Contacts of the helix formed by residues 253 - 282 (chain B) in PDB entry 5J0Z
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 253 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B PHE* 3.5 36.6 - - + +
117B ARG* 3.8 4.7 - - - +
119B TYR* 5.0 2.9 - - + -
246B LEU* 4.4 22.0 - - + +
249B THR* 3.9 18.2 + - + +
251B TYR* 3.4 4.6 + - + -
252B MET* 1.3 83.0 - - - +
254B TYR* 1.3 59.5 + - - +
255B THR* 4.4 2.5 - - - -
256B GLY* 3.3 22.2 + - - -
257B ALA* 3.1 22.9 + - - +
314B PHE* 3.7 1.2 - - - -
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Residues in contact with TYR 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PHE 4.5 0.4 + - - -
117B ARG 2.8 23.2 + - - +
118B ARG* 4.4 2.7 - - - -
119B TYR 3.7 14.6 + - - +
120B PRO* 5.3 0.4 - - + -
121B PHE* 4.0 29.3 - + - -
253B THR* 1.3 70.6 - - - +
255B THR* 1.3 69.7 + - - +
257B ALA* 3.3 3.8 + - - +
258B ILE* 3.1 51.1 + - + +
307B ASN* 5.2 4.5 + - - -
310B LEU* 4.6 4.5 - - + -
311B ALA* 4.3 26.5 - - - +
314B PHE* 3.6 37.9 - + + -
315B PHE* 4.1 21.8 - + - -
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Residues in contact with THR 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B TYR* 2.5 48.0 + - + -
120B PRO* 3.3 10.8 - - + +
201B ILE* 5.4 6.5 - - + -
202B ILE* 6.6 0.2 - - + -
242B VAL* 4.1 29.2 - - + -
246B LEU* 5.7 1.1 - - - -
253B THR* 3.5 2.6 - - - -
254B TYR* 1.3 81.1 - - - +
256B GLY* 1.3 57.3 + - - +
258B ILE* 3.5 9.8 + - + +
259B ILE* 2.9 36.2 + - + +
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Residues in contact with GLY 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A PRO* 5.8 0.3 - - - +
200A ASN* 5.6 8.5 + - - -
242B VAL* 5.7 2.9 - - - +
252B MET* 4.7 7.1 - - - +
253B THR* 3.3 21.9 + - - -
254B TYR 3.2 0.8 - - - -
255B THR* 1.3 76.5 - - - +
257B ALA* 1.3 56.1 + - - +
259B ILE* 3.8 7.7 - - - +
260B PHE* 2.8 35.4 + - - +
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Residues in contact with ALA 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B MET* 4.3 14.5 - - + +
253B THR 3.1 14.1 + - - +
254B TYR 3.5 8.3 - - - +
256B GLY* 1.3 72.3 - - - +
258B ILE* 1.3 56.7 + - - +
260B PHE* 2.9 8.0 + - - +
261B MET* 2.7 35.5 + - - +
310B LEU* 3.8 23.1 - - + -
314B PHE* 4.1 14.6 - - + -
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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
----------------------------------------------------------
202B ILE* 6.5 1.3 - - + -
205B MET* 5.4 3.1 - - - -
254B TYR* 3.1 52.5 + - + +
255B THR* 3.6 12.6 - - + +
257B ALA* 1.3 76.7 - - - +
259B ILE* 1.3 62.7 + - + +
261B MET* 3.3 6.9 + - - +
262B ILE* 3.0 45.7 + - + +
303B PHE* 5.8 1.8 - - + -
307B ASN* 4.0 26.9 - - - +
310B LEU* 4.0 16.8 - - + +
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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
----------------------------------------------------------
201B ILE* 5.7 0.7 - - + -
205B MET* 3.8 38.1 - - + -
235B HIS* 3.9 2.4 + - + +
238B PHE 4.2 4.0 - - - +
239B ASN* 3.7 31.9 - - + +
242B VAL* 3.6 37.5 - - + -
255B THR* 2.9 23.9 + - + +
256B GLY* 3.8 7.2 - - - +
258B ILE* 1.3 79.0 - - + +
260B PHE* 1.3 63.4 + - - +
262B ILE* 3.2 17.0 + - - +
263B TYR* 3.2 21.7 + - + -
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Residues in contact with PHE 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A PRO* 3.5 40.4 - - + +
200A ASN* 6.2 0.2 - - - +
203A LEU* 3.6 45.1 - - + -
204A PRO* 4.9 4.3 - - + -
207A PHE* 4.1 15.7 - + - -
252B MET* 5.7 4.5 - - + -
256B GLY 2.8 23.7 + - - +
257B ALA* 3.6 6.3 - - - +
259B ILE* 1.3 73.2 - - + +
261B MET* 1.3 72.2 + - + +
263B TYR* 3.3 22.0 + - + +
264B LEU* 3.9 18.2 + - + +
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Residues in contact with MET 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ALA 2.7 20.9 + - - +
258B ILE* 3.7 8.5 - - + +
260B PHE* 1.3 78.0 - - + +
262B ILE* 1.3 65.6 + - - +
264B LEU* 3.0 30.5 + - + +
265B PHE* 3.5 22.9 - - + -
303B PHE* 3.3 39.7 - - + -
306B ALA* 4.0 29.6 - - + +
307B ASN* 3.3 16.4 - - - +
310B LEU* 4.4 13.5 - - + -
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Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B MET* 4.1 18.8 - - + +
206B LEU* 5.3 4.3 - - + -
209B LEU* 4.5 13.9 - - + -
235B HIS* 3.1 37.5 - - + +
258B ILE* 3.0 37.9 + - + +
259B ILE* 3.2 8.0 + - - +
261B MET* 1.3 76.3 - - - +
263B TYR* 1.3 56.8 + - - +
264B LEU 2.8 7.1 + - - -
265B PHE* 2.9 17.9 + - - +
266B TYR* 3.2 31.2 + - + -
303B PHE* 4.2 25.4 - - + -
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Residues in contact with TYR 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A PRO* 3.5 37.2 - - + -
207A PHE* 3.7 23.8 - + + +
208A ILE* 5.2 4.0 - - + -
238A PHE* 3.5 16.7 - + - -
232B LEU* 4.6 12.3 - - + +
235B HIS* 3.4 26.5 - + - -
236B ILE* 3.5 20.1 - - + +
239B ASN* 2.7 46.0 + - - +
259B ILE* 3.2 23.3 - - + -
260B PHE* 3.3 16.0 + - + +
261B MET 3.2 0.8 - - - -
262B ILE* 1.3 75.8 - - - +
264B LEU* 1.3 57.8 + - - +
266B TYR* 4.2 8.3 - - - +
267B PHE* 3.4 20.9 + - - +
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A PHE* 3.2 44.2 - - + -
260B PHE* 4.0 22.7 - - + +
261B MET* 3.0 22.1 + - + +
262B ILE 2.8 1.4 + - - -
263B TYR* 1.3 73.8 - - - +
265B PHE* 1.3 64.3 + - + +
266B TYR 3.0 3.8 - - - -
267B PHE* 2.6 11.7 + - + -
268B VAL* 2.5 44.5 + - + +
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Residues in contact with PHE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 4.3 14.2 - - + +
212B SER* 4.2 4.5 + - - -
213B TRP* 3.9 26.8 + + - +
261B MET* 3.5 35.2 - - + +
262B ILE* 2.9 11.3 + - - +
264B LEU* 1.3 82.9 - - + +
266B TYR* 1.3 58.4 + - - +
268B VAL* 4.7 6.5 - - + -
269B ALA* 3.3 20.6 + - - +
299B PHE* 4.0 16.9 - + - -
302B VAL* 3.9 27.1 - - + -
303B PHE* 3.3 49.6 - + + -
306B ALA* 5.0 2.0 - - + -
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Residues in contact with TYR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ILE* 4.9 1.1 - - + -
208B ILE* 3.2 38.1 + - - +
209B LEU* 3.3 16.1 - - + +
212B SER* 3.8 15.9 - - - -
228B VAL* 3.9 19.0 - - + +
231B THR* 3.4 25.9 + - - -
232B LEU* 3.6 38.1 - - + -
235B HIS* 3.8 11.7 - + + -
262B ILE* 3.2 45.3 + - + +
263B TYR* 4.4 4.9 - - - +
264B LEU 3.0 0.4 - - - -
265B PHE* 1.3 78.1 - - - +
267B PHE* 1.3 66.2 + - - +
269B ALA* 3.3 4.1 + - - +
270B VAL* 3.0 27.9 + - - +
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Residues in contact with PHE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A PHE* 3.9 30.5 - + + -
210A PHE* 3.4 42.2 - + + -
211A ILE* 3.7 28.2 - - + +
214A THR* 6.0 0.2 - - + -
263B TYR 3.4 15.6 + - - +
264B LEU* 2.6 18.3 + - + +
266B TYR* 1.3 75.6 - - - +
268B VAL* 1.3 65.8 + - + +
270B VAL* 3.3 5.9 + - + +
271B ILE* 3.1 49.4 + - + +
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Residues in contact with VAL 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 2.5 28.3 + - + +
265B PHE* 4.7 3.4 - - + -
267B PHE* 1.3 80.1 - - + +
269B ALA* 1.3 63.9 + - - +
271B ILE* 3.0 13.0 + - + +
272B GLU* 2.9 22.2 + - + +
299B PHE* 3.4 28.5 - - + -
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Residues in contact with ALA 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B SER* 4.5 6.7 - - - +
216B PHE* 4.5 9.6 - - + -
228B VAL* 4.3 18.2 - - + -
265B PHE 3.3 21.4 + - - +
266B TYR* 3.3 8.5 + - - +
268B VAL* 1.3 77.8 - - - +
270B VAL* 1.3 63.7 + - - +
272B GLU* 3.2 5.0 + - - +
273B VAL* 2.9 27.8 + - - +
299B PHE* 3.8 20.2 - - + -
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ILE* 3.9 38.1 - - + -
214A THR* 3.6 31.4 - - + +
227A LEU* 5.0 1.8 - - + -
228B VAL* 3.3 26.7 - - + +
229B VAL* 4.8 6.3 - - + -
232B LEU* 6.1 0.7 - - + -
266B TYR 3.0 13.5 + - - +
267B PHE 3.5 8.7 - - - +
269B ALA* 1.3 74.1 - - - +
271B ILE* 1.3 54.3 + - + +
273B VAL* 3.2 6.9 + - + +
274B THR* 2.7 44.0 + - - +
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Residues in contact with ILE 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A THR* 4.9 12.6 - - + -
267B PHE* 3.1 45.4 + - + +
268B VAL* 3.0 17.5 + - + +
270B VAL* 1.3 77.5 - - + +
272B GLU* 1.3 53.1 + - - +
274B THR* 3.1 5.9 + - + -
275B VAL* 2.8 46.6 + - + +
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B ALA 4.4 0.3 - - - +
216B PHE* 3.2 27.0 - - + -
268B VAL 2.9 11.9 + - - +
269B ALA* 3.5 7.0 - - - +
271B ILE* 1.3 75.7 - - - +
273B VAL* 1.3 88.2 + - - +
275B VAL* 3.3 9.0 + - - +
276B GLN* 2.9 32.6 + - - +
291B ILE* 4.0 13.0 - - + +
292B THR* 2.6 35.5 + - - -
295B SER* 3.5 21.5 - - - +
299B PHE* 4.5 6.3 - - + -
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ALA* 4.1 13.5 - - + +
216B PHE* 5.1 1.6 - - + -
221B TYR* 3.6 24.0 - - + -
224B ASN* 3.7 42.2 - - + +
225B VAL* 4.6 3.6 - - + +
228B VAL* 4.6 8.7 - - + -
269B ALA 2.9 16.8 + - - +
270B VAL* 3.7 5.6 - - + +
272B GLU* 1.3 98.1 + - - +
274B THR* 1.3 64.6 + - - +
276B GLN* 3.4 6.2 + - - +
277B HIS* 3.0 23.9 + - - +
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Residues in contact with THR 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A THR* 3.1 50.9 + - + +
217A TRP* 4.2 20.1 - - + +
221B TYR* 3.3 19.9 + - + +
225B VAL* 5.8 0.3 - - - +
270B VAL* 2.7 25.2 + - - +
271B ILE* 3.6 5.4 - - + +
273B VAL* 1.3 72.4 - - - +
275B VAL* 1.3 57.4 + - + +
277B HIS* 3.8 5.5 - - - +
278B TYR* 2.9 25.0 + - - +
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ILE* 2.8 26.6 + - + +
272B GLU* 3.4 11.0 - - - +
274B THR* 1.3 75.7 - - + +
276B GLN* 1.3 70.4 + - - +
277B HIS 3.1 1.3 - - - -
278B TYR* 2.7 19.3 + - + +
279B LEU* 2.8 25.5 + - + +
291B ILE* 3.9 31.6 - - + -
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Residues in contact with GLN 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ALA 4.2 0.7 - - - +
218B SER 3.0 19.3 + - - -
219B THR* 3.7 19.1 - - - +
224B ASN* 3.5 21.1 + - - -
272B GLU* 2.9 28.1 + - - +
273B VAL* 3.7 9.5 - - - +
275B VAL* 1.3 75.9 - - - +
277B HIS* 1.3 63.3 + - - +
279B LEU 3.6 0.3 + - - -
280B LYS* 3.2 31.1 + - - +
288B ALA* 3.7 25.7 - - + +
289B ALA* 5.3 0.6 - - - +
291B ILE* 5.7 1.1 - - + -
292B THR* 2.8 39.7 + - - +
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Residues in contact with HIS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TRP 3.9 17.4 + - - -
218A SER* 4.0 17.1 + - - -
219A THR* 4.5 4.8 + - - -
220A SER* 4.9 9.6 - - - -
221B TYR* 3.4 61.3 - + + +
273B VAL 3.0 10.7 + - - +
274B THR 3.8 3.8 - - - +
276B GLN* 1.3 75.7 + - - +
278B TYR* 1.3 71.8 + + - +
280B LYS* 3.2 15.6 + - - +
281B VAL* 3.3 31.9 + - + +
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Residues in contact with TYR 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TRP* 3.8 36.3 - + + +
293A ARG* 5.7 1.0 - - - -
296A ARG* 3.7 34.7 + - - -
274B THR 2.9 16.9 + - - +
275B VAL* 2.7 20.1 + - + +
277B HIS* 1.3 74.3 - + - +
279B LEU* 1.3 66.3 + - + +
281B VAL* 2.9 28.4 + - + +
282B GLU* 3.0 51.1 + - + +
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B VAL* 2.8 27.6 + - + +
278B TYR* 1.3 86.7 - - + +
280B LYS* 1.3 51.4 + - - +
282B GLU* 3.0 10.6 + - + +
283B SER 2.7 31.0 + - - -
284B GLN* 3.2 25.7 + - + +
287B ARG* 3.9 22.0 - - + +
288B ALA* 3.5 40.6 - - + +
291B ILE* 3.9 15.0 - - + -
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Residues in contact with LYS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B THR* 4.1 35.5 - - - +
276B GLN* 3.2 23.7 + - + +
277B HIS* 3.7 11.4 - - - +
278B TYR 3.2 0.4 - - - -
279B LEU* 1.3 77.8 - - - +
281B VAL* 1.3 61.6 + - + +
283B SER* 3.7 9.6 + - - +
285B PRO* 3.8 43.4 + - + +
288B ALA* 4.2 8.0 - - + +
289B ALA* 4.4 11.8 - - - +
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A THR* 4.9 15.0 - - + +
277B HIS* 3.3 35.1 + - + +
278B TYR* 2.9 14.3 + - + +
280B LYS* 1.3 77.1 - - + +
282B GLU* 1.3 72.6 + - - +
283B SER* 3.3 8.0 + - - -
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Residues in contact with GLU 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B TYR* 3.0 56.7 + - + +
279B LEU* 3.0 12.4 + - + +
281B VAL* 1.3 93.6 - - - +
283B SER* 1.3 68.9 + - - +
284B GLN* 3.3 15.6 - - - +
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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).
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