Contacts of the helix formed by residues 519 - 550 (chain A) in PDB entry 5N7K
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 ASP 519 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A LYS 3.6 7.9 - - - +
516A LYS* 3.5 18.8 + - - +
517A LYS 3.3 6.3 + - - -
518A ASN* 1.3 74.4 - - - +
520A PRO* 1.4 66.0 - - - +
521A THR* 2.6 31.7 + - - +
522A PHE* 2.8 16.8 + - + +
523A LEU* 2.8 35.6 + - - +
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Residues in contact with PRO 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A ASN* 3.8 8.3 - - - +
519A ASP* 1.4 90.9 - - - +
521A THR* 1.3 55.4 + - - +
523A LEU* 3.4 12.0 + - + +
524A GLU* 3.0 34.7 + - - +
519B ASP* 5.9 0.9 - - - +
520B PRO* 4.6 22.7 - - + -
521B THR* 3.9 16.9 + - - +
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Residues in contact with THR 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ASP* 2.6 26.4 + - - +
520A PRO* 1.3 74.9 - - - +
522A PHE* 1.4 61.0 + - - +
524A GLU* 3.2 8.8 + - - +
525A LYS* 3.1 28.8 + - - +
520B PRO* 3.9 25.8 - - + +
521B THR* 5.6 0.2 - - - -
524B GLU* 3.4 31.8 - - + +
441D ASP* 5.0 0.2 - - - -
443D VAL* 4.4 8.3 - - + +
444D ALA* 4.0 21.8 - - - +
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Residues in contact with PHE 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A GLU 5.4 0.2 - - - -
476A VAL* 3.6 36.6 - - + -
479A VAL* 3.7 36.8 - - + -
480A LEU* 4.1 22.9 - - + -
516A LYS 4.3 7.6 - - - +
517A LYS* 3.8 23.8 - - + -
519A ASP* 2.8 23.9 + - + +
521A THR* 1.4 82.4 + - - +
523A LEU* 1.3 62.1 - - + +
525A LYS* 3.1 17.8 + - + +
526A LYS* 2.9 34.6 + - + +
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Residues in contact with LEU 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A LYS 3.7 21.1 - - - +
518A ASN* 3.5 24.7 - - - +
519A ASP 2.8 25.8 + - - +
520A PRO* 3.8 9.2 - - + +
522A PHE* 1.3 79.9 - - + +
524A GLU* 1.4 58.8 + - - +
526A LYS* 3.5 17.1 + - + +
527A GLU* 2.9 28.5 + - - +
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Residues in contact with GLU 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A PRO 3.0 18.6 + - - +
521A THR* 3.4 11.7 - - - +
522A PHE 3.2 0.2 - - - -
523A LEU* 1.4 74.4 - - - +
525A LYS* 1.4 58.9 + - - +
527A GLU* 3.0 27.5 + - - +
528A ARG* 2.9 29.5 + - - +
521B THR* 3.5 42.7 + - + +
524B GLU* 4.9 13.7 - - + +
525B LYS* 4.6 10.9 - - - +
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Residues in contact with LYS 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A LEU* 3.7 23.9 - - + +
475A GLU* 2.8 40.9 + - + +
476A VAL* 4.4 15.7 - - + -
521A THR* 3.1 19.0 + - - +
522A PHE* 3.4 17.7 - - + +
524A GLU* 1.4 73.1 - - + +
526A LYS* 1.4 62.6 + - - +
528A ARG* 3.3 3.5 + - - -
529A CYS* 3.1 24.9 + - - -
438B SER* 4.9 8.3 - - - +
524B GLU* 4.7 4.7 - - - +
441D ASP* 3.3 36.7 + - - +
444D ALA* 4.3 10.1 - - - +
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Residues in contact with LYS 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A VAL* 4.6 20.1 - - + +
522A PHE* 2.9 23.0 + - + +
523A LEU* 3.6 21.8 - - + +
524A GLU 3.3 0.2 - - - -
525A LYS* 1.4 75.1 - - - +
527A GLU* 1.3 62.2 + - - +
529A CYS* 3.1 9.1 + - + +
530A ASP* 3.0 50.6 + - - +
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Residues in contact with GLU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A LEU 2.9 17.0 + - - +
524A GLU* 3.0 31.0 + - - +
526A LYS* 1.3 75.5 - - - +
528A ARG* 1.4 57.4 + - - +
530A ASP* 3.5 9.1 + - + +
531A TYR* 3.0 27.4 + - + +
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Residues in contact with ARG 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A GLN* 3.8 3.0 - - - +
468A GLU* 3.2 18.2 + - - +
472A LEU* 3.8 17.6 - - + +
524A GLU 2.9 12.8 + - - +
525A LYS* 3.3 8.9 + - - +
527A GLU* 1.4 71.7 - - - +
529A CYS* 1.3 55.5 + - - +
531A TYR* 3.1 20.3 + - + +
532A LEU* 2.8 64.5 + - + +
468B GLU* 3.3 24.5 + - - -
528B ARG* 3.2 42.3 - - - +
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Residues in contact with CYS 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A TYR* 3.4 25.9 - - + +
472A LEU* 3.7 25.8 - - - -
473A SER* 3.8 27.4 - - - +
476A VAL* 4.0 10.8 - - + -
525A LYS 3.1 17.8 + - - -
526A LYS* 3.1 10.0 + - + +
528A ARG* 1.3 74.6 - - - +
530A ASP* 1.3 61.7 + - - +
532A LEU* 3.3 1.3 + - - -
533A LYS* 2.8 28.6 + - - +
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Residues in contact with ASP 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A LYS* 3.0 46.6 + - - +
527A GLU* 3.9 8.3 - - + +
529A CYS* 1.3 78.1 - - - +
531A TYR* 1.3 60.7 + - - +
533A LYS* 3.8 10.1 + - - +
534A ASN* 3.0 33.4 + - - +
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Residues in contact with TYR 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A PRO* 5.0 4.9 - - + -
441A ASP* 2.7 37.9 + - - -
442A TYR* 3.3 33.2 - + - -
465A GLN* 5.5 0.9 - - - -
527A GLU* 3.0 15.0 + - + +
528A ARG* 3.4 29.6 - - + +
530A ASP* 1.3 74.4 - - - +
532A LEU* 1.3 62.8 + - + +
534A ASN* 3.1 9.3 + - + +
535A LYS* 2.8 56.6 + - + +
468B GLU* 5.7 3.8 - - - -
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Residues in contact with LEU 532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A GLN* 3.6 42.6 - - + +
468A GLU* 4.4 7.2 - - + +
469A TYR* 3.9 38.4 - - + +
472A LEU* 4.8 6.5 - - + -
528A ARG* 2.8 57.2 + - + +
529A CYS 3.8 3.4 - - - +
531A TYR* 1.3 78.9 - - + +
533A LYS* 1.4 56.2 + - - +
535A LYS* 3.7 6.9 - - + +
536A LEU* 2.9 40.0 + - + +
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Residues in contact with LYS 533 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A TYR* 4.1 28.8 + - + +
529A CYS 2.8 20.2 + - - +
530A ASP* 3.9 10.8 - - - +
532A LEU* 1.4 71.0 - - - +
534A ASN* 1.3 59.9 + - - +
536A LEU* 4.0 6.0 - - - +
537A SER* 2.7 41.5 + - - +
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Residues in contact with ASN 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A TYR* 3.2 21.0 + - - +
530A ASP* 3.0 20.3 + - - +
531A TYR* 3.1 10.8 + - + +
533A LYS* 1.3 79.6 - - - +
535A LYS* 1.4 64.6 + - - +
537A SER* 3.3 7.7 + - - -
538A HIS* 3.2 22.2 + - - +
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Residues in contact with LYS 535 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ASP* 5.0 4.4 + - - -
442A TYR* 3.5 33.5 - - + +
446A TYR* 4.4 6.3 - - - -
465A GLN* 3.5 29.0 - - + +
531A TYR* 2.8 45.3 + - + +
532A LEU* 3.7 8.7 - - + +
534A ASN* 1.4 70.0 - - - +
536A LEU* 1.3 64.2 + - + +
538A HIS* 3.2 6.4 + - - +
539A ILE* 3.1 40.7 + - + +
464B ASP* 3.0 36.1 + - - -
468B GLU* 4.8 7.1 + - - +
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Residues in contact with LEU 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A PHE* 3.3 54.4 - - + +
465A GLN* 3.7 15.7 - - + +
466A PHE* 3.6 22.4 - - + +
469A TYR* 3.8 36.8 - - + -
532A LEU* 2.9 27.7 + - + +
533A LYS* 4.1 4.3 - - - +
535A LYS* 1.3 69.6 - - + +
537A SER* 1.4 60.1 + - - +
539A ILE* 3.5 5.2 + - + +
540A LYS* 2.9 31.5 + - - +
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Residues in contact with SER 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A LYS* 2.7 29.9 + - - +
534A ASN* 3.3 8.3 + - - -
536A LEU* 1.4 73.9 - - - +
538A HIS* 1.4 53.6 + - - +
540A LYS* 3.4 7.9 + - - +
541A GLN* 2.8 38.1 + - - +
----------------------------------------------------------
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Residues in contact with HIS 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A TYR* 4.1 25.3 - + + -
443A VAL* 4.2 22.1 - - + +
446A TYR* 2.8 42.7 + + + +
534A ASN 3.2 8.3 + - - +
535A LYS 3.2 9.1 + - - +
537A SER* 1.4 78.0 - - - +
539A ILE* 1.4 59.9 + - + +
541A GLN* 3.2 17.7 + - - +
542A ARG* 2.9 65.0 + - + +
----------------------------------------------------------
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Residues in contact with ILE 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A TYR* 4.0 35.9 - - + -
458A TYR* 3.4 40.8 - - + +
461A VAL* 3.9 27.6 - - + -
462A PHE* 4.0 13.7 - - + +
465A GLN* 6.0 0.4 - - + -
535A LYS* 3.1 29.1 + - + +
536A LEU* 4.0 5.8 - - + +
538A HIS* 1.4 76.5 - - + +
540A LYS* 1.4 60.9 + - - +
542A ARG* 3.1 9.1 + - - +
543A ILE* 3.0 28.0 + - + +
----------------------------------------------------------
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Residues in contact with LYS 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A PHE* 3.8 26.3 - - + -
536A LEU 2.9 22.3 + - - +
537A SER* 3.6 7.2 - - - +
539A ILE* 1.4 71.6 - - - +
541A GLN* 1.4 56.3 + - - +
543A ILE* 3.4 9.3 + - - +
544A GLN* 3.0 63.3 + - + +
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Residues in contact with GLN 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A SER* 2.8 21.7 + - - +
538A HIS* 3.2 15.9 + - - +
540A LYS* 1.4 70.1 - - - +
542A ARG* 1.4 62.4 + - - +
544A GLN* 3.5 10.4 + - - +
545A GLU* 2.9 34.1 + - + +
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Residues in contact with ARG 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A VAL* 4.6 8.3 + - - +
446A TYR 2.9 25.2 + - - +
447A PRO* 3.4 20.9 - - - +
448A VAL* 3.5 30.1 - - - +
449A ILE* 3.5 7.6 + - + +
458A TYR* 3.9 20.0 - - + -
538A HIS* 2.9 43.4 + - + +
539A ILE 3.1 8.5 + - - +
541A GLN* 1.4 79.5 - - + +
543A ILE* 1.4 59.7 + - - +
545A GLU* 3.6 21.0 + - - +
546A TYR* 3.2 24.3 + - - +
----------------------------------------------------------
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Residues in contact with ILE 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A ILE* 3.6 19.3 - - + -
455A ARG* 3.4 43.3 - - + +
458A TYR* 3.9 6.3 - - + -
459A LYS* 3.8 33.4 - - + +
462A PHE* 4.8 5.6 - - + -
539A ILE* 3.0 32.1 + - + +
540A LYS* 3.8 8.7 - - - +
542A ARG* 1.4 70.6 - - - +
544A GLN* 1.3 56.8 - - + +
546A TYR* 3.4 3.5 + - - +
547A ASP* 2.7 41.5 + - - +
----------------------------------------------------------
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Residues in contact with GLN 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A LYS* 3.0 50.2 + - + +
541A GLN* 3.8 10.2 - - - +
543A ILE* 1.3 73.9 - - + +
545A GLU* 1.4 55.2 + - - +
547A ASP* 3.2 9.9 + - - +
548A LYS* 2.9 34.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A VAL* 3.9 29.6 - - - +
449A ILE 5.2 0.2 + - - -
541A GLN* 2.9 18.8 + - + +
542A ARG* 3.7 34.1 + - - +
544A GLN* 1.4 74.3 - - - +
546A TYR* 1.3 64.5 + - - +
548A LYS* 3.3 8.1 + - - +
549A VAL* 3.3 28.7 + - + +
----------------------------------------------------------
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Residues in contact with TYR 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A VAL* 6.4 0.4 - - + -
449A ILE* 3.4 39.9 - - + +
450A GLN 3.8 17.6 + - - -
451A THR* 3.2 8.0 - - - -
452A ASP* 2.9 41.5 + - - -
455A ARG* 3.9 29.8 - - + -
542A ARG 3.2 14.5 + - - +
543A ILE 3.6 2.7 - - - +
545A GLU* 1.3 79.8 - - - +
547A ASP* 1.3 64.1 + - - +
549A VAL* 3.1 9.0 + - + +
550A MET* 2.9 69.9 + - + +
----------------------------------------------------------
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Residues in contact with ASP 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ARG* 2.9 44.3 + - - -
543A ILE* 2.7 28.2 + - - +
544A GLN* 3.2 11.8 + - + +
546A TYR* 1.3 78.1 - - - +
548A LYS* 1.3 61.1 + - - +
550A MET* 3.7 2.8 - - - +
551A ASN 2.9 35.0 + - - +
----------------------------------------------------------
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Residues in contact with LYS 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A GLN 2.9 12.7 + - - +
545A GLU* 3.6 10.8 - - - +
547A ASP* 1.3 77.6 - - - +
549A VAL* 1.3 65.1 + - + +
551A ASN* 3.4 13.4 + - - +
----------------------------------------------------------
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Residues in contact with VAL 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A GLU* 3.5 18.8 - - + +
546A TYR* 3.1 11.7 + - + +
548A LYS* 1.3 80.4 - - + +
550A MET* 1.3 69.3 + - + +
551A ASN* 3.3 9.4 - - - +
----------------------------------------------------------
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Residues in contact with MET 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A GLN 5.8 1.3 - - - +
452A ASP* 4.5 9.2 - - - +
546A TYR* 2.9 63.2 + - + +
547A ASP* 3.4 3.1 + - - +
549A VAL* 1.3 87.0 - - + +
551A ASN* 1.3 72.6 + - - +
----------------------------------------------------------
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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