Contacts of the helix formed by residues 498 - 527 (chain A) in PDB entry 4IM0
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 ILE 498 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ILE* 3.5 36.3 - - + +
478A THR* 5.5 2.7 - - - +
479A VAL* 4.5 18.2 - - + -
497A GLU* 1.3 78.9 - - + +
499A SER* 1.3 54.7 + - - +
501A ILE* 2.7 35.9 + - + +
502A HIS* 2.8 23.3 + - + +
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Residues in contact with SER 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A GLU 4.1 4.9 - - - +
498A ILE* 1.3 80.8 - - - +
500A ASP* 1.3 55.8 + - - +
502A HIS* 4.1 5.8 - - - +
503A THR* 2.7 45.9 + - - +
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Residues in contact with ASP 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A GLU* 2.9 42.0 + - - +
499A SER* 1.3 80.8 - - - +
501A ILE* 1.3 60.3 + - + +
503A THR* 3.2 15.0 + - - -
504A LYS* 3.2 23.4 - - + +
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Residues in contact with ILE 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ILE* 3.6 28.0 - - + -
497A GLU* 3.8 17.3 - - + +
498A ILE* 2.7 28.4 + - + +
500A ASP* 1.3 78.5 - - + +
502A HIS* 1.3 62.2 + - - +
504A LYS* 3.6 4.5 + - - +
505A LEU* 3.1 27.5 + - + +
647A TYR* 4.6 26.3 - - + -
650A TYR* 5.9 3.1 - - + +
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Residues in contact with HIS 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ILE* 3.3 38.3 + - + +
475A ILE* 3.9 34.3 - - + +
476A GLU* 4.7 16.4 + - + +
498A ILE* 2.8 18.8 + - + +
499A SER* 4.1 6.7 - - - +
501A ILE* 1.3 75.8 - - - +
503A THR* 1.3 57.1 + - + +
505A LEU* 4.3 4.5 - - + -
506A LEU* 2.7 40.2 + - - +
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Residues in contact with THR 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A SER* 2.7 30.3 + - - +
500A ASP* 3.2 15.9 + - - -
502A HIS* 1.3 79.1 - - + +
504A LYS* 1.3 57.9 + - - +
506A LEU* 3.9 4.1 + - - +
507A ARG* 3.0 33.3 + - - +
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Residues in contact with LYS 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A ASP 3.2 20.1 + - - +
501A ILE* 4.1 4.0 - - - +
502A HIS 3.3 0.2 - - - -
503A THR* 1.3 79.2 + - - +
505A LEU* 1.3 61.5 + - - +
507A ARG* 3.4 19.6 - - - +
508A LEU* 3.4 15.9 - - - +
647A TYR* 4.7 17.5 - - + +
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Residues in contact with LEU 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A LEU* 3.4 33.0 - - + -
471A CYS* 4.9 5.6 - - + +
472A ILE* 3.4 47.6 - - + +
475A ILE* 5.1 4.7 - - + -
501A ILE* 3.1 25.8 + - + +
502A HIS* 3.2 5.8 + - + +
504A LYS* 1.3 74.7 - - - +
506A LEU* 1.3 54.9 + - - +
507A ARG 3.0 4.7 - - - -
508A LEU* 2.7 38.6 + - + +
509A SER* 3.2 5.5 + - - +
644A VAL* 6.0 1.1 - - + -
647A TYR* 4.3 24.9 - - + -
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Residues in contact with LEU 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ILE* 4.6 14.5 - - + +
502A HIS* 2.7 23.6 + - + +
503A THR* 4.4 4.5 - - - +
505A LEU* 1.3 72.6 - - - +
507A ARG* 1.3 59.1 + - - +
509A SER* 4.0 6.2 - - - +
510A SER* 3.1 26.2 + - - -
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Residues in contact with ARG 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A THR* 3.0 24.6 + - - +
504A LYS* 3.4 12.8 + - - +
505A LEU 3.0 0.6 - - - -
506A LEU* 1.3 78.9 - - - +
508A LEU* 1.3 56.4 + - + +
510A SER* 2.5 27.9 + - - -
511A SER* 2.7 22.2 + - - -
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Residues in contact with LEU 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A LEU* 4.1 16.2 - - + -
504A LYS 3.4 18.2 - - - +
505A LEU* 2.7 25.4 + - + +
507A ARG* 1.3 73.9 - - + +
509A SER* 1.3 52.5 + - - +
511A SER* 3.0 10.0 + - - +
512A GLN* 2.7 37.1 + - - +
640A ILE* 4.3 19.5 - - + +
643A GLU* 4.0 29.2 - - + +
644A VAL* 4.1 24.2 - - + -
647A TYR* 5.1 9.6 - - + -
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Residues in contact with SER 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A LEU* 4.0 18.2 - - - +
469A ASP* 4.4 14.2 + - - -
472A ILE* 4.6 14.5 - - - +
505A LEU 3.2 5.8 + - - -
506A LEU* 4.0 10.5 - - - -
508A LEU* 1.3 78.2 - - - +
510A SER* 1.3 57.6 + - - +
512A GLN* 3.0 12.8 + - - +
513A GLY* 2.9 23.7 + - - -
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Residues in contact with SER 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A LEU 3.1 15.0 + - - -
507A ARG* 2.5 36.8 + - - +
509A SER* 1.3 75.5 - - - +
511A SER* 1.3 61.1 + - - +
513A GLY* 3.2 10.9 + - - +
514A THR* 3.2 18.6 + - - +
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Residues in contact with SER 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A ARG 2.7 21.4 + - - -
508A LEU* 3.0 15.9 + - - +
510A SER* 1.3 74.4 + - - +
512A GLN* 1.3 57.7 + - - +
514A THR* 2.5 27.5 + - - -
515A ILE* 3.0 17.1 - - - +
640A ILE* 4.1 14.4 - - - -
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Residues in contact with GLN 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A LYS* 4.0 15.5 + - + +
464A VAL* 3.4 28.3 - - - +
465A VAL* 3.1 38.2 - - - +
468A LEU* 3.6 23.7 - - + +
469A ASP* 5.6 0.8 + - - -
508A LEU 2.7 16.1 + - - +
509A SER* 3.0 13.2 + - - +
511A SER* 1.3 71.5 - - - +
513A GLY* 1.3 61.5 + - - +
514A THR 3.2 0.4 - - - -
515A ILE* 3.5 9.0 + - + +
516A GLU* 3.1 25.1 + - - +
640A ILE* 3.9 18.2 - - + +
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Residues in contact with GLY 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A SER 2.9 12.4 + - - -
510A SER* 3.2 6.1 + - - -
512A GLN* 1.3 76.1 - - - +
514A THR* 1.3 63.3 + - - +
516A GLU* 3.4 6.5 + - - +
517A THR* 3.2 25.3 + - - +
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Residues in contact with THR 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A SER 3.2 16.6 - - - +
511A SER* 2.5 26.2 + - - -
513A GLY* 1.3 76.2 - - - +
515A ILE* 1.3 65.3 + - - +
517A THR* 3.2 20.1 - - - +
518A SER* 3.4 15.2 + - - -
633A LEU* 4.9 0.6 - - - +
636A GLN* 4.9 2.4 + - - -
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Residues in contact with ILE 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A LYS* 3.3 28.3 - - + -
511A SER* 3.0 27.2 + - - +
512A GLN* 3.5 8.3 + - + +
513A GLY 3.2 0.4 - - - -
514A THR* 1.3 82.9 + - - +
516A GLU* 1.3 59.8 + - - +
518A SER* 3.0 3.5 + - - -
519A LEU* 2.8 41.9 + - + +
633A LEU* 3.6 31.4 - - + +
636A GLN* 3.2 31.4 - - + +
637A CYS* 4.4 9.9 - - - -
640A ILE* 4.2 13.5 - - + -
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Residues in contact with GLU 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A LYS* 2.4 40.1 + - - +
512A GLN 3.1 17.0 + - - +
513A GLY* 3.4 8.9 + - - +
515A ILE* 1.3 78.4 - - - +
517A THR* 1.3 57.6 + - - +
519A LEU* 3.3 7.9 + - - +
520A GLN* 3.0 33.1 + - + +
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Residues in contact with THR 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLY 3.2 13.9 + - - +
514A THR* 3.2 23.3 - - - +
516A GLU* 1.3 79.5 - - - +
518A SER* 1.3 62.2 + - - +
520A GLN* 3.7 8.0 + - - +
521A ASP* 3.3 20.3 + - - +
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Residues in contact with SER 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A THR 3.4 16.1 + - - -
515A ILE 3.0 5.6 + - - -
517A THR* 1.3 80.6 - - - +
519A LEU* 1.3 62.3 + - - +
521A ASP* 3.2 8.4 + - - +
522A ILE* 3.1 26.0 + - - +
633A LEU* 3.6 25.0 - - - +
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Residues in contact with LEU 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A TYR* 3.3 34.9 - - + +
457A THR* 4.1 18.8 - - - +
458A VAL* 3.7 20.4 - - + -
461A LYS* 3.7 21.8 - - + -
515A ILE* 2.8 38.0 + - + +
516A GLU* 3.6 8.5 - - - +
518A SER* 1.3 73.4 - - - +
520A GLN* 1.3 60.0 + - - +
521A ASP 3.0 2.0 - - - -
522A ILE* 3.0 3.2 + - + +
523A ASP* 2.8 27.9 + - - +
630A LEU* 4.2 8.7 - - + -
633A LEU* 3.7 21.1 - - + -
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Residues in contact with GLN 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A TYR* 4.7 2.2 + - - -
516A GLU* 3.0 20.9 + - + +
517A THR* 3.8 9.9 - - - +
519A LEU* 1.3 77.1 - - - +
521A ASP* 1.3 57.2 + - - +
523A ASP* 4.0 6.8 - - - +
524A SER* 3.2 25.8 + - - -
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Residues in contact with ASP 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A THR 3.3 12.2 + - - +
518A SER* 3.2 13.3 + - - +
519A LEU 3.0 0.4 - - - -
520A GLN* 1.3 78.9 - - - +
522A ILE* 1.3 61.1 + - - +
524A SER* 3.5 7.8 + - - -
525A ARG* 3.2 55.9 + - - +
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Residues in contact with ILE 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A TYR* 4.1 11.9 - - + -
518A SER 3.1 8.0 + - - +
519A LEU* 3.0 7.9 + - + +
521A ASP* 1.3 75.4 - - - +
523A ASP* 1.3 67.0 + - - +
525A ARG* 3.0 27.9 + - - +
526A LEU* 3.0 32.8 + - + +
626A LEU* 3.9 28.3 - - + +
629A GLN* 4.3 5.2 - - + -
630A LEU* 3.8 37.0 - - + +
633A LEU* 3.7 27.6 - - + -
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Residues in contact with ASP 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A TYR* 3.1 44.5 - - + +
519A LEU 2.8 10.2 + - - +
520A GLN* 4.0 6.5 - - - +
522A ILE* 1.3 75.1 - - - +
524A SER* 1.3 58.8 + - - +
526A LEU* 3.0 19.0 + - - +
527A SER* 2.8 31.9 + - - -
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Residues in contact with SER 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A GLN 3.2 17.9 + - - -
521A ASP* 3.5 12.4 + - - -
522A ILE 3.2 0.2 - - - -
523A ASP* 1.3 81.2 + - - +
525A ARG* 1.3 60.2 + - - +
527A SER* 3.5 15.4 + - - -
530A GLY* 3.2 17.9 + - - -
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Residues in contact with ARG 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A ASP* 3.2 38.5 + - - +
522A ILE* 3.0 25.5 + - - +
524A SER* 1.3 80.6 - - - +
526A LEU* 1.3 59.6 + - - +
527A SER 3.2 1.9 - - - +
530A GLY* 3.2 20.0 - - - -
531A SER* 3.1 26.2 - - - +
532A LEU* 3.2 20.1 + - - +
622A LYS* 5.2 2.0 + - - +
625A HIS* 4.0 17.0 + - - -
626A LEU* 3.7 32.1 - - + +
629A GLN* 2.3 34.5 + - - +
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Residues in contact with LEU 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ILE* 5.1 6.5 - - + +
450A ILE* 4.2 16.4 - - + -
451A LYS* 3.2 52.2 + - + -
454A TYR* 4.1 22.7 - - + -
522A ILE* 3.0 31.9 + - + +
523A ASP* 3.0 11.2 + - - +
525A ARG* 1.3 74.8 - - - +
527A SER* 1.3 63.9 + - - +
532A LEU* 3.9 29.5 - - + +
626A LEU* 3.9 20.9 - - + -
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Residues in contact with SER 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A LYS* 5.5 0.7 - - - +
523A ASP* 2.8 27.4 + - - -
524A SER* 3.5 14.9 - - - -
525A ARG 3.2 2.3 - - - +
526A LEU* 1.3 83.2 - - - +
528A PRO* 1.4 69.4 - - - +
529A GLY 3.2 3.4 - - - -
530A GLY* 2.7 23.1 + - - +
533A ALA* 4.8 5.2 - - - +
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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