Contacts of the helix formed by residues 255 - 281 (chain B) in PDB entry 2Y4T
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 HIS 255 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B THR* 3.5 20.0 + - + +
223B GLU* 4.7 4.7 - - - -
226B TYR* 4.9 4.7 - - + -
248B CYS* 4.4 0.9 - - - -
249B LEU* 3.9 0.7 - - - +
252B ASP* 3.2 32.3 + - + +
253B GLN 3.4 1.4 - - - -
254B ASP* 1.3 74.9 - - - +
256B LYS* 1.3 64.8 + - + +
257B ARG* 3.2 51.2 + - + +
258B CYS* 3.2 37.5 - - + +
259B PHE* 2.8 33.2 + - - +
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Residues in contact with LYS 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ASP 3.4 8.0 + - - +
255B HIS* 1.3 76.6 - - + +
257B ARG* 1.3 55.4 + - + +
259B PHE* 3.9 4.2 - - - +
260B ALA* 2.8 37.2 + - - +
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Residues in contact with ARG 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B GLU* 3.1 35.6 + - - -
226B TYR* 3.7 42.1 + - + +
255B HIS* 3.2 35.0 + - + +
256B LYS* 1.3 81.0 - - + +
258B CYS* 1.3 57.4 + - - +
260B ALA* 3.6 6.0 - - - +
261B HIS* 3.0 29.3 + - - +
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Residues in contact with CYS 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B TYR* 4.0 22.7 - - - -
245B VAL* 3.3 19.0 - - + +
248B CYS* 2.0 51.1 - - + -
249B LEU* 3.8 12.6 - - + -
255B HIS* 3.2 25.0 + - + +
256B LYS 3.3 0.4 - - - -
257B ARG* 1.3 75.7 - - - +
259B PHE* 1.3 55.4 + - - +
261B HIS 3.4 0.5 + - - -
262B TYR* 2.8 30.7 + - - +
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Residues in contact with PHE 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LEU* 3.6 30.5 - - + +
253B GLN 4.2 12.6 - - - +
254B ASP 5.9 0.2 - - - -
255B HIS 2.8 22.6 + - - +
256B LYS* 3.9 4.3 - - - +
258B CYS* 1.3 68.6 - - - +
260B ALA* 1.3 69.6 + - - +
262B TYR* 3.0 12.1 + + - +
263B LYS* 2.8 60.7 + - + +
259C PHE* 3.5 33.7 - + - -
262C TYR* 4.7 15.3 - + - -
263C LYS* 6.3 2.2 - - + -
266C LYS* 5.2 7.2 - - - -
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Residues in contact with ALA 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LYS 2.8 23.7 + - - +
257B ARG* 3.6 7.4 - - - +
259B PHE* 1.3 76.6 - - - +
261B HIS* 1.3 61.1 + - - +
263B LYS* 3.5 8.0 + - - +
264B GLN* 3.2 19.2 + - - +
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Residues in contact with HIS 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B TYR* 4.0 16.3 - + + +
229B SER* 2.9 35.0 + - - -
230B THR* 4.5 11.8 + - + -
233B TYR* 3.7 29.5 - + + -
241B SER* 3.1 8.1 + - - -
245B VAL* 3.7 18.2 - - + -
257B ARG 3.0 18.8 + - - +
258B CYS 3.6 3.4 - - - +
259B PHE 3.2 0.2 - - - -
260B ALA* 1.3 73.4 - - - +
262B TYR* 1.3 59.9 + - - +
264B GLN* 3.1 12.0 + - - +
265B VAL* 2.9 52.2 + - + +
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Residues in contact with TYR 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 3.7 25.6 - - + -
245B VAL* 3.9 16.3 - - + +
246B ARG* 3.9 24.0 + - + -
249B LEU* 3.6 27.8 - - + -
258B CYS 2.8 20.8 + - - +
259B PHE* 3.0 21.7 + + - +
261B HIS* 1.3 72.7 - - - +
263B LYS* 1.3 68.0 + - - +
264B GLN 3.2 0.2 + - - -
265B VAL* 4.0 1.0 - - - +
266B LYS* 3.0 59.9 + - + +
253C GLN* 3.7 24.5 + - + +
259C PHE* 5.0 11.3 - + - -
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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
----------------------------------------------------------
259B PHE* 2.8 51.2 + - + +
260B ALA* 3.5 7.6 - - - +
262B TYR* 1.3 79.0 - - + +
264B GLN* 1.3 63.5 + - - +
266B LYS* 4.2 4.4 - - - +
267B LYS* 3.4 19.9 + - - +
259C PHE* 4.5 16.2 - - - -
263C LYS* 5.5 5.3 - - - +
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Residues in contact with GLN 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B TYR* 2.8 36.4 + - + +
260B ALA 3.2 10.8 + - - +
261B HIS* 3.1 16.3 + - - +
263B LYS* 1.3 82.1 - - - +
265B VAL* 1.3 63.6 + - + +
267B LYS* 3.4 11.4 - - - +
268B LEU* 3.2 22.0 + - - +
297B THR* 3.3 26.8 + - - +
298B GLU* 3.6 5.1 + - - -
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Residues in contact with VAL 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B TYR* 3.8 21.5 - - + -
238B HIS* 3.4 35.7 - - + +
241B SER* 3.8 7.9 - - - +
242B LEU* 4.1 12.3 - - + +
245B VAL* 4.9 1.1 - - + -
261B HIS* 2.9 54.0 + - + +
262B TYR* 4.3 2.7 - - - +
264B GLN* 1.3 69.6 - - - +
266B LYS* 1.3 57.7 + - - +
268B LEU* 3.0 5.5 + - + -
269B ASN* 2.6 38.5 + - + +
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Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 4.0 28.1 - - + +
262B TYR* 3.0 48.5 + - + +
263B LYS* 4.2 4.5 - - - +
265B VAL* 1.3 75.2 - - - +
267B LYS* 1.3 58.6 + - - +
269B ASN* 3.8 0.5 - - - +
270B LYS* 2.9 35.8 + - + +
253C GLN* 3.4 22.4 + - + -
254C ASP* 3.4 37.6 + - - +
259C PHE* 5.6 6.9 - - - -
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Residues in contact with LYS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LYS 3.4 12.6 + - - +
264B GLN* 3.4 16.6 - - - +
266B LYS* 1.3 80.4 - - - +
268B LEU* 1.3 57.1 - - - +
270B LYS* 3.6 6.3 - - - +
271B LEU* 3.0 51.7 + - + +
297B THR* 3.2 39.2 - - + +
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B TYR* 3.5 30.1 - - + +
238B HIS* 4.7 4.3 - - + -
264B GLN* 3.2 11.1 + - - +
265B VAL* 3.0 9.3 + - + +
267B LYS* 1.3 77.3 - - + +
269B ASN* 1.3 60.8 + - - +
271B LEU* 3.6 4.9 + - + +
272B ILE* 3.0 43.2 + - + +
294B VAL* 3.8 24.2 - - + +
297B THR* 3.4 28.3 - - - +
298B GLU* 4.1 10.5 - - + -
304B TYR* 3.5 34.1 - - + +
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Residues in contact with ASN 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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238B HIS* 2.9 39.0 + - + +
239B GLU* 3.9 16.3 + - - +
242B LEU* 3.5 28.9 - - + +
265B VAL 2.6 20.7 + - - +
266B LYS* 3.8 2.9 + - - +
268B LEU* 1.3 70.4 - - - +
270B LYS* 1.3 67.6 + - - +
272B ILE* 3.2 0.7 + - - +
273B GLU* 2.9 46.2 + - - +
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Residues in contact with LYS 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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266B LYS* 2.9 24.9 + - - +
267B LYS* 3.6 6.7 - - - +
269B ASN* 1.3 75.3 - - - +
271B LEU* 1.3 64.2 + - + +
273B GLU* 3.9 4.3 - - - +
274B SER* 3.0 32.8 + - - -
254C ASP* 3.8 24.5 - - - +
256C LYS* 5.3 11.8 - - - +
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Residues in contact with LEU 271 (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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267B LYS* 3.0 46.4 + - + +
268B LEU* 3.8 6.1 - - - +
269B ASN 3.2 0.2 - - - -
270B LYS* 1.3 87.1 - - + +
272B ILE* 1.3 56.6 + - - +
274B SER* 3.4 7.3 + - - -
275B ALA* 3.0 28.2 + - - +
290B LYS* 4.4 22.5 - - + +
293B SER* 3.7 43.1 - - - +
294B VAL* 4.0 11.4 - - + +
297B THR* 4.3 14.1 - - + +
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Residues in contact with ILE 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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238B HIS* 3.6 44.2 - - + +
268B LEU* 3.0 31.0 + - + +
269B ASN 3.2 2.0 + - - +
271B LEU* 1.3 72.3 - - - +
273B GLU* 1.3 68.2 + - - +
275B ALA* 3.1 8.5 + - - +
276B GLU* 3.0 27.7 + - + +
291B TYR* 3.8 22.4 - - + +
294B VAL* 3.8 32.3 - - + -
304B TYR* 4.2 10.8 - - + -
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Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B HIS* 4.0 9.6 - - + -
239B GLU* 3.1 24.5 - - - +
269B ASN* 2.9 44.1 + - - +
270B LYS* 3.9 4.3 - - - +
272B ILE* 1.3 72.9 - - - +
274B SER* 1.3 57.5 + - - +
276B GLU* 3.2 8.0 + - - +
277B GLU* 2.9 32.1 + - - +
280B ARG* 4.7 7.6 + - - -
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Residues in contact with SER 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LYS* 3.0 22.0 + - - -
271B LEU 3.5 5.6 - - - -
273B GLU* 1.3 76.7 - - - +
275B ALA* 1.3 59.2 + - - +
277B GLU* 3.5 16.4 + - - +
278B LEU* 3.1 32.3 + - - +
290B LYS* 3.4 28.2 + - - +
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Residues in contact with ALA 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU 3.0 14.1 + - - +
272B ILE* 3.1 8.5 + - - +
274B SER* 1.3 75.5 - - - +
276B GLU* 1.3 59.9 + - - +
278B LEU* 3.3 9.6 + - - +
279B ILE* 3.1 30.6 + - - +
287B ALA* 3.5 3.9 - - - +
290B LYS* 3.7 22.8 - - + +
291B TYR* 3.6 32.1 - - + +
294B VAL* 5.5 0.2 - - + -
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Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ILE* 3.0 20.9 + - + +
273B GLU* 3.7 8.7 - - - +
275B ALA* 1.3 72.4 - - - +
277B GLU* 1.3 67.9 + - - +
279B ILE* 3.1 38.3 - - - +
280B ARG* 3.4 28.5 + - - +
291B TYR* 2.5 33.9 + - - +
311B ARG* 2.7 31.3 + - - -
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Residues in contact with GLU 277 (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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273B GLU 2.9 17.2 + - - +
274B SER* 3.5 16.9 + - - +
276B GLU* 1.3 75.0 - - - +
278B LEU* 1.3 74.0 + - - +
280B ARG* 3.3 33.1 + - - +
281B ASP* 3.3 26.4 + - - +
283B ARG* 5.4 2.3 + - - -
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B SER* 3.1 20.6 + - - +
275B ALA* 3.4 6.7 - - - +
276B GLU 3.2 0.6 - - - -
277B GLU* 1.3 88.2 - - - +
279B ILE* 1.3 64.2 + - - +
281B ASP* 3.1 13.2 + - - +
283B ARG* 3.1 78.1 + - + +
286B ASP* 3.8 12.6 - - + +
287B ALA* 3.7 25.1 - - + +
290B LYS* 4.0 18.6 - - + +
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Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ALA 3.1 14.7 + - - +
276B GLU* 3.1 39.0 - - - +
278B LEU* 1.3 74.8 - - - +
280B ARG* 1.3 73.7 + - + +
282B GLY* 3.3 8.1 + - - -
284B TYR* 3.4 29.7 + - + -
287B ALA* 3.5 17.3 - - + -
291B TYR* 5.1 4.3 - - + -
311B ARG* 3.5 26.9 - - - +
314B HIS* 4.8 10.1 - - + +
315B CYS* 3.7 18.8 - - - -
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Residues in contact with ARG 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B GLU* 4.7 7.3 + - - -
276B GLU* 3.5 29.0 + - - +
277B GLU* 3.3 32.4 + - - +
278B LEU 3.2 0.6 - - - -
279B ILE* 1.3 85.8 - - + +
281B ASP* 1.3 62.9 + - - +
282B GLY 3.1 8.1 + - - -
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Residues in contact with ASP 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLU* 3.3 27.1 + - - +
278B LEU* 3.1 10.0 + - - +
280B ARG* 1.3 80.3 - - - +
282B GLY* 1.3 60.8 + - - +
283B ARG* 3.3 27.1 + - - +
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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