Contacts of the helix formed by residues 201 - 247 (chain A) in PDB entry 6W4E
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 LEU 201 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LYS* 1.3 63.7 + - - +
203A LEU* 3.3 4.1 - - - +
204A LEU* 3.2 30.7 + - + +
205A ASP* 2.8 33.7 + - + +
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Residues in contact with LYS 202 (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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201A LEU* 1.3 78.3 - - - +
203A LEU* 1.3 67.4 + - + +
205A ASP* 4.7 3.1 - - - -
206A ASN* 2.8 67.5 + - - +
420A PCW 5.7 10.5 - - + -
569D LEU* 3.8 15.2 - - - +
573D LEU* 4.8 18.8 - - - +
576D VAL* 6.4 2.2 - - + -
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Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 3.3 1.4 - - - +
202A LYS* 1.3 85.6 - - + +
204A LEU* 1.3 62.4 + - + +
206A ASN* 4.0 4.1 - - + +
207A TRP* 3.0 30.3 + - - +
420A PCW 4.3 24.5 - - + -
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Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 3.2 34.1 + - + +
203A LEU* 1.3 79.0 - - + +
205A ASP* 1.3 59.9 + - - +
207A TRP* 3.4 18.3 + - + +
208A ASP* 3.0 27.1 + - - +
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Residues in contact with ASP 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 2.8 18.3 + - + +
202A LYS* 4.0 3.5 - - - +
204A LEU* 1.3 73.2 - - - +
206A ASN* 1.3 88.5 + - - +
208A ASP* 3.1 23.8 + - - +
209A SER* 3.3 13.4 + - - -
568D ASP* 4.2 22.5 - - - +
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Residues in contact with ASN 206 (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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202A LYS* 2.8 56.5 + - + +
203A LEU* 4.1 5.6 - - + +
205A ASP* 1.3 92.5 + - - +
207A TRP* 1.3 60.9 + - - +
209A SER* 3.5 9.1 + - - -
210A VAL* 3.2 25.1 + - - +
420A PCW 5.7 4.1 - - + +
569D LEU* 3.8 18.7 - - - +
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Residues in contact with TRP 207 (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 LEU 3.0 21.3 + - - +
204A LEU* 3.6 17.7 - - + +
205A ASP 3.2 0.2 - - - -
206A ASN* 1.3 74.9 - - - +
208A ASP* 1.3 64.4 + - + +
210A VAL* 3.1 14.7 + - + +
211A THR* 2.7 66.7 + - + -
214A PHE* 6.0 4.2 - + - -
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Residues in contact with ASP 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU 3.0 13.5 + - - +
205A ASP* 3.2 15.6 - - - +
207A TRP* 1.3 85.3 - - + +
209A SER* 1.3 61.1 + - - +
211A THR* 3.2 10.0 + - - -
212A SER* 2.9 27.1 + - - -
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Residues in contact with SER 209 (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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205A ASP* 3.3 15.0 + - - -
206A ASN* 3.7 9.6 - - - -
207A TRP 3.2 0.4 - - - -
208A ASP* 1.3 80.1 + - - +
210A VAL* 1.3 54.8 + - - +
212A SER* 2.9 17.8 + - - -
213A THR* 2.7 24.9 + - - -
561D LYS* 3.9 15.1 - - - +
565D ALA* 5.2 13.3 - - - +
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Residues in contact with VAL 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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206A ASN 3.2 18.2 - - - +
207A TRP* 3.1 16.9 + - + +
209A SER* 1.3 75.6 - - - +
211A THR* 1.3 64.8 + - - +
213A THR* 3.0 12.5 + - - -
214A PHE* 3.0 48.2 + - + -
418A PCW 4.7 11.7 - - + -
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Residues in contact with THR 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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207A TRP* 2.7 54.8 + - + -
208A ASP* 3.4 11.9 - - - -
210A VAL* 1.3 77.3 - - - +
212A SER* 1.3 59.6 + - - +
214A PHE* 3.1 21.2 + - + +
215A SER* 2.9 19.3 + - - +
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Residues in contact with SER 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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208A ASP* 2.9 20.3 + - - -
209A SER* 2.9 16.5 + - - -
211A THR* 1.3 71.3 - - - +
213A THR* 1.3 62.5 + - - +
215A SER* 3.3 11.9 + - - -
216A LYS* 3.1 28.4 + - - +
561D LYS* 4.6 13.3 - - - +
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Residues in contact with THR 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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209A SER 2.7 21.9 + - - -
210A VAL* 3.0 17.0 + - + -
212A SER* 1.3 77.7 - - - +
214A PHE* 1.3 55.1 + - + +
216A LYS* 3.3 6.9 + - + +
217A LEU* 2.8 51.6 + - + +
405A PCW 6.3 5.2 - - + -
554D HIS* 5.6 4.0 - - - +
557D THR* 6.3 1.6 - - + -
558D LEU* 6.2 3.8 - - + -
561D LYS* 3.4 21.5 - - + +
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Residues in contact with PHE 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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207A TRP* 6.0 3.8 - + - -
210A VAL* 3.0 44.6 + - + -
211A THR* 3.1 14.8 + - + +
213A THR* 1.3 78.2 - - + +
215A SER* 1.3 56.5 + - - +
217A LEU* 3.5 19.7 - - + +
218A ARG* 2.8 55.0 + - + +
405A PCW 3.8 39.9 - - + -
418A PCW 4.2 20.4 - - + -
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Residues in contact with SER 215 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A THR* 2.9 18.7 + - - +
212A SER* 3.4 13.3 + - - -
213A THR 3.2 0.2 - - - -
214A PHE* 1.3 75.6 - - - +
216A LYS* 1.3 58.6 + - - +
218A ARG* 3.2 9.5 + - - +
219A GLU* 2.8 43.9 + - - +
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Residues in contact with LYS 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 SER* 3.1 15.1 + - - +
213A THR* 3.7 8.3 - - + +
215A SER* 1.3 79.7 - - - +
217A LEU* 1.3 59.2 + - + +
219A GLU* 3.6 15.9 - - + +
220A GLN* 2.9 31.3 + - - +
554D HIS* 6.4 0.4 - - + -
557D THR* 3.6 30.4 + - + +
560D GLU* 2.7 39.9 + - - +
561D LYS* 4.8 4.0 - - - +
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Residues in contact with LEU 217 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A THR* 2.8 39.6 + - + +
214A PHE* 3.5 27.8 - - + +
216A LYS* 1.3 77.8 - - + +
218A ARG* 1.3 52.8 + - + +
220A GLN* 3.2 6.4 + - + +
221A LEU* 2.7 44.1 + - + +
405A PCW 3.6 44.4 - - + -
418A PCW 6.4 1.1 - - + -
554D HIS* 3.7 32.1 - - + +
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Residues in contact with ARG 218 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A PHE* 2.8 41.2 + - + +
215A SER* 3.7 6.2 - - - +
217A LEU* 1.3 70.4 - - + +
219A GLU* 1.3 66.3 + - + +
221A LEU* 3.2 28.4 + - + +
222A GLY* 3.3 10.9 + - - -
405A PCW 3.9 38.3 + - - +
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Residues in contact with GLU 219 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A SER* 2.8 29.9 + - - +
216A LYS* 3.3 16.9 + - + +
218A ARG* 1.3 76.9 - - + +
220A GLN* 1.3 56.9 + - - +
222A GLY* 4.5 0.3 - - - -
223A PRO* 3.1 20.6 - - - +
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Residues in contact with GLN 220 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A LYS 2.9 17.1 + - - +
217A LEU* 3.7 6.5 - - + +
219A GLU* 1.3 74.5 - - - +
221A LEU* 1.3 66.3 + - - +
222A GLY 3.2 2.2 - - - -
223A PRO* 3.1 22.2 - - - +
224A VAL* 3.1 29.5 + - + +
550D LYS* 4.0 19.6 + - + +
553D GLU* 3.4 48.2 + - + +
554D HIS* 5.9 7.6 - - + +
557D THR* 5.5 3.2 + - - -
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Residues in contact with LEU 221 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A LEU* 2.7 28.7 + - + +
218A ARG* 3.2 25.7 + - + +
220A GLN* 1.3 75.1 - - - +
222A GLY* 1.3 53.2 + - - +
224A VAL* 3.1 18.7 + - + +
225A THR* 2.8 46.6 + - + +
405A PCW 5.5 20.4 - - + -
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Residues in contact with GLY 222 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ARG 3.3 10.2 + - - -
219A GLU 4.5 0.2 - - - -
221A LEU* 1.3 76.8 - - - +
223A PRO* 1.3 67.6 - - - +
225A THR* 2.8 20.8 + - - -
226A GLN* 3.0 24.6 + - - +
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Residues in contact with PRO 223 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A GLU 3.1 20.2 - - - +
220A GLN* 3.1 26.2 - - - +
222A GLY* 1.3 88.5 - - - +
224A VAL* 1.3 50.8 + - - +
226A GLN* 3.4 17.3 - - - +
227A GLU* 2.7 56.8 + - - +
550D LYS* 4.1 3.1 - - - +
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Residues in contact with VAL 224 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLN* 3.1 27.2 + - + +
221A LEU* 3.1 25.3 + - + +
223A PRO* 1.3 77.2 - - - +
225A THR* 1.3 62.6 + - + +
227A GLU* 3.8 4.7 - - - -
228A PHE* 2.8 61.9 + - + +
550D LYS* 4.2 25.4 - - + -
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Residues in contact with THR 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A LEU* 2.8 25.9 + - + +
222A GLY* 2.8 14.2 + - - -
224A VAL* 1.3 76.1 - - + +
226A GLN* 1.3 56.2 + - - +
228A PHE* 4.5 0.9 - - - -
229A TRP* 2.9 62.6 + - + +
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Residues in contact with GLN 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A GLY* 3.0 23.8 + - - +
223A PRO* 3.4 17.7 - - - +
225A THR* 1.3 77.4 - - - +
227A GLU* 1.3 59.5 + - + +
229A TRP* 3.9 2.4 - - - +
230A ASP* 2.8 32.8 + - - +
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Residues in contact with GLU 227 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A PRO* 2.7 33.2 + - - +
224A VAL* 3.9 2.5 - - - +
226A GLN* 1.3 71.2 - - + +
228A PHE* 1.3 67.8 + - + +
230A ASP* 3.2 7.4 + - - +
231A ASN* 2.9 31.0 + - - +
546D GLU* 3.3 35.1 - - + +
550D LYS* 2.7 45.9 + - - +
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Residues in contact with PHE 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A VAL* 2.8 54.7 + - + +
225A THR* 4.1 2.2 - - - +
227A GLU* 1.3 74.1 - - + +
229A TRP* 1.3 63.0 + - + +
231A ASN* 3.3 1.3 + - - +
232A LEU* 2.7 47.1 + - + +
405A PCW 6.0 9.0 - - + -
543D ARG* 3.6 34.2 + - + +
546D GLU* 5.1 7.4 - - + -
547D TYR* 4.3 27.4 - + - -
550D LYS* 6.4 1.3 - - + -
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Residues in contact with TRP 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A THR* 2.9 53.4 + - + +
226A GLN* 4.0 2.5 - - - +
228A PHE* 1.3 81.1 - - + +
230A ASP* 1.3 56.4 + - - +
232A LEU* 3.5 25.7 - - + +
233A GLU* 2.7 45.8 + - + +
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Residues in contact with ASP 230 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A GLN 2.8 19.7 + - - +
227A GLU* 3.2 9.4 + - - +
229A TRP* 1.3 78.4 - - - +
231A ASN* 1.3 61.0 + - - +
233A GLU* 3.5 6.9 + - - +
234A LYS* 2.7 53.8 + - - +
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Residues in contact with ASN 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLU* 2.9 17.1 + - - +
228A PHE 3.8 0.2 - - - +
230A ASP* 1.3 75.2 - - - +
232A LEU* 1.3 60.9 + - - +
234A LYS* 2.8 35.6 + - - +
235A GLU* 2.9 23.6 + - - +
539D ASN* 3.2 30.2 + - + +
542D ALA* 4.2 4.0 - - - +
543D ARG* 3.3 32.8 - - - +
546D GLU* 2.7 41.2 + - - +
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Residues in contact with LEU 232 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A PHE* 2.7 39.2 + - + +
229A TRP* 3.2 38.1 + - + +
231A ASN* 1.3 72.4 - - - +
233A GLU* 1.3 53.0 + - - +
235A GLU* 3.1 21.6 + - + +
236A THR* 2.7 41.2 + - + +
405A PCW 6.6 0.4 - - + -
543D ARG* 3.4 7.2 - - - +
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Residues in contact with GLU 233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A TRP* 2.7 28.4 + - + +
230A ASP* 3.6 8.5 - - - +
232A LEU* 1.3 76.2 - - - +
234A LYS* 1.3 53.6 + - + +
236A THR* 3.0 5.8 + - - +
237A GLU* 2.7 34.1 + - - +
240A ARG* 2.7 44.9 + - - -
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Residues in contact with LYS 234 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ASP* 2.7 47.7 + - - +
231A ASN* 2.8 26.0 + - - +
233A GLU* 1.3 75.3 - - + +
235A GLU* 1.3 61.0 + - - +
237A GLU* 3.4 17.4 - - - +
238A GLY* 2.9 24.9 + - - -
535D ALA* 4.7 4.9 - - + +
538D GLU* 6.2 1.1 - - + -
539D ASN* 3.2 27.1 - - - +
542D ALA* 5.5 3.6 - - - +
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Residues in contact with GLU 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ASN 2.9 7.4 + - - +
232A LEU* 3.3 19.6 - - + +
234A LYS* 1.3 76.7 - - - +
236A THR* 1.3 58.1 + - + +
238A GLY* 3.2 3.5 + - - -
239A LEU* 3.0 33.6 + - + +
535D ALA* 4.1 11.6 - - + +
536D LEU* 4.4 24.3 - - + +
539D ASN* 2.8 26.0 + - - +
543D ARG* 2.7 46.5 + - - -
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Residues in contact with THR 236 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A LEU* 2.7 25.1 + - + +
233A GLU* 3.0 19.2 + - - +
235A GLU* 1.3 74.2 - - + +
237A GLU* 1.3 53.2 + - - +
239A LEU* 3.1 16.8 + - + +
240A ARG* 2.6 65.9 + - - +
408A PCW 5.4 11.0 - - + -
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Residues in contact with GLU 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A GLU 2.7 23.0 + - - +
234A LYS* 3.4 18.0 - - - +
235A GLU 3.2 0.2 - - - -
236A THR* 1.3 73.1 - - - +
238A GLY* 1.3 62.9 + - - +
240A ARG* 3.1 19.1 + - + +
241A GLN* 2.9 48.8 + - + +
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Residues in contact with GLY 238 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LYS 2.9 14.2 + - - -
235A GLU* 3.2 4.2 + - - -
236A THR 3.2 0.2 - - - -
237A GLU* 1.3 76.9 + - - +
239A LEU* 1.3 50.0 + - - +
241A GLN* 3.1 11.3 + - - +
242A GLU* 2.7 43.8 + - - +
535D ALA* 5.4 8.5 - - - -
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Residues in contact with LEU 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A GLU* 3.0 20.9 + - + +
236A THR* 3.1 16.6 + - + +
238A GLY* 1.3 75.3 - - - +
240A ARG* 1.3 54.2 + - - +
242A GLU* 3.6 11.8 - - + +
243A MET* 2.7 36.7 + - + +
246A ASP* 6.1 0.4 - - - +
408A PCW 4.1 32.8 - - + -
532D ARG* 4.0 38.1 - - + +
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Residues in contact with ARG 240 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A GLU* 2.7 57.3 + - - -
236A THR* 2.6 44.3 + - - +
237A GLU* 3.3 13.2 - - - +
239A LEU* 1.3 75.5 - - + +
241A GLN* 1.3 62.5 + - + +
243A MET* 3.3 30.2 - - + +
244A SER* 3.7 7.4 + - - -
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Residues in contact with GLN 241 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A GLU* 2.9 45.0 + - + +
238A GLY* 3.5 9.5 - - - +
240A ARG* 1.3 75.5 - - + +
242A GLU* 1.3 66.7 + - + +
244A SER* 3.2 23.2 + - - -
245A LYS* 4.3 6.4 + - - +
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Residues in contact with GLU 242 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLY* 2.7 24.6 + - - +
239A LEU* 3.6 14.8 - - + +
241A GLN* 1.3 71.8 - - - +
243A MET* 1.3 51.6 + - - +
244A SER 3.0 0.7 - - - -
245A LYS* 2.7 13.9 + - + +
246A ASP* 2.6 38.5 + - + +
528D ARG* 3.4 28.4 - - + +
531D ALA* 4.4 10.8 - - + -
532D ARG* 2.6 68.7 + - - +
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Residues in contact with MET 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 2.7 17.5 + - + +
240A ARG* 3.3 26.0 - - + +
241A GLN 3.1 0.2 - - - -
242A GLU* 1.3 77.3 - - - +
244A SER* 1.3 55.6 + - - +
245A LYS 2.9 5.4 + - - -
246A ASP* 4.7 2.7 - - - -
247A LEU* 3.2 37.7 + - + +
248A GLU* 3.0 25.9 + - + +
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Residues in contact with SER 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ARG 3.7 8.3 + - - -
241A GLN* 3.3 16.1 + - - -
242A GLU 3.0 0.2 - - - -
243A MET* 1.3 76.2 - - - +
245A LYS* 1.3 66.7 + - - +
248A GLU* 3.2 27.5 - - - +
249A GLU* 4.1 4.7 - - - +
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Residues in contact with LYS 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLN 4.6 8.5 + - - +
242A GLU* 2.7 11.1 + - + +
243A MET 2.9 0.2 - - - -
244A SER* 1.3 89.3 + - - +
246A ASP* 1.3 63.5 + - - +
247A LEU 3.2 1.6 - - - -
249A GLU* 2.8 60.6 + - + +
250A VAL 3.5 0.3 + - - -
527D GLN* 5.7 8.1 - - + +
528D ARG* 3.3 24.0 + - + +
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Residues in contact with ASP 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 6.1 0.3 - - - +
242A GLU* 2.6 23.8 + - + +
243A MET* 4.7 1.8 - - - -
245A LYS* 1.3 73.7 - - - +
247A LEU* 1.3 59.2 + - + +
250A VAL* 3.2 21.0 - - - +
412A PCW 3.3 29.2 - - + +
521D TYR* 3.5 4.3 + - - -
525D LEU* 3.6 11.1 - - - +
528D ARG* 2.7 37.4 + - - +
532D ARG* 3.2 26.4 + - - +
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Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A MET* 3.2 42.2 + - + +
246A ASP* 1.3 80.3 - - + +
248A GLU* 1.3 68.8 + - - +
250A VAL* 3.3 18.7 - - + +
251A LYS* 3.3 25.1 - - + +
412A PCW 3.6 32.5 - - + -
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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