Contacts of the helix formed by residues 250 - 273 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B PHE* 3.4 8.1 - - - -
247B ALA* 3.6 17.5 + - - +
248B GLU 3.4 3.6 + - - -
249B LYS* 1.3 73.3 - - - +
251B VAL* 1.3 60.8 + - - +
252B ASP* 3.4 17.2 + - - +
253B LEU* 3.2 21.2 + - + +
254B CYS* 3.0 23.4 + - - +
483B HIS* 4.0 0.9 + - - -
553G VAL 3.8 5.7 + - - -
554G THR* 3.5 41.8 + - - +
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Residues in contact with VAL 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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214B VAL* 5.0 5.8 - - + +
217B PHE* 3.6 16.2 - - + -
218B ALA* 4.0 31.0 - - + +
221B ALA* 5.8 2.7 - - + -
249B LYS 3.2 7.8 + - - +
250B ASN* 1.3 74.4 + - - +
252B ASP* 1.3 70.9 + - - +
254B CYS* 3.3 3.1 - - - +
255B LYS* 3.1 40.5 + - + +
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Residues in contact with ASP 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ASN* 3.3 10.3 + - - +
251B VAL* 1.3 83.2 - - - +
253B LEU* 1.3 65.7 + - - +
255B LYS* 3.3 21.2 + - - +
256B GLU* 3.3 25.4 + - - +
554G THR* 4.9 8.5 - - - +
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ALA* 3.6 35.4 - - + -
250B ASN* 3.2 20.5 + - + +
252B ASP* 1.3 76.1 - - - +
254B CYS* 1.3 65.0 + - - +
256B GLU* 3.4 8.5 + - - +
257B MET* 3.3 17.5 + - - +
479B ALA* 4.5 5.2 - - + -
483B HIS* 3.7 15.7 + - + +
553G VAL* 4.0 11.7 - - + +
554G THR* 3.5 28.9 + - - +
555G SER* 3.6 7.2 - - - +
556G PHE* 3.5 40.4 - - + -
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Residues in contact with CYS 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TYR* 3.4 35.9 - - - -
214B VAL* 4.5 9.2 - - - -
217B PHE* 3.5 41.7 - - + -
250B ASN 3.0 5.5 + - - -
251B VAL 3.3 10.8 - - - +
253B LEU* 1.3 75.8 - - - +
255B LYS* 1.3 63.8 + - - +
257B MET* 2.9 15.3 + - - +
258B VAL* 3.1 21.3 + - - +
483B HIS* 3.8 12.9 + - - +
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Residues in contact with LYS 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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214B VAL* 4.1 27.6 - - + -
251B VAL* 3.1 27.7 + - - +
252B ASP* 3.3 22.2 + - - +
254B CYS* 1.3 79.4 - - - +
256B GLU* 1.3 62.6 + - - +
258B VAL* 3.4 9.2 + - - +
259B ASP* 3.1 24.4 + - - +
441D PHE* 3.7 18.3 - - + +
442D ASP* 3.5 34.7 + - - +
443D GLN* 3.8 20.1 + - - +
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Residues in contact with GLU 256 (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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252B ASP* 3.3 13.7 + - - +
253B LEU* 3.6 11.0 - - - +
254B CYS 3.2 0.6 - - - -
255B LYS* 1.3 73.6 - - - +
257B MET* 1.3 68.0 + - - +
259B ASP* 3.3 6.4 + - - +
260B GLY* 2.8 21.5 + - - -
443D GLN* 5.3 5.6 - - - +
577F PHE* 4.5 4.6 + - - -
554G THR 4.2 1.9 - - - +
555G SER* 2.7 28.9 + - - -
556G PHE* 3.0 36.8 + - + -
557G PHE* 3.5 32.8 - - + -
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Residues in contact with MET 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TYR* 4.2 16.6 - - + -
253B LEU 3.3 8.4 + - - +
254B CYS* 2.9 9.8 + - - +
256B GLU* 1.3 78.3 - - - +
258B VAL* 1.3 82.6 + - + +
260B GLY 3.1 2.3 + - - -
261B LEU* 2.8 48.3 + - + +
480B LEU* 4.4 6.7 - - + -
483B HIS* 3.4 40.8 - - + +
484B PHE* 3.5 34.1 - - + -
487B PHE* 4.5 9.6 - - + -
577F PHE* 3.2 17.4 - - + -
556G PHE* 4.3 3.3 - - + -
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Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 3.2 52.6 - - + +
213B TYR* 4.3 5.4 - - + -
214B VAL* 3.7 22.4 - - + -
254B CYS* 3.1 21.7 + - - +
255B LYS* 3.8 5.6 - - - +
257B MET* 1.3 95.2 - - + +
259B ASP* 1.3 61.9 + - - +
261B LEU* 3.2 7.4 + - - +
262B ARG* 3.1 18.4 + - - +
441D PHE* 4.0 14.1 - - + -
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Residues in contact with ASP 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 LYS 3.1 17.3 + - - +
256B GLU* 3.7 4.9 - - - +
258B VAL* 1.3 75.1 - - - +
260B GLY* 1.3 65.5 + - - +
262B ARG* 2.3 41.4 + - - +
263B ILE* 3.1 35.9 + - - +
441D PHE* 4.6 11.0 - - + -
443D GLN* 3.8 27.8 - - - +
557G PHE* 6.1 1.2 - - - -
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Residues in contact with GLY 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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256B GLU 2.8 12.9 + - - -
257B MET 3.4 4.3 - - - -
259B ASP* 1.3 75.2 - - - +
261B LEU* 1.3 48.7 - - - +
263B ILE* 3.3 4.7 + - - +
264B THR* 2.6 40.5 + - - -
576F ALA* 3.9 13.4 - - - +
577F PHE* 3.4 26.9 - - - -
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Residues in contact with LEU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 6.1 0.2 - - - -
210B LEU* 4.4 18.6 - - + -
257B MET* 2.8 51.4 + - + +
258B VAL* 3.3 10.3 - - - +
259B ASP 3.2 0.2 - - - -
260B GLY* 1.3 74.9 - - - +
262B ARG* 1.3 57.5 + - - +
264B THR* 3.7 2.8 - - - -
265B PHE* 2.8 32.4 + - - +
456B LEU* 4.3 7.8 - - + +
459B LEU* 3.9 23.6 - - + +
460B PHE* 3.6 35.7 - - + -
463B LEU* 4.8 5.6 - - + -
484B PHE* 4.4 10.8 - - + -
487B PHE* 4.6 4.0 - - + -
577F PHE* 3.5 4.9 - - + -
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Residues in contact with ARG 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 5.1 1.8 - - + -
207B ILE* 3.8 22.9 - - + +
210B LEU* 3.8 21.5 - - + -
258B VAL 3.1 5.3 + - - +
259B ASP* 2.3 43.2 + - - +
261B LEU* 1.3 77.3 - - - +
263B ILE* 1.3 80.1 + - - +
265B PHE* 4.4 2.9 - - - -
266B ASP* 2.9 50.1 + - - +
448B SER* 3.2 14.4 + - - +
449B TYR* 5.7 3.0 - - - -
440D GLU* 4.8 12.0 + - - -
441D PHE* 4.3 13.2 - - + -
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Residues in contact with ILE 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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259B ASP* 3.1 36.9 + - - +
260B GLY* 3.7 7.2 - - - +
262B ARG* 1.3 94.5 - - - +
264B THR* 1.3 66.7 + - - +
266B ASP* 3.3 8.6 + - + +
267B TYR* 3.2 20.8 + - - +
574F VAL* 3.9 27.8 - - + -
575F VAL 3.7 22.4 - - - +
576F ALA* 4.5 3.4 - - + -
581F LEU* 4.0 9.6 - - + -
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Residues in contact with THR 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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260B GLY 2.6 29.3 + - - -
261B LEU* 3.8 5.8 - - - -
263B ILE* 1.3 74.8 - - - +
265B PHE* 1.3 53.6 + - - +
267B TYR* 3.3 2.3 + - + +
268B THR* 2.4 45.1 + - - +
459B LEU* 4.3 15.9 - - + -
463B LEU* 4.7 7.2 - - + -
466B ILE* 4.7 15.0 - - + -
470B MET* 5.3 1.6 - - + -
576F ALA* 3.5 7.6 - - - +
577F PHE* 3.2 21.9 - - + -
581F LEU* 4.3 20.2 - - + -
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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
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206B ILE* 3.3 37.0 - - + -
261B LEU 2.8 21.4 + - - +
262B ARG* 4.0 4.7 - - - +
264B THR* 1.3 71.7 - - - +
266B ASP* 1.3 68.3 + - - +
268B THR* 3.0 3.4 + - - -
269B LEU* 2.9 55.6 + - + +
273B LEU* 3.9 14.6 - - + -
447B PRO* 3.6 31.9 - - + -
448B SER* 4.0 12.1 - - - -
451B TYR* 3.7 9.4 - - + -
455B HIS* 3.7 22.2 - - + -
456B LEU* 4.3 11.0 - - + -
459B LEU* 4.2 13.9 - - + +
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Residues in contact with ASP 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 ARG* 2.9 32.6 + - - +
263B ILE* 3.5 7.7 - - - +
265B PHE* 1.3 78.5 - - - +
267B TYR* 1.3 60.8 + - - +
270B PRO* 3.8 6.9 - - - +
446B PRO* 3.3 16.0 - - + +
447B PRO* 3.1 33.6 - - + +
448B SER* 2.8 40.9 + - - -
449B TYR* 6.1 0.2 - - - -
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Residues in contact with TYR 267 (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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263B ILE 3.2 4.4 + - - +
264B THR 3.8 5.2 - - - +
265B PHE 3.1 0.4 - - - -
266B ASP* 1.3 78.4 - - - +
268B THR* 1.3 71.3 + - - +
270B PRO* 3.5 10.7 - - - +
271B LEU* 3.6 32.0 - - + +
466B ILE* 6.5 0.2 - - + -
567E LEU* 4.3 13.6 - - + +
581F LEU* 3.7 32.1 - - + -
582F PRO* 3.3 27.9 + - + -
583F LYS* 4.1 2.6 - - - -
584F LEU* 3.7 28.3 + - + -
572H LEU* 3.6 37.9 - - + +
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Residues in contact with THR 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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264B THR* 2.4 37.5 + - - +
265B PHE 3.8 1.8 - - - -
267B TYR* 1.3 83.1 - - - +
269B LEU* 1.3 66.9 + - - +
271B LEU* 2.8 17.7 + - - -
272B VAL* 2.9 48.4 + - + -
273B LEU* 3.7 14.8 - - + -
459B LEU* 3.9 15.6 - - + +
466B ILE* 4.1 13.0 - - + +
584F LEU* 4.3 6.0 - - + +
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Residues in contact with LEU 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 PHE* 2.9 47.1 + - + +
268B THR* 1.3 76.5 - - - +
270B PRO* 1.3 62.8 - - + +
271B LEU 3.0 5.7 + - - -
273B LEU* 3.2 32.1 + - + +
274B LEU* 3.7 15.7 + - + +
282B TYR* 3.9 22.9 - - + -
447B PRO* 3.9 12.6 - - + -
451B TYR* 3.5 34.1 - - + +
455B HIS* 4.0 26.9 - - + -
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Residues in contact with PRO 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 ASP 3.8 11.4 - - - +
267B TYR 3.5 11.9 - - - +
268B THR 3.5 3.6 - - - -
269B LEU* 1.3 99.2 - - + +
271B LEU* 1.3 67.4 + - + +
274B LEU* 4.5 14.6 - - + +
279B GLN* 5.0 6.6 + - - +
282B TYR* 3.3 44.8 - - + +
447B PRO* 4.5 2.0 - - + -
586F PRO* 5.9 0.3 - - - +
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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 TYR* 3.6 50.5 - - + +
268B THR* 2.8 8.5 + - - +
270B PRO* 1.3 88.8 - - + +
272B VAL* 1.3 63.5 + - + +
273B LEU 3.8 0.2 - - - -
274B LEU* 5.3 1.5 + - - -
584F LEU* 3.8 24.0 - - + +
586F PRO* 3.4 33.3 - - + +
587F GLN 3.0 27.4 + - - +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B THR* 2.9 41.8 + - + -
271B LEU* 1.3 81.7 - - + +
273B LEU* 1.3 59.7 + - + +
274B LEU 3.7 1.6 - - - -
462B LYS* 3.5 44.2 - - + +
466B ILE* 4.9 0.7 - - + -
584F LEU* 4.2 19.5 - - + -
585F ALA 4.9 4.5 - - - +
587F GLN* 3.6 27.1 - - + +
589F PHE* 3.6 20.6 - - - +
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B PHE* 3.9 20.4 - - + -
268B THR* 3.7 19.3 - - + -
269B LEU* 3.2 32.9 + - + +
272B VAL* 1.3 80.9 - - + +
274B LEU* 1.3 62.8 + - - +
455B HIS* 4.3 3.6 - - + +
458B ARG* 3.2 36.7 + - + +
459B LEU* 3.7 44.6 - - + +
462B LYS* 3.7 27.8 - - + -
589F PHE* 3.8 11.0 - - + +
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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