Contacts of the helix formed by residues 190 - 220 (chain B) in PDB entry 2VRW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 190 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 4.0 18.2 + - - +
191B GLU* 1.3 87.6 + - + +
192B TYR* 3.3 4.0 - - - +
193B ASP* 3.2 26.2 + - - +
194B LYS* 3.0 58.5 + - - +
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B THR* 1.3 99.5 + - + +
192B TYR* 1.3 58.0 + - - +
194B LYS* 3.3 10.2 + - - +
195B ARG* 2.9 26.7 + - - +
346B HIS* 3.5 25.6 - - - +
347B THR* 5.8 0.2 - - - -
348B GLN* 3.5 31.3 - - + +
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Residues in contact with TYR 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B THR* 3.3 1.7 - - - +
191B GLU* 1.3 75.9 + - - +
193B ASP* 1.3 71.9 + - - +
195B ARG* 3.3 38.8 + - - +
196B CYS* 3.0 44.1 + - - -
347B THR* 6.3 0.4 - - - +
348B GLN* 5.4 1.4 - - + +
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Residues in contact with ASP 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B THR* 3.2 28.6 + - - +
192B TYR* 1.3 85.6 - - - +
194B LYS* 1.3 56.1 + - + +
196B CYS* 3.4 5.3 + - - +
197B CYS* 3.1 36.1 + - - -
200B ARG* 4.7 0.7 + - - -
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Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 3.4 33.7 + - - +
32A TYR* 3.8 19.7 - - + -
190B THR* 3.0 43.3 + - + +
191B GLU* 3.6 6.1 - - - +
192B TYR 3.3 0.2 - - - -
193B ASP* 1.3 74.0 - - + +
195B ARG* 1.3 60.4 + - - +
197B CYS* 3.6 2.5 - - - +
198B CYS* 3.0 30.8 + - - +
346B HIS* 3.5 42.0 + - + +
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Residues in contact with ARG 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLU 2.9 14.0 + - - +
192B TYR* 3.3 43.4 + - - +
194B LYS* 1.3 75.5 - - - +
196B CYS* 1.3 65.4 + - - +
198B CYS* 3.3 5.7 + - - +
199B LEU* 3.0 56.6 + - - +
262B GLY* 3.0 27.9 + - - -
263B ALA* 4.2 0.6 - - - +
343B LEU* 3.8 12.2 - - + +
346B HIS* 3.7 13.2 - - + +
347B THR* 3.9 22.0 - - - +
348B GLN 5.6 0.2 - - - +
352B GLU* 2.8 41.3 + - - -
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Residues in contact with CYS 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B TYR* 3.0 52.4 + - - +
193B ASP* 4.0 5.6 - - - +
195B ARG* 1.3 85.0 - - - +
197B CYS* 1.3 66.2 + - - +
199B LEU* 3.4 9.7 + - - +
200B ARG* 3.1 46.5 + - - +
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Residues in contact with CYS 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 3.6 39.7 + - + -
193B ASP* 3.1 26.4 + - - +
194B LYS 3.6 4.9 - - - +
195B ARG 3.4 0.2 - - - -
196B CYS* 1.3 75.4 - - - +
198B CYS* 1.3 58.8 + - - +
200B ARG* 3.3 30.4 + - - +
201B GLU* 2.9 28.2 + - - +
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Residues in contact with CYS 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 3.2 22.6 + - + +
194B LYS 3.0 18.8 + - - +
195B ARG 3.5 5.4 - - - +
196B CYS 3.3 0.2 - - - -
197B CYS* 1.3 75.1 - - - +
199B LEU* 1.3 65.4 + - - +
201B GLU* 3.1 2.8 + - - +
202B ILE* 3.0 33.0 + - - +
339B LEU* 3.7 28.7 - - - -
342B GLU* 4.3 8.5 - - - -
343B LEU* 3.7 28.9 - - + -
346B HIS* 4.2 3.8 - - - +
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ARG* 3.0 56.4 + - - +
196B CYS* 3.7 11.0 - - - +
197B CYS 3.4 0.2 - - - -
198B CYS* 1.3 74.7 - - - +
200B ARG* 1.3 64.0 + - + +
202B ILE* 3.3 9.2 + - + +
203B GLN 3.3 15.9 + - - -
258B LEU* 3.8 25.1 - - + +
263B ALA* 4.3 13.0 - - + -
266B LEU* 3.7 31.0 - - + -
343B LEU* 3.7 19.7 - - + -
352B GLU* 5.3 1.6 - - - +
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Residues in contact with ARG 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ASP 4.7 0.6 + - - -
196B CYS* 3.1 34.5 + - - +
197B CYS* 3.3 41.1 - - - +
199B LEU* 1.3 76.8 - - + +
201B GLU* 1.3 56.3 + - - +
203B GLN* 3.3 6.3 + - - +
204B GLN* 2.9 52.9 + - - +
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Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 2.5 32.7 + - + +
34A PRO* 3.5 12.8 - - - +
35A THR* 3.1 17.6 + - - -
36A VAL* 2.8 36.1 + - - +
197B CYS 2.9 14.8 + - - +
198B CYS 3.1 7.2 + - - +
200B ARG* 1.3 73.1 - - - +
202B ILE* 1.3 59.3 + - - +
204B GLN* 4.5 7.4 - - - +
205B THR* 2.7 48.0 + - + +
339B LEU* 4.0 12.0 - - + +
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Residues in contact with ILE 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B CYS* 3.0 26.8 + - - +
199B LEU* 3.5 12.1 - - - +
200B ARG 3.3 0.4 - - - -
201B GLU* 1.3 76.5 - - - +
203B GLN* 1.3 61.6 + - - +
205B THR* 3.3 5.6 + - - -
206B GLU* 3.1 23.4 + - - +
254B LEU* 3.9 29.6 - - + -
258B LEU* 5.0 2.9 - - + -
266B LEU* 4.4 9.9 - - + -
270B PHE* 4.3 17.9 - - + -
332B ARG* 3.8 3.1 + - - +
336B TYR* 6.1 1.3 - - + -
339B LEU* 4.1 36.1 - - + +
340B LEU* 5.1 2.9 - - + -
343B LEU* 4.0 26.2 - - + -
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Residues in contact with GLN 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU 3.3 4.7 + - - +
200B ARG* 3.8 7.9 - - - +
201B GLU 3.2 0.2 - - - -
202B ILE* 1.3 80.4 - - - +
204B GLN* 1.3 59.8 + - + +
206B GLU* 3.2 3.5 + - - +
207B GLU* 2.9 57.9 + - + +
251B LEU* 4.2 1.1 - - + +
254B LEU* 4.4 10.3 - - + -
255B LYS* 3.7 34.7 - - + +
258B LEU* 3.6 33.1 - - + +
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Residues in contact with GLN 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ARG* 2.9 44.8 + - - +
201B GLU* 4.2 5.2 - - - +
203B GLN* 1.3 74.2 - - + +
205B THR* 1.3 60.7 + - + +
207B GLU* 3.4 18.8 + - - +
208B LYS* 3.0 27.5 + - - +
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Residues in contact with THR 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 3.8 26.0 - - + +
38A ASP* 5.1 5.8 - - - +
201B GLU* 2.7 45.1 + - + +
202B ILE* 3.3 3.3 + - - -
204B GLN* 1.3 75.9 - - + +
206B GLU* 1.3 60.2 + - - +
208B LYS* 3.4 7.5 + - + +
209B TYR* 3.0 29.1 + - - +
332B ARG* 3.1 31.4 + - - -
339B LEU* 4.2 4.7 - - - +
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE 3.1 19.2 + - - +
203B GLN 3.2 4.2 + - - +
205B THR* 1.3 74.4 - - - +
207B GLU* 1.3 59.3 + - - +
209B TYR* 3.7 2.9 - - - +
210B THR* 2.9 42.5 + - - -
247B HIS* 2.8 32.8 - - - +
250B PHE* 3.4 15.7 - - + -
251B LEU* 4.0 15.9 - - + -
254B LEU* 3.8 22.2 - - + -
332B ARG* 2.8 26.3 + - - +
336B TYR* 2.6 27.0 + - - -
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Residues in contact with GLU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLN* 2.9 44.2 + - - +
204B GLN* 3.5 24.6 - - - +
206B GLU* 1.3 76.9 - - - +
208B LYS* 1.3 57.4 + - - +
210B THR* 3.9 1.2 - - - -
211B ASP* 3.0 40.4 + - - +
251B LEU* 3.7 28.0 - - + +
255B LYS* 4.1 6.7 - - + +
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Residues in contact with LYS 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 3.4 39.2 + - - +
39A ASN 5.7 0.8 + - - -
204B GLN 3.0 16.5 + - - +
205B THR* 3.8 7.9 - - + +
206B GLU 3.3 0.2 - - - -
207B GLU* 1.3 74.5 - - - +
209B TYR* 1.3 59.9 + - - +
211B ASP* 3.3 8.6 + - - +
212B THR* 2.9 37.2 + - - +
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Residues in contact with TYR 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B THR 3.0 18.3 + - - +
206B GLU* 3.7 7.0 - - - +
207B GLU 3.3 0.2 - - - -
208B LYS* 1.3 74.5 - - - +
210B THR* 1.3 67.4 + - - +
212B THR* 3.0 7.3 + - - -
213B LEU* 3.0 51.4 + - + +
243B LEU* 4.1 1.2 - - - +
247B HIS* 3.5 26.9 - + - -
280B TYR* 2.5 30.5 + - - -
328B VAL* 3.9 22.7 - - + -
329B PRO* 3.3 29.4 - - + +
332B ARG* 3.5 44.0 - - + +
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Residues in contact with THR 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLU* 2.9 30.3 + - - -
207B GLU 3.9 3.6 - - - -
209B TYR* 1.3 76.7 - - - +
211B ASP* 1.3 60.9 + - - +
213B LEU* 3.2 9.6 + - - +
214B GLY 2.9 24.1 + - - -
244B PHE* 3.6 14.0 - - + -
247B HIS* 3.8 13.4 + - + +
248B THR* 3.7 36.3 - - + +
251B LEU* 4.0 15.9 - - + +
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Residues in contact with ASP 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLU* 3.0 24.4 + - - +
208B LYS* 3.6 8.0 - - - +
210B THR* 1.3 80.6 - - - +
212B THR* 1.3 56.6 + - - +
214B GLY* 3.3 3.0 + - - +
215B SER* 2.8 28.8 + - - -
251B LEU* 6.1 0.9 - - - +
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Residues in contact with THR 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LYS* 2.9 25.1 + - - +
209B TYR* 3.0 11.7 + - + -
211B ASP* 1.3 72.5 - - - +
213B LEU* 1.3 67.3 + - + +
215B SER* 2.6 24.1 + - - +
216B ILE* 3.0 15.8 + - + +
325B LEU* 4.0 26.5 - - + -
328B VAL* 4.1 26.2 - - + +
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B TYR* 3.0 58.9 + - + +
210B THR* 3.5 8.7 - - - +
212B THR* 1.3 76.3 - - + +
214B GLY* 1.3 62.4 + - - +
216B ILE* 3.2 11.6 + - + +
217B GLN* 3.0 22.5 + - - +
240B ILE* 3.8 34.9 - - + +
243B LEU* 3.8 33.4 - - + +
244B PHE* 3.8 17.8 - - + +
247B HIS* 4.2 7.0 - - + +
329B PRO* 4.1 5.2 - - + -
----------------------------------------------------------
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Residues in contact with GLY 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B THR 2.9 11.6 + - - -
211B ASP* 3.3 5.1 + - - -
212B THR 3.3 0.2 - - - -
213B LEU* 1.3 76.8 - - - +
215B SER* 1.3 54.8 + - - +
217B GLN* 3.3 6.5 + - - +
218B GLN* 2.8 33.7 + - - +
244B PHE* 3.6 23.7 - - - -
----------------------------------------------------------
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Residues in contact with SER 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ASP 2.8 13.5 + - - -
212B THR* 2.6 28.7 + - - +
214B GLY* 1.3 72.1 - - - +
216B ILE* 1.3 60.1 + - - +
218B GLN* 5.0 0.4 - - - +
219B HIS* 2.7 57.8 - - - -
220B PHE* 3.7 2.6 - - - -
315B ALA* 4.8 10.4 - - - +
325B LEU* 4.8 7.6 - - - +
----------------------------------------------------------
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Residues in contact with ILE 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B THR* 3.0 20.2 + - + +
213B LEU* 3.2 14.6 + - + +
215B SER* 1.3 81.5 + - - +
217B GLN* 1.3 58.4 + - - +
220B PHE* 3.2 13.4 + - - +
221B MET* 2.9 28.2 + - + +
237B PHE* 4.1 26.9 - - + -
240B ILE* 4.1 33.2 - - + -
322B LEU* 4.4 8.7 - - + -
325B LEU* 3.8 49.1 - - + +
326B LEU* 4.8 3.4 - - + +
329B PRO* 5.3 0.9 - - + -
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Residues in contact with GLN 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LEU 3.0 12.3 + - - +
214B GLY* 3.6 9.8 - - - +
216B ILE* 1.3 77.5 - - - +
218B GLN* 1.3 71.8 + - - +
221B MET* 3.3 22.8 - - + +
222B LYS* 3.1 29.3 + - - +
240B ILE* 5.9 1.1 - - + +
241B GLU* 3.7 34.5 + - + +
244B PHE* 3.8 34.1 - - + -
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Residues in contact with GLN 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B GLY 2.8 19.6 + - - +
215B SER* 4.6 0.4 - - - +
217B GLN* 1.3 95.5 + - - +
219B HIS* 1.3 71.1 + - + +
220B PHE 3.5 0.2 - - - -
222B LYS* 3.8 24.3 - - + +
223B PRO* 3.4 18.2 - - - +
----------------------------------------------------------
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Residues in contact with HIS 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B SER* 2.7 36.4 - - - -
218B GLN* 1.3 82.3 + - + +
220B PHE* 1.3 59.2 + - + +
223B PRO* 3.5 8.4 - - - +
311B CYS* 3.1 30.1 - - - +
314B ARG* 4.1 27.0 + - + +
315B ALA* 3.6 36.9 + - + -
----------------------------------------------------------
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Residues in contact with PHE 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B SER 3.8 11.7 - - - -
216B ILE* 3.2 15.9 + - - +
218B GLN 3.5 0.2 - - - -
219B HIS* 1.3 81.3 - - - +
221B MET* 1.3 60.6 + - - +
222B LYS 3.5 1.1 - - - -
223B PRO* 3.5 1.8 - - - +
224B LEU* 3.0 39.2 + - + +
237B PHE* 4.5 4.5 - - + -
308B LEU* 4.2 12.6 - - + -
311B CYS* 3.6 22.4 - - + -
312B SER* 3.7 27.8 - - - -
315B ALA* 3.6 21.5 - - + -
316B ASN* 4.6 0.2 - - - -
320B PHE 4.5 1.6 - - - -
322B LEU* 3.8 49.4 - - + -
325B LEU* 3.5 28.9 - - + -
----------------------------------------------------------
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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