Contacts of the helix formed by residues 267 - 288 (chain B) in PDB entry 6F0X
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 GLY 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ALA* 5.9 6.7 - - - +
264A CYS* 5.7 4.0 - - - +
264B CYS* 3.1 21.1 + - - -
266B ALA* 1.3 72.4 - - - +
268B THR* 1.3 56.0 + - - +
269B GLU 3.4 0.4 - - - -
270B PRO* 3.7 5.6 - - - +
271B SER* 2.8 30.9 + - - -
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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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266A ALA 5.1 6.5 - - - -
267A GLY* 5.6 1.6 - - - -
268A THR* 3.4 31.2 - - - -
266B ALA 2.7 8.8 + - - -
267B GLY* 1.3 70.4 - - - +
269B GLU* 1.3 66.6 + - - -
271B SER* 3.2 6.8 + - - -
272B ASP* 3.0 22.7 + - - +
2Z ALA 5.1 1.8 - - - -
3Z LEU* 3.4 27.1 - - - +
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Residues in contact with GLU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ALA* 5.5 1.1 - - - -
265B ARG 4.8 2.9 - - - +
266B ALA* 3.0 7.1 + - - +
268B THR* 1.3 76.1 - - - +
270B PRO* 1.3 62.5 - - - +
272B ASP* 4.5 0.3 - - - +
273B ALA* 2.9 29.5 + - - +
222C PHE* 4.5 11.9 - - + -
268C THR* 2.8 19.6 - - - +
269C GLU* 3.1 19.7 - - - +
270C PRO* 3.4 7.4 - - - +
271C SER* 4.6 6.9 + - - -
272C ASP* 4.6 4.2 - - - +
2Z ALA* 2.7 57.6 + - - +
3Z LEU* 3.3 14.8 - - + +
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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
----------------------------------------------------------
304A LYS* 4.0 10.5 - - - +
260B ALA* 4.7 4.7 - - + -
263B ALA 3.1 28.2 - - - +
264B CYS* 3.7 17.5 - - + -
265B ARG 4.9 0.6 - - - +
266B ALA 3.9 0.6 - - - -
267B GLY* 3.5 10.6 - - - +
268B THR 3.4 0.4 - - - -
269B GLU* 1.3 77.8 - - - +
271B SER* 1.3 63.5 + - - +
273B ALA* 4.5 3.8 - - + -
274B ILE* 2.9 36.1 + - + +
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Residues in contact with SER 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ALA* 3.1 37.0 - - - +
260A ALA* 5.4 0.4 - - - -
268A THR* 5.7 3.6 - - - -
267B GLY 2.8 21.7 + - - -
268B THR* 3.3 9.6 - - - -
270B PRO* 1.3 73.3 - - - +
272B ASP* 1.3 66.0 + - - +
274B ILE* 3.8 2.3 - - - +
275B ARG* 2.9 29.7 + - - +
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Residues in contact with ASP 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 4.4 3.7 + - - +
218B PHE* 5.0 2.5 - - + -
221B TRP 5.7 0.5 - - - +
222B PHE* 3.1 23.0 - - - -
223B SER 5.5 2.0 - - - +
225B SER* 5.8 3.8 - - - +
268B THR 3.0 14.2 + - - +
269B GLU 4.5 0.7 - - - +
271B SER* 1.3 77.2 - - - +
273B ALA* 1.3 66.9 + - - +
275B ARG* 2.4 41.2 + - - +
276B VAL* 3.0 27.6 + - + +
222C PHE* 5.2 11.7 - - + -
3Z LEU* 3.9 23.7 - - + +
5Z LEU* 5.0 0.2 - - - +
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Residues in contact with ALA 273 (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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218B PHE* 4.4 13.5 - - + -
257B LEU 4.4 3.4 - - - +
258B THR 6.4 0.2 - - - -
260B ALA* 3.9 25.6 - - + -
269B GLU 2.9 20.2 + - - +
270B PRO 3.9 0.4 - - - +
272B ASP* 1.3 76.9 - - - +
274B ILE* 1.3 56.4 + - - +
276B VAL* 2.9 8.1 + - - +
277B VAL* 2.9 30.9 + - + +
222C PHE* 4.8 4.1 - - + -
271C SER* 4.6 14.8 - - - -
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Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLU* 3.9 30.7 - - + +
256A SER* 6.1 1.3 - - - -
304A LYS* 3.5 22.7 - - - +
260B ALA 4.1 5.4 - - - +
261B ARG* 3.4 64.2 - - - +
270B PRO* 2.9 24.8 + - + +
271B SER* 4.0 2.2 - - - +
273B ALA* 1.3 71.7 - - + +
275B ARG* 1.3 59.0 + - - +
276B VAL 2.8 10.5 + - - -
277B VAL* 3.9 6.5 - - + -
278B ASN* 3.0 25.8 + - + -
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Residues in contact with ARG 275 (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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215A HIS* 3.1 24.8 - - + +
218A PHE* 4.1 28.2 - - + -
256A SER* 4.5 10.5 + - - +
259A ALA* 3.2 40.9 + - + +
260A ALA* 5.4 2.8 - - - +
273A ALA* 5.6 1.8 - - - +
222B PHE* 3.1 30.1 - - - -
223B SER* 3.6 25.2 + - - +
225B SER* 4.9 5.4 - - - +
226B GLY 6.2 0.2 - - - +
271B SER 2.9 15.7 + - - +
272B ASP* 2.4 44.4 + - - +
274B ILE* 1.3 75.5 - - - +
276B VAL* 1.3 52.6 + - - +
278B ASN* 2.6 30.9 + - - +
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Residues in contact with VAL 276 (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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215A HIS* 4.7 3.4 - - + -
217B LEU* 4.8 6.7 - - + +
218B PHE* 3.3 42.4 - - + -
225B SER* 3.5 31.2 - - - +
229B VAL* 4.3 16.8 - - + +
257B LEU* 5.1 3.8 - - + +
272B ASP 3.3 9.6 - - - +
273B ALA 2.9 7.7 + - - +
274B ILE 2.8 0.8 + - - -
275B ARG* 1.3 76.8 - - - +
277B VAL* 1.3 67.1 + - - +
278B ASN* 3.0 6.0 - - - +
279B ALA* 3.0 3.1 + - - +
280B VAL* 2.9 33.3 + - + +
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Residues in contact with VAL 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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257B LEU 3.1 24.9 - - - +
258B THR* 3.6 35.2 - - - +
261B ARG* 3.2 28.3 - - - +
273B ALA* 2.9 23.7 + - + +
274B ILE* 3.0 9.4 + - + +
276B VAL* 1.3 74.9 - - - +
278B ASN* 1.3 66.1 + - - +
280B VAL* 3.1 14.9 + - + +
281B LEU* 3.0 28.9 + - + +
306B ASP* 5.3 2.5 - - - +
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Residues in contact with ASN 278 (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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214A SER* 4.4 0.8 + - - -
215A HIS* 3.7 16.8 - - - +
253A GLN* 3.5 32.3 + - + +
255A GLU* 5.1 0.4 - - - +
256A SER* 3.8 19.0 + - - -
261B ARG* 3.9 10.2 - - - +
274B ILE* 3.0 12.2 + - + +
275B ARG* 2.6 40.8 + - - +
276B VAL 3.0 3.6 - - - +
277B VAL* 1.3 76.0 - - - +
279B ALA* 1.3 85.0 + - - +
281B LEU* 3.0 5.7 + - - +
282B THR* 2.9 26.7 + - - +
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Residues in contact with ALA 279 (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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213A ASN* 5.2 1.3 - - - +
215A HIS* 3.2 49.4 - - + +
229B VAL* 4.1 11.2 - - + -
276B VAL 3.7 3.6 - - - +
278B ASN* 1.3 85.8 + - - +
280B VAL* 1.3 66.1 + - - +
282B THR* 2.5 27.1 + - - +
283B GLN* 2.8 17.4 + - + +
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Residues in contact with VAL 280 (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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217B LEU* 5.8 3.1 - - + -
229B VAL* 5.2 2.9 - - + +
232B MET* 6.5 0.4 - - + -
233B PHE* 4.2 16.5 - - + -
251B ILE* 5.6 2.9 - - + -
257B LEU* 4.3 35.7 - - + -
258B THR* 6.3 1.3 - - - -
276B VAL* 2.9 29.2 + - + +
277B VAL* 3.1 17.2 + - + +
279B ALA* 1.3 78.9 - - - +
281B LEU* 1.3 66.8 + - + +
283B GLN* 3.7 2.1 - - - +
284B ILE* 3.0 39.0 + - + +
309B PHE* 4.6 11.9 - - + -
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Residues in contact with LEU 281 (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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253A GLN* 6.1 0.4 - - - +
300A ASN* 5.6 2.7 - - + +
901A AGS 5.3 7.9 - - - +
261B ARG* 4.0 24.0 - - - +
277B VAL* 3.5 13.2 - - + +
278B ASN* 3.0 7.6 + - - +
280B VAL* 1.3 76.2 - - + +
282B THR* 1.3 64.1 + - + +
284B ILE* 3.1 21.8 + - + +
285B ASP* 3.0 25.7 + - - +
306B ASP* 5.3 0.4 - - - +
308B ALA* 4.4 15.7 - - + -
309B PHE* 4.0 27.4 - - + +
312B ARG* 3.7 37.3 - - + +
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Residues in contact with THR 282 (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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211A GLU* 5.6 2.2 - - - +
213A ASN* 4.4 20.2 + - - +
252A ASP* 4.2 8.3 - - - +
253A GLN* 3.5 24.7 - - - +
901A AGS 6.6 0.2 - - - -
278B ASN 2.9 17.2 + - - +
279B ALA* 2.5 28.8 + - - +
281B LEU* 1.3 76.5 - - + +
283B GLN* 1.3 64.0 + - - +
285B ASP* 3.0 8.3 + - - +
286B GLN* 2.8 41.2 + - - +
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Residues in contact with GLN 283 (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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229B VAL* 4.7 4.5 - - + -
230B THR* 6.2 2.0 - - - +
233B PHE* 3.2 59.8 - - + +
279B ALA* 2.8 18.7 + - + +
282B THR* 1.3 83.3 + - - +
284B ILE* 1.3 65.0 + - - +
286B GLN* 3.0 23.4 + - - +
287B ILE* 2.9 38.1 + - - +
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Residues in contact with ILE 284 (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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172B ASN* 4.8 12.3 - - + +
174B VAL* 3.8 27.1 - - + -
233B PHE* 4.6 5.8 - - + -
251B ILE* 6.1 2.9 - - + -
280B VAL* 3.0 29.1 + - + +
281B LEU* 3.2 20.6 - - + +
283B GLN* 1.3 76.3 - - - +
285B ASP* 1.3 71.7 - - - +
287B ILE* 3.0 11.4 - - - +
288B LYS* 3.0 21.7 + - + +
295B ILE* 4.9 7.6 - - + -
309B PHE* 3.5 36.8 - - + -
312B ARG* 5.2 9.0 - - - +
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Residues in contact with ASP 285 (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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386A ARG* 4.2 4.6 + - - -
901A AGS 3.7 7.4 + - - -
172B ASN* 5.0 1.6 - - - +
281B LEU 3.0 12.7 + - - +
282B THR* 3.7 7.2 - - - +
284B ILE* 1.3 82.7 - - - +
286B GLN* 1.3 61.2 + - + +
287B ILE 2.9 6.3 + - - -
288B LYS* 3.1 52.9 + - - +
289B ARG* 4.3 8.5 + - - +
312B ARG* 2.7 34.8 + - - +
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Residues in contact with GLN 286 (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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123A ASN* 4.8 7.4 + - - +
125A TRP* 5.8 0.6 - - - -
211A GLU* 3.0 34.1 + - - -
213A ASN* 5.6 2.6 - - - +
237B GLN* 5.1 1.0 - - - +
282B THR* 2.8 26.3 + - - +
283B GLN* 3.0 28.8 + - - +
285B ASP* 1.3 75.2 - - + +
287B ILE* 1.3 60.8 + - + +
289B ARG* 5.0 3.5 - - - +
290B HIS* 3.9 13.1 - - - -
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Residues in contact with ILE 287 (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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173B ARG* 4.2 1.4 + - - -
233B PHE* 4.4 21.8 - - + +
236B ILE* 4.8 12.1 - - + -
237B GLN* 4.2 15.9 - - + +
240B ILE* 4.4 15.3 - - + -
249B VAL* 5.4 1.1 - - + -
283B GLN* 2.9 29.6 + - - +
284B ILE* 3.0 17.5 - - - +
286B GLN* 1.3 84.3 - - - +
288B LYS* 1.3 57.5 + - - +
289B ARG 2.7 13.2 + - - -
290B HIS* 2.8 25.6 + - - +
293B VAL* 4.9 11.2 - - + +
295B ILE* 3.9 28.0 - - + -
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Residues in contact with LYS 288 (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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386A ARG* 4.1 15.4 - - - +
901A AGS 4.1 17.0 + - - -
170B THR* 4.1 16.9 - - - +
171B TRP* 4.4 8.2 - - - +
172B ASN* 3.8 36.6 - - + +
173B ARG* 2.1 44.5 + - - +
284B ILE* 3.0 12.2 + - + +
285B ASP* 3.2 43.8 + - - +
287B ILE* 1.3 74.7 - - + +
289B ARG* 1.3 64.1 + - + +
293B VAL* 6.2 0.2 - - - -
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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
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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) + - + + + + + -
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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