Contacts of the helix formed by residues 474 - 507 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472G PHE* 3.8 22.7 + - - -
473G ASN* 1.3 76.0 - - - +
475G PHE* 1.3 54.5 + - - +
476G GLU* 3.2 19.0 + - - -
477G GLN* 2.6 43.5 + - - +
478G LEU 3.3 4.2 + - - -
590G TYR* 4.1 1.6 - - - -
591G ASN* 3.2 6.2 + - - -
593G SER 4.7 0.9 + - - -
595G TRP* 2.8 34.2 + - - -
598G MLY 4.2 11.3 + - - -
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Residues in contact with PHE 475 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269G LEU* 6.5 0.7 - - + -
474G SER* 1.3 78.6 + - - +
476G GLU* 1.3 75.9 + - + +
478G LEU* 3.1 14.0 + - + +
479G CYS* 3.2 36.3 + - - -
533G PHE* 4.3 12.1 - + - -
536G LEU* 4.2 15.3 - - + -
595G TRP* 3.0 50.9 - + + +
598G MLY 3.9 28.3 - - + -
599G ASN* 3.6 25.4 - - + -
649G VAL* 3.8 24.7 - - + -
650G SER* 4.3 1.6 - - - -
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Residues in contact with GLU 476 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G LEU* 5.5 8.0 - - + +
474G SER* 3.9 7.8 - - - -
475G PHE* 1.3 89.9 + - + +
477G GLN* 1.3 80.4 + - - +
479G CYS* 3.3 7.8 + - - +
480G ILE* 3.1 26.4 + - + +
598G MLY 2.7 50.2 + - + +
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Residues in contact with GLN 477 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468G GLU 4.9 4.0 - - - +
470G PHE* 3.8 38.1 - - + -
472G PHE* 3.6 5.4 - - - +
473G ASN* 3.4 19.9 - - + +
474G SER* 2.6 51.2 + - - +
476G GLU* 1.3 88.0 + - - +
478G LEU* 1.3 57.8 + - - +
480G ILE* 3.3 2.9 + - + +
481G ASN* 2.7 45.3 + - - +
590G TYR* 4.0 3.6 - - + -
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Residues in contact with LEU 478 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474G SER 3.3 2.2 + - - -
475G PHE* 3.1 12.3 + - + +
477G GLN* 1.3 80.5 - - - +
479G CYS* 1.3 56.6 + - - +
482G PHE* 2.7 35.2 + - + +
526G ILE* 4.2 24.0 - - + -
532G ILE* 4.4 14.1 - - + -
533G PHE* 3.5 35.2 - - + -
579G PHE* 5.2 3.1 - - + -
581G LEU* 4.6 5.4 - - + -
583G HIS* 4.9 0.4 - - + -
590G TYR* 3.4 38.7 - - + +
595G TRP* 4.0 24.9 - - + -
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Residues in contact with CYS 479 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269G LEU* 4.4 16.6 - - + -
475G PHE* 3.2 45.8 + - - -
476G GLU* 3.3 6.5 + - - +
477G GLN 3.2 0.2 - - - -
478G LEU* 1.3 80.1 - - - +
480G ILE* 1.3 54.4 + - - +
482G PHE* 3.5 2.5 - - - +
483G THR* 2.5 33.5 + - - -
533G PHE* 4.3 8.5 - - - -
649G VAL 5.8 0.4 - - - -
650G SER* 5.7 1.1 - - - -
653G PHE* 3.2 41.6 - - + -
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Residues in contact with ILE 480 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269G LEU* 3.9 29.6 - - + -
464G ILE* 4.6 11.4 - - + -
465G ALA* 4.4 26.7 - - + +
466G GLY 4.5 9.4 - - - +
468G GLU* 5.1 1.1 - - + +
476G GLU* 3.1 17.1 + - + +
477G GLN* 3.9 2.9 - - + +
479G CYS* 1.3 74.6 - - - +
481G ASN* 1.3 80.3 + - - +
483G THR* 2.8 22.2 + - - +
484G ASN* 2.9 22.9 + - - +
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Residues in contact with ASN 481 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467G PHE* 3.9 31.7 - - + +
468G GLU 3.7 22.5 + - - +
477G GLN* 2.7 28.0 + - - +
478G LEU 3.8 0.4 - - - +
480G ILE* 1.3 86.0 - - - +
482G PHE* 1.3 54.5 + - - +
484G ASN* 3.0 4.5 + - - +
485G GLU* 2.7 35.9 + - - +
583G HIS* 3.6 13.0 - - + -
588G VAL* 4.2 7.1 - - - +
590G TYR* 3.2 26.5 + - - +
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Residues in contact with PHE 482 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478G LEU* 2.7 20.1 + - + +
479G CYS* 3.5 3.6 - - - +
481G ASN* 1.3 79.2 - - - +
483G THR* 1.3 64.7 + - - +
485G GLU* 3.4 5.0 + - + -
486G MLY 3.4 33.7 + - + +
523G ILE* 4.2 19.1 - - + -
526G ILE* 3.7 42.6 - - + -
527G GLU* 3.5 34.3 - - + -
533G PHE* 4.0 23.8 - + + -
583G HIS* 4.7 1.3 - - - -
653G PHE* 4.2 5.8 - + - -
654G ARG* 4.7 9.2 - - + -
657G LEU* 3.5 29.6 - - + -
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Residues in contact with THR 483 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269G LEU* 5.1 1.2 - - - +
464G ILE* 4.4 21.8 - - + -
479G CYS 2.5 23.4 + - - -
480G ILE* 2.8 14.2 + - - +
482G PHE* 1.3 78.2 - - - +
484G ASN* 1.3 65.9 + - - +
486G MLY 3.2 5.0 + - - +
487G LEU* 3.1 39.9 + - + +
653G PHE* 3.3 16.6 - - + -
657G LEU* 3.9 27.8 - - + -
660G LEU* 5.2 2.2 - - + -
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Residues in contact with ASN 484 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178G THR* 4.0 10.7 + - - +
465G ALA 2.5 30.3 + - - +
466G GLY* 2.9 5.6 - - - -
467G PHE* 2.8 40.3 - - + +
480G ILE* 2.9 19.0 + - - +
481G ASN 3.7 5.8 - - - +
483G THR* 1.3 75.8 - - - +
485G GLU* 1.3 62.7 + - - +
486G MLY 2.8 6.2 + - - -
487G LEU* 3.0 18.4 + - - +
488G GLN* 2.9 24.1 + - - +
584G TYR* 3.9 9.9 + - - +
673G ARG* 5.4 2.9 + - - -
697G CYS 6.0 0.2 - - - -
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Residues in contact with GLU 485 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467G PHE* 4.1 1.0 - - - -
481G ASN 2.7 18.3 + - - +
482G PHE* 3.4 7.6 + - + +
484G ASN* 1.3 72.3 - - - +
486G MLY 1.3 60.6 + - - +
488G GLN 4.0 0.2 - - - -
489G GLN* 3.5 14.4 + - - +
519G LEU* 3.7 18.4 - - + +
522G CYS* 4.1 16.7 - - + +
523G ILE* 4.0 18.5 - - + +
582G VAL 4.3 0.2 - - - +
583G HIS* 2.5 44.2 + - - +
584G TYR* 2.5 53.1 + - + +
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Residues in contact with MLY 486 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482G PHE* 3.4 27.0 + - + +
483G THR* 3.2 11.0 + - - +
484G ASN 2.9 0.2 - - - -
485G GLU* 1.3 78.9 + - - +
487G LEU* 1.3 65.7 + - - +
489G GLN* 3.1 8.8 + - - +
490G PHE* 3.0 20.4 + - - +
523G ILE* 4.4 21.1 - - + -
527G GLU* 2.8 45.1 - - - -
657G LEU* 4.3 20.2 - - + -
658G ASN* 3.1 36.6 - - - -
661G MET* 4.2 32.5 - - + +
665G ARG* 4.8 17.4 + - - -
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Residues in contact with LEU 487 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176G LEU* 4.6 16.2 - - + -
178G THR* 5.4 4.0 - - - +
462G LEU* 4.6 13.0 - - + -
464G ILE* 5.2 6.5 - - + -
465G ALA 5.6 1.1 - - - +
483G THR* 3.1 37.0 + - + +
484G ASN* 3.4 23.6 - - - +
486G MLY 1.3 77.1 + - - +
488G GLN* 1.3 58.8 + - - +
490G PHE* 2.8 29.2 - - + +
491G PHE* 3.1 8.5 + - - +
660G LEU* 5.5 3.4 - - + -
661G MET* 3.6 24.5 - - + -
664G LEU* 3.9 15.7 - - + -
671G PHE* 4.8 2.9 - - + -
673G ARG* 5.1 11.9 - - - +
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Residues in contact with GLN 488 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G PHE* 5.3 1.1 - - - -
484G ASN 2.9 7.4 + - - +
485G GLU 3.8 3.6 - - - +
487G LEU* 1.3 73.3 - - - +
489G GLN* 1.3 57.1 + - - +
490G PHE 2.9 4.3 - - - -
491G PHE* 2.9 40.6 + - - +
492G ASN* 2.7 45.5 + - - +
519G LEU* 4.1 6.5 - - + -
584G TYR* 3.4 49.2 + - + +
673G ARG* 4.6 7.4 + - - +
698G ASN 3.9 6.6 - - - +
699G GLY* 3.5 29.5 + - - -
702G GLU* 4.9 8.2 - - + +
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Residues in contact with GLN 489 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485G GLU 3.5 9.7 + - - +
486G MLY 3.1 12.0 + - - +
488G GLN* 1.3 78.3 - - - +
490G PHE* 1.3 62.1 + - - +
492G ASN* 3.8 6.1 - - - +
493G HIS* 3.1 25.0 + - + +
516G GLY* 3.2 36.4 + - - +
517G MET* 4.1 1.4 - - - +
519G LEU* 3.9 11.8 - - + +
520G ALA* 3.4 31.1 - - - +
523G ILE* 3.7 15.3 - - + +
665G ARG* 5.8 2.1 + - - -
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Residues in contact with PHE 490 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G SER* 5.1 0.2 - - - -
176G LEU* 4.5 12.1 - - + -
486G MLY 3.0 8.7 + - - +
487G LEU* 2.8 22.0 - - - +
488G GLN 2.9 0.2 - - - -
489G GLN* 1.3 80.2 - - - +
491G PHE* 1.3 60.6 + - - +
493G HIS* 3.9 5.5 - + + +
494G HIS* 3.4 17.8 + - + +
661G MET* 4.1 19.5 - - + -
664G LEU* 3.3 48.2 - - + -
665G ARG* 4.3 19.3 - - + -
667G THR 4.9 0.2 - - - -
669G PRO* 3.5 38.1 - - + -
671G PHE* 4.1 11.4 - + - -
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Residues in contact with PHE 491 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G LEU* 4.0 26.0 - - + -
122G PHE* 3.3 41.5 - + - -
487G LEU 3.8 4.9 - - - +
488G GLN* 2.9 31.2 + - - +
490G PHE* 1.3 77.7 - - - +
492G ASN* 1.3 70.6 + - - +
493G HIS 2.7 5.9 + - - -
494G HIS* 2.6 27.2 + + - +
495G MET* 2.8 28.0 + - + +
671G PHE* 3.2 51.8 - + + -
673G ARG* 5.9 1.3 - - - +
699G GLY 4.7 0.4 - - - -
702G GLU 5.4 0.2 - - - -
703G GLY* 4.3 17.7 - - - -
706G ILE* 5.0 2.5 - - + -
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Residues in contact with ASN 492 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488G GLN* 2.7 44.7 + - - +
489G GLN* 3.8 5.2 - - - +
491G PHE* 1.3 76.5 - - - +
493G HIS* 1.3 60.2 + - - +
495G MET* 3.9 5.2 - - - +
496G PHE* 3.3 13.0 + - - +
515G PHE* 3.4 48.9 + - + +
516G GLY* 3.7 3.6 - - - +
518G ASP* 5.6 0.4 - - - +
519G LEU* 3.8 12.1 - - - +
702G GLU* 3.7 26.7 + - - +
706G ILE* 4.1 13.7 - - - +
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Residues in contact with HIS 493 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489G GLN* 3.1 17.3 + - + +
490G PHE* 3.9 6.7 - + + +
491G PHE 2.7 5.1 + - - -
492G ASN* 1.3 73.0 - - - +
494G HIS* 1.3 54.1 + - - +
495G MET 2.9 3.8 - - - -
496G PHE* 2.5 27.2 + + - +
497G VAL* 2.7 41.2 + - + +
514G ASP* 2.4 39.9 + - - +
516G GLY* 4.9 0.7 - - - -
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Residues in contact with HIS 494 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G LEU* 4.2 23.4 - - + +
490G PHE* 3.4 13.1 + - + +
491G PHE* 2.6 14.1 + + - +
493G HIS* 1.3 79.6 - - - +
495G MET* 1.3 58.6 + - - +
497G VAL* 3.5 8.9 - - - +
498G LEU* 2.9 53.2 + - + +
668G HIS* 3.6 31.9 + + - -
669G PRO* 3.6 29.4 + - + +
671G PHE* 4.2 18.2 - + - -
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Residues in contact with MET 495 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G GLY* 5.2 4.0 - - - -
121G LEU* 3.5 39.3 - - + +
491G PHE* 2.8 32.6 + - + +
492G ASN* 4.0 9.6 - - - +
494G HIS* 1.3 79.7 - - - +
496G PHE* 1.3 58.7 + - - +
498G LEU* 3.5 5.9 - - + +
499G GLU* 2.7 44.8 + - + +
515G PHE* 4.5 0.4 - - - -
703G GLY* 4.3 8.3 - - - +
706G ILE* 3.7 29.4 - - + -
707G CYS* 4.0 24.0 - - - -
714G ARG* 4.3 7.2 - - - +
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Residues in contact with PHE 496 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492G ASN 3.3 13.4 + - - +
493G HIS* 2.5 15.6 + + - +
495G MET* 1.3 74.2 - - - +
497G VAL* 1.2 81.9 + - + +
499G GLU* 3.8 0.9 - - - +
500G GLN* 3.3 45.0 + - - +
512G PHE* 3.0 39.8 - + - -
513G ILE* 3.1 7.2 - - - -
514G ASP* 2.9 51.6 - - + -
515G PHE* 3.4 18.8 - + + +
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Residues in contact with VAL 497 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493G HIS* 2.7 43.9 + - + +
494G HIS* 3.5 11.4 - - - +
496G PHE* 1.2 93.3 - - + +
498G LEU* 1.3 67.6 + - + +
500G GLN* 3.6 10.9 + - - +
501G GLU* 3.5 23.3 + - - +
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Residues in contact with LEU 498 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G LEU* 4.1 34.1 - - + -
494G HIS* 2.9 40.3 + - + +
495G MET* 3.5 7.2 - - + +
497G VAL* 1.3 79.5 - - + +
499G GLU* 1.3 68.5 + - - +
501G GLU* 3.0 31.6 + - - +
502G GLU* 3.6 3.3 + - - +
668G HIS* 5.3 4.0 - - - +
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Residues in contact with GLU 499 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495G MET* 2.7 35.3 + - + +
496G PHE 3.8 0.7 - - - +
498G LEU* 1.3 72.2 - - - +
500G GLN* 1.3 56.3 + - - +
502G GLU* 2.8 38.9 + - - +
503G TYR* 3.0 35.9 + - + -
512G PHE* 3.6 20.2 - - + -
515G PHE* 4.7 8.7 - - + -
706G ILE* 4.9 6.7 - - + +
707G CYS* 5.5 1.7 - - - -
710G GLY* 4.4 9.0 - - - -
711G PHE* 4.4 3.5 + - - +
714G ARG* 4.8 10.4 + - - -
766G PHE* 4.6 16.6 - - - -
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Residues in contact with GLN 500 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496G PHE* 3.3 38.5 + - - +
497G VAL* 3.9 8.8 - - - +
498G LEU 3.3 0.4 - - - -
499G GLU* 1.3 78.1 - - - +
501G GLU* 1.3 61.4 + - - +
503G TYR* 3.9 6.8 + - - +
504G MLY 3.2 21.9 + - + +
510G TRP 5.8 0.8 + - - +
512G PHE* 3.3 35.8 + - + +
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Residues in contact with GLU 501 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497G VAL* 3.5 19.3 + - - +
498G LEU* 3.0 23.2 + - - +
499G GLU 2.8 1.2 + - - -
500G GLN* 1.3 75.9 - - - +
502G GLU* 1.3 55.9 + - - +
504G MLY 2.9 9.3 + - + +
505G MLY 2.6 70.5 + - - +
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Residues in contact with GLU 502 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498G LEU 3.6 3.3 + - - +
499G GLU* 2.8 16.5 + - - +
501G GLU* 1.3 75.1 - - - +
503G TYR* 1.3 60.9 + - + +
504G MLY 2.6 15.7 + - - -
505G MLY 2.7 30.2 + - - +
506G GLU* 2.7 26.6 + - + +
759G ALA* 5.1 5.2 - - + -
760G PHE 2.7 28.3 - - - +
761G GLY* 2.9 19.5 - - - -
762G HIS* 5.3 0.3 + - - -
766G PHE* 4.7 26.8 - - + -
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Residues in contact with TYR 503 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499G GLU* 3.0 36.0 + - - -
500G GLN* 4.1 5.6 - - - +
501G GLU 3.4 0.2 - - - -
502G GLU* 1.3 84.5 - - + +
504G MLY 1.3 55.7 + - - +
507G GLY* 3.1 4.6 + - - -
508G ILE* 2.9 61.8 + - + +
510G TRP* 3.3 40.4 - + + +
512G PHE* 3.6 21.8 - + - -
710G GLY* 3.5 5.9 - - - -
711G PHE* 2.2 60.2 + + - -
759G ALA* 5.2 1.3 - - + -
766G PHE* 5.8 2.2 - + + -
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Residues in contact with MLY 504 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500G GLN* 3.2 16.4 + - + +
501G GLU* 2.9 15.0 + - + +
502G GLU 2.6 5.1 + - - -
503G TYR* 1.3 75.8 + - - +
505G MLY 1.3 64.0 + - - +
507G GLY* 3.8 7.3 + - - -
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Residues in contact with MLY 505 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501G GLU* 2.6 57.1 + - - +
502G GLU* 2.7 26.6 + - - +
504G MLY 1.3 76.9 + - - +
506G GLU* 1.3 73.1 + - - +
762G HIS* 1.4 76.4 - - + +
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Residues in contact with GLU 506 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502G GLU* 2.7 19.3 + - + +
505G MLY 1.3 90.0 + - - +
507G GLY* 1.3 61.2 + - - +
508G ILE* 3.9 17.9 - - + -
759G ALA* 3.6 11.0 - - + -
760G PHE* 1.9 70.0 - - + +
761G GLY* 4.1 1.9 - - - -
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Residues in contact with GLY 507 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503G TYR 3.1 9.9 + - - -
504G MLY 3.8 5.8 + - - -
505G MLY 3.5 1.6 - - - -
506G GLU* 1.3 82.6 - - - +
508G ILE* 1.3 69.4 + - - +
509G GLU* 3.8 1.9 + - - +
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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) + - + + + + + -
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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