Contacts of the helix formed by residues 475 - 502 (chain A) in PDB entry 2MYS
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 PHE 475 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LEU* 6.5 0.4 - - + -
474A SER* 1.3 77.7 + - - +
476A GLU* 1.3 76.6 + - + +
478A LEU* 3.1 13.8 + - + +
479A CYS* 3.2 35.5 + - - -
533A PHE* 4.3 11.7 - + - -
536A LEU* 4.2 15.0 - - + -
595A TRP* 3.0 51.2 - + + +
598A MLY 3.9 31.0 - - + -
599A ASN* 3.6 26.2 - - + -
649A VAL* 4.5 15.9 - - + -
650A SER* 4.3 6.3 - - - -
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Residues in contact with GLU 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LEU* 5.5 7.8 - - + +
474A SER* 3.9 7.4 - - - -
475A PHE* 1.3 89.3 + - + +
477A GLN* 1.3 81.2 + - - +
479A CYS* 3.3 8.2 + - - +
480A ILE* 3.1 27.1 + - + +
598A MLY 2.7 50.2 + - + +
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Residues in contact with GLN 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A GLU 4.9 3.8 - - - +
470A PHE* 3.8 37.8 - - + -
472A PHE* 3.6 5.4 - - - +
473A ASN* 3.4 19.1 - - + +
474A SER* 2.6 50.7 + - - +
476A GLU* 1.3 87.9 + - - +
478A LEU* 1.3 58.8 + - - +
480A ILE* 4.5 3.1 - - + +
481A ASN* 2.7 45.0 + - - +
590A TYR* 4.0 2.9 - - + -
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Residues in contact with LEU 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A SER 3.3 2.0 + - - -
475A PHE* 3.1 12.9 + - + +
477A GLN* 1.3 79.5 - - - +
479A CYS* 1.3 58.7 + - - +
482A PHE* 2.7 34.9 + - + +
526A ILE* 4.2 24.2 - - + -
532A ILE* 4.4 15.0 - - + -
533A PHE* 3.5 35.9 - - + -
579A PHE* 5.2 2.9 - - + -
581A LEU* 4.6 5.4 - - + -
583A HIS* 4.9 0.7 - - + -
590A TYR* 3.4 39.1 - - + +
595A TRP* 4.0 25.1 - - + -
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Residues in contact with CYS 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LEU* 4.4 17.0 - - + -
475A PHE* 3.2 45.5 + - - -
476A GLU* 3.9 6.3 - - - +
478A LEU* 1.3 79.5 - - - +
480A ILE* 1.3 54.9 + - - +
482A PHE* 3.5 2.5 - - - +
483A THR* 2.5 33.7 + - - -
533A PHE* 4.3 8.3 - - - -
650A SER* 5.7 0.9 - - - -
653A PHE* 3.2 40.1 - - + -
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Residues in contact with ILE 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LEU* 3.9 29.4 - - + -
464A ILE* 4.6 11.4 - - + -
465A ALA* 4.4 27.6 - - + +
466A GLY 4.5 8.5 - - - +
468A GLU* 5.1 1.6 - - + +
476A GLU* 3.1 16.9 + - + +
477A GLN* 3.9 2.5 - - + +
479A CYS* 1.3 75.4 - - - +
481A ASN* 1.3 81.0 + - - +
483A THR* 2.8 22.0 + - - +
484A ASN* 2.9 24.3 + - - +
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Residues in contact with ASN 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A PHE* 3.9 32.0 - - + +
468A GLU 3.7 21.6 + - - +
477A GLN* 2.7 28.5 + - - +
478A LEU 3.8 0.4 - - - +
480A ILE* 1.3 86.4 - - - +
482A PHE* 1.3 53.8 + - - +
484A ASN* 3.0 4.2 + - - +
485A GLU* 2.7 36.2 + - - +
583A HIS* 3.6 12.8 - - + -
588A VAL* 4.2 7.4 - - - +
590A TYR* 3.1 26.2 + - - +
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Residues in contact with PHE 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A LEU* 2.7 19.4 + - + +
479A CYS* 3.5 2.7 - - - +
481A ASN* 1.3 78.2 - - - +
483A THR* 1.3 64.4 + - - +
485A GLU* 3.4 5.3 + - + +
486A MLY 3.4 35.3 + - + +
523A ILE* 4.2 18.2 - - + -
526A ILE* 3.7 40.8 - - + -
527A GLU* 3.5 33.9 - - + -
533A PHE* 4.0 22.7 - + + -
583A HIS* 4.7 1.3 - - - -
653A PHE* 4.2 5.8 - + - -
654A ARG* 4.7 9.2 - - + -
657A LEU* 3.5 30.7 - - + -
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Residues in contact with THR 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LEU* 5.1 1.0 - - - +
464A ILE* 4.4 21.1 - - + -
479A CYS 2.5 24.4 + - - -
480A ILE* 2.8 14.1 + - - +
482A PHE* 1.3 78.3 - - - +
484A ASN* 1.3 64.9 + - - +
486A MLY 3.2 5.0 + - - +
487A LEU* 3.1 40.5 + - + +
653A PHE* 3.3 17.2 - - + -
657A LEU* 3.9 26.7 - - + -
660A LEU* 5.2 2.2 - - + -
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Residues in contact with ASN 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR* 4.0 10.9 + - - +
465A ALA 2.5 30.1 + - - +
466A GLY* 2.9 5.9 - - - -
467A PHE* 2.8 39.4 - - + +
480A ILE* 2.9 18.4 + - - +
481A ASN 3.7 5.4 - - - +
483A THR* 1.3 75.8 - - - +
485A GLU* 1.3 64.2 + - - +
486A MLY 2.8 6.2 + - - -
487A LEU* 3.0 18.9 + - - +
488A GLN* 2.9 23.9 + - - +
584A TYR* 3.9 8.9 + - - +
673A ARG* 5.4 2.9 + - - -
697A CYS 6.0 0.2 - - - -
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Residues in contact with GLU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A PHE* 4.1 1.4 - - + -
481A ASN 2.7 17.9 + - - +
482A PHE* 4.1 6.7 - - + +
483A THR 3.4 0.4 - - - -
484A ASN* 1.3 73.8 - - - +
486A MLY 1.3 61.4 + - - +
489A GLN* 3.5 14.4 + - - +
519A LEU* 3.7 18.9 - - + +
522A CYS* 4.1 17.3 - - + +
523A ILE* 4.0 18.5 - - + +
526A ILE* 6.3 1.1 - - + -
582A VAL 4.3 0.2 - - - +
583A HIS* 2.5 43.8 + - - +
584A TYR* 2.5 52.9 + - + +
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Residues in contact with MLY 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A PHE* 3.4 28.8 + - + +
483A THR* 3.2 11.2 + - - +
484A ASN 2.9 0.2 - - - -
485A GLU* 1.3 78.7 + - - +
487A LEU* 1.3 65.6 + - - +
489A GLN* 3.1 8.5 + - - +
490A PHE* 3.0 20.7 + - - +
523A ILE* 4.4 21.3 - - + -
527A GLU* 2.8 44.9 - - - -
657A LEU* 4.3 19.1 - - + -
658A ASN* 3.1 36.6 - - - -
661A MET* 4.2 32.6 - - + +
665A ARG* 4.8 17.7 + - - -
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Residues in contact with LEU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 4.6 16.2 - - + -
178A THR* 5.4 4.0 - - - +
462A LEU* 4.6 13.2 - - + -
464A ILE* 5.2 6.1 - - + -
465A ALA 5.6 1.1 - - - +
483A THR* 3.1 37.1 + - + +
484A ASN* 3.4 23.3 - - - +
486A MLY 1.3 77.9 + - - +
488A GLN* 1.3 57.7 + - - +
490A PHE* 2.8 29.4 - - + +
491A PHE* 3.1 8.3 + - - +
660A LEU* 5.5 3.4 - - + -
661A MET* 3.6 24.5 - - + -
664A LEU* 3.9 16.4 - - + -
671A PHE* 4.8 3.3 - - + -
673A ARG* 5.1 12.8 - - - +
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Residues in contact with GLN 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PHE* 5.3 0.9 - - - -
484A ASN 2.9 8.0 + - - +
485A GLU 3.8 3.6 - - - +
487A LEU* 1.3 72.8 - - - +
489A GLN* 1.3 55.9 + - - +
490A PHE 2.9 4.7 - - - -
491A PHE* 2.9 41.0 + - - +
492A ASN* 2.7 46.2 + - - +
519A LEU* 4.1 6.3 - - + -
584A TYR* 3.4 48.2 + - + -
673A ARG* 4.6 8.1 + - - +
698A ASN 3.9 6.8 - - - +
699A GLY* 3.5 28.9 + - - -
702A GLU* 4.9 7.9 - - + +
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Residues in contact with GLN 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A GLU 3.5 9.9 + - - +
486A MLY 3.1 11.1 + - - +
488A GLN* 1.3 78.3 - - - +
490A PHE* 1.3 62.1 + - - +
492A ASN* 3.8 6.1 - - - +
493A HIS* 3.1 25.4 + - + +
516A GLY* 3.2 37.1 + - - +
517A MET* 4.1 0.8 - - - +
519A LEU* 3.9 12.1 - - + +
520A ALA* 3.4 30.7 - - - +
523A ILE* 3.7 16.5 - - + +
665A ARG* 5.8 2.4 + - - -
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Residues in contact with PHE 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A SER* 5.1 0.2 - - - -
176A LEU* 4.5 12.6 - - + -
486A MLY 3.0 8.7 + - - +
487A LEU* 2.8 22.0 - - - +
488A GLN 2.9 0.2 - - - -
489A GLN* 1.3 79.2 - - - +
491A PHE* 1.3 60.4 + - - +
493A HIS* 3.9 5.7 + + + +
494A HIS* 3.4 18.0 + - + +
661A MET* 4.1 20.0 - - + -
664A LEU* 3.3 49.1 - - + -
665A ARG* 4.3 17.7 - - + -
667A THR 4.9 0.4 - - - -
669A PRO* 3.5 37.0 - - + -
671A PHE* 4.1 11.2 - + - -
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Residues in contact with PHE 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.0 25.8 - - + -
122A PHE* 3.3 41.1 - + - -
487A LEU 3.1 5.3 + - - +
488A GLN* 2.9 31.1 + - - +
490A PHE* 1.3 77.2 - - - +
492A ASN* 1.3 70.2 + - - +
493A HIS 2.7 5.1 + - - -
494A HIS* 2.6 27.5 + + - +
495A MET* 2.8 29.6 + - + +
671A PHE* 3.2 50.3 - + + -
673A ARG* 5.9 1.8 - - - +
699A GLY 4.7 0.4 - - - -
702A GLU 5.4 0.2 - - - -
703A GLY* 4.3 16.8 - - - -
706A ILE* 5.0 2.9 - - + -
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Residues in contact with ASN 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A GLN* 2.7 45.2 + - - +
489A GLN* 3.8 4.5 - - - +
491A PHE* 1.3 77.1 - - - +
493A HIS* 1.3 59.6 + - - +
495A MET* 3.9 5.3 - - - +
496A PHE* 3.3 13.3 + - - +
515A PHE* 3.4 49.4 + - + +
516A GLY* 3.7 3.4 - - - +
518A ASP* 5.6 0.6 - - - +
519A LEU* 3.8 11.5 - - - +
702A GLU* 3.7 27.0 + - - +
706A ILE* 4.1 12.8 - - - +
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Residues in contact with HIS 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A GLN* 3.1 18.1 + - + +
490A PHE* 3.9 7.0 - + + +
491A PHE 2.7 5.1 + - - -
492A ASN* 1.3 72.2 - - - +
494A HIS* 1.3 53.7 + - - +
495A MET 2.9 3.8 - - - -
496A PHE* 2.5 28.0 + + - +
497A VAL* 2.7 42.1 + - + +
514A ASP* 2.4 38.5 + - - +
516A GLY* 4.9 0.9 - - - -
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Residues in contact with HIS 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.2 24.2 - - + +
490A PHE* 3.4 13.0 + - + +
491A PHE* 2.6 14.1 + + - +
493A HIS* 1.3 79.0 - - - +
495A MET* 1.3 58.8 + - - +
497A VAL* 3.5 10.2 + - + +
498A LEU* 2.9 52.6 + - + +
668A HIS* 3.6 32.1 + + - -
669A PRO* 3.6 29.0 + - + +
671A PHE* 4.2 18.2 - + + -
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Residues in contact with MET 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLY* 5.2 5.4 - - - -
121A LEU* 3.5 39.7 - - + +
491A PHE* 2.8 32.5 + - + +
492A ASN* 4.0 8.7 - - - +
494A HIS* 1.3 79.2 - - - +
496A PHE* 1.3 59.1 + - - +
498A LEU* 3.5 6.5 - - + +
499A GLU* 2.7 43.9 + - + +
515A PHE* 4.5 0.9 - - - -
703A GLY* 4.3 8.5 - - - +
706A ILE* 3.7 30.1 - - + -
707A CYS* 4.0 23.8 - - - -
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Residues in contact with PHE 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ASN 3.3 13.0 + - - +
493A HIS* 2.5 16.4 + + - +
495A MET* 1.3 74.4 - - - +
497A VAL* 1.2 80.8 + - + +
499A GLU* 3.8 0.7 - - - +
500A GLN* 3.3 44.6 + - - +
512A PHE* 3.0 40.1 - + - -
513A ILE* 3.1 7.2 - - - -
514A ASP* 2.9 51.6 - - + -
515A PHE* 3.4 18.8 - + + +
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Residues in contact with VAL 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A HIS* 2.7 43.9 + - + +
494A HIS* 3.5 10.8 - - - +
496A PHE* 1.2 93.4 - - + +
498A LEU* 1.3 66.4 + - + +
500A GLN* 3.6 9.1 + - - +
501A GLU* 3.5 23.9 + - - +
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Residues in contact with LEU 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.1 33.7 - - + -
494A HIS* 2.9 38.8 + - + +
495A MET* 3.5 7.6 - - + +
497A VAL* 1.3 79.8 - - + +
499A GLU* 1.3 67.9 + - - +
501A GLU* 3.0 31.7 + - - +
502A GLU* 3.6 3.8 + - - +
668A HIS* 5.3 3.6 - - - +
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Residues in contact with GLU 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A MET* 2.7 35.9 + - + +
496A PHE 3.8 0.9 - - - +
498A LEU* 1.3 71.4 - - - +
500A GLN* 1.3 54.7 + - - +
502A GLU* 2.8 35.0 + - - +
503A TYR* 3.0 35.6 + - - -
512A PHE* 3.6 20.2 - - + -
515A PHE* 4.7 8.7 - - + -
706A ILE* 4.9 10.1 - - + +
707A CYS* 5.2 7.5 - - - +
710A GLY* 5.0 2.8 - - - -
714A ARG* 3.4 29.7 + - - -
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Residues in contact with GLN 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A PHE* 3.3 38.7 + - - +
497A VAL* 3.9 9.3 - - - +
498A LEU 3.3 0.4 - - - -
499A GLU* 1.3 78.6 - - - +
501A GLU* 1.3 60.7 + - - +
502A GLU 3.3 0.2 - - - -
503A TYR* 3.9 6.6 + - - +
504A MLY 3.2 22.7 + - + +
510A TRP 5.8 0.8 + - - -
512A PHE* 3.3 34.1 + - + +
----------------------------------------------------------
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Residues in contact with GLU 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A VAL* 3.5 19.9 + - - +
498A LEU* 3.0 23.0 + - - +
499A GLU 2.8 1.2 + - - -
500A GLN* 1.3 75.5 - - - +
502A GLU* 1.3 55.6 + - - +
504A MLY 2.9 8.9 + - + +
505A MLY 2.6 70.0 + - - +
----------------------------------------------------------
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Residues in contact with GLU 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A LEU 3.6 2.7 + - - +
499A GLU* 2.8 12.2 + - - +
501A GLU* 1.3 74.5 - - - +
503A TYR* 1.3 56.2 + - + +
504A MLY 2.6 14.7 + - - -
505A MLY 2.7 33.7 + - - +
506A GLU* 2.7 35.4 + - - +
714A ARG* 4.2 16.6 + - - +
764A MLY 3.4 35.0 - - - -
766A PHE* 3.5 27.1 - - + -
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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