Contacts of the helix formed by residues 374 - 400 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ARG* 3.5 32.1 - - + +
358A LEU* 3.6 31.0 - - + -
372A VAL 3.6 6.2 - - - +
373A ASN* 1.3 81.8 - - + +
375A THR* 1.3 64.0 + - - +
376A GLN 3.3 2.7 - - - -
377A CYS* 3.2 24.1 + - + +
378A GLU* 3.2 25.6 + - - +
434A CYS* 6.2 0.2 - - - -
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Residues in contact with THR 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ASN* 3.5 28.1 + - + +
362A GLU* 3.5 42.2 - - + +
373A ASN* 2.8 23.7 + - + +
374A PRO* 1.3 72.3 - - - +
376A GLN* 1.3 70.8 + - - +
378A GLU* 3.0 22.4 + - - +
379A ALA* 3.1 12.8 + - - +
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Residues in contact with GLN 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ASN* 4.0 12.1 + - - +
374A PRO 3.3 0.6 - - - -
375A THR* 1.3 85.1 + - - +
377A CYS* 1.3 61.1 + - - +
378A GLU 3.2 0.2 + - - -
379A ALA* 3.2 13.5 + - - +
380A MET* 2.9 30.8 + - - +
429A SER* 2.6 36.7 + - - +
430A PHE* 3.8 21.2 + - + +
433A ASN* 3.7 41.9 - - + +
434A CYS* 4.0 9.4 - - + -
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Residues in contact with CYS 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ALA* 3.5 28.7 - - - +
342A ILE* 3.9 13.7 - - - -
343A ARG* 3.8 22.9 - - + +
358A LEU* 4.5 3.8 - - - -
374A PRO* 3.2 25.4 + - + +
376A GLN* 1.3 76.6 - - - +
378A GLU* 1.3 57.5 + - - +
380A MET* 3.9 0.3 - - - +
381A THR* 2.9 36.6 + - - +
430A PHE* 3.7 24.0 - - - -
434A CYS* 4.5 3.1 - - - -
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Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ARG* 3.6 20.3 + - - +
373A ASN* 5.2 5.5 - - - +
374A PRO* 3.2 30.2 + - + +
375A THR* 3.0 14.4 + - - +
377A CYS* 1.3 74.8 - - - +
379A ALA* 1.3 63.8 + - - +
381A THR* 3.2 7.2 + - - -
382A MET* 3.0 37.9 + - + +
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Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A THR 3.1 11.3 + - - +
376A GLN* 3.2 18.6 + - - +
378A GLU* 1.3 77.5 - - - +
380A MET* 1.3 55.4 + - - +
382A MET* 3.7 13.7 - - + +
383A VAL* 3.0 35.8 + - + +
426A ALA* 5.4 2.9 - - + -
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Residues in contact with MET 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 5.0 0.4 - - + -
335A LEU* 3.8 39.0 - - + +
339A ALA* 3.8 21.3 - - + -
376A GLN 2.9 16.8 + - - +
377A CYS 3.9 3.8 - - - +
379A ALA* 1.3 78.3 - - - +
381A THR* 1.3 56.6 + - - +
383A VAL* 3.2 9.4 + - - +
384A ALA* 2.9 25.6 + - - +
423A LEU* 4.8 1.3 - - - +
426A ALA* 3.4 46.4 - - + +
427A SER* 3.6 15.5 - - - +
430A PHE* 3.9 22.4 - - + -
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Residues in contact with THR 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A MET* 3.5 36.1 - - - +
339A ALA* 3.6 21.8 - - + -
340A ASN* 4.1 6.1 - - - +
343A ARG* 3.4 28.3 + - - +
377A CYS 2.9 22.3 + - - +
378A GLU* 3.2 11.3 + - - -
380A MET* 1.3 72.6 - - - +
382A MET* 1.3 65.9 + - - +
384A ALA* 3.4 2.4 + - - -
385A ALA* 3.1 20.3 + - - +
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Residues in contact with MET 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLU* 3.0 29.5 + - + +
379A ALA* 3.7 14.1 - - + +
381A THR* 1.3 76.2 + - - +
383A VAL* 1.3 65.4 + - + +
385A ALA* 3.3 7.2 + - - +
386A GLN* 3.0 22.9 + - - +
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Residues in contact with VAL 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ALA* 3.0 19.8 + - + +
380A MET* 3.2 11.6 + - - +
382A MET* 1.3 77.1 - - + +
384A ALA* 1.3 62.4 + - - +
386A GLN* 3.1 7.9 + - - +
387A VAL* 2.9 23.7 + - + +
422A LEU* 3.6 51.4 - - + +
423A LEU* 4.0 17.0 - - + -
426A ALA* 4.1 16.4 - - + -
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Residues in contact with ALA 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ALA* 3.5 36.8 - - + +
335A LEU* 5.0 3.4 - - + -
336A MET* 3.9 19.3 - - + +
380A MET* 2.9 14.0 + - - +
381A THR* 3.6 9.4 - - - +
382A MET 3.3 0.2 - - - -
383A VAL* 1.3 77.5 - - - +
385A ALA* 1.3 63.8 + - - +
387A VAL* 3.2 5.5 + - - +
388A MET* 3.2 27.6 + - + +
423A LEU* 5.1 2.0 - - + -
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Residues in contact with ALA 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A MET* 3.9 9.7 - - + +
381A THR 3.1 14.6 + - - +
382A MET* 3.7 9.0 - - - +
383A VAL 3.3 0.2 - - - -
384A ALA* 1.3 75.2 - - - +
386A GLN* 1.3 62.3 + - - +
388A MET* 3.1 23.8 + - - +
389A GLY* 3.2 10.4 + - - -
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Residues in contact with GLN 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A MET 3.0 13.8 + - - +
383A VAL* 3.1 12.1 + - - +
385A ALA* 1.3 77.0 - - - +
387A VAL* 1.3 56.8 + - - +
389A GLY* 3.1 4.9 + - - +
390A ASN* 2.8 65.8 + - - +
418A HIS* 4.1 11.6 - - + -
422A LEU* 4.1 17.9 - - + -
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Residues in contact with VAL 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A SER* 5.2 1.5 + - - +
328A MET* 3.5 35.4 - - + +
329A ASN* 4.1 4.3 - - + +
332A ALA* 3.9 6.7 - - + -
383A VAL* 2.9 22.7 + - + +
384A ALA 3.2 7.6 + - - +
386A GLN* 1.3 75.9 - - + +
388A MET* 1.3 58.0 + - - +
390A ASN* 3.3 2.2 + - - +
391A HIS* 2.9 28.0 + - + +
419A SER* 3.8 34.0 + - - +
422A LEU* 5.2 1.6 - - + -
423A LEU* 3.8 28.0 - - + -
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Residues in contact with MET 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ASN* 3.5 22.4 - - - +
332A ALA* 4.0 9.2 - - + +
333A CYS* 4.0 26.5 - - - +
336A MET* 4.2 12.8 - - + -
384A ALA 3.2 16.5 + - - +
385A ALA* 3.1 15.3 + - - +
387A VAL* 1.3 76.2 - - - +
389A GLY* 1.3 61.8 + - - +
391A HIS* 3.4 4.7 + - - +
392A VAL* 3.4 24.4 + - - +
395B THR* 3.7 16.8 - - + +
396B VAL* 5.7 4.9 - - - -
399B SER* 3.6 32.3 - - - -
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Residues in contact with GLY 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ALA 3.2 8.9 + - - -
386A GLN* 3.1 8.5 + - - -
388A MET* 1.3 74.8 - - - +
390A ASN* 1.3 65.7 + - - +
392A VAL* 3.1 9.7 + - - +
393A ALA* 3.1 20.3 + - - +
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Residues in contact with ASN 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A SER* 4.7 0.2 - - - -
386A GLN* 2.8 49.8 + - - +
387A VAL* 3.6 1.5 - - - +
389A GLY* 1.3 72.2 - - - +
391A HIS* 1.3 56.8 + - - +
393A ALA* 3.1 4.7 + - - +
394A VAL* 2.8 32.9 + - - +
415A ASN* 3.2 28.8 - - + +
418A HIS* 3.2 32.7 + - - +
419A SER* 3.2 28.8 + - - +
422A LEU* 4.9 0.6 - - - +
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Residues in contact with HIS 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 3.7 11.2 - - + -
325A SER* 2.9 34.7 + - - +
326A GLY* 3.4 23.6 - - - -
329A ASN* 3.9 21.3 - - + +
387A VAL* 2.9 16.7 + - + +
388A MET 3.6 5.8 - - - +
389A GLY 3.2 0.2 - - - -
390A ASN* 1.3 77.6 - - - +
392A VAL* 1.3 62.7 + - + +
394A VAL* 3.2 2.1 + - - +
395A THR* 2.8 38.1 + - - -
326B GLY* 5.3 1.3 - - - -
329B ASN* 3.2 28.7 + - - -
391B HIS* 3.3 32.3 + + - -
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Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A MET 3.4 12.1 + - - +
389A GLY* 3.1 11.5 + - - +
391A HIS* 1.3 81.8 - - + +
393A ALA* 1.3 59.1 + - - +
395A THR* 3.1 9.1 + - - -
396A VAL* 2.9 39.7 + - + +
388B MET 5.8 0.4 - - - +
391B HIS* 6.3 0.2 - - + -
392B VAL* 3.4 32.3 - - + -
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Residues in contact with ALA 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A GLY 3.1 12.2 + - - +
390A ASN* 3.1 8.5 + - - +
392A VAL* 1.3 79.1 - - - +
394A VAL* 1.3 62.4 + - - +
396A VAL* 3.4 6.9 + - - +
397A GLY 3.2 17.0 + - - -
411A MET* 3.5 33.0 - - + +
415A ASN* 3.8 14.4 - - - +
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Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU* 4.0 4.9 - - + +
322A VAL* 3.9 31.1 - - + +
325A SER* 3.9 19.5 - - - +
390A ASN 2.8 21.7 + - - +
391A HIS 3.5 6.7 - - - +
393A ALA* 1.3 72.1 - - - +
395A THR* 1.3 58.1 + - - +
397A GLY* 3.4 0.7 + - - -
398A GLY* 2.9 26.5 + - - -
411A MET* 4.7 0.7 - - - -
412A MET* 3.6 33.7 - - + +
415A ASN* 3.5 22.7 - - + -
416A VAL* 4.0 9.4 - - + +
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Residues in contact with THR 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 4.4 2.5 - - - +
391A HIS* 2.8 34.5 + - - -
392A VAL* 3.1 10.4 + - + -
394A VAL* 1.3 74.8 - - - +
396A VAL* 1.3 64.2 + - + +
398A GLY 3.4 0.2 + - - -
399A SER* 3.1 21.0 + - - -
329B ASN* 2.9 38.0 + - - +
333B CYS* 3.4 24.2 - - - -
388B MET* 3.7 22.7 - - + -
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Residues in contact with VAL 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A VAL* 2.9 32.4 + - + +
393A ALA* 3.9 6.7 - - - +
395A THR* 1.3 76.8 - - + +
397A GLY* 1.3 61.5 + - - +
399A SER* 2.9 22.0 + - - +
400A ASN* 3.0 30.6 + - - +
408A PHE* 5.6 4.0 - - + -
388B MET* 5.6 5.4 - - - -
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Residues in contact with GLY 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ALA 3.2 12.2 + - - -
394A VAL 3.8 1.8 - - - -
396A VAL* 1.3 80.9 - - - +
398A GLY* 1.3 60.8 + - - +
399A SER 3.2 0.7 + - - -
400A ASN 3.2 7.3 + - - -
406A ASN* 3.1 16.8 + - - -
408A PHE* 3.8 35.3 - - - +
411A MET* 4.6 2.2 - - - -
412A MET* 3.7 11.2 - - - -
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Residues in contact with GLY 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ALA* 5.0 5.5 - - - +
318A HIS 5.1 3.1 + - - -
319A ASP* 4.2 8.9 - - - +
322A VAL* 4.1 8.5 - - - -
394A VAL 2.9 14.8 + - - -
395A THR 3.9 1.3 - - - -
397A GLY* 1.3 75.5 - - - +
399A SER* 1.3 58.8 + - - +
400A ASN 3.4 0.4 + - - -
401A GLY 4.4 0.9 + - - -
406A ASN* 3.8 10.0 + - - -
412A MET* 3.4 24.7 - - - +
333B CYS* 4.0 14.8 - - - +
337B LYS* 5.2 2.4 - - - +
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Residues in contact with SER 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A THR 3.1 13.2 + - - -
396A VAL* 2.9 19.9 + - - +
397A GLY 3.1 0.2 - - - -
398A GLY* 1.3 76.3 - - - +
400A ASN* 1.3 66.1 + - - +
401A GLY 3.5 3.5 + - - +
333B CYS* 3.9 14.3 - - - +
336B MET* 3.3 31.3 - - - +
337B LYS* 3.9 9.2 + - - -
340B ASN* 5.9 0.5 - - - +
388B MET* 3.6 28.0 - - - +
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Residues in contact with ASN 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A VAL* 3.0 35.2 + - - +
397A GLY 3.2 6.4 + - - +
399A SER* 1.3 84.6 + - - +
401A GLY* 1.3 65.0 + - - +
402A HIS* 3.4 24.9 + - - +
406A ASN* 4.2 1.1 - - - -
407A VAL 5.2 0.3 + - - -
408A PHE* 3.5 35.7 - - + -
336B MET* 5.3 3.1 - - - +
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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