Contacts of the helix formed by residues 229 - 257 (chain B) in PDB entry 6B3I
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 SER 229 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B THR* 1.3 78.2 + - - +
230B GLY* 1.3 69.7 + - - +
232B LEU* 3.7 9.7 + - - +
233B GLN* 3.3 22.1 + - - +
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Residues in contact with GLY 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B SER* 1.3 75.4 + - - +
231B ASP* 1.3 67.0 + - - -
233B GLN* 3.3 12.0 + - - +
234B LYS* 3.3 11.6 + - - +
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Residues in contact with ASP 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B THR 4.6 5.0 - - - +
105B ASP* 5.1 2.6 - - - +
106B GLU* 3.6 30.0 + - - +
110B ILE* 3.4 17.3 - - + +
148B LEU* 3.7 24.7 - - + +
230B GLY* 1.3 70.6 - - - -
232B LEU* 1.3 59.3 + - - +
234B LYS* 3.2 17.8 + - - +
235B ALA* 3.0 25.3 + - - +
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ASN* 3.7 42.4 - - + +
148B LEU* 4.2 13.6 - - + +
151B ILE* 4.3 8.1 - - + -
190B GLU* 3.8 27.1 - - + +
228B THR* 4.5 7.9 - - + -
229B SER 3.7 7.8 + - - +
230B GLY 3.2 0.4 - - - -
231B ASP* 1.3 78.8 - - - +
233B GLN* 1.3 62.4 + - - +
235B ALA* 3.2 2.2 + - + +
236B TYR* 3.0 60.1 + - + +
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Residues in contact with GLN 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ILE* 4.0 7.9 - - + +
225B GLU* 3.5 25.7 + - - +
228B THR* 2.7 48.3 + - - +
229B SER* 3.3 18.3 + - - +
230B GLY 3.3 10.6 + - - +
232B LEU* 1.3 79.0 - - - +
234B LYS* 1.3 58.9 + - - +
236B TYR* 3.3 1.2 + - - +
237B LEU* 2.9 54.3 + - + +
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Residues in contact with LYS 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASP* 4.8 4.6 + - - -
107B SER* 3.8 28.9 - - - +
110B ILE* 3.9 23.3 - - + -
230B GLY 3.3 9.1 + - - +
231B ASP* 3.2 20.8 + - - +
233B GLN* 1.3 79.1 - - - +
235B ALA* 1.3 53.8 + - - +
237B LEU* 4.0 7.1 - - - +
238B THR* 2.5 45.1 + - - +
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ILE* 3.8 20.4 - - + +
114B CYS* 4.0 10.5 - - - -
148B LEU* 4.3 16.8 - - + -
151B ILE* 4.7 12.8 - - + -
152B LEU* 5.1 0.9 - - + -
231B ASP 3.0 13.1 + - - +
232B LEU* 3.6 8.1 - - - +
233B GLN 3.2 0.2 - - - -
234B LYS* 1.3 74.1 - - - +
236B TYR* 1.3 64.4 + - + +
238B THR* 3.2 2.3 + - - -
239B LEU* 2.9 36.0 + - + +
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Residues in contact with TYR 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ASN* 5.0 0.2 - - - +
151B ILE* 4.4 9.9 - - + -
190B GLU* 3.5 21.2 + - + +
193B PHE* 3.6 31.6 - + + -
194B ASN* 2.4 31.1 + - - -
197B LEU* 3.7 18.7 - - + +
224B ILE* 3.7 25.4 - - + -
228B THR* 3.9 31.2 - - + -
232B LEU* 3.0 42.8 + - + +
235B ALA* 1.3 77.7 - - + +
237B LEU* 1.3 58.9 + - - +
239B LEU* 3.3 7.6 + - + +
240B VAL* 3.0 33.1 + - - +
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Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLU* 4.0 34.3 - - + +
224B ILE* 3.7 27.8 - - + -
225B GLU* 4.2 15.0 - - + +
233B GLN* 2.9 44.1 + - + +
234B LYS* 4.0 6.3 - - - +
236B TYR* 1.3 75.9 - - - +
238B THR* 1.3 55.7 + - - +
240B VAL* 3.3 3.1 + - - +
241B ARG* 2.8 39.8 + - + +
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Residues in contact with THR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ILE* 3.7 16.5 - - + +
114B CYS* 3.6 22.4 - - + -
115B THR* 4.1 10.5 - - + -
234B LYS* 2.5 30.3 + - - +
235B ALA 3.6 4.5 - - - -
237B LEU* 1.3 77.9 - - - +
239B LEU* 1.3 55.5 + - - +
241B ARG* 3.8 5.4 - - - +
242B CYS* 2.8 33.1 + - - +
249B TYR* 3.7 36.5 + - + +
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Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B CYS* 3.7 38.8 - - + +
151B ILE* 4.2 27.6 - - + -
155B LEU* 4.1 8.1 - - + -
160B ARG* 3.6 26.9 - - - +
197B LEU* 3.9 33.9 - - + +
202B TYR* 5.3 3.9 - - + -
205B LEU* 5.0 2.8 - - + +
209B PHE* 5.5 0.9 - - - -
235B ALA 2.9 23.9 + - - +
236B TYR* 3.7 7.9 - - + +
238B THR* 1.3 76.1 - - - +
240B VAL* 1.3 62.3 + - - +
242B CYS* 3.9 1.2 - - - +
243B ALA* 3.1 24.4 + - - +
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU* 4.1 10.8 - - + -
209B PHE* 3.9 26.6 - - + -
220B ILE* 3.9 17.5 - - + -
221B GLU* 3.8 25.1 - - + -
224B ILE* 3.7 21.3 - - + -
236B TYR 3.0 21.3 + - - +
237B LEU* 3.7 5.8 - - - +
239B LEU* 1.3 73.7 - - - +
241B ARG* 1.3 66.9 + - - +
243B ALA* 3.2 2.9 + - - +
244B GLN* 3.0 36.3 + - - +
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Residues in contact with ARG 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLU* 3.9 22.2 - - + +
237B LEU* 2.8 30.8 + - + +
238B THR* 3.9 3.4 - - - +
240B VAL* 1.3 72.3 - - + +
242B CYS* 1.3 58.1 + - - +
244B GLN* 4.1 6.0 - - - +
245B ASP 2.8 37.9 + - - +
248B ASP* 3.0 27.9 + - - -
249B TYR* 3.6 43.3 - - + +
252B GLU* 3.0 37.9 + - - +
290B LYS* 4.9 0.2 - - - +
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Residues in contact with CYS 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B CYS 3.6 22.4 - - - +
115B THR* 3.7 16.8 - - + -
202B TYR* 3.7 29.4 - - + -
238B THR 2.8 18.2 + - - +
239B LEU 3.9 3.6 - - - +
241B ARG* 1.3 77.2 - - - +
243B ALA* 1.3 61.1 + - - +
245B ASP 4.0 0.2 + - - -
246B CYS* 3.5 48.2 + - - +
249B TYR* 4.9 2.6 - - + +
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Residues in contact with ALA 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B TYR* 3.8 29.1 - - + +
205B LEU* 3.9 21.8 - - + -
206B ARG* 2.8 34.7 + - - +
209B PHE* 4.1 11.4 - - + -
239B LEU 3.1 17.9 + - - +
240B VAL 3.2 3.8 + - - +
242B CYS* 1.3 80.1 - - - +
244B GLN* 1.3 58.4 + - - +
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Residues in contact with GLN 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ARG* 4.1 21.7 + - + +
209B PHE* 3.5 42.7 - - + +
220B ILE* 5.0 1.6 - - - +
221B GLU* 3.7 24.8 + - - +
240B VAL* 3.0 22.4 + - - +
241B ARG* 4.1 5.4 - - - +
242B CYS 4.4 0.2 - - - -
243B ALA* 1.3 79.9 - - - +
245B ASP* 1.3 65.4 + - + +
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Residues in contact with ASP 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ARG* 2.8 21.1 + - - +
243B ALA 3.6 0.2 - - - -
244B GLN* 1.3 79.1 - - + +
246B CYS* 1.3 63.0 + - - +
247B GLU* 3.4 14.6 + - - +
248B ASP* 3.2 31.9 + - + +
249B TYR* 3.3 16.5 + - - +
286B LYS* 3.2 31.0 + - - +
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Residues in contact with CYS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B THR* 4.2 6.7 - - - -
242B CYS* 3.5 49.6 + - - +
245B ASP* 1.3 71.3 + - - +
247B GLU* 1.3 74.2 + - - +
249B TYR* 3.3 5.3 + - - +
250B PHE* 3.1 54.8 + - - -
275B ARG* 4.0 10.8 - - - +
279B ASP* 4.5 3.1 - - - +
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Residues in contact with GLU 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ASP* 3.3 6.6 + - - +
246B CYS* 1.3 86.7 + - - +
248B ASP* 1.3 56.8 + - - +
250B PHE* 3.4 1.7 + - - +
251B ALA* 3.0 30.0 + - - +
279B ASP* 3.7 28.9 - - - +
282B GLY* 3.5 32.1 - - - +
283B ILE* 3.6 12.9 - - - +
286B LYS* 3.7 24.7 - - + +
----------------------------------------------------------
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Residues in contact with ASP 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ARG* 3.0 33.1 + - - -
245B ASP* 3.2 33.8 + - + +
247B GLU* 1.3 77.2 - - - +
249B TYR* 1.3 62.6 + - - +
251B ALA* 3.5 3.3 + - - +
252B GLU* 3.2 18.2 + - - +
286B LYS* 4.1 15.0 - - + +
290B LYS* 3.3 32.3 - - - +
----------------------------------------------------------
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Residues in contact with TYR 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ILE* 5.7 0.2 - - - +
111B GLU* 3.8 16.6 - - + +
115B THR* 3.7 24.5 - - + -
238B THR* 3.7 31.0 + - + +
241B ARG* 3.6 41.9 - - + +
242B CYS 4.9 1.6 - - - +
245B ASP 3.3 9.3 + - - +
246B CYS* 3.3 11.6 + - - +
247B GLU 3.2 0.4 - - - -
248B ASP* 1.3 79.7 + - - +
250B PHE* 1.3 85.3 + + - +
252B GLU* 3.2 5.8 + - + +
253B ARG* 3.0 64.4 + - + +
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Residues in contact with PHE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLU* 4.3 15.9 - - + -
115B THR* 3.6 27.1 - - + -
116B ARG* 4.0 3.8 - - - -
246B CYS* 3.1 39.7 + - - +
249B TYR* 1.3 91.2 - + - +
251B ALA* 1.3 60.8 + - - +
253B ARG* 3.3 3.5 + - + +
254B LEU* 2.8 34.5 + - - +
271B ILE* 3.8 32.0 - - + +
274B THR* 5.9 0.2 - - - -
275B ARG* 3.3 45.8 - - + -
279B ASP* 4.3 0.2 - - - -
283B ILE* 3.6 28.5 - - + -
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B GLU 3.0 19.0 + - - +
248B ASP* 3.7 6.7 - - - +
249B TYR 3.3 0.2 - - - -
250B PHE* 1.3 76.7 - - - +
252B GLU* 1.3 57.7 + - - +
254B LEU* 3.4 1.6 + - - -
255B TYR* 3.0 24.3 + - - +
283B ILE* 3.9 12.2 - - - +
286B LYS 4.3 4.0 - - - +
287B PHE* 3.4 50.5 - - + +
290B LYS* 5.1 2.2 - - + -
291B TYR* 4.3 4.5 - - + -
----------------------------------------------------------
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Residues in contact with GLU 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ARG* 3.0 31.8 + - - +
248B ASP 3.2 8.7 + - - +
249B TYR* 3.2 9.6 + - + +
251B ALA* 1.3 76.7 - - - +
253B ARG* 1.3 60.4 + - + +
255B TYR* 3.2 0.9 + - - +
256B LYS* 2.9 63.3 + - + +
290B LYS* 3.6 19.5 + - - +
291B TYR* 3.3 20.8 + - - +
----------------------------------------------------------
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Residues in contact with ARG 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B SER* 4.5 19.6 + - - -
108B VAL* 5.7 0.2 - - - +
111B GLU* 2.4 33.4 + - - +
249B TYR* 3.0 56.9 + - + +
250B PHE* 3.3 8.0 + - - +
252B GLU* 1.3 76.8 - - + +
254B LEU* 1.3 61.3 + - - +
256B LYS* 4.1 9.3 - - - +
257B SER* 3.2 26.4 + - - +
267B THR* 3.8 18.4 + - - +
270B ARG* 3.8 9.5 - - - +
271B ILE* 3.8 15.5 - - + -
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Residues in contact with LEU 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B PHE 2.8 15.2 + - - +
251B ALA* 3.6 5.6 - - - +
253B ARG* 1.3 75.5 - - - +
255B TYR* 1.3 62.9 + - - +
257B SER* 2.8 18.8 + - - +
258B MET* 3.7 15.7 - - - +
268B LEU* 3.6 28.8 - - + +
271B ILE* 3.7 36.6 - - + -
272B ILE* 4.3 11.9 - - + -
280B LEU* 5.5 1.8 - - + -
283B ILE* 3.6 31.2 - - + -
287B PHE* 4.3 1.8 - - + -
295B LEU* 3.7 33.4 - - + -
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Residues in contact with TYR 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ALA 3.0 11.3 + - - +
252B GLU 3.6 1.1 - - - +
254B LEU* 1.3 77.4 - - - +
256B LYS* 1.3 73.2 + - + +
258B MET* 3.0 15.1 + - - +
259B LYS* 3.4 47.6 + - + +
287B PHE* 3.7 8.0 - + + -
291B TYR* 3.5 60.6 - + + +
293B LYS* 4.2 13.1 + - - -
298B MET* 3.6 39.7 - - + -
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Residues in contact with LYS 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B GLU* 2.9 53.8 + - + +
253B ARG* 4.4 10.3 - - - +
255B TYR* 1.3 83.1 - - + +
257B SER* 1.3 59.3 + - - +
258B MET 3.2 1.1 + - - -
259B LYS* 4.0 11.6 + - + +
291B TYR* 5.3 1.0 + - - -
401B EDO 3.8 16.7 + - - -
----------------------------------------------------------
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Residues in contact with SER 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ARG* 3.2 16.9 + - - +
254B LEU* 2.8 23.9 + - - -
255B TYR 3.2 0.2 - - - -
256B LYS* 1.3 76.8 - - - +
258B MET* 1.3 55.5 - - - +
263B THR* 3.3 8.1 - - - +
264B ASP* 3.0 45.0 + - - +
267B THR* 4.1 17.2 - - - +
268B LEU* 4.0 14.7 + - - +
401B EDO 4.2 8.1 - - - -
----------------------------------------------------------
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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