Contacts of the helix formed by residues 259 - 283 (chain B) in PDB entry 1ZDT
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 PRO 259 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B ASP 4.3 3.1 - - - +
258B GLN* 1.3 101.2 - - + +
260B ALA* 1.3 67.9 + - - +
261B ALA* 4.5 3.4 - - + +
262B PHE* 3.1 31.2 + - + +
263B GLY 3.6 4.0 + - - -
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Residues in contact with ALA 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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258B GLN 3.3 5.8 + - - +
259B PRO* 1.3 70.9 - - - +
261B ALA* 1.3 62.4 + - - +
263B GLY* 3.3 4.3 + - - -
264B LEU* 3.1 21.3 + - - +
267B ARG* 5.3 2.3 + - - -
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Residues in contact with ALA 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B PRO* 3.2 3.5 - - + -
260B ALA* 1.3 77.9 - - - +
262B PHE* 1.3 63.5 + - - +
264B LEU* 3.5 12.2 - - + +
265B LEU* 3.1 37.7 + - + +
1002B PEF 5.2 0.2 - - - -
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Residues in contact with PHE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLN* 4.7 6.5 - - + -
259B PRO* 3.1 28.8 + - + +
261B ALA* 1.3 78.7 - - - +
263B GLY* 1.3 66.3 + - - +
265B LEU* 3.4 1.9 + - - +
266B CYS* 3.0 51.5 + - - -
436B TYR* 3.6 22.9 - + - -
440B LYS* 3.7 22.7 - - + -
445B GLU* 3.1 33.4 - - + -
446B MET* 3.6 17.7 - - - -
447B PRO* 4.7 0.9 - - + -
1002B PEF 3.4 38.8 + - + +
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Residues in contact with GLY 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B PRO 3.6 4.6 + - - -
260B ALA* 3.3 6.5 + - - -
262B PHE* 1.3 81.0 - - - +
264B LEU* 1.3 52.7 + - - +
266B CYS* 3.3 9.2 + - - +
267B ARG* 2.8 45.3 + - - +
447B PRO* 4.2 14.2 - - - +
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Residues in contact with LEU 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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248B LEU* 3.6 43.6 - - + +
260B ALA 3.1 14.3 + - - +
261B ALA* 3.5 15.5 - - + +
263B GLY* 1.3 75.9 - - - +
265B LEU* 1.3 69.0 + - + +
267B ARG* 3.2 21.0 + - - +
268B MET* 3.0 26.6 + - + +
329B GLN* 4.2 23.6 - - - +
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Residues in contact with LEU 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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261B ALA* 3.1 26.3 + - + +
262B PHE 3.9 1.1 - - - +
264B LEU* 1.3 83.8 - - + +
266B CYS* 1.3 65.3 + - - +
268B MET* 3.4 22.1 + - + +
269B ALA* 3.1 23.7 + - - +
325B LEU* 3.6 30.7 - - + -
329B GLN* 4.6 3.1 - - - +
1002B PEF 3.8 66.4 - - + +
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Residues in contact with CYS 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 PHE* 3.0 53.6 + - - +
263B GLY 3.3 9.2 - - - +
265B LEU* 1.3 76.7 - - - +
267B ARG* 1.3 62.1 + - - +
269B ALA* 3.4 3.4 + - - +
270B ASP* 3.1 26.5 + - - +
446B MET* 3.7 19.1 - - - -
447B PRO* 3.8 12.3 - - + -
450B ASN* 3.7 15.4 + - - +
452B LEU* 5.5 0.7 - - - +
1002B PEF 4.1 15.7 - - - -
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Residues in contact with ARG 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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247B SER 4.5 4.3 + - - -
248B LEU* 3.3 35.7 + - + +
250B GLU* 3.6 20.0 + - - +
252B THR* 2.9 36.1 + - - +
260B ALA 5.3 2.2 + - - -
263B GLY 2.8 21.2 + - - +
264B LEU* 3.2 26.8 + - - +
266B CYS* 1.3 74.0 - - + +
268B MET* 1.3 58.2 + - - +
270B ASP* 3.2 12.1 + - + +
271B GLN* 2.9 34.2 + - + +
447B PRO* 5.7 5.6 - - + -
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Residues in contact with MET 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ILE* 4.2 9.4 - - + +
248B LEU* 3.8 15.0 - - + +
264B LEU* 3.0 16.9 + - + +
265B LEU* 3.5 35.4 - - + +
267B ARG* 1.3 78.0 - - - +
269B ALA* 1.3 53.4 + - - +
271B GLN* 3.5 3.1 + - - +
272B THR* 2.6 34.8 + - - +
325B LEU* 3.9 26.0 - - + -
326B VAL* 3.6 21.3 - - + +
327B THR* 3.8 24.2 - - + -
329B GLN* 4.5 0.7 - - - +
1002B PEF 4.3 31.4 - - + -
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Residues in contact with ALA 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 LEU 3.1 16.2 + - - +
266B CYS 3.9 3.8 - - - +
267B ARG 3.3 0.2 - - - -
268B MET* 1.3 76.9 - - - +
270B ASP* 1.3 66.3 + - - +
272B THR* 3.3 9.2 + - - -
273B PHE* 3.1 23.4 + - - +
306B LEU* 3.8 5.9 - - + +
452B LEU* 4.2 20.6 - - + +
1002B PEF 4.3 35.0 - - + -
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Residues in contact with ASP 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 CYS 3.1 16.6 + - - +
267B ARG* 3.2 15.3 + - - +
269B ALA* 1.3 76.8 - - - +
271B GLN* 1.3 61.4 + - - +
273B PHE* 3.2 6.7 + - - +
274B ILE* 2.9 31.7 + - - +
449B ASN 4.0 2.6 - - - +
450B ASN* 3.6 14.5 + - - -
451B LEU* 3.1 42.2 + - + +
452B LEU* 3.4 29.2 + - - +
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Residues in contact with GLN 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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243B ARG* 5.9 4.6 - - - +
244B ILE* 3.8 29.9 - - + +
247B SER* 3.5 35.4 + - - +
248B LEU* 5.3 2.5 - - + -
267B ARG* 2.9 22.3 + - + +
268B MET 3.8 2.9 - - - +
269B ALA 3.3 0.2 - - - -
270B ASP* 1.3 76.2 - - - +
272B THR* 1.3 64.9 + - - +
274B ILE* 3.5 33.1 + - - +
275B SER* 3.2 21.1 + - - -
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Residues in contact with THR 272 (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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240B VAL* 5.7 2.7 - - + -
244B ILE* 3.8 8.7 - - + +
268B MET* 2.6 23.7 + - - +
269B ALA* 3.5 11.3 - - - -
270B ASP 3.2 0.2 - - - -
271B GLN* 1.3 76.6 - - - +
273B PHE* 1.3 58.8 + - - +
275B SER* 3.2 7.2 + - - -
276B ILE* 3.0 29.3 + - + +
306B LEU* 4.0 14.6 - - + -
309B ASP* 3.4 31.9 - - - +
313B ARG* 4.8 5.8 - - - +
326B VAL* 3.7 17.8 - - + +
1002B PEF 6.0 2.7 - - + +
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Residues in contact with PHE 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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269B ALA 3.1 13.3 + - - +
270B ASP 3.2 7.6 + - - +
272B THR* 1.3 76.5 - - - +
274B ILE* 1.3 64.7 + - - +
276B ILE* 3.1 19.1 + - + +
277B VAL* 2.9 44.3 + - + +
298B LEU* 4.9 10.5 - - + -
302B TRP* 3.4 37.9 - - + -
305B LEU* 5.6 0.2 - - + -
306B LEU* 3.9 29.6 - - + -
451B LEU* 3.5 22.9 - - + -
452B LEU* 4.1 7.0 - - + -
455B MET* 3.9 31.0 - - + -
745Q LEU* 5.2 2.0 - - + -
748Q LEU* 5.1 2.9 - - + -
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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
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270B ASP 2.9 16.9 + - - +
271B GLN* 3.5 39.9 - - - +
272B THR 3.3 0.2 - - - -
273B PHE* 1.3 75.9 - - - +
275B SER* 1.3 56.7 + - - +
277B VAL* 3.3 9.2 + - - +
278B ASP* 3.0 27.0 + - + +
451B LEU* 4.1 27.4 - - + -
744Q LEU* 6.5 0.2 - - + -
748Q LEU* 4.3 23.1 - - + +
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Residues in contact with SER 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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235B PRO* 4.1 22.2 - - - +
240B VAL* 4.3 19.9 - - - +
243B ARG* 6.2 3.8 - - - -
244B ILE* 5.5 0.7 - - - -
271B GLN 3.2 14.3 + - - -
272B THR* 3.4 11.7 - - - -
273B PHE 3.2 0.4 - - - -
274B ILE* 1.3 77.2 - - - +
276B ILE* 1.3 57.8 + - - +
278B ASP* 3.4 8.2 + - - +
279B TRP* 3.0 26.0 + - - +
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Residues in contact with ILE 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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235B PRO* 6.0 0.4 - - - -
272B THR* 3.0 24.5 + - + +
273B PHE* 3.1 19.5 + - + +
275B SER* 1.3 75.2 - - - +
277B VAL* 1.3 65.3 + - - +
279B TRP* 3.3 17.9 + - + +
280B ALA* 3.1 19.1 + - - +
298B LEU* 5.1 3.1 - - + -
305B LEU* 4.0 54.3 - - + +
306B LEU* 4.1 23.1 - - + +
309B ASP* 4.4 10.3 - - + +
372B LYS* 4.8 12.6 - - - +
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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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273B PHE* 2.9 45.9 + - + +
274B ILE 3.6 8.1 - - - +
276B ILE* 1.3 78.1 - - - +
278B ASP* 1.3 60.7 + - - +
280B ALA* 3.3 5.9 + - - +
281B ARG* 3.0 22.9 + - + +
298B LEU* 4.4 14.4 - - + -
745Q LEU* 4.4 3.8 - - + -
748Q LEU* 3.7 42.0 - - + +
749Q LEU* 4.1 22.1 - - + +
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Residues in contact with ASP 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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243B ARG* 5.5 4.4 + - - -
274B ILE* 3.0 14.8 + - + +
275B SER* 3.7 10.7 - - - +
276B ILE 3.3 0.4 - - - -
277B VAL* 1.3 76.7 - - - +
279B TRP* 1.3 62.7 + - - +
281B ARG* 3.1 52.1 + - - +
282B ARG* 3.4 21.9 - - - +
748Q LEU 5.8 0.7 - - - -
751Q LYS* 5.2 1.0 - - - +
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Residues in contact with TRP 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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230B LEU* 4.5 13.5 + - + +
233B LEU* 3.5 31.0 - - + +
234B GLU* 3.9 9.8 + - - -
235B PRO* 4.0 20.6 - - + +
275B SER 3.0 14.0 + - - +
276B ILE* 3.4 19.7 - - + +
277B VAL 3.2 0.2 - - - -
278B ASP* 1.3 77.7 + - - +
280B ALA* 1.3 75.8 + - + +
282B ARG* 3.3 11.1 + - - +
283B CYS* 3.3 41.1 + - - -
305B LEU* 4.5 16.2 - - + -
369B VAL* 4.9 1.7 - - - +
372B LYS* 3.4 58.6 - - + +
373B PHE* 4.1 8.3 - - - -
376B LEU* 3.8 28.3 - - + -
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Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ILE 3.1 13.2 + - - +
277B VAL 3.7 4.0 - - - +
279B TRP* 1.3 98.5 - - + +
281B ARG* 1.3 57.0 + - - +
283B CYS* 2.9 27.0 + - - +
286B PHE* 3.1 26.7 - - + -
298B LEU* 4.3 18.4 - - + -
376B LEU* 4.2 11.2 - - + -
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Residues in contact with ARG 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B VAL 3.0 16.3 + - - +
278B ASP* 3.1 38.8 + - - +
280B ALA* 1.3 76.2 - - - +
282B ARG* 1.3 76.9 + - - +
286B PHE* 3.9 10.9 - - + -
287B LYS* 3.4 23.2 - - - +
294B GLN* 4.9 4.6 + - - +
748Q LEU 4.3 10.3 - - - +
749Q LEU* 4.2 29.2 - - + +
751Q LYS* 3.5 54.5 - - - +
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Residues in contact with ARG 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B GLN 4.6 3.6 + - - -
233B LEU* 3.3 61.7 + - + +
278B ASP* 3.4 30.3 - - - +
279B TRP* 3.3 9.6 + - - +
280B ALA 3.1 0.4 - - - -
281B ARG* 1.3 101.3 - - - +
283B CYS* 1.3 64.5 + - - +
284B MET 3.8 0.2 + - - -
287B LYS* 3.7 14.4 - - - +
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Residues in contact with CYS 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LEU* 4.1 15.9 - - - -
233B LEU* 3.7 9.9 - - - -
279B TRP* 3.3 54.4 + - - -
280B ALA* 2.9 14.2 + - - +
282B ARG* 1.3 79.5 - - - +
284B MET* 1.3 71.8 + - - +
286B PHE* 4.3 5.2 - - + -
287B LYS* 3.0 28.3 + - - +
373B PHE* 4.1 10.3 - - + -
376B LEU* 4.7 1.8 - - + -
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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