Contacts of the helix formed by residues 247 - 275 (chain B) in PDB entry 3AXJ
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 ALA 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B CYS* 3.6 34.1 + - + +
245B GLN 2.8 8.7 + - - +
246B ARG* 1.3 68.5 - - - +
248B ARG* 1.3 58.1 + - - +
249B GLU* 3.5 2.5 - - - -
250B LEU* 3.4 17.1 + - + +
251B TRP* 3.0 28.0 + - - +
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Residues in contact with ARG 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ARG 2.9 12.6 + - - +
247B ALA* 1.3 69.4 - - - +
249B GLU* 1.3 65.3 + - - +
251B TRP* 3.4 9.7 + - + +
252B ARG* 3.2 53.0 + - + +
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Residues in contact with GLU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B GLN* 4.5 8.1 + - - +
200B LEU* 3.7 31.9 - - + +
247B ALA 3.5 0.2 - - - -
248B ARG* 1.3 76.7 - - - +
250B LEU* 1.3 64.1 + - - +
252B ARG* 3.3 26.6 + - - +
253B LYS* 3.1 34.0 + - - +
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 4.3 11.4 - - + +
199B ILE* 4.0 21.8 - - + +
200B LEU* 4.1 17.1 - - + +
239B TYR* 4.0 17.3 - - + -
242B LEU* 4.1 17.9 - - + -
244B CYS* 3.9 32.1 - - + -
247B ALA* 3.4 16.6 + - + +
248B ARG 3.3 0.2 - - - -
249B GLU* 1.3 79.3 - - - +
251B TRP* 1.3 62.5 + - - +
253B LYS* 3.1 9.9 + - + +
254B ILE* 3.0 40.5 + - + +
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Residues in contact with TRP 251 (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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247B ALA 3.0 17.0 + - - +
248B ARG* 3.8 11.0 - - + +
249B GLU 3.3 0.4 - - - -
250B LEU* 1.3 75.7 - - - +
252B ARG* 1.3 78.9 + - + +
254B ILE* 3.3 11.9 + - + +
255B THR* 3.1 48.5 + - + -
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Residues in contact with ARG 252 (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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248B ARG* 3.2 46.2 + - + +
249B GLU* 3.6 35.6 + - - +
251B TRP* 1.3 96.5 - - + +
253B LYS* 1.3 58.5 + - - +
255B THR* 3.5 6.0 + - - -
256B THR* 3.0 29.7 + - - -
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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
----------------------------------------------------------
122B GLN* 4.6 7.3 + - - -
200B LEU* 3.9 30.9 + - + -
203B SER* 3.2 32.5 - - - +
204B ASP* 3.0 27.2 + - - +
249B GLU* 3.1 23.2 + - - +
250B LEU* 3.1 12.7 + - + +
252B ARG* 1.3 76.4 - - - +
254B ILE* 1.3 58.4 + - + +
256B THR* 3.4 7.9 + - - +
257B MSE 2.8 31.3 + - - +
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Residues in contact with ILE 254 (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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236B TYR* 3.9 9.8 - - + +
239B TYR* 3.7 43.7 - - + +
240B ILE* 3.9 27.6 - - + -
242B LEU* 5.3 3.8 - - + +
250B LEU* 3.0 37.7 + - + +
251B TRP* 3.8 9.2 - - + +
253B LYS* 1.3 73.4 - - - +
255B THR* 1.3 60.6 + - - +
257B MSE 3.2 7.5 + - - +
258B LYS* 2.9 27.7 + - - +
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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
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251B TRP* 3.1 44.1 + - + -
252B ARG* 3.6 9.0 - - - +
254B ILE* 1.3 76.2 - - - +
256B THR* 1.3 62.6 + - - +
258B LYS* 3.3 16.1 + - - +
259B GLN* 3.5 18.9 + - + +
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Residues in contact with THR 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B MSE 6.2 1.1 - - + -
252B ARG* 3.0 15.4 + - - +
253B LYS* 3.6 10.7 - - - -
255B THR* 1.3 77.4 - - - +
257B MSE 1.3 63.6 + - - +
259B GLN* 3.2 11.0 + - + +
260B SER* 3.1 24.7 + - - +
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Residues in contact with MSE 257 (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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203B SER* 3.6 32.3 - - - +
206B THR* 3.8 32.5 - - + +
232B LEU* 5.2 1.3 - - + -
235B PHE 4.1 0.2 - - - -
236B TYR* 3.8 34.8 - - + +
239B TYR* 3.6 45.3 - - + -
253B LYS 2.8 22.5 + - - +
254B ILE* 3.2 7.6 + - - +
256B THR* 1.3 74.4 - - - +
258B LYS* 1.3 61.2 + - - +
260B SER* 3.2 8.3 + - - -
261B VAL* 3.0 29.9 + - + +
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Residues in contact with LYS 258 (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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236B TYR* 3.6 42.8 + - + +
254B ILE 2.9 9.2 + - - +
255B THR* 3.5 11.9 - - - +
256B THR 3.2 0.2 - - - -
257B MSE 1.3 75.7 - - - +
259B GLN* 1.3 67.9 - - - +
261B VAL* 3.4 5.8 + - + +
262B LEU* 3.0 52.7 + - + +
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Residues in contact with GLN 259 (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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255B THR* 3.5 15.6 + - + +
256B THR* 3.2 10.4 + - + +
258B LYS* 1.3 88.3 - - - +
260B SER* 1.3 57.6 + - - +
262B LEU* 3.4 25.4 + - - +
263B LYS* 3.0 48.8 + - - +
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Residues in contact with SER 260 (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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206B THR* 4.2 12.7 + - - -
207B GLY* 4.5 4.2 + - - -
210B MSE 3.0 50.4 - - - +
232B LEU* 3.9 8.9 - - - +
256B THR* 3.1 17.3 + - - +
257B MSE 3.4 12.1 - - - -
259B GLN* 1.3 72.1 - - - +
261B VAL* 1.3 65.7 + - - +
263B LYS* 3.3 1.0 + - - -
264B ALA* 3.0 23.0 + - - +
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B CYS* 5.1 0.2 - - - -
232B LEU* 3.6 25.4 - - + +
233B GLN* 4.4 13.0 - - + +
236B TYR* 3.6 37.9 - - + -
257B MSE 3.0 21.9 + - + +
258B LYS* 3.5 9.6 - - + +
260B SER* 1.3 75.3 - - - +
262B LEU* 1.3 60.7 + - + +
264B ALA* 3.4 1.7 + - - +
265B GLU* 2.9 53.8 + - + +
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Residues in contact with LEU 262 (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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258B LYS* 3.0 43.7 + - + +
259B GLN* 3.8 30.3 - - - +
260B SER 3.3 0.2 - - - -
261B VAL* 1.3 80.9 - - + +
263B LYS* 1.3 55.6 + - + +
265B GLU* 3.5 17.3 + - - +
266B ASN* 2.4 48.9 + - - +
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Residues in contact with LYS 263 (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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210B MSE 3.8 34.9 - - + +
214B ILE* 5.4 6.3 - - + -
259B GLN* 3.0 31.0 + - - +
260B SER 3.6 4.7 - - - +
261B VAL 3.3 0.2 - - - -
262B LEU* 1.3 72.9 - - + +
264B ALA* 1.3 61.6 + - - +
266B ASN* 3.2 6.1 + - - +
267B VAL* 3.0 32.7 + - + +
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Residues in contact with ALA 264 (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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210B MSE 4.5 2.8 - - + +
213B CYS* 4.0 24.9 - - + -
229B CYS* 4.1 14.1 - - - -
232B LEU* 3.5 32.3 - - + -
260B SER 3.0 8.7 + - - +
261B VAL* 3.8 3.1 - - - +
263B LYS* 1.3 76.2 - - - +
265B GLU* 1.3 61.2 + - - +
267B VAL* 3.4 4.7 + - - +
268B CYS* 3.2 27.4 + - - -
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Residues in contact with GLU 265 (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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229B CYS* 3.6 20.4 - - - -
233B GLN* 2.6 33.9 + - - +
261B VAL* 2.9 30.8 + - + +
262B LEU* 3.8 24.1 - - - +
264B ALA* 1.3 76.2 - - - +
266B ASN* 1.3 61.1 - - - +
268B CYS* 3.7 3.4 + - - +
269B TYR* 3.1 26.3 + - - +
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Residues in contact with ASN 266 (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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262B LEU* 2.4 47.5 + - - +
263B LYS* 3.2 6.7 + - - +
265B GLU* 1.3 79.8 - - - +
267B VAL* 1.3 58.1 + - - +
269B TYR* 3.4 13.7 - - - +
270B ASN* 3.0 41.3 + - - +
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Residues in contact with VAL 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B CYS* 3.8 25.8 - - - +
214B ILE* 4.6 17.5 - - + -
217B LEU* 4.2 29.6 - - + -
225B CYS* 3.9 21.8 - - + -
263B LYS 3.0 20.2 + - - +
264B ALA* 3.4 7.6 + - - +
266B ASN* 1.3 73.8 - - - +
268B CYS* 1.3 64.6 + - - +
270B ASN* 3.0 7.8 + - - +
271B VAL* 2.9 30.3 + - + +
279B ALA* 5.0 0.3 - - - +
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Residues in contact with CYS 268 (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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213B CYS* 4.9 0.2 - - - -
225B CYS* 3.5 34.5 - - - -
226B LEU* 3.7 28.9 - - + +
229B CYS* 3.6 15.3 - - - -
264B ALA 3.2 15.7 + - - +
265B GLU* 4.0 6.3 - - - +
267B VAL* 1.3 79.1 - - - +
269B TYR* 1.3 57.4 + - - +
271B VAL* 3.5 9.6 + - - +
272B LYS* 3.0 28.4 + - - +
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Residues in contact with TYR 269 (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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265B GLU 3.1 15.2 + - - +
266B ASN* 3.4 18.8 - - - +
268B CYS* 1.3 75.6 - - - +
270B ASN* 1.3 84.3 + - - +
272B LYS* 3.3 5.6 + - + +
273B VAL* 3.0 58.7 + - + +
274B ARG* 4.3 5.6 + - - -
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Residues in contact with ASN 270 (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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217B LEU* 6.4 0.4 - - + -
266B ASN* 3.0 29.7 + - - +
267B VAL* 3.0 7.4 + - - +
269B TYR* 1.3 85.0 - - - +
271B VAL* 1.3 60.3 + - - +
273B VAL* 3.9 3.8 - - - -
274B ARG* 2.7 67.6 + - - +
275B GLY 3.6 0.2 + - - -
279B ALA* 3.5 24.7 - - + +
282B GLY 6.1 2.4 - - - -
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Residues in contact with VAL 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LEU* 3.8 26.9 - - + -
222B THR* 4.0 35.9 - - + +
225B CYS* 4.9 4.7 - - + -
226B LEU* 6.4 1.3 - - + -
267B VAL* 2.9 23.1 + - + +
268B CYS* 3.5 11.9 - - - +
270B ASN* 1.3 77.1 - - - +
272B LYS* 1.3 63.3 + - - +
275B GLY* 3.1 24.5 + - - -
276B GLY* 4.6 6.5 - - - +
279B ALA* 4.1 4.7 - - + -
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Residues in contact with LYS 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B CYS 3.0 16.9 + - - +
269B TYR* 3.3 8.5 + - + +
271B VAL* 1.3 79.2 - - - +
273B VAL* 1.3 64.8 + - + +
275B GLY* 4.8 0.7 + - - -
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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
----------------------------------------------------------
269B TYR* 3.0 50.1 + - + +
270B ASN* 3.9 2.7 - - - -
272B LYS* 1.3 86.3 - - + +
274B ARG* 1.3 92.7 + - + +
275B GLY 3.6 0.2 - - - -
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Residues in contact with ARG 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B TYR* 4.3 7.7 + - - -
270B ASN* 2.7 52.9 + - - +
273B VAL* 1.3 92.7 - - + +
275B GLY* 1.3 61.5 + - - +
278B ALA* 3.4 42.1 + - + +
279B ALA* 4.2 2.2 - - - +
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Residues in contact with GLY 275 (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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270B ASN 3.6 0.2 + - - -
271B VAL* 3.1 17.9 + - - -
272B LYS 4.7 0.6 + - - -
273B VAL 3.6 1.0 - - - -
274B ARG* 1.3 78.8 - - - +
276B GLY* 1.3 66.8 + - - -
277B GLU 3.2 3.5 + - - -
278B ALA 3.4 0.3 + - - -
279B ALA* 3.1 22.9 + - - +
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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