Contacts of the helix formed by residues 185 - 217 (chain U) in PDB entry 5L4K
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 GLY 185 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347T GLU* 4.7 12.2 + - - -
182U THR 5.2 0.2 - - - -
183U THR 3.6 4.6 + - - -
184U VAL* 1.3 74.3 - - - +
186U THR* 1.3 66.2 + - - -
187U LEU 3.7 1.1 - - - -
188U SER* 3.1 9.4 + - - -
189U GLN* 2.9 24.9 + - - +
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Residues in contact with THR 186 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347T GLU* 5.4 0.2 + - - -
185U GLY* 1.3 68.5 - - - -
187U LEU* 1.3 60.5 + - - +
189U GLN* 2.6 36.0 + - + +
190U ARG* 3.0 25.5 + - - +
293V THR* 4.9 18.4 - - + +
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Residues in contact with LEU 187 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375O LEU* 5.2 0.9 - - + -
343T ALA* 3.8 46.4 - - + +
346T LEU* 4.0 26.2 - - + +
347T GLU* 4.0 16.1 + - + +
185U GLY 3.7 0.2 - - - -
186U THR* 1.3 82.0 - - - +
188U SER* 1.3 66.0 + - - +
190U ARG* 3.2 6.5 + - - +
191U ILE* 3.1 21.7 + - + +
293V THR* 4.9 22.0 - - + +
296V ILE* 5.2 9.2 - - + -
297V VAL* 4.2 20.9 - - + +
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Residues in contact with SER 188 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375O LEU* 3.8 39.4 + - - -
376O THR* 4.0 2.6 - - - +
347T GLU* 3.5 21.3 + - - +
184U VAL* 3.6 12.1 - - - +
185U GLY 3.1 16.6 + - - -
187U LEU* 1.3 80.6 - - - +
189U GLN* 1.3 61.2 + - - +
191U ILE* 3.2 9.0 + - - +
192U THR* 2.9 27.0 + - - -
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Residues in contact with GLN 189 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181U ASP 4.5 6.8 - - - +
184U VAL* 4.0 25.3 - - - +
185U GLY 2.9 15.2 + - - +
186U THR* 2.6 21.8 + - - +
188U SER* 1.3 71.3 - - - +
190U ARG* 1.3 60.5 + - + +
192U THR* 3.1 16.4 - - - +
193U ASN* 3.0 40.8 + - - +
221V HIS* 6.2 1.4 - - - -
223V LYS* 4.1 10.3 - - - +
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Residues in contact with ARG 190 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186U THR* 3.0 29.5 + - + +
187U LEU* 3.2 7.4 + - - +
189U GLN* 1.3 78.4 - - + +
191U ILE* 1.3 67.6 + - - +
192U THR 3.1 0.9 - - - -
193U ASN* 3.0 17.7 + - - +
194U GLN* 3.0 17.4 + - - +
227V GLU* 3.1 37.2 + - - +
232V GLN* 4.5 17.0 - - - +
293V THR* 4.8 14.7 + - - -
294V SER* 5.1 10.7 + - - +
297V VAL* 4.8 24.2 - - + +
298V GLN* 4.8 7.9 - - - +
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Residues in contact with ILE 191 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371O ALA* 4.2 21.8 - - + -
372O HIS* 5.2 1.3 - - - +
375O LEU* 4.1 21.3 - - + -
376O THR* 5.9 1.3 - - + +
340T ILE* 3.9 22.4 - - + -
343T ALA* 3.7 29.8 - - + -
187U LEU* 3.1 19.9 + - + +
188U SER* 3.2 8.7 + - - +
190U ARG* 1.3 75.2 - - - +
192U THR* 1.3 65.3 + - - +
194U GLN* 2.9 16.9 + - - +
195U VAL* 3.0 22.2 + - + +
297V VAL* 4.2 17.2 - - + +
300V LEU* 4.7 7.0 - - + -
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Residues in contact with THR 192 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372O HIS* 5.7 3.1 + - + +
376O THR* 2.9 37.8 + - + +
184U VAL* 5.3 0.2 - - - +
188U SER 2.9 8.9 + - - -
189U GLN* 3.1 18.9 - - - +
190U ARG 3.1 0.2 - - - -
191U ILE* 1.3 77.6 - - - +
193U ASN* 1.3 64.3 + - - +
195U VAL* 3.2 4.6 + - - +
196U HIS* 2.8 36.5 + - + +
223V LYS* 4.4 14.1 - - - +
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Residues in contact with ASN 193 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189U GLN* 3.0 20.5 + - - +
190U ARG* 3.0 14.6 + - - +
192U THR* 1.3 74.7 - - - +
194U GLN* 1.3 58.4 + - - +
196U HIS* 3.8 0.7 - - - +
197U GLY* 2.9 25.5 + - - -
221V HIS* 6.0 1.0 - - - -
223V LYS* 2.7 45.0 + - + +
226V MET* 4.6 13.7 - - + +
227V GLU* 3.2 39.4 + - + +
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Residues in contact with GLN 194 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190U ARG 3.0 12.3 + - - +
191U ILE* 2.9 10.0 + - - +
193U ASN* 1.3 74.2 - - - +
195U VAL* 1.3 65.2 + - + +
197U GLY* 3.9 0.8 - - - -
198U LEU* 3.5 22.7 + - - +
227V GLU* 4.2 11.8 - - + +
228V GLY* 3.7 32.1 + - - +
230V THR 5.1 0.3 - - - +
297V VAL* 3.6 17.8 - - - +
300V LEU* 3.7 26.3 - - + +
301V ALA* 3.5 39.9 - - - +
304V LEU* 3.9 17.5 - - + +
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Residues in contact with VAL 195 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364O GLU* 4.4 7.5 - - + +
367O VAL* 3.5 41.1 - - + +
368O GLU* 4.0 23.6 - - + -
372O HIS* 5.1 8.7 - - + +
191U ILE* 3.0 25.6 + - + +
192U THR* 4.1 4.3 - - - +
194U GLN* 1.3 76.6 - - + +
196U HIS* 1.3 64.9 + - - +
197U GLY 3.0 1.9 + - - -
198U LEU* 3.1 10.0 + - - +
199U LYS* 3.0 37.0 + - - +
300V LEU* 6.3 1.8 - - + -
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Residues in contact with HIS 196 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131U LEU* 3.2 51.3 + - + +
192U THR* 2.8 27.4 + - + +
193U ASN 4.1 2.2 - - - +
195U VAL* 1.3 76.9 - - - +
197U GLY* 1.3 59.7 + - - +
199U LYS* 3.4 33.2 + - + +
200U GLY* 3.4 4.9 + - - -
221V HIS 5.1 2.0 + - - -
223V LYS* 3.9 35.9 - - + +
224V SER 5.4 1.0 + - - -
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Residues in contact with GLY 197 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193U ASN 2.9 18.7 + - - -
194U GLN 3.9 1.8 - - - -
195U VAL 3.0 0.6 - - - -
196U HIS* 1.3 75.2 - - - +
198U LEU* 1.3 56.5 + - - +
200U GLY* 2.7 22.9 + - - -
201U LEU 3.0 10.9 + - - -
223V LYS 4.2 21.1 - - - -
224V SER* 4.4 0.3 - - - -
227V GLU 4.6 4.9 - - - -
228V GLY 5.8 0.4 - - - -
229V LEU* 3.8 15.8 - - - +
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Residues in contact with LEU 198 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360O VAL* 4.3 6.5 - - + +
363O MET 4.3 2.2 - - - -
364O GLU* 3.4 40.6 - - + +
367O VAL* 4.6 5.4 - - + -
194U GLN 3.5 13.8 + - - +
195U VAL 3.1 6.0 + - - +
197U GLY* 1.3 74.8 - - - +
199U LYS* 1.3 63.9 + - - +
201U LEU* 4.0 5.6 - - + +
202U ASN* 2.9 28.4 + - - +
228V GLY 4.4 3.6 - - - +
229V LEU* 4.4 15.3 - - + -
304V LEU* 3.9 31.0 - - + -
305V ASP* 5.6 0.2 - - - +
308V VAL* 3.8 35.4 - - + -
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Residues in contact with LYS 199 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364O GLU* 3.1 26.3 + - - +
368O GLU* 3.5 19.2 + - - +
372O HIS* 5.3 10.8 + - - -
131U LEU* 4.2 33.6 - - + +
195U VAL* 3.0 32.7 + - - +
196U HIS* 3.4 37.1 + - + +
197U GLY 3.1 0.4 - - - -
198U LEU* 1.3 75.0 - - - +
200U GLY* 1.3 58.5 + - - +
202U ASN* 4.3 4.0 + - - +
203U SER* 4.0 15.2 + - - -
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Residues in contact with GLY 200 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131U LEU* 6.1 2.7 - - - -
196U HIS 3.4 5.1 + - - -
197U GLY 2.7 16.0 + - - -
199U LYS* 1.3 71.3 - - - +
201U LEU* 1.3 66.1 + - - -
202U ASN 3.0 1.3 - - - -
203U SER* 2.9 18.2 + - - -
204U LYS* 3.0 15.5 + - - +
224V SER* 4.0 22.2 - - - -
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Residues in contact with LEU 201 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356O TRP* 4.6 3.8 - - + -
360O VAL* 4.0 13.5 - - + -
436P MET* 4.2 21.3 - - + -
439P VAL* 5.2 8.1 - - + -
197U GLY 3.0 10.5 + - - +
198U LEU* 4.0 6.7 - - + +
200U GLY* 1.3 72.6 - - - +
202U ASN* 1.3 62.5 + - - +
204U LYS* 3.8 7.1 - - + +
205U LEU* 3.0 52.3 + - + +
224V SER* 4.6 3.6 - - - -
229V LEU* 4.0 14.0 - - + +
308V VAL* 3.7 25.1 - - + -
309V PHE* 3.7 36.1 - - + -
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Residues in contact with ASN 202 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357O CYS* 4.3 14.9 - - - +
360O VAL* 4.0 13.6 - - + +
361O LYS* 3.7 42.5 + - - +
364O GLU* 4.3 11.5 + - - +
198U LEU 2.9 18.8 + - - +
199U LYS* 4.4 4.2 + - - +
200U GLY 2.9 0.2 + - - -
201U LEU* 1.3 77.2 - - - +
203U SER* 1.3 62.1 + - - +
205U LEU* 4.0 3.5 - - - +
206U LEU* 3.0 34.7 + - - +
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Residues in contact with SER 203 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131U LEU* 6.5 0.2 - - - -
199U LYS 4.0 10.5 + - - -
200U GLY* 2.9 11.8 + - - -
202U ASN* 1.3 81.8 - - - +
204U LYS* 1.3 71.0 + - - +
206U LEU* 3.3 14.5 + - - +
207U ASP* 2.9 30.1 + - - +
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Residues in contact with LYS 204 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436P MET* 4.0 12.6 - - + +
439P VAL* 4.4 12.8 - - + -
440P ASN* 2.6 32.7 + - - +
443P THR* 4.2 25.9 - - + +
200U GLY 3.0 15.7 + - - +
201U LEU* 3.8 3.8 - - - +
203U SER* 1.3 76.7 + - - +
205U LEU* 1.3 67.4 + - - +
207U ASP* 2.8 22.3 + - - +
208U ILE* 3.1 9.4 + - - +
222V LYS* 5.4 4.4 - - - +
224V SER* 2.4 51.2 + - - +
225V TRP* 4.2 1.8 - - - -
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Residues in contact with LEU 205 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353O LEU* 4.4 14.6 - - + +
356O TRP* 3.3 64.8 - - + +
357O CYS* 4.8 15.7 - - + +
360O VAL* 4.4 10.1 - - + -
439P VAL* 4.4 19.0 - - + +
201U LEU* 3.0 33.1 + - + +
202U ASN* 4.0 2.9 - - - +
204U LYS* 1.3 74.0 - - - +
206U LEU* 1.3 65.4 + - - +
208U ILE* 2.9 13.6 + - + +
209U ARG* 2.9 22.3 + - - +
233U VAL* 6.1 0.2 - - + -
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Residues in contact with LEU 206 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357O CYS* 4.7 16.7 - - - -
202U ASN* 3.0 27.2 + - - +
203U SER* 3.3 16.8 - - - +
204U LYS 3.1 0.2 - - - -
205U LEU* 1.3 74.9 - - - +
207U ASP* 1.3 64.3 + - - +
209U ARG* 3.2 36.5 + - - +
210U SER* 3.0 23.2 + - - -
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Residues in contact with ASP 207 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443P THR* 5.0 8.6 - - + +
446P ILE* 5.4 2.9 - - + +
203U SER* 2.9 20.1 + - - +
204U LYS* 2.8 18.2 + - - +
206U LEU* 1.3 72.4 - - - +
208U ILE* 1.3 63.9 + - - +
210U SER* 2.8 25.9 + - - +
211U TYR* 3.0 8.8 + - - +
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Residues in contact with ILE 208 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353O LEU* 3.5 22.9 - - + -
439P VAL* 4.5 14.8 - - + -
442P THR* 3.2 31.9 - - + -
443P THR* 4.2 17.9 - - + -
446P ILE* 3.5 23.8 - - + -
204U LYS 3.1 6.2 + - - +
205U LEU* 2.9 15.6 + - + +
207U ASP* 1.3 75.0 - - - +
209U ARG* 1.3 63.2 + - - +
211U TYR* 3.0 3.0 + - - +
212U LEU* 2.9 28.7 + - + +
230U LEU* 3.8 26.5 - - + -
233U VAL* 6.3 0.4 - - + -
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Residues in contact with ARG 209 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350O LYS* 3.8 33.7 - - + +
353O LEU* 3.8 19.5 - - + -
354O GLU* 3.4 35.8 + - - +
357O CYS* 5.8 5.9 - - + -
205U LEU 2.9 12.0 + - - +
206U LEU* 3.2 35.4 + - - +
208U ILE* 1.3 76.3 - - - +
210U SER* 1.3 63.5 + - - +
212U LEU* 3.6 2.7 + - - +
213U GLU* 3.0 43.5 + - - +
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Residues in contact with SER 210 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206U LEU* 3.0 13.9 + - - -
207U ASP* 2.8 23.1 + - - -
209U ARG* 1.3 81.0 - - - +
211U TYR* 1.3 57.3 + - - +
213U GLU* 3.7 9.3 + - - +
214U LYS* 2.9 29.0 + - - +
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Residues in contact with TYR 211 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446P ILE* 3.6 38.4 - - + -
449P GLU* 3.6 33.2 + - - -
450P GLU* 6.1 1.1 - - - -
207U ASP 3.0 9.2 + - - +
208U ILE 3.0 6.7 + - - +
210U SER* 1.3 78.8 + - - +
212U LEU* 1.3 73.1 + - + +
214U LYS* 2.6 38.9 + - + +
215U VAL* 3.0 31.4 + - + +
220U LEU* 4.7 4.5 - - + -
221U PRO 4.9 0.2 + - - -
223U ASN 4.3 12.8 + - - -
226U ILE* 3.0 45.7 - - + +
227U ILE* 4.5 5.1 - - + +
230U LEU* 5.2 0.4 - - + -
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Residues in contact with LEU 212 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346O ILE* 4.5 14.6 - - + +
349O MET* 4.2 28.3 - - + -
350O LYS* 4.4 22.0 - - + +
353O LEU* 4.3 20.9 - - + -
208U ILE* 2.9 19.3 + - + +
209U ARG 4.1 3.1 - - - +
211U TYR* 1.3 79.8 - - + +
213U GLU* 1.3 64.4 + - - +
214U LYS 3.0 1.2 + - - -
215U VAL* 3.1 6.4 + - + +
216U ALA* 3.0 24.6 + - - +
227U ILE* 3.6 22.2 - - + -
230U LEU* 3.6 33.0 - - + -
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Residues in contact with GLU 213 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350O LYS* 4.0 25.8 + - + +
209U ARG* 3.0 36.9 + - - +
210U SER* 3.9 8.5 - - - +
212U LEU* 1.3 76.0 - - - +
214U LYS* 1.3 58.3 + - - +
216U ALA* 4.1 5.5 - - + +
217U THR* 3.1 26.2 + - - +
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Residues in contact with LYS 214 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450P GLU* 3.2 29.4 + - - +
454P ASN* 3.4 15.5 + - - +
210U SER* 2.9 16.4 + - - +
211U TYR* 2.6 28.9 + - + +
213U GLU* 1.3 74.3 - - - +
215U VAL* 1.3 59.9 + - + -
217U THR 3.0 15.7 - - - +
218U GLY 3.0 20.5 - - - +
220U LEU* 3.9 28.5 + - + +
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Residues in contact with VAL 215 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343O LEU* 4.0 7.0 - - + +
346O ILE* 4.4 24.9 - - + -
211U TYR* 3.0 41.9 + - + +
212U LEU* 3.6 14.6 - - + +
214U LYS* 1.3 74.4 - - - +
216U ALA* 1.3 74.4 + - - +
217U THR 3.1 2.7 + - - -
219U LYS* 3.5 17.8 - - - +
220U LEU* 3.4 32.8 + - + +
221U PRO 4.7 2.2 - - - +
222U ILE* 4.4 16.2 - - + +
227U ILE* 5.2 3.6 - - + -
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Residues in contact with ALA 216 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343O LEU* 4.3 12.3 - - - +
346O ILE* 4.3 11.7 - - + -
347O LYS* 4.0 33.4 - - + -
350O LYS* 6.0 2.7 - - + -
212U LEU 3.0 17.2 + - - +
213U GLU* 4.4 7.0 - - + +
214U LYS 3.5 0.4 - - - -
215U VAL* 1.3 81.8 - - - +
217U THR* 1.3 67.4 + - - +
219U LYS* 3.3 17.3 + - - -
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Residues in contact with THR 217 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347O LYS* 4.9 6.1 - - - +
213U GLU* 3.1 16.8 + - - +
214U LYS* 3.0 15.2 - - - +
215U VAL 3.1 0.6 + - - -
216U ALA* 1.3 86.2 + - - +
218U GLY* 1.3 65.7 + - - +
219U LYS* 4.1 10.5 + - - +
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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