Contacts of the helix formed by residues 204 - 238 (chain B) in PDB entry 4AD7
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 GLU 204 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B ARG* 5.2 15.3 + - - +
202B PHE 3.9 0.2 + - - -
203B GLY* 1.3 74.1 - - - -
205B ALA* 1.3 64.8 + - - +
206B PRO* 3.4 2.0 - - - -
207B ARG* 3.2 11.9 + - + +
208B GLU* 3.0 39.3 + - + +
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Residues in contact with ALA 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TRP* 5.2 1.1 - - - -
202B PHE 3.9 2.9 - - - +
204B GLU* 1.3 77.4 - - - +
206B PRO* 1.3 66.1 - - + +
208B GLU* 3.8 6.4 - - - +
209B LEU* 2.9 31.9 + - - +
320B TRP* 3.6 31.9 - - + +
323B GLU* 4.3 11.4 - - + +
324B ALA* 3.7 20.9 - - + +
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Residues in contact with PRO 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 5.2 1.6 - - - +
167B TRP* 3.4 48.1 + - + +
202B PHE* 3.7 27.6 - - + -
203B GLY 3.7 11.7 - - - +
204B GLU 3.6 2.9 - - - -
205B ALA* 1.3 95.0 - - + +
207B ARG* 1.3 56.3 + - - +
209B LEU* 3.8 2.6 - - + +
210B ARG* 2.9 28.9 + - - +
324B ALA* 4.6 0.4 - - + -
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Residues in contact with ARG 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLY 5.8 0.4 - - - +
204B GLU* 3.2 12.6 + - + +
206B PRO* 1.3 76.0 - - - +
208B GLU* 1.3 70.0 + - - +
210B ARG* 3.1 25.0 + - - +
211B LEU* 3.0 57.6 + - + +
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Residues in contact with GLU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B GLU* 3.0 37.1 + - + +
205B ALA* 3.8 3.6 - - - +
207B ARG* 1.3 80.0 + - + +
209B LEU* 1.3 58.1 + - - +
211B LEU* 3.9 9.6 - - - +
212B ARG* 2.6 68.0 + - - +
320B TRP* 3.6 21.2 + - + +
367B ARG* 5.2 2.9 + - - -
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 5.4 2.7 - - + -
148B LEU* 6.2 0.9 - - + -
163B LEU* 5.0 15.0 - - + -
167B TRP* 4.1 16.4 - - + +
205B ALA 2.9 19.0 + - - +
206B PRO 3.8 3.4 - - - +
208B GLU* 1.3 74.9 - - - +
210B ARG* 1.3 66.6 + - - +
212B ARG* 4.9 0.4 - - - -
213B ALA* 2.9 44.5 + - + +
313B VAL* 5.3 0.2 - - + -
317B VAL* 4.2 21.5 - - + -
320B TRP* 3.8 39.9 - - + -
321B LEU* 3.7 29.8 - - + -
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Residues in contact with ARG 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LEU* 4.3 0.6 - - + +
160B GLU* 3.4 47.7 + - - +
163B LEU* 3.7 29.1 - - + +
206B PRO 2.9 18.8 + - - +
207B ARG* 3.1 32.0 + - - +
209B LEU* 1.3 75.8 - - - +
211B LEU* 1.3 84.4 + - - +
213B ALA* 4.3 0.3 - - - +
214B THR* 2.4 40.6 + - - +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ARG* 3.0 57.4 + - - +
208B GLU* 3.9 9.9 - - - +
210B ARG* 1.3 107.7 - - - +
212B ARG* 1.3 64.9 + - + +
214B THR* 3.5 4.7 - - - -
215B ARG* 3.0 48.3 + - - +
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Residues in contact with ARG 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLU* 2.6 57.1 + - - +
209B LEU* 4.4 1.1 - - - +
211B LEU* 1.3 79.2 - - + +
213B ALA* 1.3 58.2 + - - +
215B ARG* 3.4 5.8 + - - +
216B ALA* 2.9 32.2 + - - +
307B THR* 3.9 32.6 + - - +
308B SER* 3.8 22.8 + - - +
313B VAL* 3.7 24.1 - - + +
320B TRP* 3.4 33.5 - - + -
367B ARG* 5.1 5.1 - - - +
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Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 5.2 6.1 - - + -
159B LEU* 4.2 10.5 - - + -
163B LEU* 5.5 1.8 - - + -
209B LEU* 2.9 31.4 + - + +
210B ARG* 4.3 0.9 - - - +
212B ARG* 1.3 74.3 - - - +
214B THR* 1.3 66.1 + - - +
216B ALA* 4.6 0.2 - - - -
217B PHE* 2.9 48.5 + - + +
313B VAL* 3.7 16.0 - - + +
317B VAL* 5.4 2.2 - - + -
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Residues in contact with THR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B TYR* 3.8 15.7 - - - +
159B LEU* 3.3 23.5 - - + +
210B ARG* 2.4 31.3 + - - +
211B LEU* 3.5 5.4 - - - -
213B ALA* 1.3 76.9 - - - +
215B ARG* 1.3 62.8 + - - +
217B PHE* 4.1 0.3 - - - +
218B VAL* 3.0 34.5 + - + +
473B GLY 4.8 9.6 - - - +
474B ASN 6.5 0.4 - - - -
475B ASP 6.4 0.4 - - - -
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Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LEU* 3.0 44.1 + - - +
212B ARG* 3.9 5.7 - - - +
214B THR* 1.3 78.0 - - - +
216B ALA* 1.3 62.8 + - - +
218B VAL* 3.1 9.8 - - - +
219B ALA* 3.0 24.8 + - - +
303B LYS* 6.1 10.1 - - + +
308B SER* 5.6 14.3 - - - +
470B ALA 5.2 2.0 - - - +
471B TYR 5.9 1.3 - - - +
472B ASN 4.0 7.6 + - - -
473B GLY* 3.8 35.1 + - - -
474B ASN* 5.6 0.2 + - - -
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B ARG 2.9 18.7 + - - +
213B ALA 4.2 1.3 - - - +
215B ARG* 1.3 75.1 - - - +
217B PHE* 1.3 61.2 + - - +
219B ALA* 3.1 4.8 + - - +
220B ALA* 2.9 26.7 + - - +
303B LYS 5.9 0.2 - - - -
308B SER 4.5 4.8 + - - +
310B VAL* 3.4 37.6 - - - +
313B VAL* 3.9 18.8 - - + -
314B ILE* 4.2 10.1 - - + -
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Residues in contact with PHE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU* 4.2 13.5 - - + -
148B LEU* 3.8 39.7 - - + -
151B TYR* 3.6 24.7 - + + -
152B TYR* 3.6 44.0 - + + -
213B ALA* 2.9 41.2 + - + +
216B ALA* 1.3 76.3 - - - +
218B VAL* 1.3 57.3 + - - +
220B ALA* 4.0 1.6 - - - +
221B ARG* 2.9 34.0 + - - +
314B ILE* 4.0 42.0 - - + -
317B VAL* 5.0 4.7 - - + -
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Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B TYR* 3.2 25.8 - - + +
214B THR* 3.0 20.9 + - + +
215B ARG* 3.1 21.1 - - - +
217B PHE* 1.3 76.5 - - - +
219B ALA* 1.3 55.4 + - - +
221B ARG* 3.5 22.7 - - - +
222B SER* 2.7 39.9 + - - +
470B ALA* 4.4 14.6 - - + +
473B GLY 4.4 7.6 - - - +
474B ASN 4.2 16.2 - - - +
475B ASP 3.8 17.3 - - - +
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Residues in contact with ALA 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B ARG* 3.0 15.0 + - + +
216B ALA* 3.3 9.0 - - - +
218B VAL* 1.3 80.3 - - + +
220B ALA* 1.3 63.6 + - - +
222B SER* 3.5 3.4 - - - -
223B PHE* 3.0 23.0 + - - +
300B ILE* 4.1 26.6 - - + +
303B LYS* 4.4 16.4 - - + -
304B PHE* 4.7 3.8 - - + -
310B VAL* 4.0 13.2 - - + -
470B ALA* 4.8 4.3 - - - +
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Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PHE* 3.5 37.0 - - + -
152B TYR* 4.0 10.3 - - + -
216B ALA 2.9 15.4 + - - +
217B PHE 4.0 3.1 - - - +
219B ALA* 1.3 74.6 - - - +
221B ARG* 1.3 64.6 + - - +
223B PHE* 3.1 4.8 + - - +
224B VAL* 3.0 27.0 + - - +
304B PHE* 4.5 4.5 - - - -
310B VAL* 4.0 13.4 - - + +
314B ILE* 4.6 4.3 - - + -
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Residues in contact with ARG 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B TYR* 3.3 50.5 + - - -
152B TYR* 3.2 31.8 - - + +
153B ARG 4.9 1.3 - - - -
154B GLY* 3.8 11.2 - - - +
157B LEU* 3.7 20.1 - - - +
217B PHE 2.9 20.8 + - - +
218B VAL* 3.5 36.0 + - - +
220B ALA* 1.3 76.3 - - - +
222B SER* 1.3 60.3 + - - +
224B VAL* 3.9 4.4 - - - +
225B GLN* 2.9 68.9 + - + +
475B ASP* 4.1 9.3 + - - -
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Residues in contact with SER 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B VAL* 2.7 24.6 + - - +
219B ALA 3.5 3.6 - - - -
221B ARG* 1.3 79.6 + - - +
223B PHE* 1.3 60.6 + - - +
225B GLN* 3.6 10.2 + - - +
226B GLY* 2.9 22.9 + - - -
300B ILE* 5.1 0.2 - - - -
463B MET* 4.3 2.6 - - - +
466B ARG* 4.3 10.3 + - - +
467B LEU* 3.3 31.6 - - - +
470B ALA* 3.2 22.1 - - - +
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Residues in contact with PHE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B PHE* 3.5 57.2 - + + -
111B PHE* 4.9 2.2 - + - -
219B ALA 3.0 12.9 + - - +
220B ALA* 3.5 7.2 - - - +
222B SER* 1.3 76.3 - - - +
224B VAL* 1.3 63.7 + - - +
226B GLY* 3.1 2.4 + - - -
227B LEU* 3.0 44.2 + - + +
297B MET* 3.2 41.8 - - + +
298B VAL* 5.3 0.2 - - - -
300B ILE* 3.5 13.9 - - + -
301B THR* 3.7 14.8 - - + -
304B PHE* 4.0 13.5 - + + -
382B ALA* 4.7 9.2 - - + -
386B LEU* 5.0 6.3 - - + -
467B LEU* 3.9 6.9 - - - +
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Residues in contact with VAL 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LEU* 3.2 30.3 - - + +
107B PHE* 4.5 5.8 - - + -
108B ASP* 4.2 28.7 - - + +
111B PHE* 4.0 14.1 - - + -
152B TYR* 3.6 22.4 - - + +
220B ALA 3.0 18.2 + - - +
221B ARG* 3.9 5.2 - - - +
223B PHE* 1.3 78.1 - - - +
225B GLN* 1.3 65.3 + - + +
227B LEU* 3.1 4.8 + - - -
228B GLY* 3.0 18.4 + - - -
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Residues in contact with GLN 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ARG 4.9 8.3 + - - -
154B GLY* 5.4 2.6 - - - -
221B ARG* 2.9 49.9 + - + +
222B SER* 3.9 6.2 + - - +
224B VAL* 1.3 79.6 - - + +
226B GLY* 1.3 57.1 + - - +
228B GLY* 3.3 2.6 + - - +
229B VAL* 2.9 34.1 + - + +
463B MET* 3.8 13.0 - - + -
466B ARG* 3.5 34.1 + - - +
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Residues in contact with GLY 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B SER 2.9 16.3 + - - -
223B PHE 3.1 5.1 + - - -
225B GLN* 1.3 74.0 - - - +
227B LEU* 1.3 65.0 + - - +
229B VAL* 3.1 4.5 + - - +
230B ALA* 2.9 23.2 + - - +
293B LEU* 4.1 2.9 - - - +
297B MET* 3.4 16.7 - - - +
463B MET* 3.9 18.8 - - - -
467B LEU* 4.3 2.7 - - - -
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Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU* 4.4 23.4 - - + +
103B GLN* 3.8 19.7 - - + +
104B LEU* 3.7 37.0 - - + +
107B PHE* 4.3 2.9 - - + -
223B PHE* 3.0 44.5 + - + +
224B VAL* 3.5 7.2 - - - +
226B GLY* 1.3 72.9 - - - +
228B GLY* 1.3 64.1 + - - +
230B ALA* 3.3 6.2 + - - +
231B SER* 3.0 23.8 + - - -
297B MET* 3.4 23.7 - - + -
382B ALA* 6.5 0.4 - - + -
386B LEU* 4.5 12.1 - - + -
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Residues in contact with GLY 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LEU* 3.8 19.6 - - - +
224B VAL 3.0 13.6 + - - -
225B GLN* 3.7 5.2 - - - -
227B LEU* 1.3 76.0 - - - +
229B VAL* 1.3 57.0 + - - +
231B SER* 3.4 6.1 + - - -
232B ASP* 2.9 36.1 + - - +
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B GLN 2.9 20.5 + - - +
226B GLY 3.1 4.0 + - - +
228B GLY* 1.3 74.1 - - - +
230B ALA* 1.3 60.4 + - - +
232B ASP* 3.1 9.6 + - + +
233B VAL* 2.9 41.3 + - + +
293B LEU* 4.3 7.6 - - + -
459B GLN* 4.4 15.5 - - + +
460B LEU* 4.7 0.7 - - + -
463B MET* 3.5 41.5 - - + -
466B ARG* 5.8 0.9 - - - +
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 3.8 21.5 - - + -
226B GLY 2.9 13.1 + - - +
227B LEU* 3.6 9.0 - - - +
229B VAL* 1.3 76.3 - - - +
231B SER* 1.3 64.5 + - - +
233B VAL* 3.3 4.4 + - - +
234B VAL* 3.0 28.2 + - - +
290B TRP* 3.8 20.4 - - + -
293B LEU* 4.0 14.3 - - + +
294B LEU* 5.0 1.3 - - + -
297B MET* 4.9 7.0 - - + -
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Residues in contact with SER 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLN* 4.5 19.8 + - - +
100B LEU* 3.6 22.5 - - - +
101B ALA* 4.9 5.5 + - - +
104B LEU* 5.7 4.5 - - - -
227B LEU 3.0 12.7 + - - -
228B GLY* 3.4 12.6 - - - -
230B ALA* 1.3 76.9 - - - +
232B ASP* 1.3 58.6 + - - +
234B VAL* 3.4 3.4 + - - +
235B ARG* 2.9 32.4 + - - +
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Residues in contact with ASP 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B GLY 2.9 19.5 + - - +
229B VAL* 3.1 11.9 + - + +
231B SER* 1.3 74.1 + - - +
233B VAL* 1.3 60.8 + - + +
235B ARG* 2.7 34.4 + - - +
236B LYS* 2.9 53.9 + - - +
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B VAL* 2.9 24.3 + - + +
230B ALA* 3.6 8.1 - - - +
232B ASP* 1.3 75.0 - - + +
234B VAL* 1.3 65.6 + - - +
236B LYS* 3.9 0.5 - - - +
237B VAL* 2.9 36.6 + - + +
286B LEU* 4.3 12.8 - - + -
290B TRP* 4.6 4.5 - - + -
393B TRP* 4.4 10.1 - - + -
456B GLN* 3.4 36.8 - - + +
459B GLN* 4.8 3.6 - - + -
460B LEU* 3.7 34.1 - - + -
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Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B SER* 3.3 25.6 - - - +
96B LEU* 3.6 25.4 - - + -
97B GLN* 3.7 16.4 - - + -
100B LEU* 4.3 3.6 - - + -
230B ALA 3.0 17.4 + - - +
231B SER* 3.7 4.9 - - - +
233B VAL* 1.3 76.9 - - - +
235B ARG* 1.3 58.0 + - - +
237B VAL* 3.8 1.2 - - - +
238B ALA* 2.9 28.9 + - - +
290B TRP* 3.5 27.6 - - + -
392B PHE* 5.1 0.7 - - + -
393B TRP* 4.0 19.1 - - + -
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Residues in contact with ARG 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLN* 3.7 31.0 - - - +
231B SER* 2.9 19.1 + - - +
232B ASP* 2.7 32.0 + - - +
233B VAL 3.3 0.2 - - - -
234B VAL* 1.3 77.7 - - - +
236B LYS* 1.3 88.0 + - - +
238B ALA* 3.5 11.6 - - - +
239B GLN* 3.8 12.7 - - + +
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Residues in contact with LYS 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ASP* 2.9 41.3 + - - +
233B VAL 4.0 0.2 - - - +
235B ARG* 1.3 94.0 - - - +
237B VAL* 1.3 66.2 + - - +
239B GLN* 3.1 21.1 + - - +
240B VAL* 4.2 1.6 + - - +
452B THR* 4.4 16.7 - - + +
456B GLN* 3.3 41.9 + - + +
459B GLN* 5.8 3.0 - - - +
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Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B VAL 2.9 22.8 + - - +
234B VAL 3.9 2.5 - - - +
236B LYS* 1.3 75.6 - - - +
238B ALA* 1.3 59.6 + - - +
239B GLN 2.9 6.1 + - - -
240B VAL* 3.0 24.4 + - - +
283B GLN* 4.1 18.2 + - + +
286B LEU* 3.6 24.2 - - + -
393B TRP* 3.6 28.5 - - + -
452B THR* 5.0 1.3 - - - -
453B ILE* 4.1 17.0 - - + +
456B GLN* 4.0 22.2 - - + -
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Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ARG* 6.0 4.3 - - - -
93B SER* 3.2 31.2 - - - +
97B GLN* 4.4 5.6 - - - +
234B VAL 2.9 13.2 + - - +
235B ARG 3.5 9.6 - - - +
236B LYS 3.1 0.4 - - - -
237B VAL* 1.3 76.4 - - - +
239B GLN* 1.3 69.4 + - - +
240B VAL 3.3 4.7 + - - +
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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