Contacts of the helix formed by residues 255 - 282 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C THR* 3.6 35.7 + - + +
223C GLU* 4.3 7.4 + - - -
226C TYR* 4.7 1.6 - - + -
248C CYS* 4.2 1.3 - - - -
249C LEU* 4.4 1.4 - - + +
252C ASP* 3.4 35.4 + - + +
253C GLN 3.4 2.0 - - - -
254C ASP* 1.3 73.3 - - - +
256C LYS* 1.3 65.0 + - - +
257C ARG* 3.4 35.6 + - - +
258C CYS* 3.0 52.1 + - + +
259C PHE* 3.2 24.3 + - - +
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Residues in contact with LYS 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LYS* 5.3 10.8 - - - +
254C ASP* 3.2 17.4 + - - +
255C HIS* 1.3 73.0 - - - +
257C ARG* 1.3 58.6 + - - +
259C PHE* 3.8 3.8 - - - +
260C ALA* 3.0 30.8 + - - +
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Residues in contact with ARG 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C GLU* 3.1 35.0 + - - -
226C TYR* 3.4 41.0 + - + +
255C HIS* 3.4 21.3 + - - +
256C LYS* 1.3 78.4 - - - +
258C CYS* 1.3 57.1 + - - +
260C ALA* 3.6 6.0 - - + +
261C HIS* 3.1 23.2 + - - +
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Residues in contact with CYS 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C TYR* 3.6 26.9 - - - -
245C VAL* 3.0 21.4 - - + +
248C CYS* 2.0 51.1 - - + -
249C LEU* 4.3 8.5 - - + -
255C HIS* 3.0 23.2 - - + +
257C ARG* 1.3 72.9 - - - +
259C PHE* 1.3 56.1 + - - +
261C HIS 3.3 0.7 + - - -
262C TYR* 2.6 32.2 + - - +
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Residues in contact with PHE 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B PHE* 3.5 38.8 - + - -
262B TYR* 5.0 11.7 - + - -
263B LYS* 4.5 13.0 - - - -
266B LYS* 5.6 4.9 - - - -
249C LEU* 3.9 21.3 - - + +
253C GLN 5.0 7.6 - - - +
254C ASP 6.0 0.2 - - - -
255C HIS 3.2 17.7 + - - +
256C LYS* 3.8 4.0 - - - +
258C CYS* 1.3 75.7 - - - +
260C ALA* 1.3 68.6 + - - +
262C TYR* 3.2 18.1 + + - +
263C LYS* 3.0 52.2 + - + +
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Residues in contact with ALA 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C LYS 3.0 17.3 + - - +
257C ARG* 3.6 8.1 - - - +
259C PHE* 1.3 82.3 - - - +
261C HIS* 1.3 60.6 + - - +
263C LYS* 3.4 14.1 + - - +
264C GLN* 3.3 18.4 + - - +
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Residues in contact with HIS 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C TYR* 4.1 18.8 - + + +
229C SER* 3.0 33.5 + - - -
230C THR* 4.8 7.4 + - - -
233C TYR* 3.5 44.1 - + + -
241C SER* 3.0 9.1 + - - -
245C VAL* 3.8 15.5 - - + -
257C ARG 3.1 17.4 + - - +
258C CYS 3.8 2.0 - - - +
260C ALA* 1.3 72.4 - - - +
262C TYR* 1.3 66.0 + - - +
264C GLN* 3.1 10.0 + - - +
265C VAL* 2.9 27.9 + - + +
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Residues in contact with TYR 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B GLN* 2.7 50.7 + - - +
259B PHE* 4.7 17.9 - + - -
242C LEU* 3.6 21.1 - - + -
245C VAL* 3.8 16.3 - - + +
246C ARG* 3.7 13.7 - - + -
249C LEU* 3.4 29.6 - - + -
258C CYS 2.6 21.9 + - - +
259C PHE* 3.2 17.7 + + - +
261C HIS* 1.3 72.2 - - - +
263C LYS* 1.3 57.7 + - + +
265C VAL* 3.4 2.1 - - - +
266C LYS* 2.8 56.0 + - + +
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Residues in contact with LYS 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B PHE* 6.3 2.0 - - + -
263B LYS* 5.5 5.4 - - - +
259C PHE* 3.0 41.4 + - + +
260C ALA* 3.4 17.0 - - - +
262C TYR* 1.3 81.8 - - + +
264C GLN* 1.3 55.8 + - - +
266C LYS* 3.7 10.7 - - - +
267C LYS* 2.9 33.6 + - + +
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Residues in contact with GLN 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C TYR* 2.9 33.5 + - + +
260C ALA 3.3 9.0 + - - +
261C HIS* 3.1 14.8 + - - +
263C LYS* 1.3 80.1 - - - +
265C VAL* 1.3 57.9 + - - +
267C LYS* 3.5 6.8 + - - +
268C LEU* 3.0 28.9 + - - +
297C THR* 2.7 39.5 + - - +
298C GLU* 3.5 5.8 + - - +
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Residues in contact with VAL 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C TYR* 3.9 27.6 - - + -
238C HIS* 3.4 32.8 - - + +
241C SER* 3.9 8.7 - - - +
242C LEU* 3.7 27.4 - - + +
245C VAL* 3.9 11.7 - - + -
261C HIS* 2.9 26.6 + - + +
262C TYR 3.4 5.8 - - - +
264C GLN* 1.3 72.9 - - - +
266C LYS* 1.3 58.8 + - - +
268C LEU* 4.4 2.0 - - + +
269C ASN* 2.7 38.7 + - + +
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Residues in contact with LYS 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B GLN* 3.5 31.0 + - - +
254B ASP* 2.8 32.4 + - - +
259B PHE* 5.2 8.9 - - - -
242C LEU* 3.8 18.1 - - + +
262C TYR* 2.8 52.2 + - + +
263C LYS* 3.7 10.8 - - - +
265C VAL* 1.3 76.7 - - - +
267C LYS* 1.3 65.0 + - - +
269C ASN* 3.9 0.9 - - - +
270C LYS* 3.1 28.9 + - + +
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Residues in contact with LYS 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C LYS* 2.9 19.5 + - + +
264C GLN* 3.5 8.5 - - - +
266C LYS* 1.3 79.2 - - - +
268C LEU* 1.3 62.4 + - - +
270C LYS* 3.5 7.8 - - - +
271C LEU* 3.2 35.4 + - + +
297C THR* 3.8 21.1 - - - +
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Residues in contact with LEU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C TYR* 3.2 31.0 - - + +
238C HIS* 5.1 3.1 - - + -
264C GLN* 3.0 17.7 + - - +
265C VAL* 3.8 6.1 - - + +
267C LYS* 1.3 73.6 - - - +
269C ASN* 1.3 60.4 + - - +
271C LEU* 3.3 9.6 + - - +
272C ILE* 3.0 52.4 + - + +
294C VAL* 3.7 16.2 - - + -
297C THR* 3.7 16.6 - - + -
298C GLU* 3.5 19.7 - - + -
304C TYR* 3.7 22.2 - - + -
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Residues in contact with ASN 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C HIS* 3.0 43.2 + - + +
239C GLU* 4.0 17.4 - - - +
242C LEU* 3.4 28.4 - - + +
265C VAL 2.7 21.9 + - - +
266C LYS 3.9 1.6 - - - +
268C LEU* 1.3 69.5 - - - +
270C LYS* 1.3 60.9 + - - +
272C ILE* 3.3 0.5 + - - -
273C GLU* 2.9 59.7 + - - +
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Residues in contact with LYS 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ASP* 3.9 37.5 + - - +
266C LYS* 3.1 20.7 + - - +
267C LYS* 3.5 8.1 - - - +
269C ASN* 1.3 76.4 + - - +
271C LEU* 1.3 56.5 + - + +
273C GLU* 4.1 3.0 - - - +
274C SER* 2.8 40.1 + - - -
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Residues in contact with LEU 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C LYS* 3.2 30.1 + - + +
268C LEU 3.6 6.7 - - - +
269C ASN 3.3 0.4 - - - -
270C LYS* 1.3 80.9 - - + +
272C ILE* 1.3 56.6 + - - +
275C ALA* 3.0 28.4 + - - +
290C LYS* 3.7 34.7 - - + +
293C SER* 3.8 28.0 - - - +
294C VAL* 3.7 15.5 - - + +
297C THR* 3.8 30.1 - - + -
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Residues in contact with ILE 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C HIS* 3.4 44.9 - - + +
268C LEU* 3.0 34.4 + - + +
269C ASN 4.0 0.4 - - - +
271C LEU* 1.3 74.2 - - - +
273C GLU* 1.3 55.9 + - - +
275C ALA* 3.0 6.0 + - - +
276C GLU* 2.7 39.8 + - + +
291C TYR* 3.6 23.5 + - + +
294C VAL* 3.7 26.2 - - + -
304C TYR* 4.4 7.6 - - + -
308C SER* 5.7 0.2 - - - +
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Residues in contact with GLU 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C HIS* 5.0 1.7 - - + -
239C GLU* 4.5 15.4 - - - +
269C ASN* 2.9 43.3 + - - +
270C LYS* 4.1 2.7 - - - +
272C ILE* 1.3 75.9 - - - +
274C SER* 1.3 53.2 + - - +
276C GLU* 3.1 8.5 + - + +
277C GLU* 2.8 34.2 + - - +
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Residues in contact with SER 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C LYS* 2.8 25.6 + - - -
271C LEU 4.0 0.2 - - - -
273C GLU* 1.3 77.8 - - - +
275C ALA* 1.3 59.3 + - - +
277C GLU* 3.3 10.1 - - - +
278C LEU* 3.3 28.5 + - - +
290C LYS* 3.4 27.0 - - - -
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Residues in contact with ALA 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C LEU 3.0 19.4 + - - +
272C ILE 3.0 5.5 + - - +
274C SER* 1.3 75.7 - - - +
276C GLU* 1.3 61.5 + - - +
278C LEU* 3.3 9.4 + - - +
279C ILE* 3.3 27.6 + - - +
287C ALA* 3.5 3.5 - - - +
290C LYS* 3.6 23.2 - - + +
291C TYR* 3.5 31.2 - - + +
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Residues in contact with GLU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ILE* 2.7 21.0 + - + +
273C GLU* 3.5 11.7 - - + +
275C ALA* 1.3 71.6 - - - +
277C GLU* 1.3 66.9 + - - +
278C LEU 3.2 0.2 - - - -
279C ILE* 3.4 29.3 - - - +
280C ARG* 3.3 25.7 + - - +
291C TYR* 2.5 34.6 + - - +
311C ARG* 3.1 38.4 + - - +
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Residues in contact with GLU 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C GLU 2.8 15.8 + - - +
274C SER* 3.3 15.9 - - - +
276C GLU* 1.3 75.1 - - - +
278C LEU* 1.3 63.4 + - + +
280C ARG* 2.9 42.7 + - - +
281C ASP* 3.5 29.1 - - - +
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Residues in contact with LEU 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C SER* 3.3 17.5 + - - +
275C ALA* 3.5 5.8 - - - +
276C GLU 3.2 0.6 - - - -
277C GLU* 1.3 80.1 - - + +
279C ILE* 1.3 63.8 + - - +
281C ASP* 3.2 7.2 + - - +
282C GLY 3.1 17.7 + - - -
283C ARG* 3.1 62.6 + - - +
286C ASP* 3.6 17.3 - - + +
287C ALA* 3.6 24.2 - - + +
290C LYS* 3.8 19.5 - - + +
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Residues in contact with ILE 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C ALA 3.3 15.7 + - - +
276C GLU* 3.4 31.2 - - - +
278C LEU* 1.3 75.4 - - - +
280C ARG* 1.3 78.1 + - + +
282C GLY* 3.3 9.2 + - - -
283C ARG 4.9 0.2 - - - -
284C TYR* 3.3 31.8 + - + -
287C ALA* 3.4 18.8 - - + +
291C TYR* 5.0 3.8 - - + -
311C ARG* 3.5 24.7 - - + +
314C HIS* 4.4 15.3 - - + +
315C CYS* 3.8 15.0 - - - -
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Residues in contact with ARG 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C GLU* 3.3 34.5 + - - +
277C GLU* 2.9 36.6 + - - +
278C LEU 3.2 1.0 - - - -
279C ILE* 1.3 96.0 - - + +
281C ASP* 1.3 65.2 + - - +
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Residues in contact with ASP 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C GLU* 3.5 24.1 + - - +
278C LEU* 3.2 8.0 + - - +
280C ARG* 1.3 84.9 + - - +
282C GLY* 1.3 57.0 + - - +
283C ARG* 4.6 19.4 + - + +
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Residues in contact with GLY 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C LEU 3.1 3.4 + - - -
279C ILE 3.3 11.2 + - - -
281C ASP* 1.3 79.2 - - - +
283C ARG* 1.3 54.9 + - - +
284C TYR* 2.8 45.2 + - - -
319C ASP* 5.2 0.3 - - - +
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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