Contacts of the helix formed by residues 261 - 292 (chain A) in PDB entry 4PJW
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 261 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ALA* 1.3 78.8 - - - +
262A GLU* 1.3 62.6 + - + +
264A LEU* 3.7 20.4 - - - +
265A GLU* 3.4 25.8 + - - +
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Residues in contact with GLU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ALA 3.0 6.2 - - - +
261A ASN* 1.3 80.1 - - + +
263A ARG* 1.3 64.6 + - - +
264A LEU 3.2 0.2 - - - -
265A GLU* 3.4 14.4 + - - +
266A LEU* 3.5 19.5 + - + +
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Residues in contact with ARG 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLN* 3.3 43.2 + - - +
251A GLU* 3.3 46.9 + - - +
260A ALA* 3.3 6.4 + - - +
262A GLU* 1.3 76.9 - - - +
264A LEU* 1.3 60.4 + - - +
266A LEU* 3.1 16.4 + - + +
267A LEU* 2.9 42.2 + - + +
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A TYR* 3.9 31.4 - - + +
251A GLU* 3.5 34.1 + - + +
252A ARG* 3.7 24.7 - - + +
260A ALA 3.2 15.5 + - - +
261A ASN* 3.7 21.1 - - - +
262A GLU 3.2 0.2 - - - -
263A ARG* 1.3 77.9 - - - +
265A GLU* 1.3 57.9 + - + +
267A LEU* 3.4 5.4 + - - +
268A LEU* 2.9 30.4 + - - +
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Residues in contact with GLU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ASN 3.4 13.5 + - - +
262A GLU* 3.6 11.4 - - - +
263A ARG 3.2 0.2 - - - -
264A LEU* 1.3 79.2 - - + +
266A LEU* 1.3 60.4 + - + +
268A LEU* 3.5 14.8 + - - +
269A GLN* 2.9 28.1 + - - +
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLU 3.5 16.8 - - - +
263A ARG* 3.1 17.3 + - + +
265A GLU* 1.3 77.9 - - + +
267A LEU* 1.3 56.9 + - + +
269A GLN* 3.2 10.1 + - + +
270A LYS* 2.7 35.4 + - - +
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A THR* 4.2 17.9 + - - +
247A GLN* 3.5 40.4 - - + +
248A TYR* 3.6 24.2 - - + +
251A GLU* 4.2 10.1 - - + -
263A ARG* 2.9 47.3 + - + +
264A LEU* 3.8 4.7 - - - +
266A LEU* 1.3 75.0 - - + +
268A LEU* 1.3 60.4 + - - +
270A LYS* 3.7 10.9 - - + +
271A ARG* 2.8 31.2 + - - +
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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
----------------------------------------------------------
248A TYR* 3.5 28.2 - - + +
264A LEU 2.9 17.9 + - - +
265A GLU* 3.7 17.3 - - - +
267A LEU* 1.3 76.3 - - - +
269A GLN* 1.3 58.8 + - - +
271A ARG* 3.3 31.8 + - - +
272A LYS* 2.9 44.3 + - - +
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Residues in contact with GLN 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A GLU 2.9 19.2 + - - +
266A LEU* 3.2 12.3 + - + +
268A LEU* 1.3 77.4 - - - +
270A LYS* 1.3 56.3 - - - +
272A LYS* 3.2 31.8 + - - +
273A GLU* 3.0 61.7 + - - +
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Residues in contact with LYS 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ASN* 3.8 29.7 + - - +
244A THR* 3.6 23.7 + - - +
266A LEU 2.7 19.9 + - - +
267A LEU* 3.7 15.5 - - + +
269A GLN* 1.3 72.4 - - - +
271A ARG* 1.3 58.6 + - - +
273A GLU* 3.2 12.2 + - + +
274A LEU* 3.0 42.2 + - + +
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Residues in contact with ARG 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A MSE 5.5 3.6 - - + +
244A THR* 4.7 15.4 + - + +
245A GLN* 2.7 42.4 + - - +
248A TYR* 5.0 15.2 - - - -
267A LEU 2.8 18.7 + - - +
268A LEU* 3.4 34.4 + - - +
270A LYS* 1.3 76.4 - - - +
272A LYS* 1.3 62.7 + - - +
274A LEU* 3.7 5.9 + - - +
275A GLN* 3.3 22.5 + - - +
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Residues in contact with LYS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 2.9 31.6 + - - +
269A GLN* 3.4 31.4 + - - +
271A ARG* 1.3 76.2 - - - +
273A GLU* 1.3 64.6 + - + +
275A GLN* 3.3 6.3 + - - +
276A GLU* 3.2 37.2 + - + +
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Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLN* 3.0 46.1 + - - +
270A LYS* 3.6 10.8 - - + +
272A LYS* 1.3 78.0 - - - +
274A LEU* 1.3 59.0 + - + +
276A GLU* 3.4 20.4 - - - +
277A ASN* 3.1 32.2 + - - +
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU* 3.9 17.1 - - + +
240A ASN* 3.5 31.0 - - - +
241A MSE 3.8 28.8 - - + +
244A THR* 3.6 32.1 - - + -
270A LYS* 3.0 31.7 + - + +
271A ARG* 4.1 4.0 - - - +
272A LYS 3.3 0.4 - - - -
273A GLU* 1.3 75.6 - - + +
275A GLN* 1.3 59.9 + - - +
277A ASN* 3.2 15.6 + - - +
278A GLN* 2.9 27.0 + - - +
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Residues in contact with GLN 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A MSE 3.2 23.3 - - + +
271A ARG 3.3 15.6 + - - +
272A LYS* 3.3 7.3 + - - +
273A GLU 3.3 0.6 - - - -
274A LEU* 1.3 75.3 - - - +
276A GLU* 1.3 66.3 + - - +
278A GLN* 2.7 24.9 + - - +
279A ASP* 3.0 38.1 + - - +
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Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS* 3.2 24.5 + - + +
273A GLU* 3.4 23.5 - - - +
275A GLN* 1.3 78.5 - - + +
277A ASN* 1.3 64.3 + - - +
279A ASP* 3.1 12.0 + - - +
280A GLU* 2.9 23.7 + - - +
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Residues in contact with ASN 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A TYR 5.8 0.2 + - - -
192A TYR* 3.5 50.9 + - - +
237A LEU* 3.7 10.3 - - + +
273A GLU* 3.1 17.2 + - - +
274A LEU* 3.3 25.4 - - - +
276A GLU* 1.3 82.2 - - - +
278A GLN* 1.3 60.1 + - - +
280A GLU* 3.5 2.2 + - - -
281A ILE* 3.1 29.5 + - - +
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Residues in contact with GLN 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ALA* 6.1 4.0 - - + +
237A LEU* 3.8 12.5 - - + +
238A SER* 6.0 3.6 - - - -
241A MSE 3.2 24.1 - - - +
274A LEU 2.9 13.8 + - - +
275A GLN* 2.7 39.7 + - - +
277A ASN* 1.3 74.0 - - - +
279A ASP* 1.3 61.5 + - - +
281A ILE* 3.3 2.9 + - - +
282A GLU* 2.9 55.0 + - - +
319A TYR* 5.5 4.2 + - - -
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Residues in contact with ASP 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLN* 3.0 39.5 + - - +
276A GLU* 3.5 10.8 - - - +
278A GLN* 1.3 76.5 - - - +
280A GLU* 1.3 62.8 + - - +
282A GLU* 3.4 12.2 + - - +
283A ASN* 3.0 32.5 + - - +
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Residues in contact with GLU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE 5.3 0.2 - - - +
192A TYR* 4.0 33.5 - - + +
194A GLU* 3.7 28.8 - - - +
198A ASP* 5.6 1.7 - - - +
276A GLU 2.9 15.4 + - - +
277A ASN* 3.7 5.4 - - - +
279A ASP* 1.3 77.6 - - - +
281A ILE* 1.3 60.8 + - - +
283A ASN* 3.3 19.0 + - - +
284A MSE 3.2 36.3 + - - +
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Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE* 3.9 9.4 - - + -
192A TYR* 3.7 27.6 - - + +
230A LEU* 4.0 25.4 - - + +
233A VAL* 3.9 15.9 - - + -
234A ALA* 4.1 16.4 - - + +
237A LEU* 4.1 8.7 - - + -
277A ASN 3.1 18.9 + - - +
278A GLN* 3.8 3.8 - - - +
280A GLU* 1.3 76.0 - - - +
282A GLU* 1.3 61.1 + - + +
284A MSE 3.1 31.3 + - + +
285A MSE 2.9 35.8 + - + +
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Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ALA* 6.1 2.1 - - + +
278A GLN* 2.9 46.4 + - - +
279A ASP* 3.8 12.2 - - - +
281A ILE* 1.3 76.9 - - + +
283A ASN* 1.3 59.1 + - - +
285A MSE 3.8 15.3 - - - +
286A ASN* 2.9 31.4 + - - +
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Residues in contact with ASN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ASP* 3.0 25.8 + - - +
280A GLU* 3.4 21.0 + - - +
282A GLU* 1.3 76.4 - - - +
284A MSE 1.3 59.5 + - + +
286A ASN* 3.0 7.3 + - - +
287A ALA* 2.8 30.6 + - - +
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Residues in contact with MSE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE* 4.0 14.4 - - + +
197A MSE 3.6 30.5 - - + -
198A ASP* 4.9 8.7 - - - +
201A ILE* 3.9 18.2 - - + +
230A LEU* 3.1 42.2 - - + -
280A GLU* 3.2 25.1 + - + +
281A ILE* 3.1 24.8 + - + +
283A ASN* 1.3 82.9 - - + +
285A MSE 1.3 61.4 + - - +
287A ALA* 3.5 5.1 + - - +
288A ILE* 3.2 28.2 + - - +
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Residues in contact with MSE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A MSE 3.5 27.5 - - + +
230A LEU* 3.3 20.9 - - + -
231A VAL* 3.2 51.6 - - + +
234A ALA* 4.4 10.3 - - - -
281A ILE* 2.9 31.5 + - + +
282A GLU* 3.8 15.9 - - + +
284A MSE 1.3 74.8 - - - +
286A ASN* 1.3 57.6 + - - +
288A ILE 3.3 0.7 + - - -
289A PHE* 2.8 32.1 + - - +
323A PHE* 4.2 16.2 - - + -
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Residues in contact with ASN 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLU 2.9 19.1 + - - +
283A ASN* 3.0 6.5 + - - +
285A MSE 1.3 74.6 - - - +
287A ALA* 1.3 65.9 + - - +
289A PHE* 4.4 8.8 - - - +
290A LYS* 2.9 63.3 + - - +
328A TYR* 5.7 2.6 + - - -
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE* 4.3 19.7 - - + -
205A THR* 5.2 2.9 + - - +
283A ASN 2.8 16.1 + - - +
284A MSE 3.6 9.2 - - - +
286A ASN* 1.3 76.1 - - - +
288A ILE* 1.3 53.6 + - - +
290A LYS* 4.5 0.8 - - - +
291A GLY* 2.7 35.7 + - - -
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Residues in contact with ILE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE* 3.7 34.8 - - + -
205A THR* 5.5 0.9 - - - +
223A ALA* 3.6 33.0 - - + +
224A MSE 4.1 13.0 - - + -
226A LEU* 3.8 28.7 - - + -
227A MSE 4.1 15.7 - - + +
230A LEU* 4.2 11.9 - - + -
284A MSE 3.2 11.0 + - - +
285A MSE 3.8 6.3 - - - +
287A ALA* 1.3 79.6 - - - +
289A PHE* 1.3 58.7 + - - +
292A VAL* 2.9 34.6 + - + +
293A PHE 3.3 1.7 + - - -
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Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A MSE 3.9 22.4 - - + -
285A MSE 2.8 18.6 + - - +
286A ASN* 4.1 8.7 - - - +
287A ALA 3.3 0.2 - - - -
288A ILE* 1.3 79.0 - - - +
290A LYS* 1.3 70.3 + - + +
293A PHE* 3.2 46.1 + + + +
294A VAL* 2.9 43.8 + - + +
312A ILE* 4.5 0.4 - - + -
315A TRP* 4.0 9.2 - + - -
327A SER 5.0 1.6 - - - -
328A TYR* 3.6 38.8 - + - +
331A TYR* 3.9 22.4 - + - -
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Residues in contact with LYS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ASN* 2.9 49.5 + - - +
287A ALA 4.5 0.2 - - - +
289A PHE* 1.3 90.5 - - + +
291A GLY* 1.3 60.2 + - - +
294A VAL* 4.0 17.0 - - + +
295A HIS* 3.2 24.1 + - - -
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Residues in contact with GLY 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A THR* 4.0 21.7 - - - +
208A SER* 4.2 4.0 + - - -
287A ALA 2.7 18.2 + - - -
290A LYS* 1.3 79.3 - - - +
292A VAL* 1.3 63.5 + - - +
295A HIS* 3.4 16.6 - - - +
296A ARG* 5.7 0.7 + - - -
----------------------------------------------------------
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 4.4 0.7 - - + +
205A THR* 4.1 20.0 - - - +
208A SER* 3.6 29.2 - - - +
220A THR* 4.3 9.0 - - + -
223A ALA* 4.2 21.8 - - + -
224A MSE 3.8 19.7 - - + -
288A ILE* 2.9 19.7 + - + +
291A GLY* 1.3 80.7 - - - +
293A PHE* 1.3 67.4 + - - +
294A VAL 3.2 1.8 - - - -
295A HIS* 3.0 7.0 + - - +
296A ARG* 2.9 35.7 + - + +
----------------------------------------------------------
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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