Contacts of the helix formed by residues 586 - 612 (chain A) in PDB entry 2P6U
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 ALA 586 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ARG* 4.1 5.8 - - - +
287A MET* 3.3 25.8 - - + -
305A GLY* 3.6 13.5 - - - -
580A CYS* 4.0 3.4 - - - -
585A ILE* 1.3 76.4 - - - +
587A PRO* 1.3 67.7 - - + -
588A GLY 3.1 0.2 - - - -
589A ASP* 2.6 41.8 + - - +
590A LEU 3.1 4.0 + - - -
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Residues in contact with PRO 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ASN* 4.3 27.6 - - - +
287A MET* 3.9 22.0 - - + -
288A SER* 4.5 0.4 - - - +
305A GLY 3.6 8.1 - - - +
307A LEU* 3.2 26.5 - - + -
576A GLU* 5.1 6.3 - - - +
580A CYS* 3.6 22.5 - - + -
585A ILE 4.5 0.7 - - - +
586A ALA* 1.3 85.6 - - + +
588A GLY* 1.3 57.1 + - - +
590A LEU* 3.4 4.3 + - + +
591A ARG* 2.9 35.0 + - + +
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Residues in contact with GLY 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ALA 3.8 5.8 - - - -
305A GLY 2.7 26.1 + - - -
306A LEU 3.2 16.6 - - - -
307A LEU* 3.9 4.9 - - - +
311A ARG* 5.2 2.6 + - - -
587A PRO* 1.3 71.2 - - - +
589A ASP* 1.3 56.5 + - - +
591A ARG* 3.3 6.8 + - - +
592A ARG* 2.8 35.6 + - - +
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Residues in contact with ASP 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ARG* 2.8 40.0 + - - -
304A ALA 3.6 1.9 - - - +
585A ILE* 3.8 18.0 - - + +
586A ALA 2.6 30.9 + - - +
588A GLY* 1.3 67.6 - - - -
590A LEU* 1.3 53.5 + - - +
592A ARG* 2.6 60.6 + - - +
593A ILE* 2.7 26.6 + - + +
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Residues in contact with LEU 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A CYS* 4.8 8.3 - - - -
570A TRP* 4.2 15.5 - - + -
576A GLU* 4.1 24.5 - - + +
579A ILE* 3.8 31.4 - - + -
580A CYS* 3.7 21.1 - - - -
585A ILE* 3.6 22.1 - - + +
586A ALA 3.1 4.9 + - - +
587A PRO* 3.6 10.5 - - + +
589A ASP* 1.3 80.1 - - - +
591A ARG* 1.3 58.3 + - + +
593A ILE* 3.2 5.2 + - + +
594A VAL* 2.9 55.2 + - + +
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Residues in contact with ARG 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLU* 4.2 19.2 + - - +
283A ASN* 5.6 1.0 + - - +
307A LEU* 3.1 36.1 - - + +
308A ASN* 6.0 1.3 - - - +
570A TRP* 4.4 13.5 - - - -
576A GLU* 2.8 43.6 + - - -
587A PRO* 2.9 27.7 + - - +
588A GLY* 3.6 5.8 - - - +
590A LEU* 1.3 78.4 - - + +
592A ARG* 1.3 57.7 - - - +
594A VAL* 4.1 5.0 - - - +
595A GLU* 2.8 34.7 + - - +
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Residues in contact with ARG 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ARG* 4.1 4.2 - - - +
304A ALA* 3.4 28.8 + - - +
521A GLU* 3.2 35.2 + - - +
588A GLY 2.8 13.8 + - - +
589A ASP* 2.6 67.4 + - - +
591A ARG* 1.3 71.6 - - - +
593A ILE* 1.3 54.4 + - - +
595A GLU* 3.3 6.8 - - - +
596A THR* 3.0 35.2 + - - +
707A PO4 5.6 6.3 - - - -
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Residues in contact with ILE 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A MET* 3.6 22.1 - - + +
521A GLU* 4.0 33.4 - - + +
522A ARG 5.3 0.2 - - - +
523A LEU* 3.5 32.8 - - + -
563A THR* 4.7 4.3 - - + -
566A CYS* 5.4 7.6 - - - -
567A LEU* 3.8 16.4 - - + -
585A ILE* 4.5 12.8 - - + -
589A ASP* 2.7 28.3 + - + +
590A LEU* 3.6 4.0 - - + +
592A ARG* 1.3 69.4 - - - +
594A VAL* 1.3 58.4 + - + +
596A THR* 3.1 6.3 + - - -
597A ALA* 2.7 36.7 + - - +
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Residues in contact with VAL 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A CYS* 6.4 0.2 - - - -
567A LEU* 4.4 7.2 - - + -
570A TRP* 3.0 53.8 - - + +
590A LEU* 2.9 46.0 + - + +
591A ARG* 4.1 5.2 - - - +
593A ILE* 1.3 73.3 - - + +
595A GLU* 1.3 66.1 + - - +
597A ALA* 3.6 6.4 - - - +
598A GLU* 2.9 24.1 + - - +
623A ILE* 3.1 15.9 - - + +
624A LYS* 4.6 4.5 - - - +
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Residues in contact with GLU 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A ARG* 2.8 23.3 + - - +
592A ARG* 3.3 8.5 - - - +
594A VAL* 1.3 79.4 - - - +
596A THR* 1.3 63.7 + - - +
598A GLU* 3.5 19.9 + - - +
599A TRP* 3.5 15.1 + - - +
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Residues in contact with THR 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ASP 3.9 11.4 - - - +
520A MET* 3.9 12.1 - - - -
521A GLU* 4.5 8.7 + - + +
592A ARG* 3.0 20.8 + - - +
593A ILE* 3.5 6.9 - - - -
595A GLU* 1.3 72.7 - - - +
597A ALA* 1.3 68.2 + - - +
598A GLU 3.0 1.3 - - - -
599A TRP* 2.7 35.7 + - + +
600A LEU* 3.1 29.7 + - + +
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Residues in contact with ALA 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ILE* 4.1 11.7 - - + +
520A MET* 4.0 14.3 - - + -
567A LEU* 3.4 38.4 - - + -
593A ILE 2.7 21.3 + - - +
594A VAL 3.6 3.1 - - - +
596A THR* 1.3 71.7 - - - +
598A GLU* 1.3 57.4 + - - +
600A LEU* 3.5 3.2 + - - +
601A SER* 2.8 28.7 + - - -
623A ILE* 4.0 8.5 - - + -
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Residues in contact with GLU 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A VAL* 2.9 16.4 + - + +
595A GLU* 3.5 20.6 - - - +
596A THR 2.9 0.6 + - - -
597A ALA* 1.3 77.4 - - - +
599A TRP* 1.3 53.5 + - - +
601A SER* 2.8 9.4 + - - -
602A ASN* 2.7 34.3 + - + +
620A THR* 3.7 25.4 - - + +
623A ILE* 3.8 12.3 - - + +
624A LYS* 3.7 42.2 + - - +
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Residues in contact with TRP 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A TYR* 4.1 26.4 - + - -
486A LEU 3.7 16.2 + - - -
487A TYR* 3.4 24.2 - + - -
488A ILE* 3.5 14.7 - - + +
519A ASP* 3.9 30.1 - - + -
595A GLU 3.5 7.8 + - - +
596A THR* 2.7 27.9 + - + +
598A GLU* 1.3 76.6 - - - +
600A LEU* 1.3 83.8 + - + +
602A ASN* 3.4 8.8 + - + +
603A ALA* 3.1 22.8 + - + +
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Residues in contact with LEU 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ILE* 4.2 7.9 - - + -
492A THR* 4.6 4.7 - - + -
496A PHE* 3.8 8.5 - - + -
514A ILE* 4.1 11.9 - - + -
517A THR* 3.8 7.4 - - + -
519A ASP* 3.5 20.4 - - + +
520A MET* 3.5 47.1 - - + +
596A THR* 3.1 14.7 + - + +
597A ALA 3.9 4.7 - - - +
599A TRP* 1.3 108.2 - - + +
601A SER* 1.3 56.0 + - - +
603A ALA* 2.9 5.5 + - + +
604A MET* 2.6 38.2 + - - +
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Residues in contact with SER 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ILE* 3.9 15.9 - - - +
597A ALA 2.8 17.0 + - - -
598A GLU* 2.8 17.7 + - - -
600A LEU* 1.3 76.5 - - - +
602A ASN* 1.3 60.6 + - - +
604A MET* 3.5 6.8 + - - +
605A ASN* 3.0 20.1 + - - +
619A LEU* 3.9 12.1 - - - +
620A THR* 3.2 34.5 + - - -
623A ILE* 3.8 9.0 - - - +
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Residues in contact with ASN 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A LEU* 5.9 1.0 - - - +
598A GLU* 2.7 15.4 + - + +
599A TRP* 3.5 11.4 - - + +
601A SER* 1.3 74.3 - - - +
603A ALA* 1.3 64.8 + - - +
605A ASN* 3.1 7.1 + - - +
606A ARG* 2.9 34.7 + - - +
620A THR* 3.5 20.2 + - + +
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Residues in contact with ALA 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A LEU* 3.7 28.6 - - + +
488A ILE* 4.0 24.0 - - + -
496A PHE* 4.3 3.8 - - + -
599A TRP* 3.1 15.0 + - + +
600A LEU* 2.9 12.7 + - - +
602A ASN* 1.3 79.8 + - - +
604A MET* 1.3 63.7 + - - +
606A ARG* 3.3 0.6 + - - -
607A ILE* 3.0 29.4 + - - +
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Residues in contact with MET 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A PHE* 3.5 39.0 - - + -
500A LEU* 3.4 14.2 - - + +
510A ALA* 4.0 10.8 - - + +
513A LEU* 4.2 11.4 - - + -
514A ILE* 3.9 24.0 - - + -
600A LEU 2.6 19.0 + - - +
601A SER* 3.7 9.6 - - - +
603A ALA* 1.3 71.5 - - - +
605A ASN* 1.3 58.7 + - + +
607A ILE* 3.4 1.4 + - - +
608A ALA* 2.8 26.5 + - - +
616A VAL* 3.1 38.8 - - + -
619A LEU* 3.5 23.8 - - + -
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Residues in contact with ASN 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A SER 3.0 14.2 + - - +
602A ASN* 3.1 9.4 + - - +
604A MET* 1.3 75.6 - - + +
606A ARG* 1.3 67.0 + - - +
608A ALA* 3.0 6.6 + - - +
609A GLU* 2.8 53.6 + - - +
613A ASN 5.6 0.9 - - - +
614A THR* 5.8 1.0 - - - -
616A VAL* 4.0 17.5 - - + +
617A SER* 4.0 31.5 + - - +
620A THR* 4.4 9.7 + - - +
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Residues in contact with ARG 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU* 2.3 36.1 + - - +
482A LEU* 3.2 32.0 - - + +
485A ARG* 3.2 24.0 - - - +
486A LEU* 4.6 9.2 - - + +
602A ASN* 2.9 24.7 + - - +
603A ALA 3.9 4.5 - - - +
605A ASN* 1.3 78.1 - - - +
607A ILE* 1.3 61.8 + - - +
609A GLU* 3.5 23.1 + - - +
610A GLU* 3.2 19.4 + - - +
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Residues in contact with ILE 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A LEU* 4.9 6.5 - - + -
482A LEU* 3.8 21.3 - - + -
483A VAL* 5.0 6.7 - - + -
486A LEU* 4.0 4.7 - - + -
488A ILE* 4.1 9.6 - - + -
493A GLY* 3.6 33.7 - - - +
496A PHE* 3.8 20.4 - - + -
497A HIS* 3.5 39.2 + - + +
500A LEU* 4.4 1.8 - - + -
603A ALA 3.0 17.5 + - - +
604A MET 3.6 4.3 - - - +
606A ARG* 1.3 74.0 - - - +
608A ALA* 1.3 70.0 + - - +
610A GLU* 3.0 15.9 + - - +
611A VAL* 3.3 9.8 + - + +
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Residues in contact with ALA 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A LEU* 3.2 28.3 - - + -
604A MET 2.8 11.1 + - - +
605A ASN* 3.2 9.2 - - - +
607A ILE* 1.3 75.5 - - - +
609A GLU* 1.3 62.8 + - - +
611A VAL* 2.8 13.1 + - - +
612A GLY 2.8 19.1 + - - -
613A ASN* 3.4 16.3 + - + +
616A VAL* 3.7 22.4 - - + -
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Residues in contact with GLU 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A ASN* 2.8 50.1 + - - +
606A ARG* 3.6 25.4 + - - +
608A ALA* 1.3 71.2 - - + +
610A GLU* 1.3 66.6 + - - +
612A GLY* 2.8 17.9 + - - +
613A ASN 4.0 7.1 + - - +
614A THR* 6.2 2.2 - - + -
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Residues in contact with GLU 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A LYS* 3.5 13.8 - - + +
479A LEU* 3.2 42.2 + - - +
482A LEU* 4.7 9.7 - - + +
497A HIS* 4.0 23.4 + - - -
606A ARG 3.2 9.5 + - - +
607A ILE* 3.0 13.2 + - - +
609A GLU* 1.3 78.2 - - - +
611A VAL* 1.3 59.4 + - - +
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Residues in contact with VAL 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A HIS* 4.2 18.2 - - + +
500A LEU* 4.5 1.1 - - + -
501A SER* 3.2 45.1 - - - +
607A ILE* 3.3 4.8 + - + +
608A ALA* 2.8 18.3 + - - +
609A GLU 3.4 0.2 - - - -
610A GLU* 1.3 83.0 + - - +
612A GLY* 1.3 60.5 + - - +
613A ASN* 3.3 22.0 - - + +
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Residues in contact with GLY 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A ALA 2.8 1.0 + - - -
609A GLU* 2.8 14.3 + - - -
611A VAL* 1.3 79.6 - - - +
613A ASN* 1.3 67.6 + - - +
614A THR* 3.6 11.7 + - - +
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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