Contacts of the helix formed by residues 474 - 506 (chain J) in PDB entry 1MVW
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 SER 474 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472J PHE* 3.8 23.1 + - - -
473J ASN* 1.3 75.9 - - - +
475J PHE* 1.3 57.3 + - - +
476J GLU* 3.2 18.1 + - - -
477J GLN* 2.6 43.2 + - - +
478J LEU 3.3 3.8 + - - -
590J TYR* 4.1 2.0 - - - -
591J ASN* 3.2 7.1 + - - -
593J SER 4.7 1.0 + - - -
595J TRP* 2.8 34.3 + - - -
598J MLY 4.2 10.5 + - - -
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Residues in contact with PHE 475 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269J LEU* 6.5 0.4 - - + -
474J SER* 1.3 78.1 + - - +
476J GLU* 1.3 76.7 + - + +
478J LEU* 3.1 14.3 + - + +
479J CYS* 3.2 35.3 + - - -
533J PHE* 4.3 11.9 - + - -
536J LEU* 4.2 15.3 - - + -
595J TRP* 3.0 51.0 - + + +
598J MLY 3.9 27.8 - - + -
599J ASN* 3.6 25.6 - - + -
649J VAL* 3.8 25.4 - - + -
650J SER* 4.3 1.8 - - - -
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Residues in contact with GLU 476 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269J LEU* 5.5 8.2 - - + +
474J SER* 3.9 7.4 - - - -
475J PHE* 1.3 89.2 + - + +
477J GLN* 1.3 81.8 + - - +
479J CYS* 3.3 8.0 + - - +
480J ILE* 3.1 25.9 + - + +
598J MLY 2.7 51.5 + - + +
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Residues in contact with GLN 477 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468J GLU 4.9 4.3 - - - +
470J PHE* 3.8 37.8 - - + -
472J PHE* 3.6 5.6 - - - +
473J ASN* 3.4 20.1 - - + +
474J SER* 2.6 50.6 + - - +
476J GLU* 1.3 88.7 + - - +
478J LEU* 1.3 58.8 + - - +
480J ILE* 4.5 2.9 - - + +
481J ASN* 2.7 45.8 + - - +
590J TYR* 4.0 3.4 - - + -
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Residues in contact with LEU 478 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474J SER 3.3 2.2 + - - +
475J PHE* 3.1 12.7 + - + +
477J GLN* 1.3 80.2 - - - +
479J CYS* 1.3 58.2 + - - +
482J PHE* 2.7 35.1 + - + +
526J ILE* 4.2 24.2 - - + -
532J ILE* 4.4 15.5 - - + -
533J PHE* 3.5 35.9 - - + -
579J PHE* 5.2 2.7 - - + -
581J LEU* 4.6 6.1 - - + -
583J HIS* 4.9 1.1 - - + -
590J TYR* 3.4 39.7 - - + +
595J TRP* 4.0 24.0 - - + -
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Residues in contact with CYS 479 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269J LEU* 4.4 15.7 - - + -
475J PHE* 3.2 46.2 + - - -
476J GLU* 3.9 6.1 - - - +
477J GLN 3.2 0.2 - - - -
478J LEU* 1.3 79.7 - - - +
480J ILE* 1.3 54.2 + - - +
482J PHE* 3.5 2.7 - - - +
483J THR* 2.5 33.5 + - - -
533J PHE* 4.3 9.0 - - - -
649J VAL 5.8 0.2 - - - -
650J SER* 5.7 0.7 - - - -
653J PHE* 3.2 42.9 - - + -
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Residues in contact with ILE 480 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269J LEU* 3.9 29.8 - - + -
464J ILE* 4.6 11.7 - - + -
465J ALA* 4.4 27.4 - - + +
466J GLY 4.5 9.0 - - - +
467J PHE* 4.8 0.2 - - - -
468J GLU* 5.1 1.6 - - + +
476J GLU* 3.1 16.9 + - + +
477J GLN* 3.9 2.7 - - + +
479J CYS* 1.3 74.5 - - - +
481J ASN* 1.3 80.2 + - - +
483J THR* 2.8 22.9 + - - +
484J ASN* 2.9 23.0 + - - +
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Residues in contact with ASN 481 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467J PHE* 3.9 31.7 - - + +
468J GLU 3.7 21.8 + - - +
477J GLN* 2.7 28.8 + - - +
478J LEU 3.8 0.9 - - - +
480J ILE* 1.3 86.5 - - - +
482J PHE* 1.3 53.2 + - - +
484J ASN* 3.0 4.9 + - - +
485J GLU* 2.7 35.5 + - - +
583J HIS* 3.6 13.2 - - + -
588J VAL* 4.2 7.1 - - - +
590J TYR* 3.1 27.5 + - - +
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Residues in contact with PHE 482 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478J LEU* 2.7 20.0 + - + +
479J CYS* 3.5 3.4 - - - +
481J ASN* 1.3 79.2 - - - +
483J THR* 1.3 64.8 + - - +
485J GLU* 3.4 5.6 + - + +
486J MLY 3.4 33.8 + - + +
523J ILE* 4.2 19.1 - - + -
526J ILE* 3.7 43.1 - - + -
527J GLU* 3.5 34.5 - - + -
533J PHE* 4.0 22.4 - + + -
583J HIS* 4.6 1.0 - - - -
653J PHE* 4.2 6.3 - + - -
654J ARG* 4.7 8.7 - - + -
657J LEU* 3.5 30.3 - - + -
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Residues in contact with THR 483 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269J LEU* 5.1 1.4 - - - +
464J ILE* 4.4 22.2 - - + -
479J CYS 2.5 24.1 + - - -
480J ILE* 2.8 14.5 + - - +
482J PHE* 1.3 77.7 - - - +
484J ASN* 1.3 65.3 + - - +
486J MLY 3.2 5.1 + - - +
487J LEU* 3.1 39.6 + - + +
653J PHE* 3.3 15.9 - - + -
657J LEU* 3.9 27.6 - - + -
660J LEU* 5.2 2.0 - - + -
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Residues in contact with ASN 484 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178J THR* 4.0 10.7 + - - +
465J ALA 2.5 29.9 + - - +
466J GLY* 2.9 6.1 - - - -
467J PHE* 2.8 40.0 - - + +
480J ILE* 2.9 19.8 + - - +
481J ASN 3.7 5.6 - - - +
483J THR* 1.3 75.5 - - - +
485J GLU* 1.3 62.6 + - - +
486J MLY 2.8 6.4 + - - -
487J LEU* 3.0 18.4 + - - +
488J GLN* 2.9 24.8 + - - +
584J TYR* 3.9 8.8 + - - +
673J ARG* 5.4 3.1 + - - -
697J CYS 6.0 0.2 - - - -
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Residues in contact with GLU 485 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467J PHE* 4.1 1.2 - - - -
481J ASN 2.7 17.0 + - - +
482J PHE* 4.1 7.2 - - + +
483J THR 3.4 0.2 - - - -
484J ASN* 1.3 72.5 - - - +
486J MLY 1.3 61.2 + - - +
488J GLN 4.0 0.2 - - - -
489J GLN* 3.5 14.7 + - - +
519J LEU* 3.7 18.5 - - + +
522J CYS* 4.1 16.9 - - + +
523J ILE* 4.0 18.3 - - + +
582J VAL 4.3 0.3 - - - +
583J HIS* 2.5 44.0 + - - +
584J TYR* 2.5 52.5 + - + +
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Residues in contact with MLY 486 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482J PHE* 3.4 29.2 + - + +
483J THR* 3.2 10.5 + - - +
484J ASN 2.9 0.4 - - - -
485J GLU* 1.3 78.4 + - - +
487J LEU* 1.3 67.0 + - - +
489J GLN* 3.1 9.1 + - - +
490J PHE* 3.0 20.3 + - - +
523J ILE* 4.4 21.1 - - + -
527J GLU* 2.8 44.6 - - - -
657J LEU* 4.3 18.8 - - + -
658J ASN* 3.1 37.0 - - - -
661J MET* 4.2 32.7 - - + +
665J ARG* 4.8 17.2 + - - -
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Residues in contact with LEU 487 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J LEU* 4.6 15.7 - - + -
462J LEU* 4.6 13.5 - - + -
464J ILE* 5.2 6.5 - - + -
465J ALA 5.6 1.1 - - - +
483J THR* 3.1 36.4 + - + +
484J ASN* 3.0 24.0 + - - +
486J MLY 1.3 78.3 + - - +
488J GLN* 1.3 58.0 + - - +
490J PHE* 2.8 29.2 - - + +
491J PHE* 3.1 8.5 + - - +
660J LEU* 5.5 3.6 - - + -
661J MET* 3.6 23.8 - - + -
664J LEU* 3.9 15.9 - - + -
671J PHE* 4.8 2.5 - - - -
673J ARG* 5.2 13.5 - - - +
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Residues in contact with GLN 488 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122J PHE* 5.3 0.5 - - - -
484J ASN 2.9 7.4 + - - +
485J GLU 3.8 3.1 - - - +
487J LEU* 1.3 72.8 - - - +
489J GLN* 1.3 56.1 + - - +
490J PHE 2.9 4.0 - - - -
491J PHE* 2.9 41.1 + - - +
492J ASN* 2.7 45.9 + - - +
519J LEU* 4.1 6.1 - - + -
584J TYR* 3.4 48.8 + - + +
673J ARG* 4.6 8.7 + - - +
698J ASN 3.9 6.4 - - - +
699J GLY* 3.5 29.2 + - - -
702J GLU* 4.9 8.0 - - - +
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Residues in contact with GLN 489 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485J GLU 3.5 10.8 + - - +
486J MLY 3.1 11.5 + - - +
488J GLN* 1.3 78.1 - - - +
490J PHE* 1.3 62.5 + - - +
492J ASN* 3.8 5.7 - - - +
493J HIS* 3.1 25.2 + - + +
516J GLY* 3.2 36.7 + - - +
517J MET* 4.1 1.4 - - - +
519J LEU* 3.9 12.2 - - + +
520J ALA* 3.4 31.5 - - - +
523J ILE* 3.7 14.9 - - + +
665J ARG* 5.8 2.4 + - - -
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Residues in contact with PHE 490 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174J SER* 5.1 0.4 - - - -
176J LEU* 4.5 12.3 - - + -
486J MLY 3.0 8.5 + - - +
487J LEU* 2.8 21.5 - - - +
489J GLN* 1.3 81.0 - - - +
491J PHE* 1.3 59.7 + - - +
493J HIS* 3.9 5.7 - + + +
494J HIS* 3.4 17.5 + - + +
661J MET* 4.2 19.3 - - + -
664J LEU* 3.3 48.0 - - + -
665J ARG* 4.3 18.2 - - + -
667J THR 4.9 0.7 - - - -
669J PRO* 3.5 38.4 - - + -
671J PHE* 4.1 11.4 - + - -
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Residues in contact with PHE 491 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J LEU* 4.0 26.5 - - + -
122J PHE* 3.3 41.5 - + - -
487J LEU 3.1 5.4 + - - +
488J GLN* 2.9 30.5 + - - +
490J PHE* 1.3 78.4 - - - +
492J ASN* 1.3 70.4 + - - +
493J HIS 2.7 5.1 + - - -
494J HIS* 2.6 27.3 + + - +
495J MET* 2.8 28.9 + - + +
671J PHE* 3.2 50.7 - + + -
673J ARG* 5.9 1.1 - - - +
699J GLY 4.7 0.7 - - - -
702J GLU 5.4 0.2 - - - -
703J GLY* 4.3 17.0 - - - -
706J ILE* 5.0 2.2 - - + -
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Residues in contact with ASN 492 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488J GLN* 2.7 43.6 + - - +
489J GLN* 3.8 5.4 - - - +
491J PHE* 1.3 77.1 - - - +
493J HIS* 1.3 60.8 + - - +
495J MET* 3.9 5.3 - - - +
496J PHE* 3.3 13.0 + - - +
515J PHE* 3.4 48.7 + - + +
516J GLY* 3.7 3.6 - - - +
518J ASP* 5.6 0.4 - - - +
519J LEU* 3.8 12.1 - - - +
702J GLU* 3.7 27.0 + - - +
706J ILE* 4.1 14.4 - - - +
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Residues in contact with HIS 493 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489J GLN* 3.1 17.8 + - + +
490J PHE* 3.9 7.0 - + + +
491J PHE 2.7 5.7 + - - -
492J ASN* 1.3 72.2 - - - +
494J HIS* 1.3 53.2 + - - +
495J MET 2.9 4.5 - - - -
496J PHE* 2.5 27.7 + + - +
497J VAL* 2.7 40.9 + - + +
514J ASP* 2.4 39.5 + - - +
516J GLY* 4.9 1.1 - - - +
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Residues in contact with HIS 494 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J LEU* 4.2 23.5 - - + +
490J PHE* 3.4 12.6 + - + +
491J PHE* 2.6 13.9 + + - +
493J HIS* 1.3 79.0 - - - +
495J MET* 1.3 59.0 + - - +
497J VAL* 3.5 9.6 - - + +
498J LEU* 2.9 53.1 + - + +
668J HIS* 3.6 31.6 + + - -
669J PRO* 3.6 30.1 + - + +
671J PHE* 4.2 17.9 - + + -
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Residues in contact with MET 495 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120J GLY* 5.2 5.6 - - - -
121J LEU* 3.5 39.3 - - + +
491J PHE* 2.8 32.9 + - + +
492J ASN* 4.0 9.0 - - - +
494J HIS* 1.3 78.9 - - - +
496J PHE* 1.3 59.8 + - - +
498J LEU* 3.5 6.0 - - + +
499J GLU* 2.7 43.3 + - + +
515J PHE* 4.5 0.9 - - - -
703J GLY* 4.3 9.0 - - - +
706J ILE* 3.7 29.4 - - + -
707J CYS* 4.0 24.9 - - - -
714J ARG* 5.1 3.4 - - - +
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Residues in contact with PHE 496 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492J ASN 3.3 13.4 + - - +
493J HIS* 2.5 15.1 + + - +
495J MET* 1.3 74.3 - - - +
497J VAL* 1.2 79.9 + - + +
499J GLU* 3.8 0.7 - - - +
500J GLN* 3.3 45.3 + - - +
512J PHE* 3.0 39.2 - + - -
513J ILE* 3.1 7.2 - - - -
514J ASP* 2.9 52.5 - - + -
515J PHE* 3.4 18.4 - + + +
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Residues in contact with VAL 497 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493J HIS* 2.7 43.8 + - + +
494J HIS* 3.5 11.9 - - - +
496J PHE* 1.2 92.8 - - + +
498J LEU* 1.3 66.8 + - + +
500J GLN* 3.6 10.1 + - - +
501J GLU* 3.5 23.7 + - - +
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Residues in contact with LEU 498 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J LEU* 4.1 33.9 - - + -
494J HIS* 2.9 39.4 + - + +
495J MET* 3.5 6.7 - - + +
497J VAL* 1.3 79.5 - - + +
499J GLU* 1.3 67.4 + - - +
501J GLU* 3.0 31.4 + - - +
502J GLU* 3.6 3.3 + - - +
668J HIS* 5.3 3.8 - - - +
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Residues in contact with GLU 499 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495J MET* 2.7 34.6 + - + +
496J PHE 3.8 0.4 - - - +
498J LEU* 1.3 73.1 - - - +
500J GLN* 1.3 55.8 + - - +
502J GLU* 2.8 37.9 + - - +
503J TYR* 3.0 36.6 + - - -
512J PHE* 3.6 21.5 - - + -
515J PHE* 4.7 8.9 - - + -
706J ILE* 4.9 7.9 - - + +
707J CYS* 5.2 0.8 - - - +
714J ARG* 3.9 27.6 + - - -
766J PHE* 4.7 8.3 - - - -
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Residues in contact with GLN 500 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496J PHE* 3.3 38.7 + - - +
497J VAL* 3.9 7.5 - - - +
498J LEU 3.3 0.8 - - - -
499J GLU* 1.3 77.6 - - - +
501J GLU* 1.3 60.8 + - - +
503J TYR* 4.1 6.4 - - - +
504J MLY 3.2 22.2 + - + +
510J TRP 5.8 1.0 + - - +
512J PHE* 3.3 34.5 + - + +
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Residues in contact with GLU 501 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497J VAL* 3.5 19.4 + - - +
498J LEU* 3.0 24.0 + - - +
499J GLU 2.8 1.0 + - - -
500J GLN* 1.3 75.3 - - - +
502J GLU* 1.3 56.6 + - - +
504J MLY 2.9 9.8 + - + +
505J MLY 2.6 69.1 + - - +
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Residues in contact with GLU 502 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498J LEU 3.6 2.3 + - - +
499J GLU* 2.8 15.8 + - - +
501J GLU* 1.3 74.9 - - - +
503J TYR* 1.3 61.9 + - + +
504J MLY 2.6 16.1 + - - -
505J MLY 2.7 32.8 + - - +
506J GLU* 2.7 41.5 + - + +
508J ILE* 6.1 1.1 - - + -
761J GLY* 3.9 14.8 - - - -
762J HIS* 4.0 7.3 + - - +
763J THR 5.2 1.6 + - - -
766J PHE* 4.4 29.7 - - + -
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Residues in contact with TYR 503 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499J GLU* 3.0 36.6 + - - -
500J GLN* 4.1 6.3 - - - +
502J GLU* 1.3 83.6 - - + +
504J MLY 1.3 54.9 + - - -
507J GLY* 3.1 4.7 + - - -
508J ILE* 2.9 72.8 + - + +
510J TRP* 3.3 50.3 - + + +
512J PHE* 3.6 21.8 - + - -
707J CYS 5.5 0.2 + - - -
710J GLY* 4.5 2.3 - - - -
711J PHE* 4.2 30.2 + + - +
714J ARG* 4.7 2.3 + - - -
766J PHE* 5.1 11.8 - + - -
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Residues in contact with MLY 504 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500J GLN* 3.2 16.0 + - + +
501J GLU* 2.9 15.2 + - + +
502J GLU 2.6 5.3 + - - -
503J TYR* 1.3 75.3 + - - +
505J MLY 1.3 64.3 + - - +
507J GLY* 3.8 7.5 + - - -
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Residues in contact with MLY 505 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501J GLU* 2.6 56.8 + - - +
502J GLU* 2.7 23.6 + - - +
504J MLY 1.3 76.9 + - - +
506J GLU* 1.3 68.1 + - - +
507J GLY* 4.5 0.2 - - - -
762J HIS* 2.3 52.6 + - + +
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Residues in contact with GLU 506 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502J GLU* 2.7 26.9 + - + +
505J MLY 1.3 77.7 + - - +
507J GLY* 1.3 59.9 + - - +
508J ILE* 3.9 24.0 - - + -
741J LYS* 5.4 1.2 + - - -
759J ALA* 5.7 0.2 - - + -
760J PHE* 2.6 23.1 - - - +
761J GLY* 2.1 38.1 - - - -
762J HIS* 3.2 25.0 + - - -
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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