Contacts of the helix formed by residues 227 - 260 (chain B) in PDB entry 2E52
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 LYS 227 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 3.0 52.2 + - + +
220B MET* 3.5 24.5 - - + +
226B ASP* 1.3 73.3 - - - +
228B ASP* 1.3 56.3 + - - +
230B LEU* 3.2 2.0 + - - +
231B ASN* 2.8 39.3 + - + +
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Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ASP* 3.3 9.7 + - - +
227B LYS* 1.3 81.0 - - - +
229B THR* 1.3 57.5 + - - +
231B ASN* 3.5 5.5 + - - +
232B GLN* 2.9 30.0 + - - +
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Residues in contact with THR 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 4.2 14.4 - - + -
225B ILE* 3.9 15.5 - - + -
226B ASP* 2.4 33.8 + - - -
228B ASP* 1.3 74.9 - - - +
230B LEU* 1.3 63.5 + - - +
232B GLN* 2.8 39.5 + - - +
233B LEU* 3.0 23.8 + - + +
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Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 3.8 21.1 - - + -
171B HIS* 5.3 2.2 - - + -
174B ILE* 3.8 37.2 - - + -
216B ASN* 4.2 21.3 - - - +
219B PHE* 4.2 16.4 - - + -
220B MET* 3.5 29.2 - - + -
225B ILE* 3.9 10.9 - - + +
226B ASP 3.0 12.5 + - - +
227B LYS 3.7 5.8 - - - +
229B THR* 1.3 77.0 - - - +
231B ASN* 1.3 57.5 + - - +
233B LEU* 3.3 2.9 + - - -
234B LEU* 2.9 38.0 + - + +
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Residues in contact with ASN 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ASN* 4.5 4.9 - - - +
297A LEU* 3.5 25.7 - - - +
299A LEU* 3.8 21.5 - - + +
227B LYS* 2.8 22.4 + - + +
228B ASP* 3.7 7.0 - - - +
230B LEU* 1.3 73.6 - - - +
232B GLN* 1.3 65.9 + - - +
234B LEU* 3.9 4.1 - - - +
235B GLN* 3.0 28.6 + - - +
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Residues in contact with GLN 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 6.0 0.4 - - - +
228B ASP 2.9 19.3 + - - +
229B THR* 2.8 37.7 + - - +
231B ASN* 1.3 75.4 - - - +
233B LEU* 1.3 84.8 + - - +
235B GLN* 3.3 6.9 + - - +
236B LYS* 3.1 55.5 + - - +
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG* 4.7 8.0 + - - +
174B ILE* 3.8 42.2 - - + +
177B GLN* 4.4 20.6 - - + -
178B LEU* 3.9 30.3 - - + -
229B THR* 3.0 23.7 + - + +
230B LEU* 3.3 4.0 + - - +
232B GLN* 1.3 97.3 - - - +
234B LEU* 1.3 57.2 + - - +
236B LYS* 3.4 15.2 + - + +
237B GLU* 3.0 32.1 + - - +
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU* 3.7 34.3 - - + +
299A LEU* 4.2 13.9 - - + -
145B PHE* 5.0 9.9 - - + -
146B PHE* 5.0 12.3 - - + -
170B GLU* 4.6 9.6 - - + -
171B HIS* 5.2 7.2 - - + +
174B ILE* 3.7 14.8 - - + -
216B ASN* 4.5 8.7 - - - +
230B LEU* 2.9 34.5 + - + +
231B ASN 3.9 2.7 - - - +
233B LEU* 1.3 74.1 - - - +
235B GLN* 1.3 59.5 + - - +
237B GLU* 3.3 21.9 + - + +
238B ILE* 3.0 33.6 + - - +
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Residues in contact with GLN 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LYS* 5.3 7.3 + - - +
297A LEU* 4.1 19.9 - - - +
231B ASN* 3.0 23.4 + - - +
232B GLN* 3.5 8.3 - - - +
233B LEU 3.3 0.2 - - - -
234B LEU* 1.3 74.5 - - - +
236B LYS* 1.3 60.2 + - + +
238B ILE* 3.2 29.0 + - - +
239B ASN* 3.0 48.2 + - - +
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Residues in contact with LYS 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG* 4.7 4.7 - - - +
232B GLN* 3.1 38.6 + - - +
233B LEU* 3.6 16.3 - - + +
235B GLN* 1.3 74.8 - - + +
237B GLU* 1.3 58.2 + - - +
239B ASN* 3.4 13.0 + - - +
240B PHE* 3.0 49.5 + - + -
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG* 3.7 29.5 + - + +
146B PHE* 5.4 1.6 - - + -
170B GLU* 2.7 55.7 - - + +
173B ALA* 3.3 18.4 - - - +
174B ILE* 3.5 22.1 - - - +
233B LEU 3.0 13.6 + - - +
234B LEU* 3.5 13.3 - - + +
235B GLN 3.3 0.2 - - - -
236B LYS* 1.3 76.3 - - - +
238B ILE* 1.3 56.2 + - - +
240B PHE* 3.3 7.6 + - - +
241B ILE* 3.0 35.6 + - + +
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Residues in contact with ILE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ILE* 3.5 42.2 - - + +
292A LYS* 4.2 17.7 - - + +
293A SER 5.9 0.2 - - - +
297A LEU* 3.6 30.7 - - + -
146B PHE* 3.6 23.8 - - + -
234B LEU 3.0 15.7 + - - +
235B GLN* 3.2 28.0 + - - +
237B GLU* 1.3 74.2 - - - +
239B ASN* 1.3 62.0 + - - +
241B ILE* 3.2 10.4 + - - +
242B GLU* 2.9 28.6 + - + +
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Residues in contact with ASN 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B GLN* 3.0 38.6 + - - +
236B LYS* 3.7 13.9 - - - +
237B GLU 3.3 0.2 - - - -
238B ILE* 1.3 77.3 - - - +
240B PHE* 1.3 57.2 + - + +
242B GLU* 3.2 15.0 + - - +
243B GLU* 2.9 44.2 + - + +
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Residues in contact with PHE 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG* 3.6 50.5 - - + -
236B LYS* 3.0 34.5 + - + -
237B GLU* 3.6 6.7 - - - +
239B ASN* 1.3 76.3 - - + +
241B ILE* 1.3 59.0 + - + +
243B GLU* 3.5 27.0 + - - +
244B ARG* 3.0 28.4 + - - +
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Residues in contact with ILE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PHE* 3.9 14.8 - - + -
288A ILE* 3.8 10.1 - - + -
291A ILE* 3.8 20.2 - - + -
44B ARG 5.5 4.7 - - - +
48B ILE* 4.3 23.6 - - + -
114B LEU* 4.4 3.3 - - + +
146B PHE* 3.8 34.3 - - + -
170B GLU* 3.9 17.5 - - + +
237B GLU* 3.0 22.5 + - + +
238B ILE 3.5 5.8 - - - +
240B PHE* 1.3 72.8 - - + +
242B GLU* 1.3 60.8 + - - +
244B ARG* 3.3 8.0 + - - +
245B SER* 2.9 26.9 + - - -
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Residues in contact with GLU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ILE* 3.8 24.3 - - + +
291A ILE* 5.8 0.4 - - + -
292A LYS* 2.8 44.4 + - + +
238B ILE* 2.9 18.5 + - + +
239B ASN* 3.2 15.5 + - - +
241B ILE* 1.3 77.3 - - - +
243B GLU* 1.3 62.8 + - + +
245B SER* 2.6 25.9 + - - +
246B LEU* 3.5 13.7 + - + +
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Residues in contact with GLU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ASN* 2.9 29.4 + - - +
240B PHE* 3.7 31.5 - - - +
242B GLU* 1.3 73.9 - - - +
244B ARG* 1.3 64.5 + - - +
246B LEU* 3.3 26.0 + - + +
247B ILE* 3.5 14.9 - - - +
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Residues in contact with ARG 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 3.7 33.5 - - - +
9B LEU* 5.7 0.2 - - - +
45B SER* 3.0 32.5 + - - +
48B ILE* 2.8 50.9 + - + +
50B PRO* 3.7 17.0 - - - +
114B LEU* 4.7 1.1 - - + -
240B PHE 3.0 18.9 + - - +
241B ILE* 3.5 8.3 - - - +
243B GLU* 1.3 78.5 - - - +
245B SER* 1.3 61.4 + - - +
246B LEU 3.3 1.0 + - - -
247B ILE* 3.3 24.9 + - - +
248B GLU* 2.8 42.2 + - + +
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Residues in contact with SER 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ILE* 4.0 7.1 - - - +
288A ILE* 3.6 28.9 - - - +
114B LEU* 3.6 20.6 - - - -
241B ILE 2.9 13.6 + - - -
242B GLU* 2.6 25.4 + - - +
244B ARG* 1.3 75.7 - - - +
246B LEU* 1.3 61.8 + - - +
248B GLU* 3.8 1.3 - - - +
249B LYS* 2.8 35.3 + - - +
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Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B GLU* 3.8 17.5 - - + +
243B GLU* 3.6 15.7 - - + +
244B ARG 3.2 0.8 - - - -
245B SER* 1.3 83.0 + - - +
247B ILE* 1.3 65.5 + - + +
249B LYS* 4.1 9.8 - - + +
250B GLU* 3.1 25.5 + - - +
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Residues in contact with ILE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLU 3.5 18.8 - - - +
244B ARG* 3.3 17.4 + - - +
246B LEU* 1.3 80.0 - - + +
248B GLU* 1.3 74.5 + - - +
250B GLU* 3.3 6.6 + - - +
251B TYR* 3.2 21.0 + - - +
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ILE* 4.1 5.6 - - + -
48B ILE* 4.8 2.9 - - + -
49B LEU 4.6 1.1 - - - -
50B PRO* 3.6 9.1 - - - +
51B GLU* 2.8 58.0 + - + +
52B ALA* 4.4 1.6 + - - +
114B LEU* 4.2 21.5 - - + -
244B ARG* 2.8 50.3 + - - +
245B SER 3.4 5.6 + - - +
247B ILE* 1.3 83.1 - - - +
249B LYS* 1.3 64.2 + - - +
251B TYR* 3.5 13.7 + - - +
252B TRP* 3.8 5.5 - - - -
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Residues in contact with LYS 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ILE* 4.0 24.0 - - + +
284A ILE* 4.0 29.1 - - + +
285A ASP* 2.8 41.0 + - - +
245B SER* 2.8 19.3 + - - +
246B LEU* 4.1 10.0 - - + +
248B GLU* 1.3 74.1 - - - +
250B GLU* 1.3 67.2 + - - +
252B TRP* 3.1 6.6 + - - +
253B LYS* 3.0 45.7 + - + +
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Residues in contact with GLU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B LEU 3.1 20.0 + - - +
247B ILE* 3.6 6.5 - - - +
248B GLU 3.3 0.2 - - - -
249B LYS* 1.3 79.2 - - - +
251B TYR* 1.3 62.4 + - - +
253B LYS* 3.2 27.5 + - - +
254B LYS* 3.0 33.1 + - + +
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Residues in contact with TYR 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLU* 3.8 25.2 + - + -
52B ALA* 3.7 35.7 + - + +
247B ILE 3.2 12.4 + - - +
248B GLU* 3.5 13.2 - - - +
250B GLU* 1.3 77.2 - - - +
252B TRP* 1.3 91.8 + + - +
254B LYS* 3.5 7.3 + - + +
255B GLN* 3.1 62.7 + - + +
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Residues in contact with TRP 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ILE* 4.2 7.9 - - + -
277A MET* 3.7 48.0 - - + +
280A LYS* 3.4 44.4 - - + +
281A ILE* 3.7 23.1 - - + +
284A ILE* 4.3 7.4 - - + -
51B GLU* 2.7 41.6 + - + +
113B ARG* 6.1 1.3 - - - -
115B SER* 5.5 0.2 - - - -
248B GLU 3.8 13.2 - - - -
249B LYS 3.1 3.7 + - - +
251B TYR* 1.3 103.0 - + - +
253B LYS* 1.3 61.0 + - - +
255B GLN* 3.9 5.7 - - + +
256B ILE* 2.9 33.4 + - - +
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Residues in contact with LYS 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ILE* 3.9 21.3 - - + -
249B LYS* 3.0 38.1 + - - +
250B GLU* 3.2 32.2 + - - +
252B TRP* 1.3 79.1 - - - +
254B LYS* 1.3 62.1 + - - +
256B ILE* 3.4 16.4 - - + +
257B ASN* 3.4 10.0 + - - +
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Residues in contact with LYS 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B GLU* 3.0 25.3 + - + +
251B TYR* 3.6 8.3 - - + +
253B LYS* 1.3 76.1 - - - +
255B GLN* 1.3 69.6 + - - +
257B ASN* 3.4 7.0 + - - +
258B ILE* 3.3 41.8 + - + +
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Residues in contact with GLN 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A MET* 3.8 20.4 - - + +
251B TYR* 3.1 57.8 + - + +
252B TRP* 3.4 8.7 + - + +
254B LYS* 1.3 84.5 - - - +
256B ILE* 1.3 57.9 + - - +
258B ILE* 3.3 21.1 + - - +
259B ILE* 3.0 45.9 + - - +
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Residues in contact with ILE 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LEU* 4.0 23.1 - - + -
277A MET* 3.7 13.9 - - + -
278A SER* 3.8 39.0 - - - +
281A ILE* 4.7 7.2 - - + -
252B TRP 2.9 16.8 + - - +
253B LYS* 3.4 16.6 - - + +
255B GLN* 1.3 76.3 - - - +
257B ASN* 1.3 61.7 + - + +
259B ILE* 3.9 1.7 - - - +
260B LYS* 3.0 60.9 + - + +
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Residues in contact with ASN 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LYS 3.4 7.4 + - - +
254B LYS* 3.4 10.9 + - - +
255B GLN 3.3 0.6 - - - -
256B ILE* 1.3 83.9 - - + +
258B ILE* 1.3 65.8 + - - +
260B LYS* 3.6 6.0 + - - +
261B ASN* 2.9 51.2 + - - +
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Residues in contact with ILE 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LYS* 3.3 34.3 + - + +
255B GLN* 3.3 28.4 + - - +
257B ASN* 1.3 81.8 - - - +
259B ILE* 1.3 69.8 + - + +
261B ASN* 3.0 15.9 + - - +
262B PHE* 3.4 32.3 + - + -
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Residues in contact with ILE 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ILE* 3.7 12.2 - - + +
271A LEU* 3.9 22.9 - - + -
272A LEU* 3.8 33.2 - - + -
277A MET* 3.7 23.8 - - + -
255B GLN* 3.0 41.2 + - - +
256B ILE* 4.0 3.8 - - - +
258B ILE* 1.3 79.4 - - + +
260B LYS* 1.3 63.7 + - - +
261B ASN 3.1 1.4 + - - -
262B PHE* 3.1 46.6 + - + +
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Residues in contact with LYS 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ARG* 4.6 3.8 + - - -
268A ILE* 3.7 22.9 - - + +
272A LEU* 4.1 21.1 - - + -
278A SER* 5.9 0.8 - - - -
256B ILE* 3.0 50.7 + - + +
257B ASN* 4.0 7.2 - - - +
258B ILE 3.3 0.2 - - - -
259B ILE* 1.3 76.0 - - - +
261B ASN* 1.3 64.9 + - - +
262B PHE 3.5 0.2 - - - -
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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).
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