Contacts of the helix formed by residues 475 - 500 (chain A) in PDB entry 2XT6
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 THR 475 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A LYS 5.1 2.7 - - - +
474A PRO* 1.3 76.0 - - + +
476A VAL* 1.3 60.3 + - - +
477A ALA* 3.6 10.2 + - - +
478A GLU* 3.0 41.4 + - - +
479A GLN* 2.9 25.7 + - - +
590A PHE* 5.7 0.2 - - - -
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Residues in contact with VAL 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A PRO 3.9 0.4 + - - +
475A THR* 1.3 72.0 - - - +
477A ALA* 1.4 52.4 + - - +
479A GLN* 3.2 15.9 + - + +
480A LYS* 2.7 37.4 + - + +
783A ASP* 3.5 31.6 - - + +
784A ILE* 4.0 16.6 - - + -
788A GLU* 4.4 12.1 - - - +
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Residues in contact with ALA 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A THR* 3.2 9.5 + - - +
476A VAL* 1.4 78.0 - - - +
478A GLU* 1.4 54.9 + - - +
480A LYS* 3.6 6.7 + - - +
481A TYR* 3.0 29.1 + - - +
590A PHE* 3.7 23.5 - - + -
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Residues in contact with GLU 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A PRO* 3.6 15.3 - - + +
475A THR* 3.0 47.0 + - - +
477A ALA* 1.4 75.7 - - - +
479A GLN* 1.3 58.1 + - - +
481A TYR* 3.5 4.7 + - - +
482A ILE* 3.1 36.1 + - + +
590A PHE* 4.2 27.2 - - + +
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Residues in contact with GLN 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A LYS* 6.0 1.2 - - - +
474A PRO* 3.9 24.1 + - + +
475A THR 2.9 11.8 + - - +
476A VAL* 3.5 25.5 - - + +
478A GLU* 1.3 73.3 - - - +
480A LYS* 1.3 59.0 + - - +
482A ILE* 3.3 3.1 + - - +
483A LEU* 2.9 30.0 + - - +
715A GLU* 2.8 30.8 + - - +
774A TYR* 3.4 16.8 - - - +
778A LEU* 3.4 19.5 - - + +
781A ARG* 4.1 1.6 - - - +
783A ASP* 3.0 38.3 + - - +
784A ILE* 6.0 0.4 - - + -
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Residues in contact with LYS 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A VAL* 2.7 25.7 + - + +
477A ALA* 3.9 6.5 - - - +
479A GLN* 1.3 71.9 - - - +
481A TYR* 1.4 56.9 + - - +
483A LEU* 3.8 9.4 - - - +
484A SER* 2.9 28.4 + - - -
778A LEU* 5.3 1.5 - - - +
784A ILE* 5.8 5.8 - - + +
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Residues in contact with TYR 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ALA 3.0 18.5 + - - +
478A GLU 3.7 6.5 - - - +
479A GLN 3.2 0.2 - - - -
480A LYS* 1.4 73.9 - - - +
482A ILE* 1.4 70.7 + - + +
484A SER* 2.7 29.2 + - - -
485A LYS* 3.2 31.8 + - + +
519A ASP* 3.0 39.0 + - - -
523A ASP* 6.0 1.8 - - - -
586A TYR* 3.5 11.4 + - - -
587A ILE 5.7 0.2 + - - -
589A MET* 3.7 43.3 + - + +
590A PHE* 4.1 19.3 - + + -
722A ARG* 6.3 1.8 - - - -
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Residues in contact with ILE 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A PRO* 5.2 7.6 - - + -
478A GLU* 3.1 27.8 + - + +
479A GLN* 3.3 4.0 + - - +
481A TYR* 1.4 80.2 - - + +
483A LEU* 1.3 63.3 + - - +
485A LYS* 3.3 10.9 + - - +
486A LEU* 3.2 19.9 + - + +
516A PRO* 4.0 13.8 - - + +
714A PRO* 3.6 37.7 - - + +
715A GLU* 4.2 23.1 - - + -
718A ALA* 4.3 23.1 - - + -
722A ARG* 6.3 1.3 - - - +
774A TYR* 4.2 7.2 - - + +
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Residues in contact with LEU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A GLN 2.9 18.0 + - - +
480A LYS* 3.8 8.1 - - - +
481A TYR 3.2 0.2 - - - -
482A ILE* 1.3 73.9 - - - +
484A SER* 1.3 57.5 + - - +
486A LEU* 3.1 7.2 + - + -
487A ASN* 2.9 48.2 + - - +
771A ARG* 4.0 13.0 - - + +
774A TYR* 3.9 20.6 - - + -
775A THR* 3.5 31.9 - - + +
778A LEU* 3.9 20.4 - - + -
784A ILE* 4.9 3.1 - - + -
792A ALA* 3.8 23.8 - - + -
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Residues in contact with SER 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LYS 2.9 17.5 + - - -
481A TYR* 2.7 31.5 + - - -
483A LEU* 1.3 74.4 - - - +
485A LYS* 1.3 59.8 + - - +
487A ASN* 3.4 4.6 - - - +
488A ALA* 3.1 26.5 + - - +
795A ASP* 4.1 18.8 - - - -
799A GLN* 3.8 7.7 + - - -
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Residues in contact with LYS 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A TYR* 3.2 40.1 + - + +
482A ILE* 3.4 10.1 - - - +
483A LEU 3.2 0.2 - - - -
484A SER* 1.3 79.1 + - - +
486A LEU* 1.4 57.7 + - - +
488A ALA* 3.4 8.3 + - - +
489A ALA* 2.9 28.8 + - - +
515A ILE* 4.1 12.2 - - + +
516A PRO* 4.1 20.4 - - + -
519A ASP* 3.5 33.0 + - + +
548A ASN* 3.1 33.9 + - - +
586A TYR* 5.8 0.4 - - - -
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Residues in contact with LEU 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ILE 3.2 10.9 + - - +
483A LEU* 3.1 10.9 + - + +
485A LYS* 1.4 73.2 - - - +
487A ASN* 1.4 56.0 + - - +
489A ALA* 3.6 3.4 - - - +
490A GLU* 2.9 37.2 + - - +
512A GLU* 4.0 22.6 - - + +
513A THR* 3.9 20.2 - - - +
516A PRO* 4.1 8.9 - - + +
714A PRO* 3.7 29.8 - - + -
770A SER* 4.0 16.6 - - - +
771A ARG* 4.2 21.7 - - + +
774A TYR* 4.0 24.5 - - + -
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Residues in contact with ASN 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A LEU* 2.9 24.1 + - - +
484A SER* 3.4 11.4 - - - +
485A LYS 3.3 0.2 - - - -
486A LEU* 1.4 75.6 - - - +
488A ALA* 1.4 53.2 + - - +
491A ALA* 2.8 37.6 + - - +
771A ARG* 3.1 29.4 + - - +
792A ALA* 2.8 34.3 + - - +
795A ASP* 2.8 26.5 + - - +
796A TYR* 3.4 19.6 - - - +
799A GLN* 4.8 2.7 - - + -
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Residues in contact with ALA 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A SER 3.1 13.2 + - - +
485A LYS* 3.6 12.1 - - - +
487A ASN* 1.4 74.0 - - - +
489A ALA* 1.3 58.3 + - - +
491A ALA* 3.5 3.1 + - - +
492A PHE* 2.9 31.9 + - - +
548A ASN* 3.4 26.5 + - + +
554A TYR* 5.5 2.1 + - - +
799A GLN* 3.5 29.3 - - - +
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Residues in contact with ALA 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A LYS 2.9 17.7 + - - +
486A LEU 3.6 5.4 - - - +
488A ALA* 1.3 77.1 - - - +
490A GLU* 1.4 56.8 + - - +
493A GLU* 3.1 24.6 + - - +
512A GLU* 3.8 32.1 - - + +
515A ILE* 3.9 17.7 - - + -
544A ASN* 3.1 24.6 + - - +
548A ASN* 4.2 1.1 - - - +
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Residues in contact with GLU 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A LEU* 2.9 20.4 + - - +
487A ASN 4.0 0.2 - - - +
489A ALA* 1.4 69.8 - - - +
491A ALA* 1.3 60.6 + - - +
493A GLU* 3.3 6.0 + - + +
494A THR* 2.9 38.3 + - - +
512A GLU* 3.8 29.2 - - + +
769A GLY* 4.4 8.0 - - - -
770A SER* 4.3 5.9 + - - -
771A ARG* 2.8 58.0 + - - +
772A LYS* 4.9 2.1 + - - +
796A TYR* 3.8 13.8 + - + +
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Residues in contact with ALA 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A ASN 2.8 19.2 + - - +
488A ALA* 3.8 3.1 - - - +
490A GLU* 1.3 74.8 - - - +
492A PHE* 1.3 62.0 + - - +
494A THR 3.3 1.0 + - - -
495A PHE* 2.9 21.8 + - - +
796A TYR* 3.4 16.9 - - + +
799A GLN* 3.8 12.1 - - + -
800A LEU* 3.3 42.1 - - - +
803A VAL* 4.9 2.7 - - + -
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Residues in contact with PHE 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ALA 2.9 17.9 + - - +
489A ALA 3.8 4.5 - - - +
491A ALA* 1.3 74.2 - - - +
493A GLU* 1.3 59.8 + - - +
495A PHE* 3.4 7.1 + + - +
496A LEU* 3.0 46.4 + - + +
543A LEU* 3.7 20.0 - - + -
544A ASN* 3.7 40.2 - - + +
547A ALA* 3.9 12.8 - - + -
548A ASN* 4.1 3.4 - - - +
554A TYR* 3.5 38.6 - + - +
557A ILE* 4.9 2.0 - - + -
558A PHE* 3.5 31.9 - + - -
803A VAL* 4.4 8.3 - - + +
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Residues in contact with GLU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ALA 3.1 13.8 + - - +
490A GLU* 3.7 7.6 - - + +
491A ALA 3.3 0.2 - - - -
492A PHE* 1.3 73.6 - - - +
494A THR* 1.3 63.9 + - - +
496A LEU* 3.2 15.1 + - - +
497A GLN* 3.1 40.9 + - + +
506A PHE 4.1 6.2 - - - +
507A SER* 3.4 17.0 + - - -
508A LEU* 3.2 40.9 + - + +
509A GLU* 4.4 11.0 - - + +
512A GLU* 4.5 10.1 - - + +
541A GLY* 4.7 1.6 - - - -
544A ASN* 3.2 28.1 + - - +
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Residues in contact with THR 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A GLU* 2.9 21.0 + - - +
491A ALA 3.6 4.3 - - - -
493A GLU* 1.3 74.5 - - - +
495A PHE* 1.3 59.3 + - - +
497A GLN* 3.6 3.9 + - - +
498A THR* 2.8 39.7 + - - +
509A GLU* 5.6 1.7 + - - -
796A TYR* 3.0 26.1 + - - +
800A LEU* 3.8 18.4 - - + -
804A PHE* 5.6 1.3 - - + -
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Residues in contact with PHE 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A ALA 2.9 17.0 + - - +
492A PHE* 3.5 6.5 - + - +
494A THR* 1.3 77.5 - - - +
496A LEU* 1.3 60.1 + - + +
498A THR 3.1 0.3 + - - -
499A LYS* 2.7 62.8 + - + +
500A TYR* 3.9 11.2 - + - -
558A PHE* 3.6 31.4 - + - -
800A LEU* 3.9 3.3 - - + +
803A VAL* 3.6 39.5 - - + -
804A PHE* 3.6 44.0 - + - -
807A VAL* 3.6 26.0 - - + -
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Residues in contact with LEU 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A PHE* 3.0 41.3 + - + +
493A GLU* 3.5 21.5 - - - +
495A PHE* 1.3 79.3 - - + +
497A GLN* 1.3 76.2 + - - +
500A TYR* 3.2 38.4 + - + +
503A GLN* 3.8 17.5 - - + +
506A PHE 5.0 4.7 - - - +
543A LEU* 4.2 9.9 - - + -
544A ASN 6.2 0.2 - - - +
558A PHE* 3.9 25.1 - - + -
561A PHE* 5.3 0.4 - - + -
578A TYR* 3.6 19.7 - - - +
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Residues in contact with GLN 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A GLU* 3.1 32.4 + - + +
494A THR* 4.2 3.4 - - - +
496A LEU* 1.3 84.8 - - - +
498A THR* 1.4 62.4 + - - +
500A TYR 3.4 11.9 - - - +
503A GLN* 3.0 47.0 + - - +
504A LYS* 3.3 10.7 + - - +
507A SER* 4.0 13.4 + - - +
509A GLU* 6.0 1.1 - - - -
745A ARG* 3.9 35.7 + - - +
749A GLU* 5.4 0.2 - - - +
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Residues in contact with THR 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A THR* 2.8 30.6 + - - +
495A PHE 3.8 2.0 - - - -
497A GLN* 1.4 78.4 - - - +
499A LYS* 1.3 63.0 + - - +
500A TYR 3.4 2.0 + - - +
804A PHE* 3.7 24.2 - - + -
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Residues in contact with LYS 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A PHE* 2.7 43.2 + - + +
498A THR* 1.3 73.3 - - - +
500A TYR* 1.3 83.5 + - + +
804A PHE* 4.0 16.6 + - + -
807A VAL* 3.7 24.9 - - - +
808A ARG* 4.4 6.5 - - - +
811A GLU* 3.2 36.7 + - - -
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Residues in contact with TYR 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A PHE* 3.9 12.6 - + - -
496A LEU* 3.2 29.3 + - + +
497A GLN* 3.4 16.2 - - - +
498A THR 3.4 1.7 - - - -
499A LYS* 1.3 105.0 - - + +
501A VAL* 1.3 61.3 + - - +
503A GLN* 3.6 21.4 + - + +
558A PHE* 3.9 24.4 + + - +
561A PHE* 3.6 45.0 - + + +
807A VAL* 3.5 22.7 - - - +
811A GLU* 4.1 11.8 + - - +
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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