Contacts of the helix formed by residues 251 - 277 (chain B) in PDB entry 6D6U
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 SER 251 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LEU* 6.0 0.9 - - - -
248B ASN* 3.7 11.4 + - - +
249B ARG 3.5 1.0 - - - -
250B GLU* 1.3 73.5 - - - +
252B VAL* 1.3 64.0 + - - +
253B PRO 3.7 0.2 - - - -
254B ALA* 4.4 12.6 - - - -
255B ARG* 3.0 31.0 + - - +
318E HIS* 3.6 16.0 + - - -
319E TYR* 3.0 48.1 + - - -
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ARG 5.6 1.1 - - - +
250B GLU 3.0 12.3 + - - +
251B SER* 1.3 70.7 - - - +
253B PRO* 1.3 77.6 - - + +
254B ALA 3.3 0.3 + - - -
255B ARG* 3.3 4.7 + - - +
256B THR* 2.9 41.4 + - + +
304B PHE* 3.8 7.4 - - + -
308B ASN* 3.3 41.1 - - - +
409B Y01 5.3 8.1 - - + -
262E VAL* 5.2 10.5 - - + -
266E THR* 6.1 1.8 - - + -
318E HIS* 3.9 1.1 - - - +
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Residues in contact with PRO 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B VAL* 1.3 94.7 - - + +
254B ALA* 1.3 60.5 + - - +
256B THR* 2.5 22.4 + - - +
257B VAL* 2.9 18.4 + - + +
262E VAL* 4.3 9.2 - - + -
266E THR* 3.6 24.9 - - + -
311E LEU* 6.4 0.2 - - + -
314E TYR* 3.7 31.2 - - + +
315E GLY* 4.3 2.9 - - - -
318E HIS* 3.3 35.4 - - + +
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LEU* 5.0 12.3 - - + -
251B SER* 4.4 17.2 - - - -
252B VAL 3.3 0.8 - - - -
253B PRO* 1.3 79.1 - - - +
255B ARG* 1.3 59.8 + - - +
257B VAL* 3.2 7.1 + - - +
258B PHE* 2.9 25.7 + - - +
315E GLY* 3.6 31.2 + - - +
318E HIS* 5.3 0.2 - - - +
319E TYR* 4.5 7.9 - - + -
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Residues in contact with ARG 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B SER* 3.2 39.4 + - - +
245B PHE* 5.3 1.2 + - - +
247B LEU* 3.7 26.4 + - + -
248B ASN 3.3 19.5 + - - -
249B ARG* 2.8 40.8 + - - +
251B SER* 3.0 22.5 + - - +
252B VAL* 3.3 4.8 + - - +
254B ALA* 1.3 74.8 - - + +
256B THR* 1.3 60.8 + - - +
258B PHE* 3.4 8.1 - - - +
259B GLY* 2.9 25.5 + - - -
301B LEU* 6.1 0.3 - - - +
304B PHE* 3.2 41.7 - - + -
307B VAL* 5.1 10.1 - - - +
308B ASN* 5.8 4.2 - - - +
322B ASP* 5.0 9.1 + - - -
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Residues in contact with THR 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B VAL* 2.9 30.0 + - + +
253B PRO* 2.5 28.6 + - - +
255B ARG* 1.3 73.7 - - - +
257B VAL* 1.3 58.7 + - - +
259B GLY* 3.3 1.5 + - - -
260B VAL* 2.9 38.4 + - - +
301B LEU* 6.4 0.7 - - - -
304B PHE* 3.6 22.4 - - + -
409B Y01 4.0 28.7 - - + +
266E THR* 4.7 9.4 - - + +
270E ILE* 5.3 8.7 - - - +
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Residues in contact with VAL 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 5.7 1.6 - - + -
253B PRO* 2.9 23.8 + - + +
254B ALA* 3.4 9.2 - - - +
256B THR* 1.3 76.4 + - - +
258B PHE* 1.3 58.6 + - - +
260B VAL* 3.3 5.9 + - - +
261B THR* 2.7 39.9 + - - +
266E THR* 6.3 0.2 - - + -
308E PHE* 4.5 4.2 - - + -
311E LEU* 3.4 49.8 - - + +
312E VAL* 3.8 33.7 - - + +
315E GLY* 4.8 2.5 - - - -
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Residues in contact with PHE 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ILE* 6.5 1.3 - - + -
259A LEU* 6.4 2.5 - - + -
240B LEU* 2.9 50.7 - - + -
241B SER* 3.4 28.5 - - - -
243B VAL* 3.7 20.6 - - + -
244B SER* 3.5 25.1 - - - -
247B LEU* 5.6 4.9 - - + -
254B ALA 2.9 13.9 + - - +
255B ARG* 3.4 13.0 - - + +
256B THR 3.2 0.2 - - - -
257B VAL* 1.3 78.2 - - - +
259B GLY* 1.3 64.8 + - - +
261B THR* 3.2 8.8 + - - -
262B THR* 3.0 32.0 + - + +
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Residues in contact with GLY 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ARG 2.9 16.6 + - - -
256B THR 3.8 1.1 - - - -
258B PHE* 1.3 74.8 - - - +
260B VAL* 1.3 60.4 + - - +
262B THR* 2.6 24.4 + - - -
263B VAL* 2.9 22.6 + - - +
301B LEU* 4.9 17.0 - - - -
409B Y01 6.0 1.1 - - - -
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B THR 2.9 22.6 + - - +
257B VAL* 3.8 6.3 - - - +
259B GLY* 1.3 75.2 - - - +
261B THR* 1.3 64.8 + - - +
263B VAL* 3.3 6.3 + - - +
264B LEU* 2.9 26.9 + - + +
409B Y01 4.9 13.9 - - + +
270E ILE* 4.3 35.2 - - + -
273E VAL* 4.8 21.3 - - + -
274E LEU* 6.2 3.6 - - + -
308E PHE* 5.6 4.7 - - + -
311E LEU* 5.7 4.9 - - + -
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Residues in contact with THR 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 3.7 30.7 - - + +
263A THR* 6.5 0.9 - - + -
240B LEU* 6.2 2.7 - - + -
257B VAL* 2.7 22.0 + - - +
258B PHE* 3.3 11.7 - - - -
260B VAL* 1.3 77.8 - - - +
262B THR* 1.3 65.0 + - + +
264B LEU* 3.9 4.1 - - - +
265B THR* 3.0 36.0 + - - +
308E PHE* 3.0 32.2 - - + -
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Residues in contact with THR 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B THR* 4.5 19.7 - - + +
240B LEU* 4.7 9.2 - - + -
241B SER* 4.1 27.1 - - - -
258B PHE* 3.0 25.4 + - + +
259B GLY* 2.6 25.6 + - - -
261B THR* 1.3 77.4 - - + +
263B VAL* 1.3 60.6 + - - +
265B THR* 3.4 1.6 + - - -
266B MET* 2.9 35.3 + - - +
297B VAL* 5.1 12.7 - - - +
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B GLY* 2.9 23.7 + - - +
260B VAL* 3.8 6.5 - - + +
262B THR* 1.3 79.1 + - - +
264B LEU* 1.3 63.4 + - - +
266B MET* 3.3 6.3 + - - +
267B THR* 2.9 34.9 + - - +
294B TYR* 6.2 0.2 - - + -
297B VAL* 5.6 4.3 - - + +
298B PHE* 3.4 35.2 - - + -
301B LEU* 4.5 13.2 - - + -
407C Y01 3.7 32.8 - - + -
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B VAL* 2.9 21.9 + - + +
261B THR* 3.9 4.3 - - - +
263B VAL* 1.3 77.5 - - - +
265B THR* 1.3 66.4 + - - +
267B THR* 3.3 3.8 + - - +
268B THR* 3.0 48.6 + - + +
407C Y01 4.7 15.7 - - + -
273E VAL* 5.2 7.4 - - + -
274E LEU* 5.5 6.5 - - + -
277E THR* 3.7 33.7 - - + +
304E PHE* 4.6 21.8 - - + -
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Residues in contact with THR 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A THR* 5.1 16.2 - - + +
266A THR* 5.6 7.9 - - + -
237B THR* 4.0 26.5 - - + +
261B THR* 3.0 25.3 + - - +
262B THR* 3.8 3.6 - - - -
264B LEU* 1.3 80.9 - - - +
266B MET* 1.3 64.8 + - - +
268B THR* 3.0 8.7 + - - +
269B LEU* 2.9 29.4 + - + +
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Residues in contact with MET 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B CYS* 3.6 25.8 - - - -
237B THR* 3.6 30.7 - - + -
238B VAL* 3.6 30.5 - - + -
262B THR 2.9 23.2 + - - +
263B VAL* 3.3 5.8 + - - +
265B THR* 1.3 77.7 - - - +
267B THR* 1.3 58.0 + - - +
269B LEU* 3.3 9.3 + - - +
270B SER* 2.9 30.1 + - - -
290B ILE* 5.8 0.2 - - - +
293B CYS* 4.1 7.4 - - + -
294B TYR* 5.1 13.5 - - + -
297B VAL* 3.7 29.8 - - + -
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Residues in contact with THR 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B VAL* 2.9 21.8 + - - +
264B LEU* 3.9 4.7 - - - -
266B MET* 1.3 76.9 - - - +
268B THR* 1.3 60.4 + - + +
270B SER* 3.2 6.3 + - - -
271B ILE* 3.0 48.9 + - + +
294B TYR* 5.2 9.4 - - - -
298B PHE* 5.9 0.3 - - - -
410B Y01 5.6 8.2 - - + +
407C Y01 3.8 42.9 - - + +
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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
----------------------------------------------------------
270A GLU* 4.0 18.9 - - - +
264B LEU* 3.0 41.9 + - + +
265B THR* 3.0 14.0 + - - +
267B THR* 1.3 77.5 - - + +
269B LEU* 1.3 61.4 + - - +
271B ILE* 4.1 14.4 - - + +
272B SER* 3.8 13.5 + - - -
407C Y01 6.2 0.9 - - + -
277E THR* 5.6 5.2 - - + -
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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
----------------------------------------------------------
229B GLN* 4.4 6.7 - - - +
230B THR* 3.7 41.5 - - + +
233B PRO* 4.8 8.5 - - + -
234B CYS* 3.8 40.4 - - + +
237B THR* 6.1 0.4 - - - +
265B THR* 2.9 24.2 + - + +
266B MET* 3.5 9.6 - - - +
268B THR* 1.3 75.6 + - - +
270B SER* 1.3 60.7 + - - +
271B ILE 3.3 0.2 + - - -
272B SER* 3.4 4.4 + - - -
273B ALA* 2.9 29.2 + - + +
290B ILE* 6.2 2.5 - - + -
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Residues in contact with SER 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B MET 2.9 16.4 + - - -
267B THR* 3.2 6.9 + - - -
269B LEU* 1.3 74.8 - - - +
271B ILE* 1.3 66.4 + - - +
273B ALA* 3.7 6.4 - - - +
274B ARG* 2.9 58.8 + - - +
290B ILE* 3.9 26.8 - - - +
294B TYR* 6.5 0.9 - - - -
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Residues in contact with ILE 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B THR* 3.0 39.2 + - + +
268B THR* 4.1 12.8 - - + +
269B LEU 3.3 0.4 - - - -
270B SER* 1.3 76.9 - - - +
272B SER* 1.3 60.0 + - - +
274B ARG* 3.4 10.0 + - - +
275B ASN* 2.9 34.1 + - + +
267C HIS* 4.2 26.7 - - + +
407C Y01 5.7 2.5 - - + -
281E THR* 5.9 3.8 - - + -
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Residues in contact with SER 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A GLU* 4.7 15.4 - - - +
268B THR 3.8 9.0 + - - -
269B LEU* 3.4 7.4 + - - -
270B SER 3.4 0.2 - - - -
271B ILE* 1.3 79.4 - - - +
273B ALA* 1.3 66.1 + - - +
275B ASN* 3.6 7.9 - - - +
276B SER* 2.9 26.3 + - - -
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B THR* 4.1 22.7 - - + +
269B LEU 2.9 18.8 + - - +
270B SER* 3.3 4.5 + - - +
272B SER* 1.3 76.8 - - - +
274B ARG* 1.3 58.9 + - - +
276B SER* 2.9 21.0 + - - -
277B LEU* 3.9 3.3 + - - +
286B MET* 3.3 23.0 - - + +
290B ILE* 3.8 25.1 - - + -
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Residues in contact with ARG 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B SER* 2.9 42.6 + - - +
271B ILE* 4.2 8.3 - - - +
273B ALA* 1.3 74.6 - - - +
275B ASN* 1.3 59.0 + - - +
276B SER 3.4 0.2 - - - -
277B LEU* 2.9 25.1 - - - +
278B PRO 4.7 1.2 - - - +
279B LYS* 5.5 4.0 - - - +
286B MET* 4.9 2.9 - - + -
287B ASP* 3.7 25.4 - - - +
290B ILE* 4.7 9.9 - - + -
410B Y01 4.8 14.3 - - - +
220C TYR* 4.5 19.3 + - - +
224C GLN* 2.9 43.0 + - - +
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Residues in contact with ASN 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B HIS* 4.0 15.0 + - - -
271B ILE* 2.9 24.1 + - + +
272B SER* 3.1 10.3 + - - +
274B ARG* 1.3 74.7 - - - +
276B SER* 1.3 65.6 + - - +
277B LEU 3.1 7.8 + - - +
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Residues in contact with SER 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LYS* 5.2 15.4 + - - +
55B ASP* 5.1 8.1 - - - +
56B HIS* 4.3 15.8 - - - -
146B PHE* 5.3 5.9 - - - -
226B PHE* 5.4 10.8 - - - -
272B SER* 2.9 13.6 + - - -
273B ALA* 2.9 17.3 + - - -
275B ASN* 1.3 76.2 - - - +
277B LEU* 1.3 57.8 + - - +
278B PRO* 4.4 2.8 - - - +
286B MET* 5.0 2.4 - - - +
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASP* 5.9 1.8 - - + +
56B HIS* 5.4 2.4 + - - -
143B LEU* 3.8 19.1 - - + -
146B PHE* 3.5 52.7 - - + -
221B ARG* 5.3 1.8 - - - +
273B ALA 4.2 10.5 - - - +
274B ARG* 2.9 22.0 + - - +
275B ASN* 3.1 5.8 - - - +
276B SER* 1.3 81.2 + - - +
278B PRO* 1.3 106.9 - - + +
279B LYS* 5.0 1.7 - - - +
280B VAL* 5.0 3.1 - - + -
284B THR* 3.7 26.5 - - + +
286B MET* 5.0 2.7 - - + -
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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