Contacts of the helix formed by residues 376 - 415 (chain A) in PDB entry 4K71
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 GLU 376 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A THR* 3.1 29.4 - - + +
356A THR* 2.8 29.5 + - - +
372A LYS 4.5 2.5 - - - +
373A VAL* 3.2 27.2 - - - +
375A ASP* 1.3 79.2 - - - +
377A PHE* 1.3 61.6 + - + +
379A PRO* 3.6 8.6 - - - +
380A LEU* 3.4 19.3 + - + +
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Residues in contact with PHE 377 (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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330A PHE* 3.7 31.9 - + - -
334A TYR* 3.8 32.3 - + - +
349A LEU* 3.7 45.3 - - + +
352A THR* 4.3 13.7 - - + -
353A TYR* 4.3 9.2 - - + -
373A VAL* 3.7 14.6 - - + -
374A PHE* 3.4 38.4 - + + +
375A ASP 3.1 1.4 - - - -
376A GLU* 1.3 82.7 - - + +
378A LYS* 1.3 60.4 + - - +
380A LEU* 2.8 19.9 + - - +
381A VAL* 2.9 19.4 + - + +
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Residues in contact with LYS 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A PHE 4.2 3.0 + - - +
375A ASP* 4.0 4.4 + - - +
377A PHE* 1.3 78.4 - - - +
379A PRO* 1.3 71.9 - - + +
381A VAL* 3.3 9.9 + - + +
382A GLU* 3.0 46.7 + - + +
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Residues in contact with PRO 379 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A ASP 3.4 17.3 - - - +
376A GLU* 3.6 6.5 - - - +
377A PHE 3.6 2.0 - - - -
378A LYS* 1.3 96.6 - - + +
380A LEU* 1.3 60.0 + - + +
382A GLU* 3.2 11.3 + - + +
383A GLU* 3.1 31.2 + - - +
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Residues in contact with LEU 380 (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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345A LEU* 3.6 13.6 - - + +
348A ARG* 4.7 19.9 + - + +
349A LEU* 4.0 20.4 - - + -
352A THR* 3.3 34.3 - - + +
376A GLU* 3.4 18.2 - - + +
377A PHE 2.8 7.8 + - - +
379A PRO* 1.3 78.4 - - + +
381A VAL* 1.3 58.4 + - - +
383A GLU* 5.1 3.7 - - + +
384A PRO* 3.2 20.7 - - - +
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Residues in contact with VAL 381 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A TYR* 5.4 1.1 - - - +
341A TYR* 4.0 36.8 - - + +
345A LEU* 4.3 20.9 - - + -
349A LEU* 4.4 10.1 - - + -
377A PHE* 2.9 23.6 + - + +
378A LYS* 3.6 9.4 - - + +
380A LEU* 1.3 77.9 - - - +
382A GLU* 1.3 64.3 + - + +
383A GLU 3.6 0.2 - - - -
384A PRO* 3.6 2.8 - - - +
385A GLN* 3.6 17.1 - - - +
446A MET* 3.5 22.5 - - + +
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Residues in contact with GLU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LYS* 3.0 45.8 + - + +
379A PRO* 3.2 9.2 + - + +
381A VAL* 1.3 80.2 - - + +
383A GLU* 1.3 60.2 + - - +
385A GLN* 3.2 14.9 + - - +
386A ASN* 2.8 45.4 + - - +
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Residues in contact with GLU 383 (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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348A ARG* 4.9 2.8 + - - -
379A PRO 3.1 14.4 + - - +
380A LEU* 4.8 3.3 - - + +
382A GLU* 1.3 75.3 - - - +
384A PRO* 1.4 66.5 - - + +
386A ASN* 3.8 6.1 - - - +
387A LEU* 2.9 37.6 + - + +
485A ARG* 3.4 35.6 + - - -
486A PRO* 5.0 8.8 - - - +
489A SER* 5.4 1.4 - - - -
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Residues in contact with PRO 384 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A LEU* 4.9 3.1 - - + -
348A ARG* 4.0 12.6 - - - +
380A LEU 3.2 23.1 - - - +
381A VAL 3.6 6.5 - - - +
383A GLU* 1.4 94.1 - - + +
385A GLN* 1.3 66.0 + - - +
387A LEU* 3.2 6.9 + - + +
388A ILE* 2.9 32.9 + - + +
446A MET* 3.8 18.2 - - + -
450A GLU* 3.8 20.2 - - - +
485A ARG* 3.9 16.8 - - - +
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Residues in contact with GLN 385 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A VAL* 3.6 24.0 - - - +
382A GLU* 3.2 21.0 + - - +
384A PRO* 1.3 77.3 - - - +
386A ASN* 1.3 62.6 + - - +
388A ILE* 3.4 2.4 + - - +
389A LYS* 2.9 30.0 + - - +
442A GLU 5.5 4.4 + - - -
443A ALA* 6.0 3.0 - - - +
446A MET* 3.6 33.6 - - + +
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Residues in contact with ASN 386 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A GLU* 2.8 30.7 + - - +
383A GLU* 3.8 5.6 - - - +
385A GLN* 1.3 79.4 - - - +
387A LEU* 1.3 63.9 + - - +
389A LYS* 3.4 13.8 + - - +
390A GLN* 3.0 37.5 + - - +
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Residues in contact with LEU 387 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A GLU* 2.9 29.3 + - + +
384A PRO* 3.2 5.1 + - + +
386A ASN* 1.3 76.2 - - - +
388A ILE* 1.3 69.4 + - + +
390A GLN* 3.3 8.8 + - - +
391A ASN* 2.7 48.8 + - - +
453A LEU* 5.2 4.9 - - + -
485A ARG* 4.0 33.9 - - - +
489A SER* 4.4 15.3 - - - +
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Residues in contact with ILE 388 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A PRO* 2.9 24.1 + - + +
385A GLN* 3.9 3.6 - - - +
387A LEU* 1.3 84.5 - - + +
389A LYS* 1.3 56.3 + - - +
391A ASN* 3.4 5.6 + - + +
392A CYS* 2.8 49.4 + - - +
437A CYS* 6.0 0.7 - - + -
445A ARG* 4.4 18.8 - - + +
446A MET* 3.6 23.1 - - + +
449A ALA* 3.6 35.2 - - + -
450A GLU* 3.9 18.6 - - - +
453A LEU* 5.5 4.5 - - + -
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Residues in contact with LYS 389 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A GLN 2.9 17.5 + - - +
386A ASN* 3.5 15.5 - - - +
388A ILE* 1.3 76.9 - - - +
390A GLN* 1.3 62.1 + - + +
392A CYS* 4.1 4.6 - - - +
393A GLU* 3.2 50.3 + - + +
442A GLU* 4.3 23.2 + - + +
445A ARG* 6.4 1.8 - - - +
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Residues in contact with GLN 390 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A ASN* 3.0 28.4 + - - +
387A LEU* 3.7 9.8 - - - +
388A ILE 3.3 0.2 - - - -
389A LYS* 1.3 75.0 - - + +
391A ASN* 1.3 66.6 + - - +
393A GLU* 3.6 13.5 + - - +
394A LEU* 3.0 28.1 + - - +
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Residues in contact with ASN 391 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A LEU* 2.7 47.1 + - - +
388A ILE* 3.9 5.8 - - + +
390A GLN* 1.3 78.7 + - - +
392A CYS* 1.3 60.9 + - - +
394A LEU* 3.3 6.8 + - - +
395A PHE* 2.8 29.9 + - - +
403A PHE* 3.6 22.2 - - + -
407A LEU* 4.7 1.2 - - - +
410A ARG* 3.2 36.2 + - - +
433A VAL* 5.9 5.2 - - + -
438A CYS* 5.0 0.7 - - - -
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Residues in contact with CYS 392 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A ILE* 2.8 42.3 + - - +
389A LYS* 4.1 5.4 - - - +
391A ASN* 1.3 68.7 - - - +
393A GLU* 1.3 61.2 + - - +
395A PHE* 3.0 3.5 + - - +
396A GLU* 2.8 42.3 + - - +
437A CYS* 5.0 0.9 - - - -
438A CYS* 2.0 57.7 - - + -
445A ARG* 4.4 12.1 - - - +
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Residues in contact with GLU 393 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A LYS* 3.2 37.4 + - + +
390A GLN* 3.7 15.8 - - - +
392A CYS* 1.3 76.0 - - - +
394A LEU* 1.3 57.9 + - - +
396A GLU* 3.2 14.8 + - - +
397A GLN* 2.9 40.5 + - - +
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Residues in contact with LEU 394 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A GLN 3.0 19.2 + - - +
391A ASN* 3.5 6.5 - - - +
392A CYS 3.2 0.2 - - - -
393A GLU* 1.3 76.8 - - - +
395A PHE* 1.3 55.8 + - - +
397A GLN* 3.4 12.4 + - - +
398A LEU* 3.0 62.7 + - + +
403A PHE* 4.1 15.9 - - + -
406A ALA* 4.7 8.7 - - + -
410A ARG* 3.6 27.1 - - - +
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Residues in contact with PHE 395 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A ASN 2.8 16.8 + - - +
392A CYS* 3.0 9.6 + - - +
394A LEU* 1.3 73.1 - - - +
396A GLU* 1.3 66.1 + - + +
399A GLY* 3.1 26.1 + - - -
400A GLU* 4.0 26.9 - - + -
403A PHE* 3.8 40.3 - + + -
431A GLY 4.9 0.9 - - - -
434A GLY* 3.2 37.9 - - - -
435A SER* 3.9 20.0 - - - -
438A CYS* 4.2 11.4 - - + -
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Residues in contact with GLU 396 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A CYS* 2.8 34.1 + - - +
393A GLU* 3.6 11.7 - - - +
395A PHE* 1.3 90.1 - - + +
397A GLN* 1.3 60.8 + - + +
398A LEU 3.6 0.3 + - - -
399A GLY* 4.2 3.8 + - - -
438A CYS* 4.0 16.5 - - + +
445A ARG* 5.2 4.5 + - - -
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Residues in contact with GLN 397 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A GLU* 2.9 26.3 + - - +
394A LEU* 4.0 13.3 + - + +
396A GLU* 1.3 78.7 - - + +
398A LEU* 1.3 68.1 + - + +
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Residues in contact with LEU 398 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A LEU* 3.0 46.1 + - + +
397A GLN* 1.3 86.3 - - + +
399A GLY* 1.3 64.6 + - - +
402A LYS* 3.5 59.3 + - + +
403A PHE* 4.0 4.5 - - - +
406A ALA* 4.3 11.9 - - + -
541A LYS* 6.1 2.9 - - - +
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Residues in contact with GLY 399 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A PHE* 3.1 18.3 + - - -
396A GLU 4.2 3.5 + - - -
397A GLN 3.7 1.6 - - - -
398A LEU* 1.3 77.9 - - - +
400A GLU* 1.3 65.9 + - - -
401A TYR 3.5 1.8 - - - -
403A PHE* 3.0 25.4 + - - +
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Residues in contact with GLU 400 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A PHE* 4.0 18.2 - - + -
399A GLY* 1.3 71.2 - - - -
401A TYR* 1.3 65.3 + - - +
403A PHE* 3.3 4.1 + - + +
404A GLN* 2.9 54.4 + - + +
428A ARG* 5.5 1.2 + - - +
431A GLY 5.2 6.4 - - - +
432A LYS* 5.5 7.0 - - - +
435A SER* 4.4 18.2 - - - +
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Residues in contact with TYR 401 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A GLU* 1.3 81.2 - - - +
402A LYS* 1.3 69.0 + - + +
404A GLN* 3.3 11.8 + - - +
405A ASN* 3.0 49.0 + - - -
522A GLN* 3.7 51.2 + - + +
525A LYS* 3.6 34.6 - - + +
526A GLN* 3.5 27.7 - - + +
548A MET* 5.6 1.0 - - - +
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Residues in contact with LYS 402 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A LEU* 3.5 45.1 + - + +
399A GLY 3.7 1.2 + - - -
400A GLU 3.5 0.4 - - - -
401A TYR* 1.3 90.7 - - + +
403A PHE* 1.3 56.6 + - - +
405A ASN* 3.2 13.2 + - + +
406A ALA* 2.8 29.1 + - - +
545A LYS* 4.8 17.3 - - - +
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Residues in contact with PHE 403 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A ASN* 3.6 41.5 - - + -
394A LEU* 4.1 23.3 - - + -
395A PHE* 3.8 39.5 - + + -
398A LEU* 4.0 7.7 - - + +
399A GLY 3.0 21.1 + - - +
400A GLU* 3.5 4.3 - - + +
402A LYS* 1.3 74.4 - - - +
404A GLN* 1.3 66.2 + - + +
406A ALA* 3.2 5.1 + - + +
407A LEU* 3.0 45.2 + - + +
410A ARG* 5.4 0.4 - - - -
431A GLY* 3.7 27.4 - - - -
433A VAL* 4.7 9.0 - - + -
434A GLY* 4.5 6.5 - - - -
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Residues in contact with GLN 404 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A GLU* 2.9 47.2 + - + +
401A TYR* 3.4 11.6 - - - +
403A PHE* 1.3 76.7 - - + +
405A ASN* 1.3 53.5 + - - +
407A LEU* 3.2 7.5 + - - +
408A LEU* 2.8 36.5 + - - +
424A VAL* 5.6 0.9 - - - +
427A SER* 3.7 14.0 + - - +
428A ARG* 3.9 44.1 + - - +
431A GLY* 4.7 8.9 - - - -
432A LYS* 6.3 0.2 - - - +
526A GLN* 3.3 25.7 + - - +
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Residues in contact with ASN 405 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A TYR* 3.0 49.0 + - - -
402A LYS* 3.2 16.5 + - + +
404A GLN* 1.3 75.6 - - - +
406A ALA* 1.3 63.7 + - - +
408A LEU* 3.1 7.2 + - - +
409A VAL* 3.0 29.3 + - - +
526A GLN* 2.9 35.6 + - - +
529A LEU* 4.0 16.4 - - + +
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Residues in contact with ALA 406 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A LEU* 4.7 13.7 - - + -
398A LEU* 4.3 16.4 - - + -
402A LYS 2.8 13.5 + - - +
403A PHE* 3.2 9.6 + - + +
405A ASN* 1.3 77.0 - - - +
407A LEU* 1.3 58.2 + - + +
409A VAL* 3.6 8.2 + - - +
410A ARG* 3.2 33.1 + - - +
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Residues in contact with LEU 407 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ASN* 4.7 4.9 - - - +
403A PHE* 3.0 32.1 + - + +
404A GLN* 3.2 6.0 + - - +
406A ALA* 1.3 73.7 - - + +
408A LEU* 1.3 60.5 + - - +
410A ARG* 3.1 39.3 + - - +
411A TYR* 2.8 47.3 + - + +
427A SER* 4.1 11.2 - - - +
430A LEU* 3.8 14.1 - - + +
431A GLY* 3.5 37.0 - - - +
433A VAL* 5.8 0.7 - - + -
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Residues in contact with LEU 408 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A GLN 2.8 19.9 + - - +
405A ASN* 3.1 5.8 + - - +
407A LEU* 1.3 73.6 - - - +
409A VAL* 1.3 58.5 + - - +
411A TYR* 3.9 2.1 - - + +
412A THR* 2.7 34.2 + - - +
423A LEU* 3.4 37.0 - - + +
424A VAL* 3.9 6.3 - - + +
427A SER* 3.8 12.7 - - - +
526A GLN* 3.6 50.3 - - + +
529A LEU* 4.4 10.8 - - + -
530A VAL* 3.6 23.1 - - + +
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Residues in contact with VAL 409 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A ASN 3.0 17.2 + - - +
406A ALA* 3.7 9.9 - - - +
408A LEU* 1.3 75.7 - - - +
410A ARG* 1.3 64.6 + - + +
412A THR* 3.9 2.8 - - - -
413A LYS* 3.0 49.7 + - + +
529A LEU* 3.7 27.6 - - + -
533A VAL* 4.5 8.7 - - + +
541A LYS* 6.5 0.2 - - - -
544A LEU* 4.0 25.8 - - + -
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Residues in contact with ARG 410 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ASN* 3.2 25.6 + - - +
394A LEU* 3.6 28.3 - - - +
403A PHE* 5.4 0.4 - - - -
406A ALA* 3.2 18.0 + - - +
407A LEU* 3.1 40.3 + - - +
409A VAL* 1.3 83.1 - - + +
411A TYR* 1.3 66.4 + - + +
413A LYS* 3.3 11.1 - - + +
414A LYS* 3.0 40.6 + - - +
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Residues in contact with TYR 411 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A LEU* 2.8 31.4 + - + +
408A LEU* 4.4 2.9 - - - +
410A ARG* 1.3 78.7 - - + +
412A THR* 1.3 60.6 + - - +
414A LYS* 3.6 30.9 - - + +
415A VAL* 2.8 38.7 + - + +
418A MET* 6.2 1.1 - - - -
423A LEU* 3.5 20.4 - - + +
426A VAL* 4.1 19.5 - - + -
427A SER* 5.9 2.2 - - - +
430A LEU* 3.5 32.3 - - + +
457A LEU* 4.3 11.6 - - + +
460A LEU* 4.8 4.0 - - + -
488A PHE* 3.8 39.6 + + + +
489A SER* 5.0 1.6 + - - -
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Residues in contact with THR 412 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A LEU* 2.7 24.7 + - - +
409A VAL* 3.9 2.0 - - - -
411A TYR* 1.3 72.5 - - - +
413A LYS* 1.3 61.5 + - - +
415A VAL 4.4 0.2 - - - -
416A PRO* 2.8 38.4 - - + +
423A LEU* 3.7 24.0 - - + +
530A VAL* 3.7 34.6 - - + +
533A VAL* 3.5 30.2 - - + +
534A LYS* 4.2 11.4 - - + -
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Residues in contact with LYS 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A VAL* 3.0 39.3 + - + +
410A ARG* 3.3 13.2 - - + +
412A THR* 1.3 77.2 - - - +
414A LYS* 1.3 58.6 + - + +
416A PRO* 3.7 4.3 - - - +
493A VAL* 3.3 21.8 - - + +
494A ASP 3.0 25.6 + - - -
533A VAL* 3.8 11.8 - - + +
537A PRO* 2.7 36.4 + - - +
538A LYS* 3.7 6.5 + - - +
539A ALA* 2.8 27.2 + - - +
540A THR 6.0 0.4 - - - -
544A LEU* 5.1 1.8 - - - -
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Residues in contact with LYS 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ARG* 3.0 29.1 + - - +
411A TYR* 3.6 44.6 - - + +
412A THR 3.2 0.2 - - - -
413A LYS* 1.3 77.4 - - + +
415A VAL* 1.3 71.0 + - + +
416A PRO* 3.6 3.7 - - - +
417A GLN* 4.8 0.2 - - - +
470A SER* 5.0 2.3 + - - -
472A ARG* 2.7 30.9 + - - +
488A PHE* 2.8 28.1 + - + +
489A SER* 3.4 14.3 + - - +
491A LEU* 2.6 49.8 + - + +
492A GLU 4.0 2.9 - - - +
494A ASP* 4.0 1.2 - - - +
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Residues in contact with VAL 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A TYR* 2.8 25.0 + - + +
412A THR 3.2 3.3 - - - +
414A LYS* 1.3 90.8 - - + +
416A PRO* 1.3 63.7 - - - +
417A GLN* 3.0 11.2 + - - +
418A MET* 3.1 44.4 + - + +
423A LEU* 3.9 7.1 - - - +
460A LEU* 6.3 1.1 - - + -
469A VAL* 4.7 2.2 - - + -
470A SER* 3.9 15.7 - - - +
472A ARG* 6.6 0.2 - - + -
473A VAL* 3.7 33.7 - - + -
488A PHE* 5.5 2.2 - - + -
491A LEU* 5.1 4.7 - - + -
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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