Contacts of the helix formed by residues 227 - 252 (chain B) in PDB entry 4O9U
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 ASN 227 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 3.9 14.4 + - - +
48A GLY* 3.6 17.8 - - - -
51A VAL* 4.9 7.3 - - - +
8B TYR* 4.2 7.4 - - - -
49B TRP* 5.0 5.3 - - + -
222B GLY 3.2 5.8 - - - +
225B VAL* 2.7 17.9 + - + +
226B GLY* 1.3 73.4 - - - -
228B PRO* 1.4 59.0 - - - +
229B ALA* 3.4 9.7 + - - +
230B LEU* 3.1 47.7 + - + +
231B MET* 3.0 32.9 + - - +
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Residues in contact with PRO 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 5.2 1.1 - - + -
5B GLN* 3.2 35.7 - - - +
8B TYR* 3.8 20.0 - - + -
49B TRP* 5.2 2.2 - - + -
226B GLY 3.5 9.6 - - - +
227B ASN* 1.4 82.7 - - - +
229B ALA* 1.3 59.3 + - - +
231B MET* 3.2 16.7 + - - +
232B VAL* 2.9 35.9 + - - +
10C TYR* 3.3 32.1 - - + +
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Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 4.7 9.1 - - + +
47A VAL* 5.0 7.2 - - + -
8B TYR* 3.9 31.8 - - + +
11B VAL* 4.1 22.4 - - + -
15B PHE* 4.9 1.6 - - - -
42B ALA* 5.1 3.6 - - + -
227B ASN* 3.4 7.4 + - - +
228B PRO* 1.3 78.1 - - - +
230B LEU* 1.3 57.9 + - + +
232B VAL* 3.3 6.3 + - - +
233B ALA* 3.0 33.0 + - - +
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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
----------------------------------------------------------
44A VAL* 3.4 47.8 - - + +
45A VAL* 3.6 13.7 - - + +
47A VAL* 5.4 1.8 - - + -
48A GLY* 3.8 15.0 - - - +
99B ILE* 5.0 8.5 - - + -
218B VAL* 3.5 14.3 - - + +
219B GLY* 4.1 0.3 - - - -
221B GLU* 4.9 3.6 - - + +
222B GLY* 3.5 23.1 - - - +
225B VAL* 5.1 4.5 - - + -
227B ASN* 3.1 40.8 + - + +
229B ALA* 1.3 72.7 - - + +
231B MET* 1.3 62.0 + - - +
234B GLY* 2.9 30.7 + - - -
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Residues in contact with MET 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLU 4.7 13.5 - - - +
3A PHE* 5.3 5.8 - - + -
8A ALA* 5.4 3.4 - - - -
11A ILE* 5.3 11.4 - - + +
15A THR* 5.0 1.7 + - - +
219B GLY* 4.5 5.1 - - - -
222B GLY* 3.3 22.2 - - - +
223B PHE* 3.6 52.8 - - + +
225B VAL 3.6 5.8 - - - +
226B GLY* 4.1 6.1 - - - -
227B ASN 3.0 36.0 + - - +
228B PRO* 3.2 20.6 + - + +
230B LEU* 1.3 76.1 - - - +
232B VAL* 1.3 64.1 + - + +
235B THR* 3.5 18.5 + - - -
10C TYR* 6.3 1.1 - - - -
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 5.7 6.3 - - + -
15A THR* 3.7 12.8 - - + +
12B ALA* 3.6 49.8 - - + +
15B PHE* 5.1 4.9 - - + -
16B ILE* 4.9 10.5 - - + -
228B PRO 2.9 21.8 + - - +
229B ALA* 3.6 4.7 - - - +
230B LEU 3.2 0.2 - - - -
231B MET* 1.3 80.6 - - + +
233B ALA* 1.3 61.9 + - - +
234B GLY 3.4 0.2 + - - -
236B LEU* 3.1 26.4 + - + +
10C TYR* 3.7 22.0 - - + -
14C LEU* 5.6 8.3 - - + -
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 3.9 12.6 - - + +
42A HIS* 4.8 0.6 - - - +
44A VAL* 3.8 31.2 - - + -
15B PHE* 3.9 18.8 - - + -
218B VAL* 5.0 0.2 - - - -
229B ALA 3.0 15.9 + - - +
232B VAL* 1.3 77.8 - - - +
234B GLY* 1.3 64.4 + - - +
236B LEU* 3.6 5.9 - - - +
237B VAL* 3.1 28.6 + - - +
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Residues in contact with GLY 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B GLY* 2.8 25.3 - - - +
218B VAL* 3.4 19.4 - - - +
219B GLY* 3.7 4.0 - - - -
230B LEU* 2.9 16.2 + - - +
232B VAL 3.3 0.2 - - - -
233B ALA* 1.3 76.3 - - - +
235B THR* 1.3 58.5 + - - +
237B VAL* 3.1 4.4 + - - -
238B GLY 2.8 22.5 + - - -
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Residues in contact with THR 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.7 36.8 + - + -
15A THR* 3.4 27.7 - - - +
16A ALA* 5.3 1.6 - - - -
215B GLY 4.6 1.1 - - - -
216B MET* 5.1 5.4 - - - +
219B GLY* 4.0 11.3 - - - -
220B PHE* 5.1 4.7 - - + -
223B PHE* 3.9 19.4 - - + -
231B MET 3.5 10.1 + - - +
234B GLY* 1.3 71.9 - - - +
236B LEU* 1.3 59.7 + - - +
237B VAL 3.3 0.2 - - - -
238B GLY* 3.7 6.1 - - - +
239B ALA* 3.0 31.9 + - - +
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Residues in contact with LEU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR* 3.9 16.6 - - + -
18A LEU* 4.9 4.3 - - + -
19A GLY* 3.9 26.2 - - - +
22A LEU* 4.4 7.4 - - + -
41A ILE* 4.9 11.7 - - + -
15B PHE* 4.7 6.3 - - + +
16B ILE* 4.6 26.2 - - + +
19B LEU* 3.6 34.4 - - + +
232B VAL* 3.1 22.1 + - + +
233B ALA* 3.6 7.9 - - - +
234B GLY 3.1 0.2 - - - -
235B THR* 1.3 81.6 + - - +
237B VAL* 1.3 58.6 + - + +
240B ALA* 3.3 22.0 + - - +
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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
----------------------------------------------------------
38A SER* 3.3 35.8 - - - +
41A ILE* 3.6 24.2 - - + -
42A HIS* 3.4 37.7 - - + +
19B LEU* 6.3 0.9 - - + -
211B ASN* 3.9 11.0 - - - +
212B ALA* 4.6 0.2 - - - -
215B GLY* 4.1 1.3 - - - -
233B ALA 3.1 18.9 + - - +
234B GLY 3.7 3.1 - - - +
236B LEU* 1.3 79.1 - - + +
238B GLY* 1.3 53.8 + - - +
240B ALA* 3.3 5.1 + - - +
241B GLY* 2.7 32.9 + - - -
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Residues in contact with GLY 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ALA* 3.8 13.6 - - - +
215B GLY* 4.0 0.2 - - - -
216B MET* 3.8 28.9 - - - -
234B GLY 2.8 15.2 + - - -
235B THR* 3.6 2.7 + - - -
236B LEU 3.5 0.2 - - - -
237B VAL* 1.3 77.9 - - - +
239B ALA* 1.3 56.9 + - - +
241B GLY* 3.1 14.9 + - - -
242B THR* 3.2 16.5 + - - +
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Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR 4.3 2.7 - - - +
16A ALA* 3.4 35.7 - - + +
19A GLY* 4.7 3.4 - - - -
20A TYR* 4.5 13.4 - - + +
235B THR* 3.0 20.3 + - - +
238B GLY* 1.3 73.0 - - - +
240B ALA* 1.3 60.6 + - - +
242B THR* 3.5 14.5 + - - -
243B LEU* 3.8 11.4 + - - +
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY 4.2 5.1 + - - +
23A ILE* 3.7 34.0 - - + +
38A SER* 5.2 7.6 - - - -
19B LEU* 4.7 9.0 - - + -
236B LEU 3.3 20.7 + - - +
237B VAL* 3.3 7.6 + - - +
238B GLY 3.2 0.2 - - - -
239B ALA* 1.3 78.6 - - - +
241B GLY* 1.3 57.9 + - - +
243B LEU* 3.5 3.1 + - - +
244B LEU* 2.8 33.2 + - + +
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Residues in contact with GLY 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A SER* 5.7 0.2 - - - -
208B SER 3.6 4.8 - - - +
211B ASN* 5.0 2.2 - - - -
212B ALA* 3.4 20.4 - - - -
237B VAL 2.7 20.0 + - - -
238B GLY 3.1 3.0 + - - -
240B ALA* 1.3 74.5 - - - +
242B THR* 1.3 51.4 + - - +
244B LEU* 3.2 16.5 - - - +
245B THR* 2.5 34.8 + - - -
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Residues in contact with THR 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PHE* 5.4 10.5 - - + -
212B ALA* 3.8 15.9 - - + -
213B PHE* 6.1 0.4 - - + -
216B MET* 4.7 16.4 - - + -
238B GLY 3.2 8.1 + - - +
239B ALA* 3.5 13.7 + - - -
241B GLY* 1.3 72.8 - - - +
243B LEU* 1.3 65.1 + - - +
245B THR* 3.3 9.2 + - - +
246B VAL* 3.2 28.6 + - - +
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 3.0 60.1 - - + +
23A ILE* 3.8 21.3 - - + +
24A THR* 3.8 13.7 - - + +
239B ALA 3.8 7.5 + - - +
240B ALA 3.5 7.5 + - - +
242B THR* 1.3 77.1 + - - +
244B LEU* 1.3 65.8 - - - +
246B VAL* 3.3 6.0 + - + +
247B LEU* 3.1 48.9 + - + +
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 4.6 11.8 - - + +
31A HIS* 3.6 18.8 - - - +
34A LEU* 4.7 5.8 - - + +
35A MET* 3.7 35.2 - - + +
38A SER* 3.8 12.8 - - - +
208B SER* 3.4 7.9 - - - +
211B ASN* 4.3 1.1 - - - +
240B ALA* 2.8 23.7 + - + +
241B GLY* 3.2 16.6 - - - +
243B LEU* 1.3 76.9 - - - +
245B THR* 1.3 56.2 + - - +
247B LEU* 4.4 3.7 - - - +
248B MET* 3.0 68.2 + - + +
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Residues in contact with THR 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B VAL* 3.7 23.9 - - + +
208B SER* 3.5 19.3 + - - -
209B PHE* 3.4 40.5 - - + -
212B ALA* 4.6 0.2 - - - +
241B GLY 2.5 22.7 + - - -
242B THR* 3.4 12.1 - - - -
243B LEU 3.1 0.6 - - - -
244B LEU* 1.3 76.7 - - - +
246B VAL* 1.3 62.5 + - - +
248B MET* 3.5 2.0 + - - +
249B ALA* 3.1 21.1 + - - +
256B VAL* 4.0 11.9 - - + -
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B THR* 3.2 18.2 + - - +
243B LEU* 3.3 6.2 + - + +
245B THR* 1.3 76.0 - - - +
247B LEU* 1.3 51.7 + - - +
249B ALA* 3.0 4.8 + - + +
250B ARG* 2.7 56.0 + - - +
256B VAL* 4.0 22.7 - - + -
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Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 4.2 3.8 - - + +
24A THR* 5.5 0.4 - - - -
25A ARG 5.3 3.6 - - - +
26A VAL* 3.9 34.3 - - + +
28A VAL* 5.9 2.2 - - + -
31A HIS* 4.2 19.5 + - + +
243B LEU* 3.1 37.0 + - + +
244B LEU* 4.5 3.8 - - - +
246B VAL* 1.3 75.5 - - - +
248B MET* 1.3 57.8 + - + +
250B ARG* 3.3 20.2 + - + +
251B ALA* 3.1 26.7 + - - +
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Residues in contact with MET 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A HIS* 4.2 25.6 - - + +
32A THR* 3.9 27.8 - - + -
35A MET* 3.8 11.4 - - + +
204B PRO* 4.8 18.6 - - + +
205B VAL* 3.8 15.1 - - + +
208B SER* 3.7 15.3 - - - -
244B LEU* 3.0 48.0 + - + +
245B THR* 3.8 4.0 - - - +
246B VAL 3.3 0.6 - - - -
247B LEU* 1.3 78.2 - - + +
249B ALA* 1.3 59.5 + - - +
251B ALA* 4.2 5.4 - - - +
252B MET* 3.4 27.0 + - - +
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B VAL* 4.3 12.3 - - + +
245B THR 3.1 12.6 + - - +
246B VAL* 3.0 10.2 + - + +
248B MET* 1.3 78.1 - - - +
250B ARG* 1.3 62.2 + - - +
251B ALA 3.3 0.8 + - - -
252B MET* 3.5 7.4 + - - +
254B ARG* 3.0 31.5 + - + +
255B SER* 4.1 6.3 - - - +
256B VAL* 3.7 32.5 - - + +
259B VAL* 5.9 2.2 - - + -
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Residues in contact with ARG 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B VAL* 2.7 35.4 + - - +
247B LEU* 3.3 25.5 + - + +
249B ALA* 1.3 78.5 - - - +
251B ALA* 1.3 60.7 + - - +
253B ASN* 3.6 16.6 + - - -
254B ARG 4.5 7.8 + - - -
255B SER* 6.1 2.0 - - - +
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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
----------------------------------------------------------
28A VAL* 4.6 24.2 - - + -
31A HIS* 4.6 6.5 - - + -
247B LEU 3.1 14.1 + - - +
248B MET* 4.2 7.9 - - - +
249B ALA 3.3 0.2 - - - -
250B ARG* 1.3 75.2 - - - +
252B MET* 1.3 58.3 + - + +
253B ASN* 3.0 21.9 + - - +
279B PRO 5.6 0.9 - - - +
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Residues in contact with MET 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLY 3.7 23.6 - - - +
202B ASP* 5.2 2.2 - - - -
204B PRO* 5.3 8.7 - - + -
205B VAL* 3.8 25.1 - - - -
248B MET 3.4 14.0 + - - +
249B ALA* 3.5 7.2 + - - +
250B ARG 3.5 0.6 - - - -
251B ALA* 1.3 75.7 - - + +
253B ASN* 1.3 71.4 + - - +
254B ARG* 3.4 31.2 + - + +
259B VAL* 5.9 1.6 - - - -
----------------------------------------------------------
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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