Contacts of the helix formed by residues 520 - 546 (chain C) in PDB entry 6T8O
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 520 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614B ARG* 5.4 7.8 + - - -
617B GLN* 5.0 5.2 - - - +
518C VAL* 3.4 8.0 - - - +
519C THR* 1.3 87.4 - - + +
521C MET* 1.3 81.7 + - - +
522C LYS* 3.5 16.9 + - - +
523C GLU* 3.6 25.5 + - + +
524C ALA* 3.2 19.8 + - - +
603C ILE* 5.8 1.7 - - - +
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Residues in contact with MET 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C ILE* 4.9 2.2 - - + -
499C PRO* 3.6 40.8 - - + -
519C THR 5.0 1.8 - - - +
520C ASP* 1.3 85.0 + - - +
522C LYS* 1.3 61.3 + - - +
523C GLU 3.3 0.4 - - - -
524C ALA* 3.3 6.0 + - - +
525C ALA* 2.9 27.9 + - - +
596C GLU 4.0 3.8 - - - +
599C ASP* 4.0 5.6 - - + -
600C MET* 3.6 58.9 - - + +
603C ILE* 3.7 29.6 - - + -
604C VAL* 3.9 21.7 - - + +
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Residues in contact with LYS 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520C ASP* 3.5 14.6 + - - +
521C MET* 1.3 76.7 - - - +
523C GLU* 1.3 60.8 + - + +
525C ALA* 3.3 8.6 + - + +
526C ASN* 2.9 37.0 + - - +
603C ILE* 4.5 13.1 + - - +
604C VAL* 4.2 27.5 - - + +
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Residues in contact with GLU 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C VAL* 3.7 14.1 - - + +
519C THR* 4.0 9.7 + - - -
520C ASP* 3.6 31.4 + - + +
521C MET 3.3 0.4 - - - -
522C LYS* 1.3 79.6 - - + +
524C ALA* 1.3 56.3 + - - +
526C ASN* 3.3 10.1 + - - +
527C ALA* 2.9 27.2 + - - +
720C ILE 4.0 2.8 - - - +
721C LEU* 4.2 31.2 - - + +
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Residues in contact with ALA 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C ILE* 3.8 19.7 - - + +
518C VAL* 3.4 6.9 - - + +
520C ASP 3.2 15.2 + - - +
521C MET* 3.6 11.4 - - - +
522C LYS 3.3 0.4 - - - -
523C GLU* 1.3 73.2 - - - +
525C ALA* 1.3 60.2 + - - +
527C ALA* 3.2 6.4 + - - +
528C LEU* 2.9 35.3 + - - +
600C MET* 3.8 28.0 - - + -
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Residues in contact with ALA 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C MET 2.9 16.5 + - - +
522C LYS* 3.3 11.0 + - + +
524C ALA* 1.3 77.3 - - - +
526C ASN* 1.3 57.3 + - - +
528C LEU* 3.4 7.3 + - - +
529C ARG* 2.9 56.8 + - - +
600C MET* 5.6 1.3 - - + -
604C VAL* 5.4 5.4 - - + -
608C VAL* 4.7 18.6 - - + -
611C LEU* 4.1 4.3 - - + +
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Residues in contact with ASN 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C LYS* 2.9 27.3 + - - +
523C GLU* 3.5 5.4 - - - +
524C ALA 3.3 0.2 - - - -
525C ALA* 1.3 77.0 - - - +
527C ALA* 1.3 56.8 + - - +
529C ARG* 3.4 15.1 + - - +
530C TRP* 2.9 26.9 + - - +
720C ILE 3.2 9.3 - - - +
721C LEU 2.7 24.7 + - - +
722C ALA* 3.3 33.7 - - - +
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Residues in contact with ALA 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C ILE* 4.5 15.7 - - + +
497C ILE* 5.1 3.4 - - + -
518C VAL* 4.7 11.4 - - + -
523C GLU 2.9 13.8 + - - +
524C ALA* 3.2 11.4 + - - +
526C ASN* 1.3 75.5 - - - +
528C LEU* 1.3 59.8 + - + +
530C TRP* 3.3 3.8 + - - +
531C SER* 2.9 31.2 + - - -
720C ILE* 3.1 30.8 + - + +
721C LEU* 5.7 0.2 - - + -
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Residues in contact with LEU 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C ILE* 6.1 0.2 - - + -
497C ILE* 4.3 12.1 - - + -
524C ALA 2.9 21.2 + - - +
525C ALA* 4.0 1.6 - - - +
527C ALA* 1.3 74.5 - - + +
529C ARG* 1.3 61.3 + - - +
531C SER* 3.2 10.9 + - - +
532C VAL* 2.9 29.8 + - - +
592C VAL* 3.9 28.3 - - + -
594C VAL* 5.4 2.2 - - + -
600C MET* 3.8 24.7 - - - -
608C VAL* 5.0 2.2 - - + -
611C LEU* 3.7 25.4 - - + -
612C ILE* 3.7 32.1 - - + -
615C ILE* 4.3 8.3 - - + +
626C LEU* 5.4 2.9 - - + -
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Residues in contact with ARG 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525C ALA* 2.9 51.8 + - - +
526C ASN* 3.8 15.3 + - - +
528C LEU* 1.3 72.1 - - - +
530C TRP* 1.3 60.3 + - - +
532C VAL* 3.2 10.1 + - - +
533C ALA* 3.0 27.7 + - - +
604C VAL* 6.2 2.0 - - - +
607C LYS* 5.3 15.2 + - - +
608C VAL* 6.0 2.8 - - - +
611C LEU* 3.9 23.0 - - + +
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Residues in contact with TRP 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C ILE* 4.0 5.8 - - + -
514C LEU* 3.6 36.8 - - + -
526C ASN 2.9 15.5 + - - +
527C ALA 3.4 7.2 - - - +
529C ARG* 1.3 75.0 - - - +
531C SER* 1.3 66.9 + - - +
533C ALA* 3.3 10.2 + - + +
534C GLU* 2.9 59.4 + - + +
590C ILE* 5.4 5.4 - - + -
717C ILE* 4.5 23.3 - - + +
719C ASP* 3.4 27.0 + - - +
720C ILE* 3.7 37.2 - - + -
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Residues in contact with SER 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C ILE* 3.5 24.4 - - - +
527C ALA 2.9 14.9 + - - -
528C LEU* 3.2 13.5 + - - +
530C TRP* 1.3 80.1 - - - +
532C VAL* 1.3 59.4 + - - +
534C GLU* 3.4 4.5 + - - +
535C MET* 2.9 29.1 + - - +
590C ILE* 5.3 1.0 - - - +
592C VAL* 3.9 13.8 - - - +
615C ILE* 4.1 15.6 - - - +
624C ILE* 4.8 12.2 - - - +
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Residues in contact with VAL 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528C LEU 2.9 19.4 + - - +
529C ARG* 3.2 8.9 + - - +
531C SER* 1.3 76.4 - - - +
533C ALA* 1.3 58.3 + - - +
535C MET* 3.2 13.8 + - + +
536C GLU* 2.9 39.3 + - + +
611C LEU* 3.7 26.7 - - + +
614C ARG* 5.3 12.1 - - + +
615C ILE* 3.6 22.9 - - + +
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Residues in contact with ALA 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529C ARG 3.0 13.4 + - - +
530C TRP* 3.7 14.4 - - + +
532C VAL* 1.3 77.6 - - - +
534C GLU* 1.3 58.2 + - - +
536C GLU* 3.4 7.1 + - - +
537C ARG* 3.0 31.9 + - - +
540C ARG* 5.3 1.2 + - - -
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Residues in contact with GLU 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530C TRP* 2.9 53.0 + - + +
531C SER* 3.7 5.4 - - - +
532C VAL 3.3 0.2 - - - -
533C ALA* 1.3 73.7 - - - +
535C MET* 1.3 60.2 + - - +
537C ARG* 2.9 39.8 + - - +
538C ARG* 2.9 65.3 + - - +
587C LEU* 5.4 1.0 - - - +
590C ILE* 5.1 4.7 - - + -
624C ILE* 4.8 6.7 - - + -
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Residues in contact with MET 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531C SER 2.9 16.3 + - - +
532C VAL* 3.2 17.7 + - + +
534C GLU* 1.3 77.2 - - - +
536C GLU* 1.3 79.2 + - + +
538C ARG* 3.3 3.1 + - - +
539C TYR* 3.0 51.4 + - + -
614C ARG* 3.7 21.5 - - + +
615C ILE* 4.3 5.4 - - + +
618C LYS* 3.8 18.4 - - + -
619C ALA* 3.6 35.4 - - + -
622C ALA* 4.1 7.4 - - + -
624C ILE* 4.2 16.0 - - + +
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Residues in contact with GLU 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532C VAL* 2.9 30.7 + - + +
533C ALA* 3.8 7.2 - - - +
535C MET* 1.3 96.2 - - - +
537C ARG* 1.3 57.3 + - - +
539C TYR* 3.4 6.2 + - - +
540C ARG* 3.0 48.8 + - - +
618C LYS* 4.2 20.2 + - - +
520D ASP* 4.9 5.6 - - - +
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Residues in contact with ARG 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533C ALA 3.0 17.6 + - - +
534C GLU* 2.9 49.9 + - - +
536C GLU* 1.3 76.4 - - - +
538C ARG* 1.3 63.7 + - - +
540C ARG* 3.4 20.7 + - - +
541C LEU* 2.9 56.7 + - - +
571C LEU* 5.2 2.5 - - + +
587C LEU* 5.2 9.9 - - - +
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Residues in contact with ARG 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534C GLU* 2.9 44.5 + - - +
535C MET* 3.8 4.7 - - - +
536C GLU 3.3 0.2 - - - -
537C ARG* 1.3 78.6 - - - +
539C TYR* 1.3 60.8 + - - +
541C LEU* 3.3 5.5 + - + +
542C MET* 2.9 39.4 + - + +
550C LEU* 4.4 10.5 - - + +
587C LEU* 3.9 38.2 - - + +
588C PRO* 3.1 34.5 + - - +
590C ILE* 3.6 28.2 - - - +
622C ALA* 3.3 33.1 + - + -
623C GLY 4.2 4.0 + - - -
624C ILE* 4.1 10.1 - - - +
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Residues in contact with TYR 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535C MET* 3.0 34.9 + - + +
536C GLU* 3.8 7.2 - - - +
538C ARG* 1.3 76.1 - - - +
540C ARG* 1.3 60.1 + - + +
542C MET* 3.4 19.4 + - + +
543C ALA* 2.9 28.6 + - - +
548C ARG 5.4 1.6 - - - -
618C LYS* 2.6 62.6 + - + +
621C ALA* 3.3 24.5 + - + +
622C ALA* 3.6 24.7 - - + -
501D MET* 3.9 36.0 + - + +
519D THR* 5.7 0.4 - - + -
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Residues in contact with ARG 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533C ALA 5.3 1.0 + - - -
536C GLU* 3.0 33.5 + - - +
537C ARG* 3.9 23.6 - - - +
538C ARG 3.3 0.2 - - - -
539C TYR* 1.3 76.4 - - + +
541C LEU* 1.3 57.9 + - - +
543C ALA* 3.4 7.9 + - - +
544C ALA* 2.9 27.2 + - - +
571C LEU* 4.4 11.8 - - + +
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Residues in contact with LEU 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C ARG* 2.9 43.6 + - - +
538C ARG* 3.9 6.3 - - + +
540C ARG* 1.3 74.1 - - - +
542C MET* 1.3 62.4 + - + +
544C ALA* 3.2 6.7 + - - +
545C MET* 2.9 28.8 + - + +
553C PHE* 3.6 39.3 - - + -
569C ASP* 4.8 7.4 - - - +
570C PRO* 4.4 9.6 - - + -
571C LEU* 4.2 13.0 - - + +
584C LEU* 4.0 20.9 - - + -
587C LEU* 5.1 9.6 - - + -
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Residues in contact with MET 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538C ARG* 2.9 28.1 + - + +
539C TYR* 3.7 37.0 - - + +
541C LEU* 1.3 76.0 - - + +
543C ALA* 1.3 60.9 + - - +
545C MET* 4.8 0.4 - - - -
546C GLY* 2.8 22.2 + - - -
547C VAL* 3.0 39.0 + - + +
548C ARG 4.5 3.6 - - - +
549C ASN* 3.5 35.0 - - - +
550C LEU* 4.1 11.2 - - + -
553C PHE* 4.6 11.2 - - + -
587C LEU* 6.4 1.3 - - + -
621C ALA 4.4 1.8 - - - +
622C ALA* 4.3 16.8 - - - -
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Residues in contact with ALA 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539C TYR 2.9 17.6 + - - +
540C ARG* 3.6 8.3 - - - +
542C MET* 1.3 76.4 - - - +
544C ALA* 1.3 61.2 + - - +
546C GLY* 3.3 12.2 + - - +
547C VAL 5.3 0.7 - - - -
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Residues in contact with ALA 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540C ARG 2.9 16.8 + - - +
541C LEU* 3.2 6.0 + - - +
543C ALA* 1.3 76.2 - - - +
545C MET* 1.3 64.4 + - - +
570C PRO* 3.9 23.1 - - + +
571C LEU* 4.1 22.4 - - + -
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Residues in contact with MET 545 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C LEU* 2.9 17.9 + - + +
542C MET 4.4 2.0 - - - +
544C ALA* 1.3 77.2 - - - +
546C GLY* 1.3 64.1 + - - +
547C VAL* 3.4 6.0 + - + -
553C PHE* 4.0 28.5 - - + -
556C LYS* 3.9 29.2 + - + +
567C LEU* 4.5 26.9 - - + -
568C THR 5.0 2.0 - - - +
570C PRO* 3.7 33.2 - - + -
584C LEU* 4.0 13.2 - - + -
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Residues in contact with GLY 546 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542C MET 2.8 10.9 + - - -
543C ALA* 3.3 12.0 + - - -
545C MET* 1.3 79.1 - - - +
547C VAL* 1.3 59.9 + - - +
556C LYS* 5.0 1.9 + - - -
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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