Contacts of the helix formed by residues 370 - 397 (chain A) in PDB entry 1YOK
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 LYS 370 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A GLU 4.1 1.2 + - - -
369A LEU* 1.3 75.6 - - - +
371A VAL* 1.3 58.7 + - - +
372A ASP* 4.1 23.1 + - + +
373A ASP* 2.8 32.9 + - - +
374A GLN* 3.0 7.6 + - - +
465A GLU* 2.8 43.5 + - - +
466A ASN* 6.0 1.5 - - + +
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Residues in contact with VAL 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU 3.5 1.6 + - - +
370A LYS* 1.3 73.4 - - - +
372A ASP* 1.3 58.9 + - - +
374A GLN* 3.5 18.5 - - - +
375A MET* 2.9 38.5 + - + +
746B ARG* 3.8 26.0 - - + +
749B LEU* 4.5 16.2 - - + +
750B ASP* 3.2 31.2 - - - +
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Residues in contact with ASP 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A LYS* 3.0 25.5 + - + +
371A VAL* 1.3 75.6 + - - +
373A ASP* 1.3 67.6 + - - +
375A MET* 3.5 6.9 + - - +
376A LYS* 3.2 44.1 + - - +
465A GLU* 5.4 2.5 - - + +
746B ARG* 3.7 25.3 + - - -
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Residues in contact with ASP 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU* 3.3 30.9 - - + +
370A LYS* 2.8 18.2 + - - +
372A ASP* 1.3 78.5 - - - +
374A GLN* 1.3 66.3 + - - +
376A LYS* 2.9 16.2 + - - +
377A LEU* 3.0 19.0 + - + +
463A ASN 4.5 1.9 - - - +
464A LEU* 3.8 17.3 - - + -
465A GLU* 2.9 35.3 + - - +
466A ASN* 3.1 23.4 + - - +
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Residues in contact with GLN 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ARG* 4.8 5.9 + - - +
366A PHE* 2.9 64.8 + - + -
367A ARG* 4.0 10.5 + - - +
369A LEU* 3.4 25.1 + - + +
370A LYS 3.0 17.1 + - - +
371A VAL* 3.5 19.1 - - - +
373A ASP* 1.3 77.3 - - - +
375A MET* 1.3 61.0 + - - +
377A LEU 3.6 0.2 + - - -
378A LEU* 3.2 22.7 + - - +
749B LEU* 3.7 31.0 - - + +
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Residues in contact with MET 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A VAL* 2.9 22.5 + - - +
372A ASP* 3.8 6.1 - - - +
373A ASP 3.1 0.2 - - - -
374A GLN* 1.3 73.7 - - - +
376A LYS* 1.3 62.0 + - + +
379A GLN* 2.8 45.7 + - - +
742B ASN* 3.7 36.3 - - + +
745B LEU* 4.0 15.9 - - + +
746B ARG* 3.7 52.3 - - - +
749B LEU* 3.9 16.4 - - + -
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Residues in contact with LYS 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ASP* 3.2 31.5 + - - +
373A ASP* 2.9 10.3 + - - +
375A MET* 1.3 78.7 - - + +
377A LEU* 1.3 62.0 + - - +
379A GLN* 4.0 9.1 - - - +
380A ASN* 3.3 22.2 + - - +
461A VAL* 4.4 5.3 - - + +
462A LYS 3.5 15.3 - - - +
463A ASN* 3.2 47.2 + - + +
464A LEU* 3.8 13.9 - - + -
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Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A PHE* 3.8 23.6 - - + -
369A LEU* 3.9 16.8 - - + -
373A ASP* 3.0 17.2 + - + +
374A GLN 3.9 3.8 - - - +
376A LYS* 1.3 76.5 - - - +
378A LEU* 1.3 62.1 + - - +
380A ASN* 3.1 15.4 + - - +
381A CYS* 3.1 19.5 + - - +
456A LEU* 3.8 23.1 - - + +
457A PHE* 4.0 18.4 - - + -
458A SER 4.5 6.3 - - - +
461A VAL* 3.3 33.4 - - + -
464A LEU* 3.8 14.4 - - + -
470A VAL* 4.6 5.2 - - + -
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Residues in contact with LEU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 5.0 6.7 - - + -
357A VAL* 4.5 13.0 - - + -
360A ALA* 4.1 15.7 - - + -
366A PHE* 3.9 21.5 - - + -
374A GLN 3.2 18.9 + - - +
375A MET 4.1 1.6 - - - +
377A LEU* 1.3 74.2 - - - +
379A GLN* 1.3 65.6 + - - +
380A ASN 3.0 2.2 - - - -
381A CYS* 4.2 2.0 - - - -
382A TRP* 2.9 33.7 + - + +
385A LEU* 4.2 16.4 - - + -
456A LEU* 3.8 20.2 - - + -
535A MET* 4.7 2.5 - - + -
745B LEU* 4.4 18.4 - - + -
749B LEU* 4.1 22.0 - - + -
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Residues in contact with GLN 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A MET* 2.8 40.7 + - - +
376A LYS* 4.0 8.7 - - - +
378A LEU* 1.3 73.3 - - - +
380A ASN* 1.3 57.5 + - - +
382A TRP* 3.4 18.1 + - + +
535A MET* 4.2 13.2 - - + +
538A ALA* 3.7 24.3 - - + +
742B ASN* 2.8 43.5 + - - +
745B LEU* 4.2 5.5 - - + +
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Residues in contact with ASN 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LYS 3.3 17.1 + - - +
377A LEU 3.1 5.5 + - - +
378A LEU 3.0 0.4 - - - -
379A GLN* 1.3 80.0 - - - +
381A CYS* 1.3 58.9 + - - +
382A TRP* 3.8 1.3 - - - -
384A GLU* 4.2 2.3 - - - +
456A LEU 5.4 0.3 - - - +
458A SER* 3.7 16.0 + - - -
460A ASP* 5.2 5.9 + - - +
461A VAL* 3.2 30.2 - - + +
507A ARG* 3.1 46.3 + - - +
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Residues in contact with CYS 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU 3.1 19.6 + - - +
378A LEU* 4.2 3.4 - - - -
380A ASN* 1.3 80.9 - - - +
382A TRP* 1.3 54.1 + - - +
383A SER* 3.4 2.5 - - - -
384A GLU* 3.1 27.5 + - + +
385A LEU* 2.7 47.6 + - - +
455A VAL* 3.6 13.2 - - + +
456A LEU* 3.7 36.3 - - - -
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Residues in contact with TRP 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A P6L 4.3 6.3 - - + -
353A LEU* 3.7 26.7 - - + -
356A ILE* 5.9 2.2 - - + -
378A LEU* 2.9 20.9 + - + +
379A GLN* 3.4 26.6 + - + +
380A ASN 5.0 0.9 - - - -
381A CYS* 1.3 75.9 - - - +
383A SER* 1.3 84.8 + - - +
385A LEU* 3.1 11.0 + - - +
386A LEU* 3.0 35.3 + - + +
514A GLU* 3.8 25.8 + - + -
517A LEU* 5.0 0.9 - - + -
532A LEU* 3.6 43.7 - - + -
535A MET* 3.7 37.2 + - + +
536A LEU* 3.8 29.1 - - + +
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Residues in contact with SER 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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100A P6L 4.3 8.3 - - - +
381A CYS 3.4 0.4 - - - -
382A TRP* 1.3 100.1 - - - +
384A GLU* 1.3 61.9 + - - +
386A LEU* 3.4 5.8 + - - +
387A ILE* 3.1 30.7 + - - +
507A ARG* 5.1 4.3 + - - -
510A SER* 3.1 21.0 + - - -
514A GLU* 2.7 39.2 + - - -
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Residues in contact with GLU 384 (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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380A ASN* 4.2 1.6 - - - +
381A CYS* 3.1 34.1 + - - +
383A SER* 1.3 78.9 + - - +
385A LEU* 1.3 64.5 + - - +
387A ILE* 4.3 0.7 - - - -
388A LEU* 3.0 26.0 + - - +
455A VAL* 3.4 27.0 - - + +
458A SER* 5.7 1.0 - - - -
503A LEU 5.0 1.6 - - - +
506A ILE* 3.8 17.6 - - + +
507A ARG* 3.1 58.6 + - - +
510A SER* 3.7 17.3 - - - +
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Residues in contact with LEU 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 3.7 35.2 - - + +
359A TRP* 4.0 20.4 - - + -
378A LEU* 4.2 10.8 - - + -
381A CYS* 2.7 40.9 + - - +
382A TRP* 3.5 6.1 - - - +
384A GLU* 1.3 74.5 - - - +
386A LEU* 1.3 58.1 + - - +
388A LEU* 3.3 4.6 + - + +
389A ASP* 2.9 31.2 + - - +
452A LYS* 4.2 38.4 - - + +
455A VAL* 4.1 15.3 - - + -
456A LEU* 4.7 2.5 - - + -
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Residues in contact with LEU 386 (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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100A P6L 4.1 30.0 - - + +
349A ALA 4.5 6.3 - - - +
352A THR* 3.7 25.3 - - + +
353A LEU* 4.2 20.2 - - + -
356A ILE* 3.1 28.0 - - + -
382A TRP* 3.0 45.0 + - + +
383A SER* 3.7 7.2 - - - +
384A GLU 3.3 0.2 - - - -
385A LEU* 1.3 77.0 - - - +
387A ILE* 1.3 57.0 + - - +
389A ASP* 3.3 4.1 - - - +
390A HIS* 3.0 28.4 + - - +
393A ARG* 5.1 0.5 + - - -
532A LEU* 4.5 9.9 - - + -
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Residues in contact with ILE 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A P6L 3.7 46.2 - - + -
383A SER 3.1 20.1 + - - +
384A GLU* 3.8 6.1 - - - +
385A LEU 3.3 0.2 - - - -
386A LEU* 1.3 73.7 - - - +
388A LEU* 1.3 56.4 + - - +
390A HIS* 3.2 5.0 + - + +
391A ILE* 2.8 55.8 + - + +
434A LEU* 4.9 1.6 - - + -
506A ILE* 4.2 19.7 - - + +
509A ILE* 4.0 26.5 - - + -
510A SER* 4.0 20.0 - - - +
513A ALA* 4.5 3.4 - - + -
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Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLU 3.0 17.4 + - - +
385A LEU* 3.8 6.3 - - + +
387A ILE* 1.3 77.5 - - - +
389A ASP* 1.3 57.6 + - - +
391A ILE* 3.3 9.6 + - + -
392A TYR* 2.9 28.9 + - - +
438A LEU* 5.5 2.0 - - + -
443A PHE* 4.7 15.0 - - + -
448A PHE* 3.7 18.4 - - + -
451A LEU* 4.1 13.7 - - + +
452A LYS* 3.6 40.8 - - + +
455A VAL* 4.3 12.3 - - + -
506A ILE* 3.6 27.8 - - + -
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Residues in contact with ASP 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A THR* 4.6 7.2 - - + +
356A ILE* 3.9 22.1 - - + +
385A LEU 2.9 17.4 + - - +
386A LEU* 3.3 9.0 - - - +
388A LEU* 1.3 79.9 - - - +
390A HIS* 1.3 62.7 + - - +
392A TYR* 3.8 2.6 - - - +
393A ARG* 2.9 57.6 + - - +
448A PHE* 4.6 12.6 - - - -
452A LYS* 4.6 14.6 + - - +
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Residues in contact with HIS 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A P6L 3.5 71.1 - - + +
386A LEU 3.0 10.9 + - - +
387A ILE* 3.7 4.5 - - + +
389A ASP* 1.3 75.4 - - - +
391A ILE* 1.3 78.8 + - + +
393A ARG* 3.3 17.5 + - - +
394A GLN* 3.2 59.0 + - + +
403A ILE* 3.7 20.1 - - + +
404A PHE 4.6 3.4 + - - -
405A LEU* 6.0 0.8 - - - -
431A ALA* 5.2 2.1 - - + +
435A VAL* 5.4 1.2 - - + +
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Residues in contact with ILE 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ILE* 2.8 43.4 + - + +
388A LEU* 3.6 10.3 - - + +
390A HIS* 1.3 85.6 - - + +
392A TYR* 1.3 64.8 + - - +
394A GLN* 3.2 12.3 + - - +
395A VAL* 3.2 13.6 + - + +
431A ALA* 4.0 15.5 - - + +
434A LEU* 4.0 21.8 - - + -
435A VAL* 3.6 34.5 - - + -
438A LEU* 3.5 31.9 - - + -
506A ILE* 5.5 0.2 - - + -
509A ILE* 5.4 0.2 - - + -
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Residues in contact with TYR 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A GLU* 5.3 9.4 - - - -
388A LEU* 2.9 8.5 + - - +
389A ASP 3.8 4.0 - - - +
391A ILE* 1.3 78.2 - - - +
393A ARG* 1.3 58.8 + - - +
395A VAL* 3.4 6.4 + - + +
396A VAL* 3.0 58.2 + - + +
443A PHE* 3.8 22.9 - + + -
444A ASP* 4.1 11.2 - - - -
445A GLN* 3.0 39.3 + - + +
448A PHE* 3.3 65.7 - + + -
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Residues in contact with ARG 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A P6L 5.9 1.4 - - - +
315A GLU* 5.1 14.5 + - - +
319A GLN* 5.9 0.7 - - - -
352A THR* 4.5 8.1 + - - +
386A LEU 5.1 0.6 + - - -
389A ASP* 2.9 39.4 + - - +
390A HIS* 3.3 31.1 + - - +
392A TYR* 1.3 78.1 - - - +
394A GLN* 1.3 60.3 + - - +
396A VAL* 4.9 0.4 - - - -
397A HIS* 2.9 36.4 + - + +
398A GLY 3.3 3.8 + - - -
404A PHE* 3.4 43.9 + - + +
405A LEU 3.9 8.5 - - - -
406A VAL* 3.6 42.6 + - - +
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Residues in contact with GLN 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A HIS* 3.2 51.6 + - - +
391A ILE 3.2 4.1 + - - +
393A ARG* 1.3 78.8 - - - +
395A VAL* 1.3 60.1 + - - +
398A GLY* 2.8 28.2 + - - +
402A SER 4.2 3.8 - - - +
403A ILE* 3.6 9.7 - - - +
404A PHE* 2.9 45.0 + - - +
435A VAL* 3.6 29.6 - - + -
439A ARG* 3.0 14.9 + - - +
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Residues in contact with VAL 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ILE* 3.2 19.2 + - + +
392A TYR* 3.7 10.1 - - + +
394A GLN* 1.3 79.9 - - - +
396A VAL* 1.3 66.7 + - + +
398A GLY 4.7 1.4 + - - +
435A VAL* 3.8 25.1 - - + +
438A LEU* 4.1 15.9 - - + +
439A ARG* 3.4 34.7 + - + +
443A PHE* 4.2 26.7 - - + +
----------------------------------------------------------
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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
----------------------------------------------------------
315A GLU* 5.1 2.7 - - - +
392A TYR* 3.0 56.5 + - + +
393A ARG* 4.9 0.2 - - - -
395A VAL* 1.3 83.3 - - + +
397A HIS* 1.3 91.4 + - + +
443A PHE 5.6 1.1 - - - +
444A ASP* 6.4 0.2 - - - -
----------------------------------------------------------
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Residues in contact with HIS 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A GLU* 3.1 35.5 + - - -
319A GLN* 5.3 2.1 + - - -
393A ARG* 2.9 25.8 + - + +
396A VAL* 1.3 98.1 + - + +
398A GLY* 1.3 70.9 + - - +
399A LYS* 4.7 0.9 - - - +
404A PHE* 3.5 44.5 - + + -
410A GLN* 3.2 13.4 - - - +
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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