Contacts of the helix formed by residues 385 - 418 (chain A) in PDB entry 5TPT
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 ASN 385 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ASP* 2.9 16.0 + - - +
384A ASP* 1.3 84.6 - - - +
386A GLU* 1.3 63.8 + - - +
387A HIS 3.3 2.0 - - - -
388A ALA* 3.6 11.3 + - + +
389A ARG* 3.1 39.2 + - - +
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Residues in contact with GLU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR* 2.6 21.9 + - - -
380A THR 4.7 0.9 - - - +
381A SER 5.1 0.5 - - - +
382A ALA* 4.2 5.5 - - + -
383A ASP* 3.1 29.0 + - - +
384A ASP 3.2 1.2 - - - -
385A ASN* 1.3 77.8 - - - +
387A HIS* 1.3 58.0 + - - +
389A ARG* 3.4 8.7 + - - +
390A PHE* 2.9 25.3 + - - +
456A HIS* 2.6 35.0 + - + +
459A ARG* 3.3 41.9 + - + -
460A VAL* 4.6 6.5 - - + -
463A MET* 4.4 7.6 - - + -
----------------------------------------------------------
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Residues in contact with HIS 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASP 4.7 4.8 + - - +
385A ASN 3.3 0.4 - - - -
386A GLU* 1.3 80.2 - - - +
388A ALA* 1.3 59.6 + - - +
390A PHE* 3.4 4.4 + + - +
391A GLN* 2.9 52.2 + - + +
456A HIS* 4.1 25.1 - + + -
460A VAL* 6.1 0.9 - - + -
509A ARG* 6.2 2.2 - - - -
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Residues in contact with ALA 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASP 5.6 0.2 + - - -
385A ASN* 3.6 16.1 + - + +
387A HIS* 1.3 79.7 + - - +
389A ARG* 1.3 66.9 + - - +
391A GLN* 3.0 8.4 + - - +
392A LYS* 3.0 34.3 + - - +
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Residues in contact with ARG 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR* 3.9 19.4 - - + +
380A THR* 3.5 34.1 + - - +
381A SER 4.0 8.5 + - - -
383A ASP* 2.6 41.8 + - - -
385A ASN* 3.1 34.6 + - - +
386A GLU* 3.8 11.1 + - - +
388A ALA* 1.3 76.4 - - - +
390A PHE* 1.3 58.4 + - - +
392A LYS* 3.5 6.5 + - - +
393A ALA* 3.0 29.3 + - + +
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Residues in contact with PHE 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR* 3.4 27.3 - + + -
386A GLU* 2.9 22.1 + - - +
387A HIS* 3.6 5.4 - + - +
389A ARG* 1.3 75.6 - - - +
391A GLN* 1.3 71.5 + - - +
393A ALA* 3.8 1.0 - - - +
394A LYS* 2.9 64.7 + - + +
452A LEU* 3.6 30.1 - - + -
453A VAL* 4.2 15.3 - - + -
456A HIS* 3.4 49.8 - + + +
----------------------------------------------------------
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Residues in contact with GLN 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A HIS* 2.9 39.9 + - + +
388A ALA* 3.0 8.7 + - - +
390A PHE* 1.3 87.4 - - - +
392A LYS* 1.3 59.8 + - + +
394A LYS* 3.5 27.7 + - - +
395A GLU* 3.1 32.8 + - - +
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Residues in contact with LYS 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ALA* 3.0 23.8 + - - +
389A ARG* 4.1 5.8 - - - +
391A GLN* 1.3 75.6 - - + +
393A ALA* 1.3 60.7 + - - +
395A GLU* 3.1 7.0 + - - +
396A GLN* 2.8 42.2 + - + +
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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
----------------------------------------------------------
373A ASP 5.5 0.7 - - - +
374A VAL* 3.5 23.6 - - + +
377A TYR* 3.8 30.7 - - + -
389A ARG 3.0 18.9 + - - +
390A PHE 3.9 3.4 - - - +
392A LYS* 1.3 76.5 - - - +
394A LYS* 1.3 61.7 + - - +
396A GLN* 4.5 5.4 - - - +
397A LEU* 3.1 24.4 + - - +
452A LEU* 3.8 6.5 - - + +
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Residues in contact with LYS 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A PHE* 2.9 49.3 + - + +
391A GLN* 3.5 27.2 + - - +
393A ALA* 1.3 78.7 - - - +
395A GLU* 1.3 61.7 + - - +
397A LEU* 3.6 3.7 + - - +
398A GLU* 3.3 29.3 + - - +
449A LYS* 3.2 39.0 + - + +
452A LEU* 3.5 13.0 - - + +
453A VAL* 5.4 4.9 - - + -
513A HIS* 5.7 8.1 + - - -
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Residues in contact with GLU 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A GLN* 3.1 22.5 + - - +
392A LYS* 3.1 8.0 + - - +
394A LYS* 1.3 76.2 - - - +
396A GLN* 1.3 69.7 + - - +
398A GLU* 3.2 24.7 + - - +
399A ILE* 3.1 41.9 + - + +
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Residues in contact with GLN 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ASP* 4.3 25.4 - - + +
374A VAL* 3.7 20.4 - - + -
392A LYS* 2.8 28.0 + - + +
393A ALA* 4.5 1.6 - - - -
395A GLU* 1.3 80.7 - - - +
397A LEU* 1.3 58.3 + - - +
399A ILE* 3.8 19.9 - - - +
400A ARG* 2.9 36.9 + - - +
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Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A VAL* 3.9 22.4 - - + +
378A PHE* 6.3 0.2 - - + -
393A ALA 3.1 17.3 + - - +
394A LYS 3.7 6.1 - - - +
395A GLU 3.2 0.2 - - - -
396A GLN* 1.3 76.0 - - - +
398A GLU* 1.3 60.3 + - + +
400A ARG* 4.0 13.8 - - + +
401A HIS* 3.0 30.9 + - + +
445A ALA* 4.9 2.9 - - - +
448A GLU* 3.6 54.1 - - + +
449A LYS* 3.8 16.2 - - + -
452A LEU* 4.1 15.3 - - + -
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Residues in contact with GLU 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LYS* 3.3 13.0 + - - +
395A GLU* 3.2 29.4 + - - +
397A LEU* 1.3 78.8 - - - +
399A ILE* 1.3 63.4 + - + +
401A HIS* 3.6 6.3 + - - +
402A ARG* 3.2 38.7 + - - +
449A LYS* 2.4 36.0 + - + +
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Residues in contact with ILE 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLU* 3.1 34.4 + - + +
396A GLN* 3.8 23.8 - - - +
398A GLU* 1.3 75.6 - - + +
400A ARG* 1.3 61.6 + - + +
402A ARG* 3.1 18.3 + - - +
403A ASN* 2.8 47.7 + - - +
----------------------------------------------------------
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Residues in contact with ARG 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ASP* 4.1 11.7 - - - +
374A VAL* 3.4 38.9 - - - +
375A ASP* 3.7 25.6 + - - -
396A GLN* 2.9 24.2 + - - +
397A LEU* 4.0 14.7 - - + +
399A ILE* 1.3 76.2 - - + +
401A HIS* 1.3 57.8 + - - +
403A ASN* 3.4 11.2 + - - +
404A ARG* 3.0 29.3 + - - +
----------------------------------------------------------
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Residues in contact with HIS 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A LEU* 3.0 20.7 + - + +
398A GLU* 3.9 5.6 - - - +
400A ARG* 1.3 75.9 - - - +
402A ARG* 1.3 58.3 + - + +
404A ARG* 3.2 22.9 + - - +
405A MET* 2.7 64.8 + - + +
441A LEU* 3.0 30.7 - - + -
442A GLU* 4.4 6.5 - - - +
445A ALA* 3.3 26.9 - - + +
448A GLU* 6.0 1.1 - - - +
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Residues in contact with ARG 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A GLU* 3.2 30.2 + - - +
399A ILE* 3.1 21.4 + - - +
401A HIS* 1.3 77.3 - - + +
403A ASN* 1.3 63.2 + - - +
405A MET* 3.6 6.7 - - + +
406A ASP* 2.9 52.4 + - - +
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Residues in contact with ASN 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ILE* 2.8 37.8 + - - +
400A ARG* 3.7 10.8 - - - +
402A ARG* 1.3 80.7 - - - +
404A ARG* 1.3 60.0 + - - +
406A ASP* 3.9 8.1 - - - +
407A ARG* 3.1 24.1 + - - +
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Residues in contact with ARG 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ARG 3.0 18.3 + - - +
401A HIS* 3.6 28.5 + - - +
403A ASN* 1.3 73.8 - - - +
405A MET* 1.3 67.0 + - - +
407A ARG* 3.4 29.8 + - - +
408A VAL* 3.1 36.3 + - + +
441A LEU* 3.2 25.8 + - + +
444A GLU* 2.5 50.2 + - - +
445A ALA* 4.7 1.0 - - - +
448A GLU* 4.2 10.1 + - - -
451B GLN* 3.9 4.0 + - - -
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Residues in contact with MET 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A HIS* 2.7 54.5 + - + +
402A ARG* 3.6 9.4 - - + +
404A ARG* 1.3 75.2 - - - +
406A ASP* 1.3 61.0 + - - +
408A VAL* 3.6 3.1 + - - +
409A LYS* 3.0 33.2 + - + +
438A VAL* 4.3 21.5 - - + +
441A LEU* 3.6 33.0 - - + +
442A GLU* 3.8 19.7 - - + +
----------------------------------------------------------
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Residues in contact with ASP 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ARG* 2.9 39.9 + - - +
403A ASN* 3.9 8.6 - - - +
405A MET* 1.3 80.4 - - - +
407A ARG* 1.3 66.0 + - - +
409A LYS* 3.3 21.6 + - - +
410A LYS* 3.0 39.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ASN 3.1 13.8 + - - +
404A ARG* 3.6 35.0 + - - +
406A ASP* 1.3 80.8 - - - +
408A VAL* 1.3 74.6 + - - +
410A LYS* 3.3 6.9 + - - +
411A GLU* 3.1 53.2 + - + +
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Residues in contact with VAL 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ARG* 3.1 22.2 + - + +
405A MET 4.0 2.7 - - - +
407A ARG* 1.3 94.7 - - - +
409A LYS* 1.3 66.8 + - - +
411A GLU* 3.2 10.8 + - - +
412A TRP* 3.1 46.4 + - + +
434A PHE* 5.1 3.4 - - + -
437A MET* 4.1 15.5 - - + -
441A LEU* 3.9 30.3 - - + -
----------------------------------------------------------
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Residues in contact with LYS 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A MET* 3.0 23.9 + - + +
406A ASP* 3.3 18.9 + - - +
408A VAL* 1.3 77.4 - - - +
410A LYS* 1.3 88.2 + - - +
412A TRP* 4.1 1.0 - - - +
413A GLU* 3.2 49.0 + - - +
434A PHE* 3.8 30.8 - - + -
438A VAL* 5.9 0.4 - - + -
----------------------------------------------------------
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Residues in contact with LYS 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ASP* 3.0 28.9 + - - +
407A ARG* 3.5 9.2 - - - +
408A VAL 3.2 0.2 - - - -
409A LYS* 1.3 106.7 - - - +
411A GLU* 1.3 62.9 + - + +
413A GLU* 3.3 17.6 + - - +
414A GLU* 3.2 21.1 + - - +
----------------------------------------------------------
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Residues in contact with GLU 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ARG* 3.1 50.2 + - + +
408A VAL* 3.2 11.2 + - - +
410A LYS* 1.3 76.9 - - + +
412A TRP* 1.3 67.7 + - + +
414A GLU* 3.3 12.9 + - - +
415A ALA* 3.3 17.5 + - - +
----------------------------------------------------------
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Residues in contact with TRP 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A VAL* 3.1 45.0 + - + +
411A GLU* 1.3 81.2 + - + +
413A GLU* 1.3 59.7 + - - +
415A ALA* 3.1 11.3 + - + +
416A GLU* 2.9 31.8 + - + +
430A LEU* 4.0 18.2 - - + -
433A HIS* 3.6 28.5 - - + -
434A PHE* 3.4 43.3 - + + -
437A MET* 3.9 22.2 - - + +
454B GLU 3.6 20.9 - - - -
455B THR* 4.0 25.4 + - + +
458B ALA* 3.7 17.7 - - + -
----------------------------------------------------------
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Residues in contact with GLU 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A LYS* 3.2 42.3 + - + +
410A LYS* 3.7 21.9 - - - +
411A GLU 3.2 0.2 - - - -
412A TRP* 1.3 75.0 - - - +
414A GLU* 1.3 61.1 + - - +
416A GLU* 3.2 23.6 + - - +
417A LEU* 3.0 25.6 + - - +
434A PHE* 5.1 8.1 - - + -
----------------------------------------------------------
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Residues in contact with GLU 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A LYS 3.2 12.5 + - - +
411A GLU* 3.6 12.4 - - - +
412A TRP 3.2 0.2 - - - -
413A GLU* 1.3 77.4 - - - +
415A ALA* 1.3 57.7 + - - +
417A LEU* 3.2 14.6 + - + +
418A GLN* 2.7 61.6 + - + +
----------------------------------------------------------
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Residues in contact with ALA 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A GLU 3.3 9.1 + - - +
412A TRP* 3.1 17.3 + - + +
414A GLU* 1.3 77.4 - - - +
416A GLU* 1.3 62.4 + - - +
418A GLN* 3.6 15.4 + - - +
419A ALA* 3.3 15.6 + - - +
430A LEU* 3.3 27.5 - - + +
----------------------------------------------------------
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A TRP* 2.9 18.2 + - + +
413A GLU* 3.4 29.8 - - - +
415A ALA* 1.3 75.6 - - - +
417A LEU* 1.3 66.3 + - - +
419A ALA* 3.5 9.4 + - - +
420A LYS* 3.6 10.7 + - - +
427A ARG* 4.9 4.9 - - - +
430A LEU* 3.8 19.3 - - + +
431A ILE* 3.4 37.7 - - + +
434A PHE* 3.8 25.0 - - + +
----------------------------------------------------------
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Residues in contact with LEU 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A GLU 3.0 12.4 + - - +
414A GLU* 3.3 17.3 - - + +
416A GLU* 1.3 74.4 - - - +
418A GLN* 1.3 59.7 + - + +
419A ALA 3.0 10.0 + - - -
420A LYS* 3.1 52.8 + - + +
----------------------------------------------------------
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Residues in contact with GLN 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A GLU* 2.7 53.1 + - + +
415A ALA* 3.8 14.1 - - - +
416A GLU 3.4 0.2 - - - -
417A LEU* 1.3 76.3 - - + +
419A ALA* 1.3 57.2 + - - +
420A LYS* 3.4 2.0 + - - +
421A ASN* 5.1 1.7 + - - +
422A LEU* 5.9 0.2 - - - +
----------------------------------------------------------
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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