Contacts of the helix formed by residues 250 - 273 (chain C) in PDB entry 2Y0N
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 250 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C PHE* 3.7 5.1 - - - -
246C PRO 4.4 8.8 + - - +
247C ALA* 3.3 21.7 - - - +
248C GLU 3.0 4.6 + - - -
249C LYS* 1.3 74.5 - - - +
251C VAL* 1.3 62.6 + - - +
252C ASP* 3.2 15.2 + - - +
253C LEU* 3.1 26.1 + - + +
254C CYS* 3.1 21.0 + - - +
483C HIS* 4.0 1.0 + - - -
553F VAL 4.3 3.4 + - - -
554F THR* 3.8 35.8 - - - +
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Residues in contact with VAL 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C VAL* 5.0 7.4 - - + +
217C PHE* 3.6 20.6 - - + -
218C ALA* 4.3 26.7 - - + -
221C ALA* 5.5 4.5 - - + -
249C LYS 3.6 5.6 + - - +
250C ASN* 1.3 72.2 + - - +
252C ASP* 1.3 73.3 + - - +
254C CYS* 3.3 3.3 - - + +
255C LYS* 3.1 40.5 + - + +
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Residues in contact with ASP 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C ASN* 3.2 10.8 + - - +
251C VAL* 1.3 83.3 - - - +
253C LEU* 1.3 64.6 + - - +
255C LYS* 3.3 21.3 + - - +
256C GLU* 3.3 26.2 + - - +
554F THR* 4.8 7.2 - - - +
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Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ALA* 3.6 36.8 - - + +
250C ASN* 3.1 22.2 + - + +
252C ASP* 1.3 74.2 - - - +
254C CYS* 1.3 64.8 + - - +
256C GLU* 3.4 10.9 + - - +
257C MET* 3.3 17.7 + - - +
479C ALA* 4.4 7.0 - - + -
483C HIS* 3.7 13.2 - - + +
553F VAL* 3.9 10.8 - - + +
554F THR 3.2 27.5 + - - +
555F SER* 3.8 3.8 - - - +
556F PHE* 3.4 49.7 - - + -
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Residues in contact with CYS 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C TYR* 3.5 35.7 - - - -
214C VAL* 4.6 9.6 - - - -
217C PHE* 3.6 34.1 - - + -
250C ASN 3.1 13.0 + - - +
251C VAL 3.3 10.5 - - - +
253C LEU* 1.3 76.5 - - - +
255C LYS* 1.3 62.6 + - - +
257C MET* 3.1 14.4 + - - +
258C VAL* 3.1 20.3 + - - +
483C HIS* 3.8 14.5 + - - +
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Residues in contact with LYS 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A PHE* 3.4 20.8 - - - +
442A ASP* 3.2 38.1 + - + +
443A GLN* 3.9 16.9 + - - +
214C VAL* 4.1 27.1 - - + -
251C VAL* 3.1 27.7 + - - +
252C ASP* 3.3 21.9 + - - +
254C CYS* 1.3 76.6 - - - +
256C GLU* 1.3 60.6 + - - +
258C VAL* 3.5 9.8 + - - +
259C ASP* 3.1 24.8 + - - +
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Residues in contact with GLU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A GLN* 4.6 10.5 - - - +
252C ASP* 3.3 13.9 + - - +
253C LEU* 3.6 8.8 - - - +
254C CYS 3.3 1.0 - - - -
255C LYS* 1.3 74.0 - - - +
257C MET* 1.3 67.0 + - - +
259C ASP* 3.4 6.4 + - - +
260C GLY* 2.9 20.6 + - - -
554F THR 4.8 1.2 - - - +
555F SER* 3.4 24.0 + - - -
556F PHE* 2.8 47.6 + - + -
557F PHE* 3.8 30.7 - - + +
577G PHE* 4.4 5.1 + - - -
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Residues in contact with MET 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C TYR* 4.2 15.9 - - + -
253C LEU 3.3 8.7 + - - +
254C CYS* 3.1 11.2 + - - +
256C GLU* 1.3 78.3 - - - +
258C VAL* 1.3 82.1 + - + +
260C GLY 3.1 2.3 + - - -
261C LEU* 2.9 49.2 + - + +
480C LEU* 4.4 4.7 - - + -
483C HIS* 3.4 41.1 - - + +
484C PHE* 3.5 33.9 - - + -
487C PHE* 4.5 10.3 - - + -
556F PHE* 4.1 8.4 - - + -
577G PHE* 3.2 14.5 - - + -
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Residues in contact with VAL 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A PHE* 3.3 17.9 - - + -
210C LEU* 3.2 48.8 - - + +
213C TYR* 4.3 6.1 - - + -
214C VAL* 3.7 20.6 - - + -
254C CYS* 3.1 22.6 + - - +
255C LYS* 3.8 5.6 - - - +
256C GLU 3.4 0.2 - - - -
257C MET* 1.3 92.8 - - + +
259C ASP* 1.3 62.6 + - - +
261C LEU* 3.3 7.9 + - - +
262C ARG* 3.1 17.7 + - - +
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Residues in contact with ASP 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A PHE* 3.6 18.4 - - + -
443A GLN* 3.5 32.0 - - - +
255C LYS 3.1 17.5 + - - +
256C GLU* 3.8 3.8 - - - +
258C VAL* 1.3 72.7 - - - +
260C GLY* 1.3 66.2 + - - +
262C ARG* 2.2 42.0 + - - +
263C ILE* 3.1 34.3 + - - +
557F PHE* 5.8 4.2 - - - -
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Residues in contact with GLY 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C GLU 2.9 12.4 + - - -
259C ASP* 1.3 76.7 - - - +
261C LEU* 1.3 49.7 + - - +
263C ILE* 3.2 5.0 + - - +
264C THR* 2.6 39.8 + - - -
576G ALA* 4.0 6.5 - - - +
577G PHE* 3.3 38.1 - - - -
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Residues in contact with LEU 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ILE* 6.1 0.2 - - - -
210C LEU* 4.4 18.2 - - + -
257C MET* 2.9 54.2 + - + +
258C VAL* 3.3 10.1 + - - +
260C GLY* 1.3 72.5 - - - +
262C ARG* 1.3 56.8 + - - +
264C THR* 3.9 2.1 - - - -
265C PHE* 2.8 32.3 + - - +
456C LEU* 4.3 8.0 - - + +
459C LEU* 3.9 24.2 - - + +
460C PHE* 3.6 34.8 - - + -
463C LEU* 4.7 5.6 - - + -
484C PHE* 4.4 6.5 - - + -
487C PHE* 4.6 4.0 - - + -
577G PHE* 3.2 11.9 - - + -
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Residues in contact with ARG 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A GLU* 4.0 21.3 + - - +
441A PHE* 3.7 21.3 - - + -
206C ILE* 5.1 2.5 - - + -
207C ILE* 3.8 20.8 - - + +
210C LEU* 3.8 21.3 - - + -
258C VAL 3.1 5.8 + - - +
259C ASP* 2.2 41.1 + - - +
261C LEU* 1.3 74.3 - - - +
263C ILE* 1.3 80.6 + - - +
265C PHE* 4.4 2.2 - - - -
266C ASP* 2.9 50.3 + - - +
448C SER* 3.1 11.8 + - - +
449C TYR* 5.6 2.6 - - - -
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Residues in contact with ILE 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C ASP* 3.1 36.1 + - - +
260C GLY* 3.7 8.3 - - - +
262C ARG* 1.3 95.1 - - - +
264C THR* 1.3 65.2 + - - +
265C PHE 3.3 0.2 + - - -
266C ASP* 3.3 9.2 + - - +
267C TYR* 3.2 20.5 + - + +
557F PHE* 6.4 1.8 - - + -
574G VAL* 3.8 28.3 - - + -
575G VAL 3.8 20.2 - - - +
576G ALA* 4.4 6.7 - - + -
581G LEU* 4.4 2.7 - - + -
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Residues in contact with THR 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C GLY 2.6 30.3 + - - -
261C LEU* 3.9 4.0 - - - -
263C ILE* 1.3 74.5 - - - +
265C PHE* 1.3 53.2 + - - +
267C TYR* 3.3 2.1 + - - +
268C THR* 2.3 46.4 + - - +
459C LEU* 4.4 14.6 - - + -
463C LEU* 4.8 4.9 - - + -
466C ILE* 4.7 13.9 - - + -
470C MET* 5.2 0.9 - - + -
576G ALA* 3.5 8.5 - - - +
577G PHE* 3.3 25.3 - - + -
581G LEU* 4.1 24.7 - - + -
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Residues in contact with PHE 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C ILE* 3.3 34.1 - - + -
261C LEU 2.8 22.6 + - - +
262C ARG* 4.0 4.9 - - - +
264C THR* 1.3 70.3 - - - +
266C ASP* 1.3 68.2 + - - +
267C TYR 3.0 0.2 + - - -
268C THR* 4.2 3.1 - - - -
269C LEU* 2.9 55.1 + - + +
273C LEU* 3.9 14.6 - - + -
447C PRO* 3.6 30.7 - - + -
448C SER* 3.9 11.9 - - - -
451C TYR* 3.7 8.7 - - + -
455C HIS* 3.7 26.0 - - + -
456C LEU* 4.3 12.6 - - + -
459C LEU* 4.1 13.6 - - + +
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Residues in contact with ASP 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ARG* 2.9 34.2 + - - +
263C ILE* 3.3 7.3 + - + +
265C PHE* 1.3 77.1 - - - +
267C TYR* 1.3 59.6 + - - +
270C PRO* 3.8 6.4 - - - +
446C PRO* 3.2 16.9 - - + +
447C PRO* 3.1 33.3 - - + +
448C SER* 2.8 41.1 + - - -
449C TYR* 6.0 0.3 - - - -
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Residues in contact with TYR 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C ILE* 3.2 8.9 + - + +
264C THR* 3.8 5.2 - - + +
265C PHE 3.1 0.6 - - - -
266C ASP* 1.3 78.3 - - - +
268C THR* 1.3 72.3 + - - +
269C LEU 3.6 0.2 - - - -
270C PRO* 3.5 11.3 - - - +
271C LEU* 3.6 31.6 - - + +
572E LEU* 3.6 36.0 - - + +
574G VAL* 6.0 0.7 - - + -
581G LEU* 3.6 24.7 - - + -
582G PRO 3.4 21.1 - - - -
583G LYS* 3.2 13.3 - - - +
584G LEU* 2.9 36.1 + - + -
568H ILE* 5.8 0.3 - - - +
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Residues in contact with THR 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C THR* 2.3 38.4 + - - +
265C PHE 3.9 1.3 - - - -
267C TYR* 1.3 83.5 - - - +
269C LEU* 1.3 69.2 + - - +
271C LEU* 2.8 16.3 + - - -
272C VAL* 2.9 47.8 + - + -
273C LEU* 3.8 13.2 + - + -
459C LEU* 3.9 17.2 - - + +
466C ILE* 4.0 12.5 - - + +
584G LEU* 4.5 4.1 - - + +
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Residues in contact with LEU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C PHE* 2.9 48.2 + - + +
268C THR* 1.3 78.2 - - - +
270C PRO* 1.4 66.0 - - + +
271C LEU 3.0 3.5 + - - -
273C LEU* 3.2 29.9 + - + +
274C LEU* 3.6 17.1 + - + +
282C TYR* 3.8 20.0 - - + -
447C PRO* 3.9 9.0 - - + -
451C TYR* 3.5 37.2 - - + +
455C HIS* 4.0 25.8 - - + -
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Residues in contact with PRO 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C ASP 3.8 11.7 - - - +
267C TYR 3.5 15.7 - - - +
269C LEU* 1.4 99.9 - - + +
271C LEU* 1.3 65.5 + - + +
274C LEU* 4.4 17.7 - - + +
279C GLN* 5.0 6.2 + - - +
282C TYR* 3.3 42.6 - - + +
447C PRO* 4.5 1.6 - - + -
586G PRO* 5.6 1.2 - - - +
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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 TYR* 3.6 46.2 - - + +
268C THR* 2.8 7.6 + - - +
270C PRO* 1.3 89.6 - - + +
272C VAL* 1.3 59.8 + - + +
273C LEU 3.9 0.2 - - - -
274C LEU* 5.3 1.1 - - - -
584G LEU* 3.4 29.8 - - + +
586G PRO* 3.4 30.9 - - + +
587G GLN 2.7 34.6 + - - +
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Residues in contact with VAL 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C THR* 2.9 41.7 + - + +
271C LEU* 1.3 80.0 - - + +
273C LEU* 1.3 61.0 + - + +
462C LYS* 3.4 42.5 - - + +
465C GLU* 4.9 5.4 - - - +
466C ILE* 4.9 0.7 - - + -
584G LEU* 4.4 15.5 - - + -
585G ALA 5.0 4.5 - - - +
587G GLN* 3.3 29.8 - - + +
589G PHE* 3.6 21.7 - - - +
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Residues in contact with LEU 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C PHE* 3.9 20.9 - - + -
268C THR* 3.8 16.4 - - + -
269C LEU* 3.2 33.8 + - + +
272C VAL* 1.3 78.7 - - - +
274C LEU* 1.3 63.3 + - - +
455C HIS* 4.2 3.3 - - + +
458C ARG* 3.1 36.3 + - + +
459C LEU* 3.7 46.7 - - + +
462C LYS* 3.8 27.4 - - + -
589G PHE* 3.8 11.2 - - + +
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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