Contacts of the helix formed by residues 528 - 555 (chain A) in PDB entry 4L6V
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 GLY 528 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A ASP* 3.9 11.4 - - - -
479A GLN* 3.6 11.9 - - - -
480A PRO* 3.6 13.1 - - - +
526A THR 4.1 0.8 + - - -
527A LEU* 1.3 73.2 - - - +
529A THR* 1.3 60.7 + - - -
530A ALA* 3.1 3.6 - - - -
531A ASP* 3.1 13.6 + - - +
532A PHE 2.9 22.2 + - - -
636A ALA* 6.3 0.4 - - - -
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Residues in contact with THR 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A PHE 4.7 1.3 - - - +
472A SER* 3.4 15.2 + - - -
473A ASP* 3.2 41.1 + - - +
477A GLN* 3.9 5.0 - - + -
478A LEU* 3.2 55.9 + - - +
479A GLN* 4.1 1.8 - - - +
528A GLY* 1.3 70.4 - - - -
530A ALA* 1.3 69.8 + - + +
532A PHE* 3.5 0.7 - - - +
533A MET* 3.1 28.7 + - - +
636A ALA 5.4 0.4 - - - +
640A ILE* 5.0 2.5 - - + -
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Residues in contact with ALA 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A TYR* 4.3 1.6 + - - -
473A ASP* 5.0 0.2 - - - +
528A GLY* 3.1 1.1 - - - -
529A THR* 1.3 84.3 - - - +
531A ASP* 1.3 61.5 + - - +
533A MET* 3.9 3.2 + - - +
534A VAL* 3.5 24.3 + - - +
635A PHE* 4.1 18.7 - - + +
636A ALA* 3.6 39.0 - - + +
639A ALA* 4.4 4.1 - - + +
640A ILE* 3.8 20.6 - - + -
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Residues in contact with ASP 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A PRO* 5.5 0.4 - - + -
527A LEU* 3.6 30.6 - - + +
528A GLY* 3.1 18.1 + - - +
530A ALA* 1.3 79.8 - - - +
532A PHE* 1.3 63.8 + - - +
533A MET 3.2 1.8 - - - -
534A VAL* 3.0 15.9 - - + +
535A HIS* 2.9 24.8 + - - +
608A HIS* 4.1 10.9 + - - -
612A LYS* 2.9 45.5 + - - +
635A PHE* 3.8 11.0 - - - -
636A ALA* 5.8 0.9 - - - +
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Residues in contact with PHE 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A HIS 5.8 0.4 - - - -
454A LEU* 5.0 8.7 - - + -
478A LEU* 3.3 59.9 - - + +
479A GLN 4.6 5.8 - - - -
480A PRO* 3.9 29.3 - - + +
528A GLY 2.9 9.7 + - - +
529A THR 3.5 4.9 - - - +
531A ASP* 1.3 76.5 - - - +
533A MET* 1.3 67.8 + - + +
535A HIS* 3.4 5.7 + - - +
536A HIS* 3.2 63.9 + + + -
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Residues in contact with MET 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A SER* 4.7 1.9 - - - +
454A LEU* 3.5 46.9 - - + +
455A TYR* 3.5 47.3 - - + +
458A ASN* 4.8 2.0 - - - +
471A PHE* 4.4 14.1 - - + -
478A LEU* 4.3 9.0 - - + -
529A THR* 3.1 23.4 + - - +
530A ALA 4.1 2.5 - - - +
532A PHE* 1.3 77.2 - - + +
534A VAL* 1.3 60.5 + - - +
535A HIS 3.1 1.1 - - - -
536A HIS* 2.9 9.6 + - - +
537A ILE* 2.9 28.4 + - - +
640A ILE* 4.2 26.2 - - - +
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Residues in contact with VAL 534 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A TYR* 3.0 22.7 - - + +
530A ALA 3.5 13.6 + - - +
531A ASP* 3.0 21.8 - - - +
533A MET* 1.3 75.9 - - - +
535A HIS* 1.3 55.5 + - - +
537A ILE* 3.5 10.4 - - + +
538A HIS* 3.0 35.4 + - + +
604A ILE* 5.7 4.9 - - + -
608A HIS* 3.1 35.9 - - + +
635A PHE* 4.9 5.8 - - + -
639A ALA 4.7 1.3 - - - +
645A TRP* 3.9 27.1 - - + -
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Residues in contact with HIS 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A LEU* 4.2 24.8 - - + +
531A ASP 2.9 27.6 + - - +
532A PHE* 3.5 9.2 - - - +
533A MET 3.1 0.6 - - - -
534A VAL* 1.3 78.1 - - - +
536A HIS* 1.3 64.3 + - + +
538A HIS* 3.2 14.8 + - + +
539A ALA* 3.0 25.3 + - - +
608A HIS* 4.2 19.1 - + - -
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Residues in contact with HIS 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A PHE* 6.4 1.8 - + - -
447A LEU* 4.4 18.7 - - + +
450A HIS* 4.8 10.8 - - + +
451A SER* 3.4 16.8 - - - -
454A LEU* 6.2 0.4 - - + -
532A PHE* 3.2 48.8 + + + +
533A MET* 2.9 10.3 + - - +
535A HIS* 1.3 79.9 - - + +
537A ILE* 1.3 60.0 + - - +
539A ALA* 3.9 9.4 - - + +
540A PHE* 3.2 24.8 + - - +
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Residues in contact with ILE 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A SER* 3.3 27.4 - - - +
452A PHE* 3.6 21.5 - - + +
455A TYR* 3.7 21.3 - - + +
533A MET 2.9 16.5 + - - +
534A VAL* 3.5 14.4 - - + +
535A HIS 3.2 0.2 - - - -
536A HIS* 1.3 78.5 - - - +
538A HIS* 1.3 58.1 + - - +
540A PHE* 3.3 6.3 + - + +
541A THR* 2.8 41.9 + - + +
604A ILE* 3.8 29.8 - - + -
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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
----------------------------------------------------------
534A VAL* 3.0 17.2 + - + +
535A HIS* 3.2 15.8 + - + +
537A ILE* 1.3 74.7 - - - +
539A ALA* 1.3 64.8 + - - +
541A THR* 3.0 6.2 + - - -
542A ILE* 2.9 39.3 + - + +
601A SER 4.6 1.6 - - - -
604A ILE* 3.3 26.2 + - + +
605A VAL* 3.2 45.8 - - + +
608A HIS* 3.4 36.9 + + + +
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Residues in contact with ALA 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LEU* 3.8 16.6 - - + -
535A HIS 3.0 15.9 + - - +
536A HIS* 4.1 10.3 - - + +
538A HIS* 1.3 75.5 - - - +
540A PHE* 1.3 62.7 + - - +
542A ILE* 3.9 6.2 - - - +
543A HIS* 2.8 38.6 + - + +
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Residues in contact with PHE 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A CYS* 3.1 23.1 - - - -
447A LEU* 3.7 17.6 - - + +
448A GLY* 3.3 28.5 - - - -
451A SER* 3.9 16.4 - - - +
452A PHE* 5.4 5.8 - - + -
536A HIS 3.2 21.3 + - - +
537A ILE* 3.4 12.3 - - + +
539A ALA* 1.3 76.3 - - - +
541A THR* 1.3 72.1 + - + +
543A HIS* 3.2 3.6 + - - +
544A VAL* 3.2 34.4 + - + +
597A TRP* 4.0 26.0 - + - -
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Residues in contact with THR 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A ILE* 2.8 32.3 + - + +
538A HIS* 3.0 18.2 + - - -
540A PHE* 1.3 82.4 - - + +
542A ILE* 1.3 53.3 + - - +
544A VAL 3.7 0.3 + - - -
545A THR* 2.7 32.6 + - - -
597A TRP* 3.8 18.9 - - + -
600A ASN* 3.9 21.8 - - - +
601A SER* 3.0 33.2 + - - -
604A ILE* 4.9 4.7 - - + -
605A VAL* 5.6 0.2 - - - +
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Residues in contact with ILE 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A HIS* 2.9 31.4 + - + +
539A ALA* 3.9 7.2 - - - +
541A THR* 1.3 74.8 - - - +
543A HIS* 1.3 68.1 + - + +
545A THR* 3.2 8.9 + - - -
546A ALA* 3.0 28.7 + - + +
601A SER* 4.0 11.7 - - - +
602A LEU* 6.2 1.6 - - + -
605A VAL* 6.2 3.4 - - + -
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Residues in contact with HIS 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A LEU* 3.8 20.5 - - + +
443A VAL* 3.7 21.9 - - + +
444A CYS* 3.3 20.1 - - - -
447A LEU* 3.7 17.5 - - + +
539A ALA* 2.8 35.1 + - + +
540A PHE 3.2 3.1 + - - +
542A ILE* 1.3 85.1 - - + +
544A VAL* 1.3 56.7 + - - +
546A ALA* 3.3 7.4 + - + +
547A LEU* 2.9 24.4 + - - +
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Residues in contact with VAL 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A CYS* 3.5 20.2 - - + -
540A PHE* 3.2 39.7 + - + +
542A ILE 3.3 0.2 - - - -
543A HIS* 1.3 75.5 - - - +
545A THR* 1.3 63.2 + - - +
547A LEU* 3.1 7.1 + - + +
548A ILE* 3.0 33.1 + - + +
597A TRP* 3.4 47.6 - - + +
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Residues in contact with THR 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A VAL* 5.0 0.4 - - + -
541A THR 2.7 20.0 + - - -
542A ILE* 3.2 9.5 + - - -
544A VAL* 1.3 78.4 - - - +
546A ALA* 1.3 61.8 + - - +
548A ILE* 3.6 3.5 + - - +
549A LEU* 3.2 42.5 + - + +
594A GLY 3.7 23.1 - - - +
597A TRP* 3.2 25.2 + - + +
598A MET* 3.8 17.7 - - + +
601A SER* 4.1 3.6 - - - -
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Residues in contact with ALA 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A LEU* 4.1 9.2 - - + -
542A ILE* 3.0 15.0 + - + +
543A HIS* 3.5 12.6 - - + +
544A VAL 3.2 0.2 - - - -
545A THR* 1.3 75.2 - - - +
547A LEU* 1.3 56.1 + - - +
549A LEU* 3.2 5.2 + - - +
550A LEU* 2.5 42.7 + - + +
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Residues in contact with LEU 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ILE* 4.0 25.1 - - + +
440A LEU* 3.4 38.3 - - + +
441A ASN* 3.8 31.9 - - + +
444A CYS* 4.0 11.4 - - + -
543A HIS 2.9 14.1 + - - +
544A VAL* 3.1 13.7 + - + +
546A ALA* 1.3 76.3 - - - +
548A ILE* 1.3 60.3 + - + +
550A LEU* 4.6 0.2 - - - -
551A LYS* 3.0 39.9 + - + +
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Residues in contact with ILE 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A VAL* 3.0 24.2 + - + +
545A THR* 4.0 4.0 - - - +
547A LEU* 1.3 80.5 - - + +
549A LEU* 1.3 61.3 + - - +
551A LYS* 4.8 2.2 - - - -
552A GLY 3.3 2.8 + - - -
590A HIS* 3.3 52.2 - - + +
593A LEU* 3.9 20.4 - - + +
594A GLY* 3.5 14.8 - - - +
597A TRP* 3.3 42.8 - - + +
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Residues in contact with LEU 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ILE 3.8 22.2 - - - +
402A VAL* 4.0 29.2 - - + +
405A GLY* 4.5 16.3 - - - +
545A THR* 3.2 30.5 + - + +
546A ALA* 3.2 5.4 + - - +
548A ILE* 1.3 77.6 - - - +
550A LEU* 1.3 65.1 + - - +
552A GLY* 3.1 11.0 + - - -
553A VAL* 3.2 19.1 + - - +
590A HIS* 3.6 21.1 - - - +
591A VAL* 4.2 10.8 - - + -
594A GLY* 4.0 13.5 - - - -
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Residues in contact with LEU 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A MET* 5.6 7.4 - - + -
436A ILE* 3.6 31.4 - - + -
437A ILE* 4.1 5.2 - - + -
440A LEU* 4.0 17.9 - - + -
546A ALA* 2.5 25.9 + - + +
547A LEU 4.2 1.1 - - - +
549A LEU* 1.3 69.6 - - - +
551A LYS* 1.3 64.1 + - - +
553A VAL* 2.9 21.6 + - + +
554A LEU* 3.2 26.0 + - + +
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Residues in contact with LYS 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ILE* 3.6 41.6 - - + +
547A LEU* 3.0 25.9 + - + +
548A ILE* 4.2 4.3 - - - +
550A LEU* 1.3 77.2 - - - +
552A GLY* 1.3 59.7 + - - +
555A TYR* 3.2 46.5 + - + +
590A HIS* 3.3 26.8 + - + +
----------------------------------------------------------
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Residues in contact with GLY 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLY 5.6 0.2 - - - -
409A ALA* 3.7 8.6 - - - +
548A ILE 3.3 4.8 + - - -
549A LEU 3.1 8.7 + - - -
550A LEU 3.0 1.4 - - - -
551A LYS* 1.3 81.3 - - - +
553A VAL* 1.3 59.9 - - - +
555A TYR 4.2 0.3 - - - -
556A ALA* 3.4 21.2 + - - +
587A GLY* 4.0 6.2 - - - -
590A HIS* 3.3 34.9 + - - -
----------------------------------------------------------
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Residues in contact with VAL 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLY* 3.5 27.4 - - - +
408A GLY* 3.3 24.5 - - - +
409A ALA* 3.7 11.9 - - - +
412A MET* 3.5 19.7 - - + +
549A LEU 3.2 13.2 + - - +
550A LEU* 2.9 14.1 + - + +
552A GLY* 1.3 77.0 - - - +
554A LEU* 1.3 71.8 + - + +
556A ALA* 3.3 15.9 - - - +
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Residues in contact with LEU 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A MET* 5.1 1.6 - - - +
426A LEU* 6.4 0.4 - - + -
429A MET* 4.5 28.3 - - + +
430A LEU* 3.8 31.9 - - + +
433A ARG* 3.8 30.5 + - + -
436A ILE* 4.0 21.1 - - + -
437A ILE* 3.9 25.8 - - + -
550A LEU* 3.2 26.1 + - + +
553A VAL* 1.3 85.2 - - + +
555A TYR* 1.3 70.9 + - + +
556A ALA 3.3 2.2 + - - -
557A ARG* 4.6 4.5 + - - +
558A SER 4.5 0.2 - - - +
----------------------------------------------------------
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Residues in contact with TYR 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ARG* 3.4 36.1 + - + -
434A ASP* 2.8 43.1 + - - -
437A ILE* 4.5 19.5 - - + +
551A LYS* 3.2 38.0 + - + +
552A GLY 4.2 3.1 - - - -
554A LEU* 1.3 83.0 - - + +
556A ALA* 1.3 59.1 + - - +
557A ARG 3.3 2.6 + - - -
558A SER 3.7 12.7 - - - +
559A SER* 4.0 23.6 - - - -
560A ARG 5.8 0.7 - - - -
565A LYS* 2.7 40.0 + - - +
585A VAL 4.4 0.3 - - - +
590A HIS* 5.5 4.0 - - + -
----------------------------------------------------------
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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