Contacts of the helix formed by residues 274 - 297 (chain A) in PDB entry 2XYX
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 PHE 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A SER 3.9 0.8 + - - -
273A LEU* 1.3 72.3 - - - +
275A LEU* 1.3 56.1 + - - +
276A ASN* 3.2 17.9 - - - +
277A ASP* 2.8 33.7 + - + +
278A GLN 3.2 7.6 + - - -
365A MET* 3.7 31.4 - - + -
366A ASN* 5.8 7.4 - - + -
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LYS* 6.5 0.2 - - + -
273A LEU 3.4 2.4 + - - -
274A PHE* 1.3 70.9 - - - +
276A ASN* 1.4 56.4 + - - +
278A GLN* 3.3 35.7 - - + +
279A VAL* 3.0 34.0 + - + +
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Residues in contact with ASN 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A PHE* 3.3 24.3 - - - +
275A LEU* 1.4 70.4 + - - +
277A ASP* 1.3 64.4 + - - +
279A VAL* 3.5 9.0 + - - +
280A THR* 3.0 30.8 + - - -
365A MET* 3.8 28.8 - - - +
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Residues in contact with ASP 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 4.5 16.5 - - + +
274A PHE* 2.8 16.3 + - - +
276A ASN* 1.3 81.5 + - - +
278A GLN* 1.3 64.9 + - - +
280A THR* 3.4 6.3 + - - -
281A LEU* 3.1 31.3 + - - +
363A GLY 4.4 2.1 - - - +
364A LEU* 3.6 18.9 - - + +
365A MET* 2.9 35.3 + - - +
366A ASN* 3.0 32.2 + - - +
370A VAL* 5.0 1.2 - - - +
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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
----------------------------------------------------------
265A LYS* 4.7 10.6 - - - +
270A PHE* 3.6 50.7 + - + +
271A SER* 3.4 20.4 + - - +
273A LEU* 2.7 31.7 + - + +
274A PHE 3.2 3.2 + - - +
275A LEU* 3.3 38.0 + - + +
277A ASP* 1.3 76.6 - - - +
279A VAL* 1.3 54.6 + - + +
281A LEU* 3.5 4.2 + - - +
282A LEU* 3.1 37.1 + - + +
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Residues in contact with VAL 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 3.0 23.4 + - + +
276A ASN* 3.6 9.0 - - - +
278A GLN* 1.3 75.0 - - + +
280A THR* 1.3 55.9 + - - +
282A LEU* 3.2 9.5 + - + +
283A LYS* 2.7 40.3 + - + +
1442A BOG 4.6 29.2 - - + +
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Residues in contact with THR 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A ASN 3.0 17.7 + - - -
277A ASP* 3.4 11.7 + - - -
279A VAL* 1.3 75.7 - - - +
281A LEU* 1.3 63.4 + - - +
283A LYS* 3.4 6.1 + - - +
284A TYR* 3.2 34.3 + - + +
361A ARG* 4.1 8.0 - - + +
362A PRO 3.5 25.2 + - - +
363A GLY 4.3 7.1 + - - -
364A LEU* 4.0 26.9 - - + +
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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
----------------------------------------------------------
270A PHE* 3.8 24.0 - - + -
273A LEU* 3.9 21.1 - - + -
277A ASP 3.1 18.4 + - - +
278A GLN 3.7 4.5 - - - +
280A THR* 1.3 74.4 - - - +
282A LEU* 1.3 52.9 + - - +
284A TYR* 3.5 0.7 + - - +
285A GLY* 2.8 34.7 + - - -
356A ILE* 3.3 24.3 - - + +
357A LEU* 3.9 15.0 - - + -
358A CYS 3.3 27.1 - - - +
361A ARG* 4.1 7.1 + - + -
364A LEU* 3.9 15.9 - - + -
370A VAL* 3.8 15.0 - - + -
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A VAL* 6.4 0.7 - - + -
260A LEU 4.2 19.7 - - - +
261A THR* 3.8 36.6 - - + +
264A ALA* 4.2 3.6 - - + -
270A PHE* 4.2 13.2 - - + -
278A GLN* 3.1 23.7 + - + +
279A VAL* 3.7 8.1 - - + +
281A LEU* 1.3 74.6 - - - +
283A LYS* 1.3 62.6 + - - +
286A VAL* 3.0 41.1 + - + +
356A ILE* 4.0 29.2 - - + -
1442A BOG 4.8 18.2 - - + -
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Residues in contact with LYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A VAL* 2.7 24.6 + - + +
280A THR* 3.4 7.4 + - - +
282A LEU* 1.3 72.8 - - - +
284A TYR* 1.3 101.3 + - + +
286A VAL* 4.8 1.0 - - - +
287A HIS* 5.3 0.3 + - - -
435A GLU* 3.4 27.1 - - + +
436A ILE* 3.3 51.0 + - - +
438A LYS* 5.2 1.3 - - - +
439A ASP* 3.6 23.0 - - - +
440A MET 4.5 1.2 + - - +
1442A BOG 4.1 22.3 - - + +
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Residues in contact with TYR 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A THR* 3.2 26.2 + - + +
282A LEU 3.2 0.2 - - - -
283A LYS* 1.3 113.8 + - + +
285A GLY* 1.3 60.6 + - - +
286A VAL 3.5 0.9 - - - -
287A HIS 4.8 1.7 + - - -
288A GLU* 3.7 21.3 + - - +
361A ARG* 3.4 34.3 + - + +
362A PRO* 3.3 47.7 + - + +
410A VAL* 5.0 7.6 - - - +
439A ASP* 3.2 19.7 + - - -
440A MET* 3.6 26.7 - - + -
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Residues in contact with GLY 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU 2.8 20.4 + - - -
284A TYR* 1.3 73.3 - - - +
286A VAL* 1.3 59.5 + - - +
287A HIS 3.5 0.7 - - - -
288A GLU* 3.1 5.6 + - - +
289A ALA* 2.9 27.2 + - - +
355A ILE* 3.4 14.0 - - - +
356A ILE* 4.1 9.2 - - - -
361A ARG* 3.5 17.8 - - - +
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A VAL* 3.8 38.4 - - + +
260A LEU* 3.6 33.7 - - + -
282A LEU* 3.0 32.9 + - + +
283A LYS 4.8 0.4 - - - +
284A TYR 3.5 0.6 - - - -
285A GLY* 1.3 76.5 - - - +
287A HIS* 1.3 72.1 + - - +
289A ALA* 3.3 2.9 + - - +
290A ILE* 2.9 32.8 + - + +
356A ILE* 4.3 5.3 - - + +
436A ILE* 4.1 16.6 - - + -
1442A BOG 6.0 0.7 - - + -
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Residues in contact with HIS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A THR* 3.9 15.1 - - + +
257A VAL* 5.7 0.2 - - + -
283A LYS 5.7 0.2 + - - -
284A TYR 4.8 2.4 + - - +
285A GLY 3.5 0.4 - - - -
286A VAL* 1.3 81.7 - - + +
288A GLU* 1.4 60.6 - - - +
290A ILE* 3.7 13.0 - - + +
291A PHE* 3.0 49.8 + + + -
410A VAL* 3.6 27.8 - - + +
413A HIS* 3.9 15.7 - + - -
433A LEU* 4.4 10.5 - - + -
436A ILE* 3.4 30.6 - - + +
437A TYR* 2.7 45.6 + + - -
1441A Z00 5.1 0.7 - - - -
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Residues in contact with GLU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A TYR 3.7 8.3 + - - +
285A GLY 3.1 8.4 + - - +
287A HIS* 1.4 78.0 - - - +
289A ALA* 1.4 59.9 + - - +
292A ALA 3.3 16.8 + - - -
355A ILE* 3.6 22.4 - - + +
361A ARG* 2.8 42.8 + - - -
403A MET 4.4 4.6 - - - +
406A LEU* 3.4 34.0 - - + +
407A ARG* 3.3 30.5 + - - +
410A VAL* 3.6 21.4 - - + +
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A LEU* 3.8 25.8 - - + -
285A GLY 2.9 12.5 + - - +
286A VAL 3.5 7.9 - - - +
288A GLU* 1.4 72.0 - - - +
290A ILE* 1.4 64.9 + - - +
292A ALA* 3.1 4.7 + - - +
293A MET* 3.0 27.2 + - - +
352A ILE* 3.6 23.8 - - + -
355A ILE* 3.7 7.9 - - + +
356A ILE* 4.1 10.1 - - + -
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A THR* 3.9 25.6 - - + +
256A THR* 3.8 26.2 - - + +
257A VAL* 3.8 28.5 - - + -
260A LEU* 3.9 6.7 - - + +
286A VAL* 2.9 27.7 + - + +
287A HIS* 3.7 13.9 - - + +
289A ALA* 1.4 69.7 - - - +
291A PHE* 1.3 74.4 + - + +
293A MET* 3.2 8.5 + - - +
294A LEU* 2.8 30.3 + - + +
1441A Z00 4.8 16.8 - - + -
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Residues in contact with PHE 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A HIS* 3.0 33.5 + + + +
288A GLU 4.8 0.2 - - - -
289A ALA 3.3 0.2 - - - -
290A ILE* 1.3 83.5 - - + +
292A ALA* 1.3 64.7 + - - +
294A LEU* 3.4 22.3 + - + +
295A ALA* 3.5 5.2 + - - +
331A LYS* 3.7 37.2 - - + -
334A PHE* 4.2 11.4 - - + -
335A ALA* 5.7 0.7 - - - +
406A LEU* 3.7 17.9 - - + -
409A LEU* 3.7 24.9 - - + -
410A VAL* 3.7 25.6 - - + -
413A HIS* 3.7 25.4 - + + -
1441A Z00 3.4 20.4 - - - -
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLU 3.3 11.8 + - - +
289A ALA* 3.1 9.9 + - - +
291A PHE* 1.3 74.7 - - - +
293A MET* 1.4 60.2 + - - +
295A ALA* 3.4 19.2 - - - +
296A SER* 4.4 3.1 + - - -
334A PHE* 4.3 11.4 - - - -
338A PHE* 3.7 13.5 - - + -
348A LEU* 4.7 4.4 - - + +
351A PHE* 3.6 32.3 - - + -
352A ILE* 3.7 12.8 - - + -
355A ILE* 5.7 0.2 - - + -
406A LEU* 4.0 4.8 - - + +
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Residues in contact with MET 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A TYR* 3.7 25.1 - - + +
190A PHE* 3.6 56.3 - - + -
192A MET 5.6 3.1 - - - +
256A THR* 4.7 13.7 - - + -
260A LEU* 4.5 8.3 - - - -
289A ALA 3.0 15.6 + - - +
290A ILE* 3.6 6.3 - - - +
292A ALA* 1.4 71.3 - - - +
294A LEU* 1.3 64.4 + - - +
295A ALA 3.2 2.2 - - - -
296A SER* 3.2 26.7 + - - +
297A ILE* 4.0 5.0 + - - +
348A LEU* 5.8 4.7 - - + -
352A ILE* 3.7 18.4 - - + -
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ILE* 2.8 18.9 + - + +
291A PHE* 3.5 19.1 - - + +
292A ALA 3.4 0.2 - - - -
293A MET* 1.3 75.5 - - - +
295A ALA* 1.4 62.3 + - - +
297A ILE* 3.1 38.4 + - + +
298A VAL* 3.2 31.9 + - + +
303A LEU* 4.5 3.1 - - + -
328A ILE* 5.2 3.6 - - + -
331A LYS* 3.9 34.8 - - + +
335A ALA* 6.0 1.6 - - + -
1441A Z00 4.2 38.4 - - + -
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ARG* 3.2 0.9 + - - -
291A PHE 3.5 5.5 + - - +
292A ALA 3.4 15.1 + - - +
293A MET 3.2 0.4 - - - -
294A LEU* 1.4 77.6 - - - +
296A SER* 1.4 56.9 + - - +
298A VAL* 3.1 11.3 - - - +
334A PHE* 5.2 0.9 - - + -
335A ALA* 3.8 30.2 - - - +
338A PHE* 3.7 18.8 - - + -
339A ASN* 2.8 38.8 + - - +
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Residues in contact with SER 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TYR* 5.0 2.3 + - - -
192A MET 5.9 1.1 - - - -
193A THR 5.1 1.8 - - - -
194A LYS* 3.7 43.3 - - - +
197A ALA* 3.3 14.0 - - - +
198A ARG* 2.9 23.9 + - - +
292A ALA 4.6 1.7 + - - -
293A MET* 3.2 19.4 + - - +
295A ALA* 1.4 77.6 - - - +
297A ILE* 1.4 60.8 + - - +
339A ASN* 4.1 0.6 + - - -
348A LEU* 3.8 14.9 - - - +
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Residues in contact with ILE 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A MET* 4.1 19.1 - - + -
197A ALA* 3.9 18.4 - - + -
198A ARG* 4.0 2.2 - - - -
201A LEU* 4.4 4.6 - - - +
252A THR* 6.3 0.7 - - + -
293A MET 4.6 2.2 - - - +
294A LEU* 3.3 37.5 - - + +
296A SER* 1.4 81.5 - - - +
298A VAL* 1.3 56.7 + - + +
299A ASN 4.4 0.2 + - - -
303A LEU* 3.3 13.4 - - + -
304A LEU* 3.0 67.0 + - + +
1441A Z00 5.1 5.6 - - + -
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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