Contacts of the helix formed by residues 520 - 546 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618E LYS* 5.1 7.6 - - - +
518F VAL* 3.7 2.1 - - - +
519F THR* 1.3 84.3 - - + +
521F MET* 1.3 78.8 + - - +
522F LYS* 3.4 17.2 + - - +
523F GLU* 3.3 25.6 + - + +
524F ALA* 2.9 22.7 + - - +
603F ILE* 5.9 0.3 - - - +
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Residues in contact with MET 521 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617E GLN* 3.4 28.7 - - - +
618E LYS* 5.5 1.1 - - - +
499F PRO* 3.6 18.2 - - + -
519F THR 4.5 4.7 - - - +
520F ASP* 1.3 86.2 + - - +
522F LYS* 1.3 61.5 + - + +
524F ALA* 3.5 7.6 - - - +
525F ALA* 2.9 28.8 + - - +
599F ASP 3.7 17.0 - - - +
600F MET* 3.7 30.5 - - - +
603F ILE* 3.7 37.9 - - + -
604F VAL* 3.7 22.0 - - + +
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Residues in contact with LYS 522 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520F ASP* 3.4 12.7 + - - +
521F MET* 1.3 78.6 - - - +
523F GLU* 1.3 59.7 + - + +
525F ALA* 3.4 7.0 + - + +
526F ASN* 2.8 38.9 + - - +
603F ILE* 5.4 10.9 + - - +
604F VAL* 5.8 5.5 - - + +
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Residues in contact with GLU 523 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518F VAL* 3.6 13.1 - - + +
519F THR* 4.3 6.8 + - - -
520F ASP* 3.3 30.8 + - + +
521F MET 3.2 0.2 - - - -
522F LYS* 1.3 78.1 - - + +
524F ALA* 1.3 58.8 + - - +
526F ASN* 4.0 4.9 - - - +
527F ALA* 2.9 25.6 + - - +
721F LEU* 3.3 43.3 - - + +
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Residues in contact with ALA 524 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497F ILE* 3.8 25.4 - - + +
518F VAL* 3.5 7.4 - - - +
519F THR 5.7 0.4 - - - +
520F ASP 2.9 14.6 + - - +
521F MET* 3.2 16.5 + - - +
523F GLU* 1.3 76.0 - - - +
525F ALA* 1.3 58.1 + - - +
527F ALA* 3.2 4.5 + - - +
528F LEU* 3.0 34.7 + - - +
600F MET* 4.0 21.3 - - + -
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Residues in contact with ALA 525 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521F MET 2.9 16.7 + - - +
522F LYS* 3.8 7.6 - - + +
524F ALA* 1.3 76.0 - - - +
526F ASN* 1.3 57.5 + - - +
528F LEU* 3.4 9.2 + - - +
529F ARG* 2.9 55.5 + - - +
604F VAL* 5.0 8.5 - - + -
607F LYS* 6.5 0.2 - - - -
608F VAL* 4.7 15.8 - - + +
611F LEU* 4.2 3.7 - - + +
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Residues in contact with ASN 526 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522F LYS* 2.8 32.4 + - - +
523F GLU* 3.6 9.9 - - - +
524F ALA 3.2 0.2 - - - -
525F ALA* 1.3 78.4 - - - +
527F ALA* 1.3 57.2 + - - +
529F ARG* 3.4 15.8 + - - +
530F TRP* 2.9 23.6 + - - +
720F ILE 3.2 9.9 - - - +
721F LEU* 3.8 33.9 - - + +
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Residues in contact with ALA 527 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495F ILE* 4.8 11.1 - - + +
497F ILE* 4.4 17.0 - - + -
518F VAL* 4.6 13.7 - - + -
523F GLU 2.9 17.4 + - - +
524F ALA* 3.2 6.7 + - - +
526F ASN* 1.3 76.1 - - - +
528F LEU* 1.3 59.1 + - - +
530F TRP* 3.4 6.7 + - - +
531F SER* 2.9 30.8 + - - -
720F ILE* 3.9 15.7 + - + -
721F LEU* 4.7 3.4 - - + -
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Residues in contact with LEU 528 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497F ILE* 4.4 18.2 - - + -
524F ALA 3.0 19.8 + - - +
525F ALA* 3.8 1.6 - - - +
526F ASN 3.3 0.2 - - - -
527F ALA* 1.3 78.9 - - - +
529F ARG* 1.3 56.3 + - - +
531F SER* 3.2 9.4 + - - +
532F VAL* 2.9 32.0 + - - +
592F VAL* 4.7 11.7 - - + -
600F MET* 4.2 11.7 - - - -
608F VAL* 4.1 25.1 - - + -
611F LEU* 3.8 25.6 - - + -
612F ILE* 3.8 34.3 - - + -
615F ILE* 5.0 6.8 - - + +
626F LEU* 5.9 3.6 - - + -
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Residues in contact with ARG 529 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525F ALA* 2.9 48.5 + - - +
526F ASN* 3.8 15.2 + - - +
527F ALA 3.3 0.2 - - - -
528F LEU* 1.3 73.1 - - - +
530F TRP* 1.3 60.6 + - - +
532F VAL* 3.3 9.4 + - - +
533F ALA* 3.0 25.6 + - - +
607F LYS* 4.0 34.1 - - - +
611F LEU* 3.9 22.7 - - + +
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Residues in contact with TRP 530 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495F ILE* 4.0 12.3 - - + -
514F LEU* 3.6 32.3 - - + -
526F ASN 2.9 17.1 + - - +
527F ALA 3.7 3.8 - - - +
528F LEU 3.3 0.2 - - - -
529F ARG* 1.3 75.9 - - - +
531F SER* 1.3 62.8 + - - +
533F ALA* 3.2 12.6 + - + +
534F GLU* 2.9 55.3 + - + +
590F ILE* 5.4 4.3 - - + -
717F ILE* 4.6 26.2 - - + +
719F ASP* 4.1 9.2 + - + +
720F ILE* 3.6 45.5 - - + +
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Residues in contact with SER 531 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495F ILE* 3.9 21.5 - - - +
527F ALA 2.9 16.4 + - - -
528F LEU* 3.2 15.9 + - - +
530F TRP* 1.3 78.2 - - - +
532F VAL* 1.3 59.4 + - - +
534F GLU* 3.4 4.6 + - - +
535F MET* 2.9 28.9 + - - +
590F ILE* 5.4 0.6 - - - +
592F VAL* 4.1 15.8 - - - +
615F ILE* 4.3 12.0 - - - +
624F ILE* 4.5 13.9 - - - +
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Residues in contact with VAL 532 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528F LEU 2.9 18.7 + - - +
529F ARG* 3.4 9.4 - - - +
531F SER* 1.3 76.6 - - - +
533F ALA* 1.3 56.8 + - - +
535F MET* 3.3 5.2 + - + +
536F GLU* 2.9 33.2 + - + +
611F LEU* 3.9 26.5 - - + +
614F ARG* 3.4 35.4 - - - +
615F ILE* 3.7 24.5 - - + -
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Residues in contact with ALA 533 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529F ARG 3.0 14.2 + - - +
530F TRP* 3.2 17.9 + - + +
532F VAL* 1.3 78.1 - - - +
534F GLU* 1.3 55.9 + - - +
536F GLU* 3.3 6.6 + - - +
537F ARG* 3.0 31.9 + - - +
540F ARG* 5.1 1.2 + - - -
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Residues in contact with GLU 534 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530F TRP* 2.9 48.0 + - + +
531F SER* 3.7 8.1 - - - +
532F VAL 3.3 0.2 - - - -
533F ALA* 1.3 72.1 - - - +
535F MET* 1.3 61.0 + - - +
537F ARG* 3.3 32.1 + - - +
538F ARG* 2.8 70.9 + - - +
587F LEU* 4.9 1.2 - - - +
590F ILE* 4.8 8.1 - - + -
624F ILE* 4.4 11.0 - - + -
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Residues in contact with MET 535 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531F SER 2.9 17.6 + - - +
532F VAL* 3.5 4.9 - - + +
534F GLU* 1.3 76.6 - - - +
536F GLU* 1.3 82.4 + - - +
538F ARG* 3.4 1.4 + - - +
539F TYR* 2.9 50.9 + - + -
614F ARG* 4.1 21.3 - - + +
615F ILE* 4.0 17.3 - - + -
618F LYS* 3.7 31.6 - - + -
619F ALA* 3.6 24.5 - - + -
622F ALA* 4.1 8.3 - - + -
624F ILE* 3.9 15.2 - - + +
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Residues in contact with GLU 536 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A MET* 3.5 23.7 - - - +
532F VAL* 2.9 25.2 + - + +
533F ALA* 3.8 7.0 - - - +
534F GLU 3.3 0.2 - - - -
535F MET* 1.3 91.8 - - - +
537F ARG* 1.3 58.2 + - - +
539F TYR* 3.4 3.5 + - - +
540F ARG* 2.9 42.1 + - - +
614F ARG* 2.8 31.2 + - - +
618F LYS* 3.4 14.4 + - - +
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Residues in contact with ARG 537 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533F ALA 3.0 18.4 + - - +
534F GLU* 3.3 47.5 + - - +
536F GLU* 1.3 76.2 - - - +
538F ARG* 1.3 62.4 + - - +
540F ARG* 3.4 25.9 + - - +
541F LEU* 2.9 53.1 + - - +
584F LEU* 5.3 6.5 - - - +
587F LEU* 4.6 14.5 - - - +
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Residues in contact with ARG 538 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534F GLU* 2.8 46.3 + - - +
535F MET 3.9 3.1 - - - +
537F ARG* 1.3 78.6 - - - +
539F TYR* 1.3 59.9 + - - +
541F LEU* 3.8 5.4 - - - +
542F MET* 2.9 40.3 + - + +
550F LEU* 4.1 9.0 - - - +
587F LEU* 3.5 31.6 - - + +
588F PRO* 2.6 54.0 + - - +
590F ILE* 3.9 21.1 - - - +
622F ALA* 2.6 47.5 + - + +
623F GLY* 4.1 4.9 - - - -
624F ILE* 4.4 2.1 - - - +
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Residues in contact with TYR 539 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A LYS* 5.4 9.4 + - + +
501A MET* 4.1 19.3 - - + +
502A LEU* 3.7 42.6 - - + +
535F MET* 2.9 34.5 + - + +
536F GLU 3.8 4.0 - - - +
538F ARG* 1.3 76.2 - - - +
540F ARG* 1.3 57.9 + - - +
542F MET* 3.6 7.0 + - + +
543F ALA* 2.9 29.3 + - - +
618F LYS* 2.7 61.8 + - + +
621F ALA* 3.4 22.3 + - + +
622F ALA* 3.7 22.4 - - + -
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Residues in contact with ARG 540 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A MET* 4.0 21.8 - - + -
533F ALA 5.1 1.0 + - - -
536F GLU* 2.9 27.9 + - - +
537F ARG* 3.7 28.1 - - - +
539F TYR* 1.3 75.7 - - - +
541F LEU* 1.3 58.4 + - - +
543F ALA* 3.3 7.2 + - - +
544F ALA* 2.9 27.7 + - - +
570F PRO* 5.9 0.4 - - - -
571F LEU* 4.3 33.0 - - + +
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Residues in contact with LEU 541 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537F ARG* 2.9 40.6 + - - +
538F ARG* 3.8 5.8 - - - +
539F TYR 3.3 0.2 - - - -
540F ARG* 1.3 77.0 - - - +
542F MET* 1.3 59.6 + - + +
544F ALA* 3.2 3.9 + - - +
545F MET* 3.0 30.6 + - - +
553F PHE* 3.5 37.9 - - + -
570F PRO* 3.8 26.7 - - + -
584F LEU* 3.9 28.9 - - + -
587F LEU* 5.2 10.8 - - + -
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Residues in contact with MET 542 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A LEU* 4.3 8.7 - - + +
538F ARG* 2.9 32.1 + - + +
539F TYR* 4.2 10.1 - - + +
541F LEU* 1.3 76.6 - - + +
543F ALA* 1.3 58.9 - - - +
545F MET* 3.8 5.4 - - - +
546F GLY* 2.9 22.3 + - - -
547F VAL* 3.1 28.6 + - + +
548F ARG 4.3 4.9 - - - +
549F ASN 4.0 28.3 - - - +
550F LEU* 4.1 12.1 - - + -
553F PHE* 4.5 21.3 - - + -
587F LEU* 6.1 2.5 - - + -
621F ALA* 3.5 23.6 - - + +
622F ALA* 4.0 13.0 - - + +
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Residues in contact with ALA 543 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A MET* 3.3 37.5 - - + +
502A LEU* 4.8 2.9 - - - +
505A SER* 5.5 6.2 + - - +
539F TYR 2.9 19.1 + - - +
540F ARG* 3.5 7.6 - - - +
542F MET* 1.3 75.9 - - - +
544F ALA* 1.3 64.6 + - - +
546F GLY* 3.6 9.3 + - - +
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Residues in contact with ALA 544 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540F ARG 2.9 16.5 + - - +
541F LEU 3.2 4.7 + - - +
543F ALA* 1.3 78.6 - - - +
545F MET* 1.3 61.5 + - + +
546F GLY 3.7 0.3 + - - -
570F PRO* 3.7 26.9 - - + -
571F LEU* 6.1 3.1 - - + -
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Residues in contact with MET 545 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541F LEU* 3.0 20.7 + - + +
542F MET* 4.6 3.4 - - - +
544F ALA* 1.3 80.2 - - + +
546F GLY* 1.3 63.9 + - - +
547F VAL* 3.3 8.8 + - + +
553F PHE* 3.6 30.3 - - + -
556F LYS* 2.6 36.3 + - - +
557F VAL* 6.4 0.2 - - + -
567F LEU* 3.7 35.4 - - + -
568F THR* 3.8 12.8 - - + +
570F PRO* 4.9 6.5 - - + -
584F LEU* 3.7 27.8 - - + -
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Residues in contact with GLY 546 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A LEU* 5.7 0.9 - - - -
542F MET 2.9 10.0 + - - -
543F ALA* 3.6 6.6 + - - -
544F ALA 3.4 3.8 + - - -
545F MET* 1.3 76.9 - - - +
547F VAL* 1.3 58.5 + - - +
548F ARG 4.1 1.2 + - - -
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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