Contacts of the helix formed by residues 261 - 290 (chain A) in PDB entry 1KPI
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 HIS 261 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.2 40.0 + - + +
257A ALA* 2.9 31.8 + - - +
258A LEU* 3.5 4.5 - - + +
260A ALA* 1.3 84.0 - - + +
262A LYS* 1.3 53.4 + - - +
263A ASP* 3.3 2.9 - - - -
264A GLU* 3.0 31.0 + - + +
265A ALA* 2.8 33.5 + - + +
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Residues in contact with LYS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LEU* 3.0 13.3 + - + +
259A GLN* 3.1 42.3 + - - +
260A ALA 3.2 2.0 + - - +
261A HIS* 1.3 75.0 - - - +
263A ASP* 1.3 55.3 + - - +
265A ALA* 3.2 5.0 + - - +
266A ILE* 2.7 63.5 + - + +
271A GLN* 4.3 12.9 - - - +
274A CYS* 5.5 6.5 - - + -
275A ASP* 5.4 2.8 + - - -
278A MET* 6.5 1.3 - - + -
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Residues in contact with ASP 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ALA 5.0 0.8 + - - -
261A HIS 3.3 0.6 - - - -
262A LYS* 1.3 81.2 - - - +
264A GLU* 1.3 62.7 + - - +
266A ILE* 3.4 14.4 + - - +
267A ALA* 3.1 21.5 + - - +
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Residues in contact with GLU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU* 5.6 1.7 - - - +
33A LEU* 3.3 28.2 - - + +
261A HIS* 3.0 31.1 + - + +
263A ASP* 1.3 79.0 - - - +
265A ALA* 1.3 60.2 + - - +
267A ALA* 2.9 26.0 - - + +
268A LEU* 3.2 10.8 + - + +
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Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 4.4 7.9 - - + -
33A LEU* 3.6 20.1 - - + +
258A LEU* 3.9 20.9 - - + -
261A HIS 2.8 16.1 + - - +
262A LYS 3.6 4.0 - - - +
264A GLU* 1.3 73.3 - - - +
266A ILE* 1.3 64.3 + - - +
267A ALA 3.0 1.5 + - - -
268A LEU* 3.3 4.3 + - - +
269A LYS* 3.0 23.6 + - - +
274A CYS* 3.6 20.5 - - - -
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Residues in contact with ILE 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LYS* 2.7 61.3 + - + +
263A ASP* 3.8 14.1 - - - +
265A ALA* 1.3 73.6 - - - +
267A ALA* 1.3 59.0 + - - +
270A GLY* 2.9 43.7 + - - +
271A GLN* 3.4 31.6 - - + +
274A CYS* 4.0 14.1 - - + -
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Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASP 3.1 13.1 + - - +
264A GLU* 2.9 15.7 - - + +
266A ILE* 1.3 81.2 - - - +
268A LEU* 1.3 65.7 + - + +
270A GLY 4.2 1.0 + - - -
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Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 4.4 4.0 - - - +
29A GLU* 3.4 56.3 - - + +
30A PHE* 3.6 20.6 - - + +
33A LEU* 4.2 12.8 - - + -
264A GLU* 3.2 8.9 + - + +
265A ALA* 3.3 6.0 + - - +
267A ALA* 1.3 84.2 - - + +
269A LYS* 1.3 74.1 + - + +
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Residues in contact with LYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 2.9 32.1 + - - -
27A SER* 3.8 18.2 - - - +
30A PHE* 3.7 32.5 - - + -
265A ALA 3.0 8.6 + - - +
268A LEU* 1.3 85.3 - - + +
270A GLY* 1.3 60.3 + - - +
273A THR* 3.5 33.3 + - + -
274A CYS* 5.1 0.2 - - - -
906A SO4 3.0 31.0 + - - -
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Residues in contact with GLY 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ILE* 2.9 30.9 + - - -
267A ALA 4.2 1.0 + - - -
268A LEU 3.7 1.2 + - - -
269A LYS* 1.3 75.5 - - - +
271A GLN* 1.3 60.7 - - - -
272A GLU 3.6 1.1 - - - -
273A THR 4.5 0.4 - - - -
274A CYS* 3.1 28.6 + - - -
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Residues in contact with GLN 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LYS* 4.3 11.6 - - - +
266A ILE* 3.4 38.9 - - + +
270A GLY* 1.3 70.7 - - - -
272A GLU* 1.3 67.0 + - - +
274A CYS* 3.2 5.0 + - - +
275A ASP* 3.0 57.2 + - - +
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Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A GLY 3.6 0.4 - - - -
271A GLN* 1.3 79.7 - - - +
273A THR* 1.3 65.3 + - - +
275A ASP* 2.8 22.2 + - + +
276A ILE* 2.9 33.3 + - + +
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Residues in contact with THR 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 4.7 11.9 + - + +
30A PHE* 4.1 11.7 - - + -
269A LYS* 3.5 42.3 + - + +
270A GLY 4.3 1.2 + - - -
271A GLN 3.5 0.4 - - - -
272A GLU* 1.3 78.1 - - - +
274A CYS* 1.3 56.8 + - - +
276A ILE* 3.6 9.7 + - - +
277A TYR* 3.1 47.4 + - + +
906A SO4 4.4 11.1 + - - -
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Residues in contact with CYS 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 4.6 9.4 - - - -
258A LEU* 4.3 7.9 - - + +
262A LYS* 4.7 6.5 - - + -
265A ALA* 3.6 40.6 - - + -
266A ILE* 3.6 13.5 - - + -
269A LYS* 5.1 0.2 - - - -
270A GLY 3.1 22.4 - - - +
271A GLN* 3.2 10.0 + - - +
272A GLU 3.0 0.8 - - - -
273A THR* 1.3 77.2 - - - +
275A ASP* 1.3 65.7 + - - +
277A TYR* 4.0 4.5 - - - +
278A MET* 3.1 30.1 + - + +
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Residues in contact with ASP 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LYS* 5.4 3.8 + - - -
271A GLN* 3.0 45.4 + - - +
272A GLU* 2.8 10.6 + - + +
274A CYS* 1.3 73.9 - - - +
276A ILE* 1.3 67.1 + - + +
278A MET* 3.4 5.3 + - - +
279A HIS* 3.0 26.8 + - - +
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Residues in contact with ILE 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PHE* 3.3 23.5 - - + -
213A GLU* 3.7 28.0 - - + +
214A ILE* 3.6 26.7 - - + -
272A GLU* 2.9 36.0 + - + +
273A THR* 3.6 11.9 - - - +
275A ASP* 1.3 77.5 - - + +
277A TYR* 1.3 68.9 + - + +
279A HIS* 3.3 1.7 + - - -
280A TYR* 2.9 24.6 + - - +
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Residues in contact with TYR 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A HIS* 3.3 40.6 + + - -
26A LYS* 3.4 32.5 - - - +
30A PHE* 3.8 28.7 - + + -
31A PHE* 4.5 2.8 - + - -
34A TRP* 3.9 19.3 - + - -
213A GLU 5.3 3.6 + - - -
214A ILE* 4.9 5.2 - - + -
258A LEU* 4.0 17.3 - - + -
273A THR* 3.1 36.5 + - + +
274A CYS 4.1 0.9 - - - +
275A ASP 3.3 0.2 - - - -
276A ILE* 1.3 90.5 - - + +
278A MET* 1.3 60.0 + - - +
280A TYR* 3.7 20.6 - + - +
281A LEU* 2.8 35.3 + - + +
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Residues in contact with MET 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ALA* 3.3 29.6 - - + +
258A LEU* 3.6 23.6 - - + -
259A GLN* 4.0 20.4 - - + +
262A LYS* 6.5 1.3 - - + -
274A CYS* 3.1 22.5 + - + +
275A ASP* 3.8 5.4 - - - +
277A TYR* 1.3 74.9 - - - +
279A HIS* 1.3 57.8 + - - +
281A LEU* 3.2 2.1 + - - +
282A ARG* 2.8 80.0 + - + +
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Residues in contact with HIS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ARG* 6.0 2.0 + - - -
206A PHE* 3.5 27.2 - + - -
209A PHE* 3.3 42.4 - + + +
275A ASP 3.0 18.7 + - - +
276A ILE* 3.4 4.3 - - - +
278A MET* 1.3 78.1 - - - +
280A TYR* 1.3 56.0 + - - +
282A ARG* 4.0 3.0 - - - +
283A GLY* 2.9 25.8 + - - -
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Residues in contact with TYR 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TRP* 4.9 0.7 - + - -
41A TYR* 2.7 30.5 + - - -
206A PHE* 3.7 3.8 - - - -
209A PHE* 3.7 19.9 - - + -
210A ILE* 3.8 7.6 - - + -
214A ILE* 3.7 33.0 - - + -
215A PHE* 3.3 18.9 - + - -
251A LEU* 5.0 0.7 - - + -
276A ILE 2.9 14.8 + - - +
277A TYR* 3.7 38.4 - + - -
279A HIS* 1.3 74.5 - - - +
281A LEU* 1.3 79.8 + - + +
284A CYS* 3.1 44.4 + - + -
901A 10A 3.4 17.3 - - + +
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TRP* 4.0 20.9 - - + -
251A LEU* 3.7 39.5 - - + +
254A TRP* 3.8 29.2 - - + +
255A ALA* 3.7 38.8 - - + +
258A LEU* 4.1 15.5 - - + -
277A TYR* 2.8 24.8 + - + +
278A MET* 3.9 1.6 - - - +
280A TYR* 1.3 91.5 - - + +
282A ARG* 1.3 62.0 + - - +
285A SER* 3.5 15.2 + - - -
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Residues in contact with ARG 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASN* 4.1 20.2 + - - +
255A ALA* 3.4 24.9 + - - +
256A ASP* 3.0 30.1 + - - +
259A GLN* 4.7 8.1 - - - +
278A MET* 2.8 52.0 + - + +
279A HIS* 4.0 4.0 - - - +
281A LEU* 1.3 71.0 - - - +
283A GLY* 1.3 66.0 + - - +
285A SER* 3.3 20.1 + - - -
286A ASP* 3.5 12.4 - - - +
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Residues in contact with GLY 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A PHE* 3.3 30.6 - - - -
279A HIS* 2.9 14.6 + - - -
282A ARG* 1.3 77.6 - - - +
284A CYS* 1.3 60.5 + - - +
285A SER 3.4 0.3 + - - -
286A ASP* 3.5 17.0 + - - +
287A LEU* 3.6 10.2 + - - +
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Residues in contact with CYS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A PHE* 3.4 7.4 - - - -
210A ILE* 4.0 13.2 - - - -
251A LEU* 3.8 21.5 - - + -
280A TYR* 3.1 41.9 + - - +
281A LEU 4.2 0.2 - - - +
282A ARG 3.3 0.2 - - - -
283A GLY* 1.3 73.1 - - - +
285A SER* 1.3 66.1 + - - +
287A LEU* 3.1 16.0 + - - +
288A PHE* 3.1 18.9 - - + -
901A 10A 3.4 37.0 - - + -
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Residues in contact with SER 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A VAL* 3.4 26.9 + - - +
251A LEU* 3.7 17.4 - - - +
252A ASN* 3.0 26.5 + - - -
281A LEU 3.5 10.6 + - - -
282A ARG* 3.3 12.9 + - - -
284A CYS* 1.3 76.6 - - - +
286A ASP* 1.3 65.3 + - - +
288A PHE* 3.1 7.5 + - - +
289A ARG* 3.1 20.6 + - - +
----------------------------------------------------------
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Residues in contact with ASP 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ARG 3.5 15.6 - - - +
283A GLY* 3.5 9.6 + - - +
284A CYS 3.3 0.8 - - - -
285A SER* 1.3 75.0 + - - +
287A LEU* 1.3 61.4 + - + +
289A ARG* 3.1 43.4 + - - +
290A ASP* 2.7 41.2 + - - +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 3.7 26.5 - - + -
206A PHE* 4.0 24.0 - - + -
207A ILE* 4.4 4.9 - - + -
283A GLY 3.6 10.7 + - - +
284A CYS* 3.1 13.0 + - - +
286A ASP* 1.3 79.4 - - + +
288A PHE* 1.3 59.6 + - + +
290A ASP* 3.7 1.3 - - + -
291A LYS 3.3 2.8 + - - -
292A TYR* 2.9 48.5 + - + +
293A THR* 3.4 14.9 + - + +
901A 10A 3.5 37.0 - - + -
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Residues in contact with PHE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ILE* 4.0 10.3 - - + -
244A GLY* 3.7 25.6 - - - +
245A ALA* 4.8 2.9 - - - -
247A TYR* 3.6 30.7 - + + -
248A VAL* 4.1 7.2 - - + +
251A LEU* 3.9 18.2 - - + -
284A CYS 3.1 24.7 - - - -
285A SER 3.1 6.0 + - - +
287A LEU* 1.3 74.5 - - - +
289A ARG* 1.3 67.3 + - - +
291A LYS* 3.5 19.8 + - - +
293A THR* 3.4 36.5 - - - +
294A ASP* 3.7 23.6 - - - -
295A VAL* 3.8 2.2 - - + -
901A 10A 3.7 33.0 - - + -
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Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ALA* 6.1 0.2 - - - +
248A VAL* 3.7 26.0 - - + +
285A SER 3.1 13.1 + - - +
286A ASP* 3.1 34.7 + - - +
288A PHE* 1.3 78.9 - - - +
290A ASP* 1.3 84.0 + - - +
291A LYS* 3.2 17.2 + - - +
----------------------------------------------------------
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Residues in contact with ASP 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 3.8 12.5 - - - +
286A ASP* 2.7 25.4 + - - +
287A LEU* 4.2 3.6 - - + +
289A ARG* 1.3 107.3 + - - +
291A LYS* 1.3 67.6 + - - +
292A TYR* 3.1 9.2 + - + +
----------------------------------------------------------
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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