3.5 4.5 - - - +
236A ASN* 1.3 74.0 - - - +
238A ILE* 1.3 68.1 + - - +
240A SER* 2.8 27.2 + - - -
241A LEU* 2.9 12.8 + - + +
275B LEU* 3.3 41.5 + - + +
276B HIS* 6.0 0.2 + - - -
278B PHE* 3.6 23.3 - - + -
279B ASP* 2.7 33.8 + - - +
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Residues in contact with ILE 238 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LEU 2.9 26.4 + - - +
235A GLN* 3.7 9.0 - - - +
237A LYS* 1.3 76.3 - - - +
239A GLY* 1.3 63.2 + - - +
241A LEU* 3.2 13.2 + - + +
242A THR* 2.7 31.4 + - - +
269A ILE* 3.8 19.7 - - + -
270A ASP 3.8 19.1 - - - +
271A ALA* 4.4 12.1 - - + +
274A PRO* 3.9 19.1 - - + -
277A ALA* 3.3 24.5 - - + -
281A LEU* 5.8 1.6 - - + -
278B PHE* 3.8 22.4 - - + -
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Residues in contact with GLY 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A GLN 3.1 12.7 + - - -
236A ASN* 3.8 3.6 - - - -
238A ILE* 1.3 80.7 - - - +
240A SER* 1.3 60.5 + - - +
242A THR* 3.3 7.2 + - - -
243A SER* 3.1 28.3 + - - -
271A ALA* 5.5 7.1 - - - +
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Residues in contact with SER 240 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ASN 2.8 19.2 + - - -
237A LYS* 2.8 28.3 + - - -
239A GLY* 1.3 73.9 - - - +
241A LEU* 1.3 58.1 + - - +
243A SER* 3.5 5.2 + - - +
244A SER* 2.9 28.4 + - - -
279B ASP* 5.4 0.2 + - - -
282B GLU* 5.3 0.5 + - - -
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Residues in contact with LEU 241 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A LYS* 2.9 17.2 + - + +
238A ILE* 3.4 15.5 - - + +
240A SER* 1.3 77.9 + - - +
242A THR* 1.3 65.6 + - - +
244A SER* 3.8 2.7 - - - -
245A ILE* 2.9 53.5 + - + +
269A ILE* 5.2 0.9 - - + -
281A LEU* 4.4 21.1 - - + -
278B PHE* 3.2 53.6 - - + +
279B ASP* 4.8 1.8 - - - +
282B GLU* 3.0 32.5 - - + +
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Residues in contact with THR 242 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ILE* 2.7 33.1 + - - +
239A GLY* 3.5 8.9 - - - -
240A SER 3.2 0.2 - - - -
241A LEU* 1.3 81.6 - - - +
243A SER* 1.3 65.1 + - - +
245A ILE* 3.9 1.5 - - - +
246A GLU* 3.1 42.1 + - - +
266A ILE* 3.5 28.3 - - + +
267A ASN* 4.3 5.4 - - + -
269A ILE* 4.3 14.2 - - + +
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Residues in contact with SER 243 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLY 3.1 14.0 + - - -
240A SER* 3.9 4.7 - - - -
242A THR* 1.3 78.8 - - - +
244A SER* 1.3 68.1 + - - +
246A GLU* 3.1 9.4 + - - +
247A TRP* 3.1 36.8 + - - +
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Residues in contact with SER 244 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A SER 2.9 20.6 + - - -
241A LEU* 3.8 9.2 - - - -
242A THR 3.3 0.2 - - - -
243A SER* 1.3 78.4 - - - +
245A ILE* 1.3 62.9 + - - +
247A TRP* 3.1 6.9 + - - +
248A TYR* 3.1 20.3 + - - +
282B GLU* 3.5 19.4 + - - -
286B ARG* 4.5 7.3 + - - -
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Residues in contact with ILE 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A LEU* 2.9 40.6 + - + +
242A THR* 3.9 4.3 - - - +
244A SER* 1.3 75.1 + - - +
246A GLU* 1.3 59.0 + - - +
248A TYR* 3.0 8.7 + - + +
249A LEU* 2.8 28.9 + - + +
262A ILE* 5.8 0.4 - - + -
266A ILE* 4.3 22.7 - - + -
281A LEU* 5.4 0.2 - - + -
282B GLU* 3.8 20.9 - - + -
285B ILE* 4.0 35.0 - - + -
286B ARG* 4.3 11.7 - - + -
289B ILE* 4.1 24.9 - - + -
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Residues in contact with GLU 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A THR* 3.1 25.8 + - - +
243A SER* 3.1 9.1 + - - +
245A ILE* 1.3 79.8 - - - +
247A TRP* 1.3 64.9 + - + +
249A LEU* 3.6 8.3 + - + +
250A ARG* 3.2 29.1 + - - +
263A GLU* 3.3 35.1 - - + +
266A ILE* 3.3 32.0 - - + +
267A ASN* 3.4 23.4 + - - +
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Residues in contact with TRP 247 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A SER* 3.1 36.3 + - - +
244A SER* 3.7 7.4 - - - +
246A GLU* 1.3 78.3 - - + +
248A TYR* 1.3 66.2 + - - +
250A ARG* 3.3 51.3 + - + +
251A SER* 3.5 12.5 + - - -
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Residues in contact with TYR 248 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A SER 3.1 11.7 + - - +
245A ILE* 3.0 12.7 + - - +
247A TRP* 1.3 76.1 - - - +
249A LEU* 1.3 63.3 + - - +
251A SER* 2.7 29.0 + - - -
252A MET* 3.7 30.5 - - + +
286B ARG* 3.3 71.0 + - + +
289B ILE* 4.3 16.4 - - + -
290B SER* 3.5 22.7 + - - -
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Residues in contact with LEU 249 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ILE* 2.8 14.9 + - + +
246A GLU* 3.7 6.7 - - + +
248A TYR* 1.3 79.2 - - - +
250A ARG* 1.3 60.2 + - - +
252A MET* 3.3 11.1 + - - +
254A LEU* 4.0 13.7 - - + -
259A LYS* 3.1 59.1 - - + +
262A ILE* 3.6 31.9 - - + -
263A GLU* 3.8 19.1 - - + +
266A ILE* 5.9 0.9 - - + -
289B ILE* 3.9 31.6 - - + -
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Residues in contact with ARG 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU* 3.2 16.4 + - - +
247A TRP* 3.3 46.5 + - + +
248A TYR 3.2 0.8 - - - -
249A LEU* 1.3 76.8 - - + +
251A SER* 1.3 56.6 - - - +
252A MET 3.1 3.3 - - - +
259A LYS* 2.9 27.4 + - + +
263A GLU* 3.2 37.1 + - - +
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Residues in contact with SER 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A TRP 3.5 8.1 + - - -
248A TYR* 2.7 27.7 + - - -
250A ARG* 1.3 78.0 - - - +
252A MET* 1.3 73.6 + - - +
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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