Contacts of the helix formed by residues 329 - 363 (chain B) in PDB entry 2Y48
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 THR 329 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ASN* 3.1 6.1 + - - -
328B ALA* 1.3 85.6 - - + +
330B ALA* 1.3 57.4 + - - +
331B ALA* 2.8 9.4 + - - +
332B THR* 3.3 19.4 + - - +
333B THR* 2.9 34.4 + - - -
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ALA 3.6 24.0 - - - +
324B VAL* 4.1 4.8 - - - -
326B ALA* 4.6 3.4 - - + +
327B ASN* 2.9 43.4 + - - +
328B ALA 3.8 1.0 - - - -
329B THR* 1.3 76.3 - - - +
331B ALA* 1.3 61.5 + - - +
333B THR* 4.2 10.1 - - - -
334B VAL* 3.5 20.8 + - + +
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Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A GLN* 3.6 32.8 - - - +
324B VAL* 3.7 20.9 + - + +
327B ASN 4.9 1.5 + - - +
328B ALA 5.0 4.3 - - - +
329B THR* 2.8 6.1 - - - -
330B ALA* 1.3 81.7 - - - +
332B THR* 1.3 66.9 + - + +
334B VAL* 3.4 4.0 + - - +
335B LEU* 3.2 25.1 + - - +
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Residues in contact with THR 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B THR* 3.3 25.8 + - - +
331B ALA* 1.3 76.9 - - + +
333B THR* 1.3 67.1 + - - +
335B LEU* 3.5 13.2 + - + +
336B ARG* 3.1 42.4 + - - +
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Residues in contact with THR 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B THR* 2.9 23.0 + - - -
330B ALA* 4.2 7.6 - - - -
332B THR* 1.3 75.9 + - - +
334B VAL* 1.3 60.9 + - + +
336B ARG* 2.8 30.6 + - - +
337B GLN* 3.0 32.6 + - - +
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Residues in contact with VAL 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LYS* 4.5 19.7 - - + -
323B ALA* 5.0 13.0 - - + +
324B VAL* 4.4 17.7 - - + -
330B ALA* 3.5 16.7 + - + +
331B ALA 3.4 5.4 + - - +
333B THR* 1.3 84.8 - - + +
335B LEU* 1.3 74.0 + - + +
336B ARG 3.3 0.5 + - - -
337B GLN* 3.6 8.0 + - + +
338B LEU* 3.4 26.9 + - + +
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Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A GLN* 4.6 15.7 - - + +
420A GLU* 3.7 29.6 - - + +
421A LYS* 3.6 42.8 - - + +
424A LYS* 4.1 17.8 - - + +
331B ALA 3.2 17.1 + - - +
332B THR* 3.7 14.8 - - + +
333B THR 3.2 1.0 - - - -
334B VAL* 1.3 80.0 - - + +
336B ARG* 1.3 59.4 + - - +
338B LEU* 4.6 3.6 - - + -
339B ASP* 3.3 30.6 + - - +
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Residues in contact with ARG 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B THR* 3.1 28.7 + - - +
333B THR* 2.8 14.8 + - - +
335B LEU* 1.3 79.6 - - - +
337B GLN* 1.3 70.8 + - - +
338B LEU 2.9 1.6 - - - -
339B ASP* 3.7 8.6 - - + +
340B MET* 2.8 38.3 + - + +
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Residues in contact with GLN 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B THR* 3.0 31.1 + - - +
334B VAL* 4.0 11.4 - - + +
336B ARG* 1.3 78.0 - - - +
338B LEU* 1.3 62.7 + - + +
340B MET* 4.2 10.1 - - - +
341B GLU* 2.9 34.0 + - + +
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Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LYS* 4.0 24.9 - - + +
424A LYS* 4.2 17.1 - - + +
425A ASP* 3.3 40.6 - - - +
428A ILE* 3.6 21.8 - - + +
334B VAL* 3.4 18.5 + - + +
335B LEU* 4.5 1.8 - - + +
336B ARG 2.9 0.8 - - - -
337B GLN* 1.3 81.9 - - + +
339B ASP* 1.3 60.2 + - - +
340B MET 3.1 1.6 - - - -
341B GLU* 4.1 7.4 - - + -
342B LEU* 2.9 30.3 + - - +
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Residues in contact with ASP 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LYS* 3.0 40.8 + - - +
335B LEU 3.3 15.1 + - - +
336B ARG* 3.0 13.8 + - + +
338B LEU* 1.3 78.2 - - - +
340B MET* 1.3 60.7 + - + +
342B LEU* 3.9 7.4 - - - +
343B VAL* 3.5 20.6 + - - +
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Residues in contact with MET 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ARG* 2.8 26.5 + - + +
337B GLN* 4.2 9.6 - - - +
339B ASP* 1.3 76.8 - - + +
341B GLU* 1.3 66.2 + - - +
342B LEU 2.8 3.4 + - - -
343B VAL* 3.0 13.3 + - + +
344B SER* 2.9 24.9 + - - -
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Residues in contact with GLU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ILE* 3.9 17.4 - - + +
432A LYS* 3.8 20.5 + - - -
337B GLN* 2.9 28.0 + - + +
338B LEU* 3.8 11.0 - - + +
340B MET* 1.3 73.9 - - - +
342B LEU* 1.3 60.6 + - - +
344B SER* 3.8 8.8 + - - -
345B VAL* 3.2 34.0 + - - +
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Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LYS* 5.0 5.8 - - + +
427A GLN* 3.8 27.4 - - + +
428A ILE* 3.7 36.5 - - + +
431A TRP* 3.8 23.5 - - + +
338B LEU 2.9 17.1 + - - +
339B ASP* 3.9 9.0 - - - +
340B MET 2.8 1.6 + - - -
341B GLU* 1.3 73.6 - - - +
343B VAL* 1.3 68.2 + - - +
345B VAL* 3.0 7.7 + - + +
346B LYS* 2.9 37.9 + - + +
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ASP 3.5 12.5 + - - +
340B MET* 3.0 19.7 + - + +
342B LEU* 1.3 74.8 - - + +
344B SER* 1.3 68.6 + - - +
346B LYS* 3.2 12.1 + - + +
347B ARG* 3.1 43.5 + - - +
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Residues in contact with SER 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B MET 2.9 16.1 + - - -
341B GLU* 3.8 11.5 + - - -
343B VAL* 1.3 80.8 - - - +
345B VAL* 1.3 68.9 + - - +
346B LYS 3.0 1.7 + - - -
347B ARG* 3.2 19.7 + - - +
348B GLN* 3.0 27.1 + - - +
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Residues in contact with VAL 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ILE* 5.2 7.0 - - + +
431A TRP* 3.9 36.3 - - + +
432A LYS* 4.3 21.1 - - + +
435A VAL* 4.3 12.8 - - + -
341B GLU* 3.2 27.8 + - - +
342B LEU* 3.0 10.4 + - + +
344B SER* 1.3 82.7 + - - +
346B LYS* 1.3 61.1 + - - +
348B GLN* 3.6 16.6 - - - +
349B ILE* 3.1 21.7 + - - +
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Residues in contact with LYS 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A GLN* 5.8 3.2 - - - +
431A TRP* 3.8 47.7 - - + +
342B LEU* 2.9 26.1 + - + +
343B VAL* 3.5 14.8 - - + +
344B SER 3.0 0.2 - - - -
345B VAL* 1.3 79.2 - - - +
347B ARG* 1.3 62.2 + - - +
349B ILE* 3.2 20.5 + - + +
350B GLN* 3.3 13.2 + - - +
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Residues in contact with ARG 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B VAL* 3.1 33.4 + - - +
344B SER* 3.3 19.1 - - - +
346B LYS* 1.3 73.2 - - - +
348B GLN* 1.3 69.9 + - - +
350B GLN* 3.2 12.8 + - - +
351B ASN* 3.1 24.4 + - - +
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Residues in contact with GLN 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A VAL* 4.3 24.1 - - + +
439A GLU* 4.6 9.2 - - - +
344B SER* 3.0 18.8 + - - +
345B VAL* 3.6 24.6 - - - +
346B LYS 3.3 0.2 - - - -
347B ARG* 1.3 79.9 - - + +
349B ILE* 1.3 61.6 + - - +
351B ASN* 3.3 8.2 + - + +
352B ILE* 3.2 31.5 + - + +
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Residues in contact with ILE 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A TRP* 3.6 52.0 - - + +
434A ILE* 3.6 26.9 - - + -
435A VAL* 3.2 22.2 - - + +
438A GLN* 4.5 6.7 - - + +
512A GLU* 5.1 5.8 - - - +
345B VAL 3.1 11.9 + - - +
346B LYS* 3.4 13.2 - - + +
347B ARG 3.2 0.4 - - - -
348B GLN* 1.3 79.8 - - - +
350B GLN* 1.3 64.5 + - + +
352B ILE* 3.4 5.8 + - - +
353B LYS* 2.9 39.2 + - + +
----------------------------------------------------------
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Residues in contact with GLN 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LYS 3.3 8.8 + - - +
347B ARG* 3.2 14.8 + - - +
349B ILE* 1.3 84.4 - - + +
351B ASN* 1.3 58.2 + - - +
353B LYS* 3.2 14.2 + - + +
354B GLN* 2.8 34.7 + - - +
----------------------------------------------------------
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Residues in contact with ASN 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B ARG 3.1 13.2 + - - +
348B GLN* 3.5 12.8 - - + +
350B GLN* 1.3 77.2 - - - +
352B ILE* 1.3 60.0 + - + +
354B GLN* 3.2 7.6 + - - +
355B THR* 2.9 32.3 + - - -
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Residues in contact with ILE 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A VAL* 5.5 6.7 - - + +
438A GLN* 3.2 41.4 - - + +
439A GLU* 3.3 38.1 - - + +
442A LYS* 4.5 26.0 - - + +
348B GLN* 3.2 21.8 + - + +
349B ILE* 4.1 3.1 - - - +
351B ASN* 1.3 78.9 - - + +
353B LYS* 1.3 60.4 + - - +
355B THR* 4.0 6.1 - - - +
356B ASN* 3.2 28.6 + - - +
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Residues in contact with LYS 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A GLN* 3.3 22.4 - - - +
512A GLU* 3.4 32.2 + - - -
349B ILE* 2.9 27.2 + - + +
350B GLN* 3.4 14.6 - - + +
351B ASN 3.2 0.2 - - - -
352B ILE* 1.3 76.5 - - - +
354B GLN* 1.3 60.2 + - - +
356B ASN* 3.6 3.4 + - - +
357B SER* 3.0 28.4 + - - -
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Residues in contact with GLN 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B GLN* 2.8 19.1 + - - +
351B ASN* 3.3 8.7 - - - +
353B LYS* 1.3 74.5 - - - +
355B THR* 1.3 68.4 + - - +
357B SER* 3.1 14.1 + - - -
358B ALA* 3.2 14.4 + - - +
----------------------------------------------------------
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Residues in contact with THR 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LYS* 3.4 36.3 + - + -
351B ASN* 2.9 22.6 + - - -
352B ILE* 4.0 7.6 - - - +
354B GLN* 1.3 75.8 - - - +
356B ASN* 1.3 73.9 + - - +
358B ALA* 3.2 5.3 + - - +
359B LEU* 3.1 30.2 + - + +
----------------------------------------------------------
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Residues in contact with ASN 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A GLN* 3.4 12.0 + - + +
441A LEU* 3.3 29.8 - - + +
442A LYS* 3.1 54.8 - - - +
445A LEU* 3.8 10.6 - - + +
352B ILE 3.2 17.6 + - - +
353B LYS* 4.0 4.5 - - - +
355B THR* 1.3 79.6 - - - +
357B SER* 1.3 61.8 + - - +
359B LEU* 3.6 7.3 + - - +
360B LYS* 3.3 27.5 + - - +
----------------------------------------------------------
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Residues in contact with SER 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LYS 3.0 18.7 + - - -
354B GLN* 3.5 8.5 - - - -
355B THR 3.1 0.4 - - - -
356B ASN* 1.3 78.0 - - - +
358B ALA* 1.3 61.1 + - - +
360B LYS* 3.4 11.8 + - - +
361B GLU* 3.3 20.4 + - - +
----------------------------------------------------------
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Residues in contact with ALA 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B GLN 3.2 7.2 + - - +
355B THR* 3.2 9.7 + - - +
357B SER* 1.3 76.2 - - - +
359B LEU* 1.3 64.8 + - + +
360B LYS 3.2 2.4 + - - -
361B GLU* 3.4 16.1 + - - +
362B LYS* 3.6 18.4 + - - +
----------------------------------------------------------
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Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LYS* 4.2 10.1 - - + +
445A LEU* 3.7 20.8 - - + +
446A ASN* 3.4 49.1 - - - +
449A VAL* 4.1 12.3 - - + +
355B THR* 3.1 26.9 + - + +
356B ASN* 4.0 7.2 - - - +
357B SER 3.4 0.4 - - - -
358B ALA* 1.3 78.4 - - + +
360B LYS* 1.3 60.5 + - - +
362B LYS* 3.8 17.8 + - + +
363B LEU* 3.7 22.7 + - - +
----------------------------------------------------------
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Residues in contact with LYS 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A LEU* 6.4 1.6 - - + -
445A LEU* 4.0 15.5 - - + -
501A GLN* 4.2 15.3 - - - +
505A GLU* 4.2 21.9 + - + +
356B ASN 3.3 15.4 + - - +
357B SER* 3.5 13.7 + - - +
358B ALA 3.2 0.6 - - - -
359B LEU* 1.3 77.5 - - - +
361B GLU* 1.3 59.8 + - - +
362B LYS 3.2 0.4 - - - -
363B LEU* 3.0 23.9 + - + +
364B ASP* 3.4 9.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B SER 3.3 10.8 + - - +
358B ALA* 3.4 11.5 + - - +
359B LEU 3.4 0.2 - - - -
360B LYS* 1.3 79.7 - - - +
362B LYS* 1.3 61.4 + - + +
364B ASP* 3.4 24.0 - - + +
----------------------------------------------------------
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Residues in contact with LYS 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A VAL* 3.8 24.6 - - + +
452A LYS* 3.3 21.8 + - - +
358B ALA* 3.6 12.4 + - - +
359B LEU* 4.0 14.0 - - + +
360B LYS 3.2 0.8 - - - -
361B GLU* 1.3 78.2 - - + +
363B LEU* 1.3 57.5 + - - +
364B ASP 3.2 2.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A LEU* 4.7 13.2 - - + +
448A MET* 3.5 47.8 - - + +
449A VAL* 3.7 35.2 - - + +
452A LYS* 3.9 21.1 - - + +
494A TYR* 4.0 10.7 + - - +
501A GLN* 4.9 4.9 - - - +
359B LEU 3.7 13.0 - - - +
360B LYS* 3.0 14.9 + - + +
362B LYS* 1.3 77.0 - - - +
364B ASP* 1.3 62.3 + - - +
365B GLY 3.3 0.2 + - - -
366B GLY* 3.2 18.2 + - - -
----------------------------------------------------------
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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