Contacts of the helix formed by residues 374 - 400 (chain B) in PDB entry 6EBT
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 374 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ARG* 3.5 32.3 - - + +
346B GLY 6.2 1.3 - - - +
358B LEU* 3.6 32.5 - - + -
372B VAL* 3.4 7.2 - - + +
373B ASN* 1.3 80.5 - - + +
375B THR* 1.3 63.1 + - - +
376B GLN 3.3 2.7 - - - -
377B CYS* 3.1 22.6 + - - +
378B GLU* 3.2 22.5 + - - +
434B CYS* 6.4 0.4 - - - -
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Residues in contact with THR 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ASN* 5.2 2.1 + - - -
362B GLU* 2.9 38.9 + - + +
373B ASN* 2.8 32.2 + - + +
374B PRO* 1.3 72.8 - - - +
376B GLN* 1.3 70.2 + - - +
378B GLU* 3.1 19.5 + - - +
379B ALA* 3.1 22.2 + - - +
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Residues in contact with GLN 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ASN* 4.2 9.6 - - - +
362B GLU* 5.2 4.2 + - - -
374B PRO 3.3 0.4 - - - -
375B THR* 1.3 80.0 + - - +
377B CYS* 1.3 65.3 + - - +
379B ALA* 3.4 10.6 + - - +
380B MET* 3.0 24.4 + - - +
429B SER* 2.6 39.5 + - - +
430B PHE* 3.6 20.4 + - + +
433B ASN* 3.5 42.3 - - + +
434B CYS* 4.0 10.5 - - + -
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Residues in contact with CYS 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ALA* 3.4 28.3 - - - +
342B ILE* 4.0 12.1 - - - -
343B ARG* 3.8 26.2 - - + +
358B LEU* 4.5 3.6 - - - -
374B PRO* 3.1 22.2 + - + +
376B GLN* 1.3 77.7 - - - +
378B GLU* 1.3 58.1 + - - +
380B MET* 3.8 0.7 - - - +
381B THR* 2.8 35.1 + - - +
430B PHE* 3.6 23.1 - - - -
434B CYS* 4.6 2.7 - - - -
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Residues in contact with GLU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ARG* 3.5 19.6 + - - +
373B ASN* 4.9 5.5 - - - +
374B PRO* 3.4 27.3 - - + +
375B THR* 3.1 22.4 + - - +
377B CYS* 1.3 75.0 - - - +
379B ALA* 1.3 59.7 + - - +
381B THR* 3.2 7.3 + - - -
382B MET* 2.9 43.5 + - + +
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Residues in contact with ALA 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B THR 3.1 12.8 + - - +
376B GLN* 3.9 14.1 - - - +
378B GLU* 1.3 75.8 - - - +
380B MET* 1.3 57.5 + - - +
382B MET* 3.8 14.8 - - + +
383B VAL* 3.0 35.9 + - + +
426B ALA* 5.3 2.9 - - + -
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Residues in contact with MET 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 4.8 0.7 - - + -
335B LEU* 3.7 37.9 - - + +
339B ALA* 3.7 21.8 - - + -
376B GLN 3.0 17.5 + - - +
377B CYS* 3.8 3.4 - - - +
379B ALA* 1.3 77.2 - - - +
381B THR* 1.3 58.8 + - - +
383B VAL* 3.1 10.4 + - - +
384B ALA* 2.9 26.0 + - - +
423B LEU* 5.4 0.7 - - - -
426B ALA* 3.4 46.7 - - + +
427B SER* 3.5 17.7 - - - +
430B PHE* 3.9 21.3 - - + -
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Residues in contact with THR 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B MET* 3.4 38.0 - - - +
339B ALA* 3.6 21.3 - - + -
340B ASN* 4.1 7.9 - - + +
343B ARG* 3.2 28.3 + - - +
377B CYS 2.8 22.7 + - - +
378B GLU* 3.2 10.6 + - - -
380B MET* 1.3 75.1 - - - +
382B MET* 1.3 61.4 + - - +
384B ALA* 3.4 2.5 + - - -
385B ALA* 3.1 19.2 + - - +
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Residues in contact with MET 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B GLU* 2.9 28.4 + - + +
379B ALA* 3.8 15.5 - - + +
381B THR* 1.3 74.6 + - - +
383B VAL* 1.3 65.3 + - - +
385B ALA* 3.2 8.3 + - - +
386B GLN* 3.0 22.1 + - - +
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Residues in contact with VAL 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ALA* 3.0 21.1 + - + +
380B MET* 3.4 10.3 - - - +
382B MET* 1.3 76.1 - - + +
384B ALA* 1.3 63.7 + - - +
386B GLN* 3.1 8.2 + - - +
387B VAL* 2.9 23.8 + - + +
422B LEU* 3.6 51.4 - - + +
423B LEU* 4.0 16.4 - - + +
426B ALA* 4.1 17.5 - - + -
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Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ALA* 3.5 35.8 - - + +
335B LEU* 5.0 3.6 - - + -
336B MET* 3.8 19.5 - - + +
380B MET* 2.9 14.2 + - - +
381B THR* 3.6 10.3 - - - +
382B MET 3.2 0.2 - - - -
383B VAL* 1.3 79.1 - - - +
385B ALA* 1.3 62.6 + - - +
387B VAL* 3.2 5.4 + - - +
388B MET* 3.2 28.0 + - + +
423B LEU* 5.3 1.8 - - - -
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Residues in contact with ALA 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B MET* 3.9 8.8 - - + +
381B THR 3.1 13.3 + - - +
382B MET* 3.2 10.7 + - - +
384B ALA* 1.3 75.6 - - - +
386B GLN* 1.3 64.4 + - - +
388B MET* 3.2 17.2 + - - +
389B GLY* 3.1 17.5 + - - -
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Residues in contact with GLN 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B MET 3.0 12.9 + - - +
383B VAL* 3.1 12.8 + - - +
385B ALA* 1.3 77.6 - - - +
387B VAL* 1.3 50.8 + - - +
389B GLY* 3.2 4.2 + - - -
390B ASN* 2.8 63.9 + - - +
418B HIS* 4.0 27.1 - - + -
422B LEU* 4.0 10.8 - - + -
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Residues in contact with VAL 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B SER* 5.2 1.9 + - - +
328B MET* 3.4 35.7 - - + +
329B ASN* 4.1 4.0 - - + +
332B ALA* 3.9 6.7 - - + -
383B VAL* 2.9 21.9 + - + +
384B ALA 3.2 7.6 + - - +
386B GLN* 1.3 75.8 - - + +
388B MET* 1.3 58.5 + - - +
390B ASN* 3.3 2.5 + - - +
391B HIS* 2.9 28.1 + - - +
419B SER* 3.8 34.7 + - - +
422B LEU* 5.2 1.8 - - + -
423B LEU* 3.7 28.7 - - + -
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Residues in contact with MET 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A THR* 3.7 16.8 - - + +
396A VAL* 5.6 4.9 - - - -
399A SER* 3.6 32.3 - - - -
329B ASN* 3.5 22.7 - - - +
332B ALA* 4.1 24.2 - - + +
333B CYS* 4.1 7.0 - - - +
336B MET* 4.0 16.2 - - + -
384B ALA 3.2 16.2 + - - +
385B ALA* 3.2 14.1 + - - +
387B VAL* 1.3 76.6 - - - +
389B GLY* 1.3 61.1 + - - +
391B HIS* 3.2 11.8 + - - +
392B VAL* 3.4 16.6 + - - +
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Residues in contact with GLY 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ALA 3.1 10.7 + - - -
386B GLN* 3.2 5.8 + - - -
388B MET* 1.3 75.5 - - - +
390B ASN* 1.3 66.8 + - - +
392B VAL* 3.1 18.1 + - - +
393B ALA* 3.1 12.4 + - - +
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Residues in contact with ASN 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B SER* 4.6 0.7 - - - +
386B GLN* 2.8 47.2 + - - +
387B VAL 3.5 1.6 - - - +
389B GLY* 1.3 72.2 - - - +
391B HIS* 1.3 56.4 + - - +
393B ALA* 3.2 4.8 + - - +
394B VAL* 2.9 33.5 + - - +
415B ASN* 3.2 32.7 + - + +
418B HIS* 3.1 29.2 + - - +
419B SER* 3.1 31.8 + - - +
422B LEU* 5.1 0.6 - - - +
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Residues in contact with HIS 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLY* 5.2 1.7 - - - -
329A ASN* 3.3 27.5 + - - +
391A HIS* 3.3 33.2 + + - -
392A VAL* 6.3 0.2 - - + -
322B VAL* 3.7 12.1 - - + -
325B SER* 2.8 31.6 + - - +
326B GLY* 3.3 25.6 - - - -
329B ASN* 4.0 20.2 - - + +
387B VAL* 2.9 13.4 + - + +
388B MET 3.5 9.6 - - - +
389B GLY 3.1 0.8 - - - -
390B ASN* 1.3 74.7 - - - +
392B VAL* 1.3 63.5 + - + +
394B VAL* 3.3 1.1 + - - +
395B THR* 2.8 38.8 + - - -
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Residues in contact with VAL 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A VAL* 3.4 33.0 - - + -
388B MET 3.4 11.8 + - - +
389B GLY* 3.1 9.7 + - - +
391B HIS* 1.3 77.8 - - + +
393B ALA* 1.3 61.8 + - - +
395B THR* 3.1 7.4 + - + +
396B VAL* 2.9 43.2 + - + +
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Residues in contact with ALA 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B GLY 3.1 11.2 + - - +
390B ASN* 3.4 8.5 - - - +
392B VAL* 1.3 78.7 - - - +
394B VAL* 1.3 62.0 + - - +
396B VAL* 3.4 5.7 + - - +
397B GLY 3.2 17.3 + - - -
411B MET* 3.5 19.0 - - + +
415B ASN* 3.8 24.0 - - - +
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Residues in contact with VAL 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B LEU 4.0 9.4 - - - +
322B VAL* 4.0 23.4 - - + +
325B SER* 3.9 15.5 - - - +
390B ASN 2.9 18.5 + - - +
391B HIS 3.6 6.5 - - - +
392B VAL 3.3 0.2 - - - -
393B ALA* 1.3 76.3 - - - +
395B THR* 1.3 57.6 + - - +
397B GLY* 3.4 0.5 + - - -
398B GLY* 2.8 27.0 + - - -
411B MET* 4.7 4.3 - - - -
412B MET* 3.6 35.3 - - + +
415B ASN* 3.4 24.2 - - + -
416B VAL* 4.1 9.9 - - + +
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Residues in contact with THR 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ASN* 2.9 35.4 + - - +
333A CYS* 3.4 23.8 - - - -
388A MET* 3.7 22.9 - - + -
322B VAL* 4.3 3.3 - - - +
391B HIS* 2.8 31.3 + - - -
392B VAL* 3.1 10.5 + - + -
394B VAL* 1.3 77.4 - - - +
396B VAL* 1.3 64.2 + - + +
398B GLY 3.4 0.5 + - - -
399B SER* 3.0 23.0 + - - -
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Residues in contact with VAL 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A MET* 5.7 5.4 - - - -
392B VAL* 2.9 33.3 + - + +
393B ALA* 3.9 5.8 - - - +
395B THR* 1.3 77.9 - - + +
397B GLY* 1.3 62.9 + - - +
399B SER* 2.9 14.6 + - - +
400B ASN* 2.8 36.6 + - - +
408B PHE* 5.5 4.3 - - + -
411B MET* 5.8 0.7 - - + -
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Residues in contact with GLY 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ALA 3.2 8.9 + - - -
394B VAL 3.8 1.1 - - - -
396B VAL* 1.3 79.4 - - - +
398B GLY* 1.3 61.9 + - - +
400B ASN* 3.1 10.7 + - - -
406B ASN* 3.1 15.4 + - - -
408B PHE* 3.7 31.6 - - - +
411B MET* 3.7 13.4 - - - +
412B MET* 3.7 7.4 - - - -
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Residues in contact with GLY 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A CYS* 4.2 13.7 - - - +
337A LYS* 5.2 2.4 - - - +
317B ALA* 5.2 3.5 - - - +
318B HIS 5.1 4.6 + - - -
319B ASP* 4.4 7.9 - - - +
322B VAL* 4.1 8.3 - - - -
394B VAL 2.8 17.3 + - - -
395B THR 3.8 2.2 - - - -
396B VAL 3.4 0.2 - - - -
397B GLY* 1.3 72.3 - - - +
399B SER* 1.3 59.5 + - - +
400B ASN 3.5 0.5 + - - -
401B GLY* 4.2 2.1 + - - -
406B ASN* 3.8 10.4 + - - -
412B MET* 3.4 24.7 - - - -
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Residues in contact with SER 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A CYS* 3.9 14.1 - - - +
336A MET* 3.4 31.0 - - - +
337A LYS* 4.0 9.3 + - - -
340A ASN* 6.0 0.5 - - - +
388A MET* 3.6 28.2 - - - +
395B THR 3.0 14.0 + - - -
396B VAL* 2.9 19.1 + - - +
397B GLY 3.1 0.4 - - - -
398B GLY* 1.3 76.1 - - - +
400B ASN* 1.3 65.6 + - - +
401B GLY 3.5 3.3 + - - +
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Residues in contact with ASN 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A MET* 5.6 2.3 - - - +
396B VAL* 2.8 36.9 + - - +
397B GLY 3.1 7.7 + - - +
399B SER* 1.3 84.3 + - - +
401B GLY* 1.3 66.3 + - - +
402B HIS* 3.5 24.4 + - + +
406B ASN* 4.1 1.1 - - - -
407B VAL 5.2 0.5 + - - -
408B PHE* 3.5 34.3 - - + -
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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