Contacts of the helix formed by residues 371 - 395 (chain F) in PDB entry 5KRA
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 371 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369F ASP 5.6 0.7 - - - +
370F LEU* 1.3 78.8 - - - +
372F LEU* 1.3 64.7 + - - +
373F HIS* 3.8 7.4 + - - +
374F ASP* 3.0 29.8 + - - +
375F GLN* 3.0 20.1 + - - +
471F GLU* 3.3 29.9 + - - +
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Residues in contact with LEU 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370F LEU 3.7 1.0 + - - -
371F THR* 1.3 72.0 - - - +
373F HIS* 1.3 62.6 + - - +
375F GLN* 3.4 16.1 + - - +
376F VAL* 3.1 31.2 + - + +
691H HIS* 3.3 43.3 - - + +
694H LEU* 3.8 36.1 - - + +
695H GLN* 3.6 23.1 - - + +
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Residues in contact with HIS 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371F THR* 3.1 8.8 - - - +
372F LEU* 1.3 79.1 - - - +
374F ASP* 1.3 65.5 + - - +
376F VAL* 3.4 9.2 + - - +
377F HIS* 3.1 20.6 + - - +
691H HIS* 5.9 2.9 - - - -
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Residues in contact with ASP 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370F LEU* 4.6 13.8 - - + +
371F THR* 3.0 21.3 + - - +
373F HIS* 1.3 78.3 - - - +
375F GLN* 1.3 61.2 + - - +
377F HIS* 3.2 11.0 + - + +
378F LEU* 2.9 37.0 + - + +
471F GLU* 2.8 32.9 - - - +
475F ILE* 5.6 5.4 - - + +
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Residues in contact with GLN 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362F LYS* 5.8 0.9 - - - +
367F PHE* 2.8 55.2 + - + +
368F VAL* 3.3 18.7 + - - +
370F LEU* 3.1 20.1 + - + +
371F THR 3.0 15.9 + - - +
372F LEU* 3.6 15.3 - - - +
374F ASP* 1.3 77.5 - - - +
376F VAL* 1.3 62.3 + - - +
378F LEU* 3.4 1.0 + - - +
379F LEU* 3.1 28.4 + - - +
694H LEU* 3.4 34.2 - - + +
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Residues in contact with VAL 376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372F LEU* 3.1 17.2 + - + +
373F HIS* 3.6 9.9 - - - +
375F GLN* 1.3 77.4 - - - +
377F HIS* 1.3 56.6 + - - +
380F GLU* 2.9 60.1 + - - +
687H HIS 4.3 12.1 - - - +
690H LEU* 3.5 16.1 - - + +
691H HIS* 4.0 35.2 - - + +
694H LEU* 4.2 11.4 - - + -
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Residues in contact with HIS 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373F HIS 3.1 11.5 + - - +
374F ASP* 3.2 14.8 + - + +
376F VAL* 1.3 79.7 - - - +
378F LEU* 1.3 66.6 + - + +
380F GLU* 3.3 14.4 + - - +
381F CYS* 3.1 25.3 + - + +
457F GLY* 3.1 23.6 + - - -
460F THR* 3.1 47.2 + - - -
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Residues in contact with LEU 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367F PHE* 4.0 17.7 - - + -
370F LEU* 3.7 30.3 - - + -
374F ASP* 2.9 18.1 + - + +
375F GLN 3.4 3.8 + - - +
377F HIS* 1.3 79.4 - - + +
379F LEU* 1.3 57.7 + - - +
381F CYS* 3.2 5.3 + - - +
382F ALA* 2.9 32.4 + - - +
453F LEU* 3.6 25.0 - - + +
454F LEU* 4.0 17.5 - - + +
457F GLY* 3.7 34.2 + - - +
458F VAL* 3.9 4.7 - - - +
475F ILE* 4.3 9.6 - - + -
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Residues in contact with LEU 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354F LEU* 6.1 0.2 - - + -
357F MET* 4.2 27.6 - - + +
358F ILE* 4.3 10.3 - - + -
361F ALA* 4.0 14.8 - - + -
367F PHE* 4.2 11.7 - - + -
375F GLN 3.1 11.2 + - - +
376F VAL 4.0 2.2 - - - +
378F LEU* 1.3 74.7 - - - +
380F GLU* 1.3 62.1 + - - +
382F ALA* 4.4 0.4 - - - +
383F TRP* 2.9 36.5 + - + +
386F ILE* 5.0 1.3 - - + -
453F LEU* 3.7 20.9 - - + -
543F MET* 4.0 4.9 - - + -
690H LEU* 3.7 31.0 - - + -
694H LEU* 3.8 28.0 - - + -
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Residues in contact with GLU 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376F VAL* 2.9 37.9 + - - +
377F HIS* 3.6 14.9 + - - +
378F LEU 3.3 0.2 - - - -
379F LEU* 1.3 77.3 - - - +
381F CYS* 1.3 49.2 + - - +
383F TRP* 3.3 5.6 + - - -
542F GLU 5.1 0.3 - - - +
543F MET* 4.0 16.2 - - - +
546F ALA* 3.6 30.2 - - + +
547F HIS* 2.7 36.6 + - - -
687H HIS* 3.2 31.6 + - - +
690H LEU* 3.6 13.4 - - + +
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Residues in contact with CYS 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516E HIS* 5.2 7.4 - - - -
377F HIS* 3.1 21.6 + - + +
378F LEU 3.6 4.0 - - - +
379F LEU 3.1 0.8 - - - -
380F GLU* 1.3 80.5 - - + +
382F ALA* 1.3 57.2 + - - +
383F TRP 3.7 0.4 - - - -
384F LEU 5.4 0.3 + - - -
385F GLU* 3.7 11.3 - - - +
456F SER* 3.3 31.6 - - - -
457F GLY* 3.8 12.8 - - - +
460F THR* 4.8 6.3 - - - -
515F ARG* 4.2 10.3 + - - -
518F SER* 5.2 2.4 + - - -
522F MET* 5.7 0.2 - - - +
547F HIS* 3.7 23.1 - - - -
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Residues in contact with ALA 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378F LEU 2.9 15.8 + - - +
379F LEU* 4.9 0.2 - - - -
381F CYS* 1.3 79.7 - - - +
383F TRP* 1.3 65.8 + - - +
384F LEU 3.3 2.7 - - - -
385F GLU* 3.1 11.7 + - - +
386F ILE* 3.0 27.6 + - + +
452F ILE* 3.8 28.9 - - + +
453F LEU* 4.2 11.7 - - + +
456F SER* 3.9 8.7 - - - +
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Residues in contact with TRP 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354F LEU* 3.8 23.6 - - + -
357F MET* 3.3 23.3 - - - +
379F LEU* 2.9 18.5 + - + +
380F GLU* 3.3 26.2 + - - -
381F CYS 3.7 0.2 - - - -
382F ALA* 1.3 76.3 - - - +
384F LEU* 1.3 79.0 + - + +
386F ILE 3.4 0.2 + - - -
387F LEU* 3.0 47.8 + - + +
522F MET* 3.8 23.3 - - + +
525F LEU* 3.8 21.8 - - + -
540F LEU* 3.6 30.1 - - + -
543F MET* 3.4 45.2 - - + +
544F LEU* 4.7 2.0 - - - -
547F HIS* 3.9 14.0 + - - -
601F 6WT 4.5 3.1 - - + -
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Residues in contact with LEU 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381F CYS 5.4 0.6 + - - -
382F ALA 3.3 0.2 - - - -
383F TRP* 1.3 93.4 - - + +
385F GLU* 1.3 60.9 + - - +
387F LEU* 3.3 7.4 + - + -
388F MET* 2.9 64.5 + - + +
518F SER* 3.3 36.1 + - - +
521F GLY* 4.0 4.0 - - - -
522F MET* 3.7 34.1 - - + +
525F LEU* 4.6 5.2 - - + -
601F 6WT 4.1 28.5 - - + -
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Residues in contact with GLU 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512E SER* 5.7 0.5 - - - -
381F CYS 3.7 11.0 - - - +
382F ALA* 3.1 10.4 + - - +
384F LEU* 1.3 78.8 - - - +
386F ILE* 1.3 56.4 + - - +
388F MET* 3.4 1.0 + - - -
389F ILE* 3.0 32.0 + - - +
452F ILE* 3.6 19.0 - - + +
456F SER* 2.8 32.4 + - - -
511F LEU* 4.2 4.9 - - - +
514F ILE* 3.8 21.8 - - + +
515F ARG* 3.3 41.1 + - - +
518F SER* 3.5 24.6 + - - +
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Residues in contact with ILE 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357F MET* 3.7 31.2 - - + -
360F TRP* 3.7 24.9 - - + -
379F LEU* 5.0 0.7 - - + -
382F ALA* 3.0 19.7 + - + +
383F TRP 3.8 3.8 - - - +
385F GLU* 1.3 74.7 - - - +
387F LEU* 1.3 65.8 + - + +
389F ILE* 3.3 6.9 - - - +
390F GLY* 3.1 20.8 + - - -
449F LYS* 3.7 29.4 - - + +
452F ILE* 4.0 14.4 - - + -
453F LEU* 4.0 29.4 - - + -
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Residues in contact with LEU 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350F ALA* 3.9 28.7 - - + +
353F GLU* 3.3 43.3 - - + +
354F LEU* 4.7 1.1 - - + +
357F MET* 3.6 18.2 - - + -
383F TRP* 3.0 48.5 + - + +
384F LEU* 3.7 9.9 - - + +
386F ILE* 1.3 77.0 - - - +
388F MET* 1.3 58.1 + - - +
390F GLY* 3.2 2.3 + - - -
391F LEU* 2.9 29.1 + - - +
601F 6WT 4.0 20.8 - - + +
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Residues in contact with MET 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384F LEU* 2.9 46.3 + - + +
385F GLU* 3.8 4.5 - - - +
387F LEU* 1.3 76.8 - - - +
389F ILE* 1.3 58.2 + - - +
391F LEU* 3.2 7.9 + - - +
392F VAL* 2.8 33.9 + - - +
424F ILE* 4.3 9.0 - - + -
428F LEU* 4.0 17.4 - - + +
514F ILE* 4.6 7.6 - - + +
517F MET* 3.4 34.3 - - + +
518F SER* 3.7 23.3 - - - -
521F GLY* 4.4 2.7 - - - -
601F 6WT 3.9 33.0 - - + -
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Residues in contact with ILE 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385F GLU 3.0 17.5 + - - +
386F ILE* 3.3 17.3 - - - +
388F MET* 1.3 76.7 - - - +
390F GLY* 1.3 60.5 + - - +
392F VAL* 3.7 5.5 - - - +
393F TRP* 2.9 28.9 + - - +
435F PHE* 4.1 21.5 - - + -
445F PHE* 4.1 16.2 - - + -
448F LEU* 4.1 22.9 - - + -
449F LYS* 4.3 16.2 - - + +
452F ILE* 3.8 23.8 - - + -
511F LEU* 4.5 1.8 - - + -
514F ILE* 3.8 25.7 - - + +
517F MET* 6.5 0.2 - - - -
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Residues in contact with GLY 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F ILE 3.1 15.3 + - - -
387F LEU 3.6 3.6 - - - -
389F ILE* 1.3 76.8 - - - +
391F LEU* 1.3 63.7 + - - +
393F TRP* 3.4 4.5 + - - +
394F ARG* 3.3 35.0 + - - +
445F PHE* 4.1 17.5 - - - -
449F LYS* 5.4 1.6 - - - -
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Residues in contact with LEU 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387F LEU 2.9 13.6 + - - +
388F MET* 3.2 6.5 + - - +
390F GLY* 1.3 77.0 - - - +
392F VAL* 1.3 59.0 + - - +
393F TRP 3.3 0.2 + - - -
394F ARG* 3.4 15.7 + - - +
395F SER* 2.6 37.0 + - - +
402F LEU* 4.3 11.0 - - + -
403F LEU 3.4 35.0 - - - +
404F PHE* 3.6 40.2 - - + +
428F LEU* 3.9 29.2 - - + -
601F 6WT 4.2 15.5 - - + -
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Residues in contact with VAL 392 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388F MET 2.8 24.6 + - - +
389F ILE* 3.7 7.2 - - - +
391F LEU* 1.3 74.6 - - + +
393F TRP* 1.3 61.8 + - - +
395F SER* 3.3 12.6 + - - -
396F MET* 3.5 3.8 + - - +
402F LEU* 5.2 0.9 - - + -
428F LEU* 3.6 39.7 - - + +
431F THR* 3.7 14.6 - - + -
432F SER* 3.3 34.1 + - - +
435F PHE* 3.4 31.6 - - + -
517F MET* 4.9 2.0 - - + -
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Residues in contact with TRP 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323F GLU* 5.2 1.6 + - - -
326F ILE* 6.4 1.1 - - + -
389F ILE 2.9 19.0 + - - +
390F GLY 3.6 5.6 - - - +
391F LEU 3.2 0.2 - - - -
392F VAL* 1.3 79.9 - - - +
394F ARG* 1.3 68.9 + - + +
395F SER 3.3 0.7 + - - -
396F MET* 3.5 46.2 + - + +
397F GLU* 4.0 3.1 - - - +
435F PHE* 4.8 3.4 - - + -
440F LEU* 3.5 42.0 - - + -
441F GLN 4.2 1.6 - - - -
442F GLY* 3.5 32.8 - - - -
445F PHE* 3.5 43.1 - + + -
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Residues in contact with ARG 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326F ILE* 3.7 41.6 - - + +
327F LEU 6.2 0.4 - - - -
353F GLU* 2.9 30.6 + - - -
390F GLY* 3.3 22.4 + - - +
391F LEU* 3.5 19.2 - - - +
393F TRP* 1.3 86.8 - - + +
395F SER* 1.3 57.7 + - - +
396F MET 3.4 0.9 - - - -
397F GLU* 3.5 14.6 - - - +
398F HIS* 3.9 4.0 + - - -
403F LEU* 2.8 49.0 + - + +
404F PHE* 2.8 27.7 + - - +
405F ALA* 5.1 0.2 - - - +
601F 6WT 3.3 15.0 - - - +
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Residues in contact with SER 395 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391F LEU* 2.6 25.9 + - - +
392F VAL 3.7 5.4 - - - -
393F TRP 3.1 1.2 - - - -
394F ARG* 1.3 78.0 - - - +
396F MET* 1.3 63.2 + - - +
397F GLU 3.3 2.9 - - - -
398F HIS* 3.1 25.3 + - - +
401F LYS 3.7 17.8 - - - +
402F LEU* 3.6 11.1 - - - +
403F LEU* 2.8 28.1 + - - +
432F SER* 3.2 12.1 + - - -
436F ARG* 4.2 0.5 + - - -
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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