Contacts of the helix formed by residues 474 - 506 (chain P) 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 P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472P PHE* 3.8 23.1 + - - -
473P ASN* 1.3 76.8 - - - +
475P PHE* 1.3 55.8 + - - +
476P GLU* 3.2 17.5 + - - -
477P GLN* 2.6 42.5 + - - +
478P LEU 3.3 4.0 + - - -
590P TYR* 4.1 1.6 - - - -
591P ASN* 3.2 6.3 + - - -
593P SER 4.7 1.0 + - - -
595P TRP* 2.8 34.2 + - - -
598P MLY 4.2 10.7 + - - -
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Residues in contact with PHE 475 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269P LEU* 6.5 0.9 - - + -
474P SER* 1.3 78.2 + - - +
476P GLU* 1.3 75.7 + - + +
478P LEU* 3.1 13.7 + - + +
479P CYS* 3.2 35.8 + - - -
533P PHE* 4.3 11.7 - + - -
536P LEU* 4.2 15.5 - - + -
595P TRP* 3.0 51.4 - + + +
598P MLY 3.9 27.4 - - + -
599P ASN* 3.6 24.9 - - + -
649P VAL* 3.8 26.0 - - + -
650P SER* 4.3 1.8 - - - -
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Residues in contact with GLU 476 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269P LEU* 5.5 8.2 - - + +
474P SER* 3.9 7.6 - - - -
475P PHE* 1.3 88.6 + - + +
477P GLN* 1.3 81.4 + - - +
479P CYS* 3.3 7.4 + - - +
480P ILE* 3.1 27.2 + - + +
598P MLY 2.7 50.7 + - + +
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Residues in contact with GLN 477 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468P GLU 4.9 3.8 - - - +
470P PHE* 3.8 38.3 - - + -
472P PHE* 3.6 5.6 - - - +
473P ASN* 3.4 19.1 - - + +
474P SER* 2.6 50.1 + - - +
476P GLU* 1.3 88.9 + - - +
478P LEU* 1.3 58.0 + - - +
480P ILE* 4.5 3.4 - - + +
481P ASN* 2.7 45.2 + - - +
590P TYR* 4.0 3.1 - - + -
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Residues in contact with LEU 478 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474P SER 3.3 1.8 + - - +
475P PHE* 3.1 11.6 + - + +
477P GLN* 1.3 79.4 - - - +
479P CYS* 1.3 58.7 + - - +
482P PHE* 2.7 34.3 + - - +
526P ILE* 4.2 23.8 - - + -
532P ILE* 4.4 15.3 - - + -
533P PHE* 3.5 35.0 - - + -
579P PHE* 5.2 3.4 - - + -
581P LEU* 4.6 5.8 - - + -
583P HIS* 4.9 0.7 - - + -
590P TYR* 3.4 39.0 - - + +
595P TRP* 4.0 24.5 - - + -
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Residues in contact with CYS 479 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269P LEU* 4.4 16.4 - - + -
475P PHE* 3.2 45.2 + - - -
476P GLU* 3.9 6.7 - - - +
477P GLN 3.2 0.2 - - - -
478P LEU* 1.3 80.7 - - - +
480P ILE* 1.3 54.5 + - - +
482P PHE* 3.5 2.7 - - - +
483P THR* 2.5 33.3 + - - -
533P PHE* 4.3 8.7 - - - -
649P VAL 5.8 0.4 - - - -
650P SER* 5.7 0.7 - - - -
653P PHE* 3.2 41.5 - - + -
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Residues in contact with ILE 480 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269P LEU* 3.9 30.1 - - + -
464P ILE* 4.6 12.1 - - + -
465P ALA* 4.4 27.6 - - + +
466P GLY 4.5 9.2 - - - +
468P GLU* 5.1 1.8 - - + +
476P GLU* 3.1 17.3 + - + +
477P GLN* 3.9 2.9 - - + +
479P CYS* 1.3 75.9 - - - +
481P ASN* 1.3 80.0 + - - +
483P THR* 2.8 22.7 + - - +
484P ASN* 2.9 23.5 + - - +
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Residues in contact with ASN 481 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467P PHE* 3.9 30.6 - - + +
468P GLU 3.7 22.0 + - - +
477P GLN* 2.7 28.2 + - - +
478P LEU 3.8 0.4 - - - +
480P ILE* 1.3 86.2 - - - +
482P PHE* 1.3 53.1 - - - +
484P ASN* 3.0 4.9 + - - +
485P GLU* 2.7 35.9 + - - +
583P HIS* 3.6 12.6 - - + -
588P VAL* 4.2 6.9 - - - +
590P TYR* 3.1 27.7 + - - +
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Residues in contact with PHE 482 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478P LEU 2.7 19.0 + - - +
479P CYS* 3.5 3.1 - - - +
481P ASN* 1.3 78.5 - - - +
483P THR* 1.3 64.9 + - - +
485P GLU* 3.4 6.3 + - + +
486P MLY 3.4 34.1 + - + +
523P ILE* 4.2 18.8 - - + -
526P ILE* 3.7 41.7 - - + -
527P GLU* 3.5 33.9 - - + -
533P PHE* 4.0 23.3 - + + -
583P HIS* 4.7 1.0 - - - -
653P PHE* 4.2 6.1 - + - -
654P ARG* 4.7 9.2 - - + -
657P LEU* 3.5 30.3 - - + -
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Residues in contact with THR 483 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269P LEU* 5.1 1.2 - - - +
464P ILE* 4.4 22.2 - - + -
479P CYS 2.5 21.8 + - - -
480P ILE* 2.8 14.2 + - - +
482P PHE* 1.3 79.7 - - - +
484P ASN* 1.3 66.2 + - - +
486P MLY 3.2 4.7 + - - +
487P LEU* 3.1 39.8 + - + +
653P PHE* 3.3 16.1 - - + -
657P LEU* 3.9 28.0 - - + -
660P LEU* 5.2 1.3 - - + -
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Residues in contact with ASN 484 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178P THR* 4.0 10.7 + - - +
465P ALA 2.5 30.5 + - - +
466P GLY* 2.9 5.7 - - - -
467P PHE* 2.8 40.5 - - + +
480P ILE* 2.9 19.8 + - - +
481P ASN 3.7 6.1 - - - +
483P THR* 1.3 76.0 - - - +
485P GLU* 1.3 63.3 + - - +
486P MLY 2.8 6.5 + - - -
487P LEU* 3.0 17.7 + - - +
488P GLN* 2.9 24.4 + - - +
584P TYR* 3.9 8.5 + - - +
673P ARG* 5.4 2.8 + - - -
697P CYS 6.0 0.2 - - - -
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Residues in contact with GLU 485 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467P PHE* 4.1 1.6 - - - -
481P ASN 2.7 18.7 + - - +
482P PHE* 4.1 7.4 - - + +
484P ASN* 1.3 71.8 - - - +
486P MLY 1.3 61.1 + - - +
488P GLN 4.0 0.2 - - - -
489P GLN* 3.5 14.2 + - - +
519P LEU* 3.7 19.2 - - + +
522P CYS* 4.1 17.0 - - + +
523P ILE* 4.0 18.0 - - + +
526P ILE* 6.3 0.9 - - + -
582P VAL 4.3 0.2 - - - +
583P HIS* 2.5 44.0 + - - +
584P TYR* 2.5 52.5 + - + +
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Residues in contact with MLY 486 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482P PHE* 3.4 26.9 + - + +
483P THR* 3.2 11.8 + - - +
484P ASN 2.9 0.2 - - - -
485P GLU* 1.3 79.2 + - - +
487P LEU* 1.3 65.2 + - - +
489P GLN* 3.1 9.3 + - - +
490P PHE* 3.0 21.1 + - - +
523P ILE* 4.4 20.4 - - + -
527P GLU* 2.8 44.6 - - - -
657P LEU* 4.3 20.6 - - + -
658P ASN* 3.1 37.2 - - - -
661P MET* 4.2 30.8 - - + +
665P ARG* 4.8 16.6 + - - -
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Residues in contact with LEU 487 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176P LEU* 4.6 15.3 - - + -
178P THR* 5.4 4.3 - - - +
462P LEU* 4.6 13.2 - - + -
464P ILE* 5.2 6.7 - - + -
465P ALA 5.6 1.1 - - - +
483P THR* 3.1 36.6 + - + +
484P ASN* 3.4 24.0 - - - +
486P MLY 1.3 77.5 + - - +
488P GLN* 1.3 58.1 + - - +
490P PHE* 2.8 28.4 - - + +
491P PHE* 3.1 8.8 + - - +
660P LEU* 5.5 3.6 - - + -
661P MET* 3.6 25.6 - - + -
664P LEU* 3.9 15.0 - - + -
671P PHE* 4.8 2.7 - - + -
673P ARG* 5.2 13.5 - - - +
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Residues in contact with GLN 488 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122P PHE* 5.6 0.7 - - - -
484P ASN 2.9 6.8 + - - +
485P GLU 3.8 2.9 - - - +
487P LEU* 1.3 71.7 - - - +
489P GLN* 1.3 58.1 + - - +
490P PHE 2.9 4.3 - - - -
491P PHE* 2.9 40.7 + - - +
492P ASN* 2.7 46.3 + - - +
519P LEU* 4.1 5.8 - - + -
584P TYR* 3.4 48.9 + - + +
673P ARG* 4.6 8.6 + - - +
698P ASN 3.9 6.4 - - - +
699P GLY* 3.5 29.5 + - - -
702P GLU* 4.9 8.2 - - + +
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Residues in contact with GLN 489 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485P GLU 3.5 9.9 + - - +
486P MLY 3.1 11.5 + - - +
488P GLN* 1.3 77.9 - - - +
490P PHE* 1.3 61.8 + - - +
492P ASN* 3.8 5.5 - - - +
493P HIS* 3.1 25.1 + - + +
516P GLY* 3.2 36.7 + - - +
517P MET* 4.1 0.8 - - - +
519P LEU* 3.9 12.9 - - + +
520P ALA* 3.4 31.5 - - - +
523P ILE* 3.7 16.1 - - + +
665P ARG* 5.8 2.1 + - - -
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Residues in contact with PHE 490 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174P SER* 5.1 0.4 - - - -
176P LEU* 4.5 12.3 - - + -
486P MLY 3.0 8.7 + - - +
487P LEU* 2.8 22.7 - - - +
489P GLN* 1.3 80.0 - - - +
491P PHE* 1.3 60.4 + - - +
493P HIS* 3.9 5.6 - + + +
494P HIS* 3.4 18.3 + - + +
661P MET* 4.1 19.3 - - + -
664P LEU* 3.3 48.7 - - + -
665P ARG* 4.3 18.4 - - + -
667P THR 4.9 0.4 - - - -
669P PRO* 3.5 37.7 - - + -
671P PHE* 4.1 10.8 - + - -
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Residues in contact with PHE 491 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121P LEU* 4.0 26.0 - - + -
122P PHE* 3.3 40.4 - + - -
487P LEU 3.8 5.4 - - - +
488P GLN* 2.9 30.4 + - - +
490P PHE* 1.3 77.6 - - - +
492P ASN* 1.3 71.8 + - - +
493P HIS 2.7 5.7 + - - -
494P HIS* 2.6 27.2 + + - +
495P MET* 2.8 28.5 + - + +
671P PHE* 3.2 50.9 - + + -
673P ARG* 5.9 2.0 - - - +
699P GLY 4.7 0.7 - - - -
703P GLY* 4.3 16.8 - - - -
706P ILE* 5.0 3.1 - - + -
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Residues in contact with ASN 492 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488P GLN* 2.7 44.2 + - - +
489P GLN* 3.8 4.5 - - - +
491P PHE* 1.3 76.8 - - - +
493P HIS* 1.3 60.0 + - - +
495P MET* 3.9 5.0 - - - +
496P PHE* 3.3 12.6 + - - +
515P PHE* 3.4 47.4 + - + +
516P GLY* 3.7 4.3 - - - +
518P ASP* 5.6 0.4 - - - +
519P LEU* 3.8 12.7 - - - +
702P GLU* 3.7 26.5 + - - +
706P ILE* 4.1 13.5 - - - +
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Residues in contact with HIS 493 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489P GLN* 3.1 18.0 + - + +
490P PHE* 3.9 6.3 - + + +
491P PHE 2.7 4.9 + - - -
492P ASN* 1.3 72.6 - - - +
494P HIS* 1.3 54.9 + - - +
495P MET 2.9 4.0 - - - -
496P PHE* 2.5 27.3 + + - +
497P VAL* 2.7 41.2 + - + +
514P ASP* 2.4 39.5 + - - +
516P GLY* 4.9 0.7 - - - -
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Residues in contact with HIS 494 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121P LEU* 4.2 23.4 - - + +
490P PHE* 3.4 12.3 + - + +
491P PHE* 2.6 14.3 + + - +
493P HIS* 1.3 79.8 - - - +
495P MET* 1.3 58.8 + - - +
497P VAL* 3.5 9.3 + - - +
498P LEU* 2.9 52.6 + - + +
668P HIS* 3.6 31.8 + + - -
669P PRO* 3.6 29.3 + - + +
671P PHE* 4.2 18.2 - + - -
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Residues in contact with MET 495 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120P GLY* 5.2 4.0 - - - -
121P LEU* 3.5 38.6 - - + +
491P PHE* 2.8 32.6 + - + +
492P ASN* 4.0 8.7 - - - +
494P HIS* 1.3 78.3 - - - +
496P PHE* 1.3 59.2 + - - +
498P LEU* 3.9 7.2 - - + -
499P GLU* 2.7 40.2 + - + +
515P PHE* 4.5 0.9 - - - -
703P GLY* 4.3 8.1 - - - +
706P ILE* 3.7 29.6 - - + -
707P CYS* 4.0 4.5 - - - -
714P ARG* 3.0 32.3 - - - +
764P MLY 5.3 1.3 - - - -
766P PHE* 5.9 0.9 - - + -
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Residues in contact with PHE 496 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492P ASN 3.3 13.0 + - - +
493P HIS* 2.5 16.0 + + - +
495P MET* 1.3 74.4 - - - +
497P VAL* 1.2 81.3 + - + +
499P GLU* 3.8 1.0 - - - +
500P GLN* 3.3 46.0 + - - +
512P PHE* 3.0 40.9 - + - -
513P ILE* 3.1 7.0 - - - -
514P ASP* 2.9 51.1 - - + -
515P PHE* 3.4 19.3 - + + +
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Residues in contact with VAL 497 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493P HIS* 2.7 43.9 + - + +
494P HIS* 3.5 11.9 - - + +
496P PHE* 1.2 93.3 - - + +
498P LEU* 1.3 66.6 + - + +
500P GLN* 3.6 9.7 + - - +
501P GLU* 3.5 24.2 + - - +
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Residues in contact with LEU 498 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121P LEU* 4.1 33.9 - - + -
494P HIS* 2.9 40.0 + - + +
495P MET* 3.5 6.7 - - + +
497P VAL* 1.3 79.9 - - + +
499P GLU* 1.3 67.5 + - - +
501P GLU* 3.0 32.4 + - - +
502P GLU* 3.6 3.3 + - - +
668P HIS* 5.3 3.6 - - - +
762P HIS* 6.2 1.1 - - - +
763P THR* 6.1 1.6 - - - +
764P MLY 5.1 11.4 - - - -
766P PHE* 5.2 13.4 - - + -
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Residues in contact with GLU 499 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495P MET* 2.7 34.1 + - + +
496P PHE 3.8 0.7 - - - +
498P LEU* 1.3 71.4 - - - +
500P GLN* 1.3 55.2 + - - +
502P GLU* 2.8 33.8 + - - +
503P TYR* 3.0 35.3 + - - -
512P PHE* 3.6 20.2 - - + -
515P PHE* 4.7 8.3 - - + -
706P ILE* 4.9 6.9 - - + +
710P GLY* 5.1 1.0 - - - -
711P PHE 4.4 1.4 + - - -
714P ARG* 4.1 15.1 + - - +
766P PHE* 2.5 42.7 - - + -
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Residues in contact with GLN 500 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496P PHE* 3.3 38.5 + - - +
497P VAL* 3.9 8.5 - - - +
498P LEU 3.3 0.6 - - - -
499P GLU* 1.3 78.5 - - - +
501P GLU* 1.3 60.6 + - - +
503P TYR* 3.9 6.7 + - - +
504P MLY 3.2 22.2 + - + +
510P TRP 5.8 1.0 + - - -
512P PHE* 3.3 34.7 + - + +
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Residues in contact with GLU 501 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497P VAL* 3.5 20.4 + - - +
498P LEU* 3.0 23.5 + - - +
499P GLU 2.8 0.8 + - - -
500P GLN* 1.3 75.1 - - - +
502P GLU* 1.3 56.6 + - - +
504P MLY 2.9 9.8 + - + +
505P MLY 2.6 43.4 + - - +
761P GLY* 5.5 0.2 - - - -
762P HIS* 1.2 60.4 + - - +
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Residues in contact with GLU 502 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498P LEU 3.6 2.0 + - - +
499P GLU 2.8 10.6 + - - +
501P GLU* 1.3 74.1 - - - +
503P TYR* 1.3 55.5 + - + +
504P MLY 2.6 15.8 + - - -
505P MLY 2.7 11.8 + - - +
506P GLU* 2.7 16.6 + - - +
759P ALA* 2.6 35.0 - - + +
760P PHE* 0.9 111.7 - - - +
761P GLY* 2.2 23.3 + - - -
764P MLY 2.8 10.6 - - - +
766P PHE* 3.3 27.3 - - + -
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Residues in contact with TYR 503 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499P GLU* 3.0 35.1 + - - -
500P GLN* 4.1 5.6 - - - +
501P GLU 3.4 0.2 - - - -
502P GLU* 1.3 77.5 - - + +
504P MLY 1.3 56.3 + - - +
507P GLY* 3.1 4.9 + - - -
508P ILE* 2.9 56.7 + - + +
510P TRP* 3.3 40.8 - + + +
512P PHE* 3.6 22.2 - + - -
710P GLY* 3.5 5.2 - - - -
711P PHE* 1.9 71.6 + + + -
759P ALA* 4.0 6.1 - - + -
766P PHE* 4.9 3.6 - - + -
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Residues in contact with MLY 504 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500P GLN* 3.2 16.9 + - + +
501P GLU* 2.9 14.5 + - + +
502P GLU 2.6 5.3 + - - -
503P TYR* 1.3 75.4 + - - +
505P MLY 1.3 63.2 + - - +
507P GLY* 3.8 6.8 + - - -
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Residues in contact with MLY 505 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501P GLU* 2.6 25.4 + - - +
502P GLU 2.7 1.1 + - - +
504P MLY 1.3 77.0 + - - +
506P GLU* 1.3 65.2 + - - +
741P LYS* 2.8 36.3 - - - +
745P GLU* 6.0 2.5 - - - +
760P PHE* 2.9 34.1 - - + +
761P GLY* 2.9 11.7 - - - +
762P HIS* 1.1 142.3 + - - -
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Residues in contact with GLU 506 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502P GLU 2.7 9.0 + - - +
505P MLY 1.3 79.4 + - - +
507P GLY* 1.3 61.0 + - - +
508P ILE* 3.9 6.1 - - + -
755P HIS 5.5 2.9 - - - +
758P TYR* 3.2 12.1 - - + +
759P ALA* 2.4 39.7 - - + +
760P PHE* 0.8 121.3 + - + +
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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