Contacts of the helix formed by residues 394 - 417 (chain A) in PDB entry 1ZY7
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 HIS 394 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLY 3.5 5.4 - - - +
375A THR* 3.0 35.4 + - - -
376A LYS* 3.5 6.3 - - - -
377A CYS* 3.7 10.6 - - - -
392A ASP* 3.1 19.1 + - - +
393A CYS* 1.3 77.0 - - - +
395A ALA* 1.3 67.0 + - - +
396A GLU* 3.2 4.3 - - - +
397A ILE* 3.0 14.3 + - + +
398A ILE* 3.1 10.8 + - - +
451A CYS* 3.5 9.0 - - + -
455A ARG* 6.1 1.3 - - - -
483A LYS* 3.3 23.0 - - + +
489A GLY 5.9 1.3 - - - -
516A CYS* 3.5 18.2 - - - -
801A ZN 2.0 33.3 - - - -
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Residues in contact with ALA 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A VAL* 3.7 19.7 - - + +
353A ALA* 3.6 16.6 - - + -
372A SER* 2.5 23.6 + - - +
373A THR* 3.5 35.4 - - - -
374A GLY 2.8 12.8 + - - +
393A CYS 3.3 0.6 + - - -
394A HIS* 1.3 72.0 - - - +
396A GLU* 1.3 59.7 + - - +
398A ILE* 3.2 2.1 + - - -
399A SER* 2.9 16.1 + - - -
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Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A VAL* 4.3 5.4 - - - +
353A ALA* 3.7 8.0 - - - +
374A GLY 4.8 0.3 - - - +
394A HIS* 3.8 4.7 + - - +
395A ALA* 1.3 88.6 + - - +
397A ILE* 1.3 66.7 + - + +
399A SER* 3.4 4.4 + - - -
400A ARG 3.3 16.8 + - - -
444A LEU* 4.7 10.8 - - + +
446A ILE* 3.8 41.0 - - + +
450A PRO* 3.4 27.9 - - - +
451A CYS 4.2 0.2 + - - -
455A ARG* 4.9 4.0 + - - -
516A CYS* 3.5 30.6 - - + +
520A ILE* 4.6 4.9 - - + -
523A TRP* 3.7 11.0 - - + -
801A ZN 3.8 3.6 - - - -
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Residues in contact with ILE 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ASP* 3.5 38.8 - - - +
394A HIS 3.0 7.5 + - - +
396A GLU* 1.3 74.5 - - + +
398A ILE* 1.3 65.0 + - - +
400A ARG* 3.2 6.1 + - - +
401A ARG* 3.2 22.1 + - - +
516A CYS* 3.5 28.5 - - + +
519A LYS* 3.5 26.9 - - + -
520A ILE* 5.6 0.2 - - + -
523A TRP* 3.7 23.3 - - + -
901A IHP 3.6 35.2 + - - +
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Residues in contact with ILE 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A SER* 3.6 13.9 - - - -
390A LEU* 3.9 27.8 - - + -
392A ASP 3.5 17.7 - - - +
393A CYS* 3.7 19.5 - - - +
394A HIS 3.1 11.9 + - - +
395A ALA* 3.6 7.4 - - - +
397A ILE* 1.3 77.1 - - - +
399A SER* 1.3 55.8 + - - +
401A ARG* 3.2 14.2 + - - +
402A SER* 3.0 31.5 + - - -
599A SER* 3.7 12.6 - - - +
600A VAL 4.0 4.0 - - - +
601A ASN* 3.5 32.3 - - + +
627A LEU* 3.7 7.2 - - + -
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Residues in contact with SER 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ALA* 3.5 3.4 + - - -
354A GLY* 3.3 29.4 - - - -
355A VAL* 4.0 10.0 - - - +
370A SER* 3.1 21.1 + - - -
371A VAL 4.0 0.2 - - - -
372A SER* 2.6 26.8 + - - -
395A ALA 2.9 10.6 + - - -
396A GLU* 3.7 6.3 - - - -
397A ILE 3.3 0.2 - - - -
398A ILE* 1.3 75.6 - - - +
400A ARG* 1.3 57.9 + - - +
402A SER* 3.4 3.2 + - - -
403A LEU* 3.0 25.5 + - - +
444A LEU* 4.7 2.7 - - - -
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Residues in contact with ARG 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A VAL* 4.8 2.6 - - - +
396A GLU 3.3 3.0 + - - +
397A ILE 3.2 8.2 + - - +
399A SER* 1.3 77.0 - - - +
401A ARG* 1.3 68.8 + - - +
403A LEU* 3.0 13.3 + - + +
404A LEU* 3.0 46.2 + - + +
444A LEU* 5.7 0.6 - - - +
523A TRP* 3.3 58.6 - - + +
527A GLY 5.5 0.2 + - - -
528A ILE* 2.9 42.0 + - + +
530A GLY* 3.9 15.4 - - - +
542A PHE* 5.1 3.8 - - + -
901A IHP 3.0 50.9 + - - -
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Residues in contact with ARG 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU* 3.7 19.2 - - - +
391A ASN 6.3 0.2 - - - -
392A ASP 5.2 1.1 - - - -
397A ILE* 3.2 15.2 + - - +
398A ILE* 3.2 20.4 + - - +
400A ARG* 1.3 80.7 - - - +
402A SER* 1.3 62.8 + - - +
404A LEU* 3.0 28.1 + - + +
405A ARG* 3.4 5.4 + - - +
627A LEU* 2.9 49.6 + - + +
628A CYS* 3.9 1.2 - - - +
629A LYS* 3.6 15.6 - - - +
632A LEU* 3.5 20.6 - - + +
901A IHP 2.7 81.5 + - - +
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Residues in contact with SER 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A SER* 3.3 23.8 - - - -
371A VAL 4.8 1.3 + - - -
398A ILE 3.0 16.7 + - - -
399A SER* 3.6 1.3 - - - -
401A ARG* 1.3 74.2 - - - +
403A LEU* 1.3 64.2 + - - +
405A ARG* 3.2 11.0 + - - +
601A ASN* 3.8 13.5 - - - +
602A TRP 3.8 4.2 + - - -
603A THR* 3.1 39.7 + - - +
627A LEU* 3.6 21.4 - - - +
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Residues in contact with LEU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A VAL* 4.3 10.3 - - + -
369A ILE* 3.8 22.0 - - + -
370A SER* 4.2 0.8 - - - -
399A SER 3.0 14.0 + - - +
400A ARG* 3.0 13.4 + - + +
402A SER* 1.3 76.1 - - - +
404A LEU* 1.3 63.5 + - + +
406A PHE* 3.0 9.7 + - + +
407A LEU* 2.9 31.1 + - + +
442A PHE* 3.7 32.8 - - + -
528A ILE* 3.2 39.5 - - + +
542A PHE* 4.1 20.0 - - + -
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Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ARG* 3.0 39.5 + - + +
401A ARG* 3.0 14.5 + - + +
403A LEU* 1.3 77.1 - - + +
405A ARG* 1.3 62.1 + - - +
407A LEU* 3.1 11.6 + - + +
408A TYR* 2.9 32.1 + - + -
528A ILE 3.4 25.4 - - - +
529A GLN* 3.5 23.6 - - - +
530A GLY* 5.7 0.9 - - - -
533A LEU* 4.0 10.5 - - + +
632A LEU* 4.0 29.4 - - + -
901A IHP 5.2 4.3 - - - +
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Residues in contact with ARG 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ARG 3.4 3.1 + - - +
402A SER 3.2 8.8 + - - +
404A LEU* 1.3 76.3 - - - +
406A PHE* 1.3 57.0 + - - +
408A TYR* 3.3 9.5 + - - +
409A THR* 2.9 33.6 + - - -
601A ASN* 4.9 0.6 + - - -
603A THR* 3.2 20.6 + - + +
606A ASP* 2.8 43.8 + - - -
626A ARG* 3.5 49.9 + - - +
627A LEU* 3.6 16.6 - - - +
632A LEU* 4.0 18.4 - - + -
635A ARG* 3.8 23.9 + - + +
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Residues in contact with PHE 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A MET* 3.9 14.4 - - + -
367A LYS* 4.4 9.0 - - - -
369A ILE* 3.6 48.5 - - + -
402A SER 3.3 2.4 + - - -
403A LEU* 3.0 17.5 + - + +
405A ARG* 1.3 76.9 - - - +
407A LEU* 1.3 62.2 + - + +
409A THR* 3.2 11.1 + - + -
410A GLN* 2.9 66.7 + - + +
425A ILE* 3.9 11.2 - - + -
442A PHE* 3.9 15.3 - + - -
603A THR* 3.8 12.9 - - + +
604A VAL* 3.5 23.3 - - + -
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Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A LEU* 2.9 28.5 + - + +
404A LEU* 3.1 12.3 + - + +
406A PHE* 1.3 79.8 - - + +
408A TYR* 1.3 62.4 + - - +
410A GLN* 3.2 5.4 + - - +
411A LEU* 2.9 29.1 + - - +
425A ILE* 4.2 8.7 - - + -
426A PHE* 3.7 21.5 - - + -
442A PHE* 4.1 25.6 - - + -
528A ILE* 5.3 1.6 - - + -
529A GLN* 4.1 22.0 - - + -
533A LEU* 4.0 17.7 - - + -
537A VAL* 5.7 0.7 - - + -
540A ILE* 3.9 24.2 - - + -
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Residues in contact with TYR 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LEU* 2.9 29.8 + - + -
405A ARG* 3.6 6.7 - - - +
407A LEU* 1.3 73.7 - - - +
409A THR* 1.3 64.1 + - - +
411A LEU* 3.2 6.8 + - + +
412A GLU* 2.9 26.5 + - - +
532A LEU* 3.9 10.7 - - - +
533A LEU* 3.5 38.1 - - + +
536A PHE* 4.5 2.7 - + - -
632A LEU* 3.9 29.7 + - + +
635A ARG* 3.5 36.1 - - + +
636A TRP* 3.5 46.3 - + + +
639A VAL* 4.0 19.8 - - + +
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Residues in contact with THR 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A ARG 2.9 12.4 + - - -
406A PHE* 3.2 14.1 + - + -
408A TYR* 1.3 76.0 - - - +
410A GLN* 1.3 65.6 + - - +
412A GLU* 3.2 8.1 + - + +
413A LEU* 2.9 37.5 + - + +
635A ARG* 2.9 22.4 + - - +
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Residues in contact with GLN 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LYS* 5.2 4.8 - - - +
406A PHE* 2.9 60.1 + - + +
407A LEU* 3.6 5.6 - - - +
409A THR* 1.3 78.1 - - - +
411A LEU* 1.3 63.9 + - - +
413A LEU* 3.5 22.0 + - - +
414A TYR 3.1 8.8 + - - -
423A ARG 3.6 3.1 + - - +
424A SER* 2.7 32.6 + - - -
425A ILE* 2.8 37.8 + - + +
426A PHE* 3.9 18.2 - - + -
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A LEU 2.9 15.5 + - - +
408A TYR* 3.6 9.6 - - + +
410A GLN* 1.3 72.3 - - - +
412A GLU* 1.3 61.7 + - - +
414A TYR* 3.2 6.2 + - + +
415A LEU* 2.9 36.0 + - + +
426A PHE* 3.7 20.0 - - + -
434A PHE* 3.7 27.4 - - + -
533A LEU* 3.6 31.4 - - + -
536A PHE* 4.0 17.9 - - + -
537A VAL* 3.6 27.8 - - + -
639A VAL* 4.5 13.9 - - + -
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Residues in contact with GLU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A TYR 2.9 14.5 + - - +
409A THR* 3.2 9.3 + - - +
411A LEU* 1.3 75.5 - - - +
413A LEU* 1.3 55.9 + - - +
415A LEU* 3.1 8.3 + - + +
416A ASN* 2.8 47.6 + - - +
635A ARG* 3.2 18.3 + - - +
638A ARG* 2.7 58.8 + - - +
639A VAL* 3.8 19.3 + - + +
642A LYS* 5.8 4.4 - - + +
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Residues in contact with LEU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A THR* 2.9 22.9 + - + +
410A GLN* 3.5 40.6 - - - +
411A LEU 3.3 0.2 - - - -
412A GLU* 1.3 76.9 - - - +
414A TYR* 1.3 63.3 + - - +
415A LEU 3.4 0.2 + - - -
416A ASN* 3.5 9.2 + - - +
417A ASN 3.9 0.5 - - - +
420A ASP* 3.3 46.5 - - + +
421A GLN 3.2 18.9 + - - -
423A ARG* 4.2 22.2 - - + +
424A SER* 4.0 3.4 - - - -
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Residues in contact with TYR 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A GLN 3.1 6.2 + - - +
411A LEU* 3.2 12.1 + - + +
413A LEU* 1.3 79.4 - - - +
415A LEU* 1.3 71.7 + - + +
416A ASN 3.7 0.2 + - - -
417A ASN 4.2 1.9 + - - +
421A GLN* 3.0 67.0 + - + +
424A SER* 3.6 17.2 - - - +
426A PHE* 3.4 30.3 - - + -
427A GLN* 4.0 12.3 - - - -
428A LYS* 3.2 36.8 + - - +
434A PHE* 3.5 30.3 - + - -
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Residues in contact with LEU 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A LEU* 2.9 25.4 + - + +
412A GLU* 3.1 6.9 + - + +
414A TYR* 1.3 87.1 - - + +
416A ASN* 1.3 64.8 + - - +
417A ASN* 3.5 0.7 + - - -
434A PHE* 4.0 26.2 - - + -
639A VAL* 3.9 17.5 - - + -
642A LYS* 3.4 46.2 + - + +
643A VAL* 3.8 25.6 - - + -
644A PRO* 5.0 4.3 - - + -
647A LEU* 6.3 0.4 - - + -
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Residues in contact with ASN 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A GLU* 2.8 39.8 + - - +
413A LEU* 3.9 9.0 - - - +
414A TYR 3.5 1.2 - - - -
415A LEU* 1.3 76.4 - - - +
417A ASN* 1.3 71.2 + - - +
420A ASP* 2.9 27.4 + - - +
642A LYS* 4.3 13.5 + - - +
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Residues in contact with ASN 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A LEU 3.9 0.2 - - - +
414A TYR 4.2 1.7 - - - +
415A LEU 3.5 2.3 - - - -
416A ASN* 1.3 92.6 - - - +
418A LYS* 1.3 59.6 + - + +
419A ASP* 2.8 17.7 + - - +
420A ASP* 2.8 39.2 + - - -
421A GLN* 2.9 31.5 + - - +
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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