Contacts of the helix formed by residues 412 - 442 (chain A) in PDB entry 3ODX
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 412 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A PRO* 1.3 68.2 + - - -
413A SER* 1.3 65.8 + - - +
414A GLN 3.0 3.9 + - - -
415A VAL* 3.2 40.7 - - + +
416A LYS* 3.5 25.4 + - - +
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Residues in contact with SER 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A PRO 3.4 2.7 - - - -
412A LYS* 1.3 78.4 - - - +
414A GLN* 1.3 61.9 + - - +
416A LYS 3.7 0.5 + - - -
417A ARG* 3.1 28.2 + - - +
578A ASN* 3.7 36.5 + - - +
580A GLU* 5.8 7.2 - - - -
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Residues in contact with GLN 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A PRO* 3.2 29.5 - - + -
412A LYS 3.0 1.0 - - - -
413A SER* 1.3 82.3 - - - +
415A VAL* 1.3 58.3 + - + +
417A ARG* 3.4 11.4 + - - +
418A GLN* 2.8 58.8 + - + +
489A ILE 5.4 1.2 + - - -
490A GLU* 5.6 2.8 + - - -
578A ASN 4.5 2.3 - - - +
580A GLU* 3.0 36.1 + - + +
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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 PRO* 4.8 9.9 - - + -
412A LYS* 3.2 47.0 + - + +
414A GLN* 1.3 76.4 - - + +
416A LYS* 1.3 65.5 + - + +
418A GLN* 3.8 4.9 - - - +
419A GLU* 2.8 51.1 + - - +
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Residues in contact with LYS 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LYS* 3.5 24.2 + - - +
413A SER 3.9 4.9 - - - +
414A GLN 3.3 0.2 - - - -
415A VAL* 1.3 79.8 - - + +
417A ARG* 1.3 56.8 + - - +
419A GLU* 3.0 29.1 + - - +
420A VAL* 2.7 57.7 + - + +
423A GLU* 5.9 0.6 + - - -
574A SER* 5.3 3.6 + - - -
578A ASN* 3.5 26.5 - - - +
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Residues in contact with ARG 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A SER 3.1 18.9 + - - +
414A GLN* 3.6 17.3 - - - +
416A LYS* 1.3 73.8 - - - +
418A GLN* 1.3 65.4 + - - +
420A VAL* 4.0 4.7 - - - +
421A ILE* 2.9 54.0 + - + +
489A ILE 3.9 12.7 + - - -
490A GLU* 3.7 13.3 + - - -
491A GLU* 3.3 29.9 - - - +
492A ILE* 4.4 3.8 - - - +
574A SER 5.2 1.1 - - - -
575A ILE* 4.3 15.0 - - + +
578A ASN* 3.8 25.8 - - + +
579A THR* 3.0 29.3 + - - +
580A GLU* 3.2 17.4 + - - -
584A GLU* 3.8 14.5 + - - +
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Residues in contact with GLN 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A GLN* 2.8 43.1 + - + +
415A VAL* 3.8 5.4 - - - +
417A ARG* 1.3 83.4 + - - +
419A GLU* 1.3 53.9 + - - +
421A ILE* 3.3 7.8 + - - +
422A SER* 2.7 37.3 + - - -
482A ARG* 5.7 0.5 + - - -
489A ILE* 3.4 54.4 + - - +
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Residues in contact with GLU 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A VAL* 2.8 38.0 + - - +
416A LYS* 3.4 29.3 - - - +
418A GLN* 1.3 72.4 - - - +
420A VAL* 1.3 52.3 + - - +
422A SER* 2.8 11.2 + - - -
423A GLU* 2.7 34.6 + - - +
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Residues in contact with VAL 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LYS* 2.7 51.8 + - + +
417A ARG* 4.0 1.6 - - - +
419A GLU* 1.3 71.8 - - - +
421A ILE* 1.3 65.2 + - - +
423A GLU* 2.9 10.7 + - - +
424A LEU* 2.8 21.7 + - - +
571A LEU* 3.4 28.9 - - + +
574A SER* 3.6 24.0 - - - +
575A ILE* 3.3 28.7 - - + -
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Residues in contact with ILE 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ARG* 2.9 51.6 + - + +
418A GLN* 3.7 13.7 - - - +
420A VAL* 1.3 76.3 - - - +
422A SER* 1.3 65.0 + - - +
424A LEU* 3.3 4.6 + - - +
425A LEU* 3.1 20.9 + - + +
478A LEU* 6.0 1.7 - - + +
489A ILE* 4.2 29.6 - - + +
492A ILE* 3.5 37.9 - - + -
575A ILE* 3.6 24.2 - - + -
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Residues in contact with SER 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLN 2.7 17.1 + - - -
419A GLU* 2.8 13.6 + - - -
421A ILE* 1.3 72.2 - - - +
423A GLU* 1.3 67.5 + - - -
425A LEU* 3.0 11.6 + - - +
426A VAL* 2.9 29.7 + - - +
482A ARG* 5.8 4.3 + - - -
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Residues in contact with GLU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LYS* 5.9 0.7 + - - -
419A GLU 2.7 14.2 + - - +
420A VAL* 2.9 14.8 + - - +
422A SER* 1.3 71.4 - - - +
424A LEU* 1.3 57.7 + - - +
426A VAL* 3.3 3.5 + - - -
427A THR* 2.9 51.8 + - + +
571A LEU* 3.7 22.1 - - + +
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Residues in contact with LEU 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A VAL 2.8 12.6 + - - +
421A ILE* 3.5 9.6 - - - +
423A GLU* 1.3 76.3 - - - +
425A LEU* 1.3 58.2 - - - +
427A THR* 3.2 4.9 + - - -
428A GLU* 2.9 31.9 + - - +
474A PHE* 4.2 15.5 - - + -
478A LEU* 4.0 26.0 - - + -
492A ILE* 4.8 3.8 - - + -
496A LEU* 4.7 7.6 - - + -
564A ARG* 3.8 15.9 - - - +
568A TYR* 4.0 17.3 - - + -
571A LEU* 3.9 25.9 - - + +
572A LEU* 4.4 17.5 - - + -
575A ILE* 4.5 13.2 - - + -
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Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ILE* 3.1 12.6 + - + +
422A SER* 3.0 12.1 + - - +
424A LEU* 1.3 75.3 - - - +
426A VAL* 1.3 71.9 + - + +
428A GLU* 3.0 4.9 + - - +
429A ALA* 2.9 22.1 + - + +
475A LEU* 4.1 7.8 - - + +
478A LEU* 3.4 44.4 - - + +
479A MET* 3.7 26.9 - - + -
482A ARG* 4.9 22.9 - - + -
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Residues in contact with VAL 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A SER* 2.9 21.7 + - - +
423A GLU* 3.8 4.5 - - + +
425A LEU* 1.3 82.8 - - + +
427A THR* 1.3 70.8 + - + +
429A ALA* 3.1 10.2 + - - +
430A ALA* 3.0 22.5 + - + +
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Residues in contact with THR 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLU* 2.9 43.6 + - + +
424A LEU* 3.2 5.0 + - - -
426A VAL* 1.3 75.7 - - + +
428A GLU* 1.3 69.0 + - - +
430A ALA* 3.3 7.7 + - - +
431A HIS* 3.1 23.4 + - - +
564A ARG* 2.6 34.6 + - - +
571A LEU* 4.2 2.5 - - + +
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Residues in contact with GLU 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LEU 2.9 17.0 + - - +
425A LEU* 3.0 6.5 + - - +
427A THR* 1.3 83.2 + - - +
429A ALA* 1.3 61.2 + - - +
431A HIS* 3.3 3.9 + - - +
432A VAL* 3.0 21.3 + - - +
471A HIS* 2.8 43.5 + - - +
474A PHE* 3.5 21.4 - - + -
475A LEU* 4.2 18.6 - - + +
478A LEU* 4.4 5.2 - - + -
564A ARG* 2.5 27.1 + - - +
568A TYR* 2.4 25.2 + - - -
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Residues in contact with ALA 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LEU* 2.9 10.3 + - + +
426A VAL* 3.1 11.2 + - - +
428A GLU* 1.3 73.1 - - - +
430A ALA* 1.3 54.0 + - - +
432A VAL* 3.2 3.6 + - - +
433A ARG* 2.7 35.1 + - - +
475A LEU* 3.6 30.0 - - + +
479A MET* 6.2 0.2 - - - -
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Residues in contact with ALA 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A VAL* 3.0 15.2 + - + +
427A THR* 3.3 11.2 + - - +
429A ALA* 1.3 75.7 - - - +
431A HIS* 1.3 56.4 + - - +
433A ARG* 3.3 31.3 + - - +
434A MET* 2.9 29.9 + - - +
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Residues in contact with HIS 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A THR 3.1 12.5 + - - +
428A GLU* 3.5 11.0 - - - +
429A ALA 3.1 0.2 - - - -
430A ALA* 1.3 73.8 - - - +
432A VAL* 1.3 67.0 + - - +
434A MET* 3.1 8.0 + - - +
435A LEU* 2.9 37.9 + - + +
471A HIS* 3.3 37.5 + + + -
560A THR* 4.1 12.0 + - - -
561A GLU* 2.7 42.3 + - - -
564A ARG* 3.6 34.5 - - + +
----------------------------------------------------------
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Residues in contact with VAL 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLU 3.0 15.6 + - - +
429A ALA 3.6 7.0 - - - +
431A HIS* 1.3 77.6 - - - +
433A ARG* 1.3 66.3 + - - +
435A LEU* 3.4 7.0 + - - +
436A ARG* 2.9 44.1 + - + +
468A ILE* 4.7 3.6 - - + +
471A HIS* 3.6 41.3 - - + +
472A SER* 3.6 18.4 - - - +
475A LEU* 4.3 19.7 - - + -
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Residues in contact with ARG 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ALA 2.7 18.3 + - - +
430A ALA* 3.4 33.1 + - - +
431A HIS 3.2 0.2 - - - -
432A VAL* 1.3 74.7 - - - +
434A MET* 1.3 64.0 + - - +
436A ARG* 3.0 11.0 + - + +
437A VAL* 2.9 32.9 + - + +
548A ARG* 5.1 0.6 + - - +
550A ARG* 3.4 55.2 - - - +
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Residues in contact with MET 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ALA 2.9 15.6 + - - +
431A HIS* 3.5 10.5 - - - +
433A ARG* 1.3 80.0 - - - +
435A LEU* 1.3 59.1 + - + +
437A VAL* 2.8 14.2 + - + +
438A LEU* 2.7 34.1 + - + +
548A ARG 4.7 4.7 - - - +
549A CYS 4.6 7.6 - - - +
550A ARG* 4.2 26.2 - - + -
552A LEU* 4.5 17.5 - - + -
557A MET* 4.0 40.2 - - + +
560A THR* 4.6 17.5 - - + +
----------------------------------------------------------
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Residues in contact with LEU 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A HIS* 2.9 44.0 + - + +
432A VAL* 3.6 6.1 - - - +
434A MET* 1.3 74.4 - - - +
436A ARG* 1.3 57.3 + - - +
438A LEU* 3.3 14.9 + - + +
439A HIS* 2.8 27.5 + - - +
464A LEU* 4.2 13.1 - - + +
467A LEU* 3.8 32.1 - - + +
468A ILE* 3.8 21.4 - - + +
471A HIS* 3.8 16.6 - - + -
515A PHE* 5.2 4.0 - - + -
560A THR* 5.1 7.4 - - - +
561A GLU* 3.8 13.2 - - + +
----------------------------------------------------------
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Residues in contact with ARG 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A VAL* 2.9 33.2 + - - +
433A ARG* 3.4 11.2 - - - +
434A MET 3.0 0.2 + - - -
435A LEU* 1.3 73.3 - - - +
437A VAL* 1.3 59.4 + - - +
439A HIS* 3.1 6.7 + - + +
440A ASP* 2.7 44.1 + - - +
468A ILE* 4.1 24.5 - - + -
472A SER* 5.6 0.4 - - - -
548A ARG* 3.9 9.4 - - - +
----------------------------------------------------------
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Residues in contact with VAL 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ARG* 2.9 20.6 + - + +
434A MET* 2.8 18.5 + - + +
436A ARG* 1.3 69.1 - - - +
438A LEU* 1.3 67.8 + - - +
440A ASP* 4.3 0.7 - - - +
441A LEU* 2.9 41.6 + - + +
442A PHE* 4.6 1.3 - - + -
548A ARG* 3.3 60.6 - - + +
549A CYS* 4.6 0.2 - - - -
557A MET* 4.1 24.7 - - + -
----------------------------------------------------------
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Residues in contact with LEU 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A MET 2.7 14.9 + - - +
435A LEU* 3.3 18.4 - - + +
437A VAL* 1.3 74.9 - - - +
439A HIS* 1.3 62.7 + - - +
442A PHE* 3.2 14.0 - - + +
443A PHE* 3.2 18.7 + - - +
461A PHE* 4.1 19.7 - - + -
464A LEU* 4.1 26.5 - - + -
515A PHE* 4.3 12.6 - - + -
554A LEU* 3.5 31.9 - - + -
557A MET* 3.6 29.4 - - + +
558A ILE* 4.5 7.9 - - + -
----------------------------------------------------------
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Residues in contact with HIS 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A LEU 2.8 13.8 + - - +
436A ARG* 3.3 9.0 - - + +
437A VAL 3.1 0.2 - - - -
438A LEU* 1.3 78.8 - - - +
440A ASP* 1.3 78.2 + - - +
443A PHE* 3.4 19.3 + + - -
444A GLN* 2.9 61.7 + - + +
464A LEU* 3.6 12.7 - - + +
465A ASP* 3.0 30.5 + - - -
468A ILE* 3.7 20.9 - - + -
----------------------------------------------------------
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Residues in contact with ASP 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ARG* 2.7 31.7 + - - +
439A HIS* 1.3 98.6 + - - +
441A LEU* 1.3 63.6 + - + +
442A PHE 3.5 0.2 - - - -
444A GLN* 4.5 6.0 - - - +
445A PRO* 3.1 19.6 - - - +
548A ARG* 2.8 39.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A VAL* 2.9 16.4 + - + +
440A ASP* 1.3 85.5 - - + +
442A PHE* 1.3 74.8 + - + +
445A PRO* 3.5 14.5 - - - +
539A PHE* 4.3 3.8 - - - -
543A ALA* 3.8 18.2 - - + +
546A ARG* 3.6 41.7 - - + -
548A ARG* 3.7 43.7 - - + +
549A CYS* 4.1 18.4 - - - -
----------------------------------------------------------
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Residues in contact with PHE 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A VAL* 4.0 5.2 - - + -
438A LEU* 3.2 19.1 + - + +
440A ASP 3.5 0.2 - - - -
441A LEU* 1.3 99.3 - - + +
443A PHE* 1.3 65.3 + - - +
444A GLN 3.5 0.7 - - - -
445A PRO* 3.4 1.9 - - - +
446A MET* 2.8 49.6 + - + +
461A PHE* 4.9 2.5 - - + -
539A PHE* 5.0 2.5 - + - -
540A VAL* 4.5 6.5 - - + -
543A ALA* 3.8 23.6 - - + -
544A GLU* 3.9 24.7 - - + -
549A CYS* 4.1 12.6 - - - -
554A LEU* 3.7 47.1 - - + -
557A MET* 4.1 17.5 - - + -
----------------------------------------------------------
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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