Contacts of the helix formed by residues 471 - 496 (chain B) in PDB entry 3VF1
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 471 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU* 3.0 57.9 - - + -
244B ASN* 3.9 0.7 - - - -
248B PRO* 3.9 18.8 - - + -
251B ILE* 5.5 1.8 - - + -
460B LEU* 4.4 4.0 - - + -
465B VAL* 3.4 44.0 - - + -
468B LEU* 3.6 24.0 - - + +
469B ARG 3.3 3.2 - - - -
470B LYS* 1.3 76.0 - - - +
472B TYR* 1.3 65.1 + - - +
473B TYR* 3.7 26.9 - + - -
474B LYS* 3.1 27.6 + - + +
475B ASP* 3.2 15.4 + - - +
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Residues in contact with TYR 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ASN* 2.9 33.1 + - - +
469B ARG 4.1 7.0 - - - -
470B LYS* 3.6 46.3 - - + +
471B PHE* 1.3 69.9 - - - +
473B TYR* 1.3 66.7 + - - +
475B ASP* 3.3 5.1 + - - -
476B ASP* 3.1 29.5 + - - +
657B ARG* 3.6 40.2 + - + +
661B MET* 3.5 30.2 - - + +
663B SER 5.9 2.0 - - - -
665B TYR* 3.8 27.1 - - + -
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Residues in contact with TYR 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU 3.6 18.8 - - - +
244B ASN* 3.3 3.6 + - - -
248B PRO* 3.8 28.5 - - + -
249B GLU* 5.8 0.7 - - - +
456B LEU* 3.7 17.5 - - + +
460B LEU* 4.7 12.8 - - + -
463B ARG* 5.6 0.7 - - - -
471B PHE* 3.3 17.5 - + + -
472B TYR* 1.3 77.2 - - - +
474B LYS* 1.3 64.5 + - - +
477B ALA* 2.8 51.9 + - + +
550B PHE* 4.8 0.4 - + - -
555B GLN* 2.8 34.4 + - - -
558B ALA* 4.0 15.5 - - + -
559B VAL* 5.7 0.2 - - + -
665B TYR* 3.5 35.9 - - + +
668B LEU* 3.9 6.4 - - + +
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Residues in contact with LYS 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B LEU* 3.7 24.0 - - + -
465B VAL 3.9 4.7 - - - -
466B ASP* 2.9 40.9 + - - +
468B LEU 2.8 27.3 + - - -
471B PHE* 3.1 33.6 + - + +
473B TYR* 1.3 89.5 - - - +
475B ASP* 1.3 82.9 + - - +
477B ALA* 4.1 0.8 - - - +
478B LEU* 3.1 36.7 + - + +
2D FRU 3.2 22.5 + - - +
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Residues in contact with ASP 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B ARG 3.7 18.9 - - - +
471B PHE 3.2 9.6 + - - +
472B TYR* 3.8 12.8 - - - +
474B LYS* 1.3 106.1 + - - +
476B ASP* 1.3 66.1 + - - +
478B LEU* 3.5 2.4 + - - +
479B LEU* 3.3 28.8 + - + +
657B ARG* 4.4 8.2 + - - +
2D FRU 3.0 27.8 + - - +
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Residues in contact with ASP 476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B TYR 3.1 14.4 + - - +
475B ASP* 1.3 75.4 - - - +
477B ALA* 1.3 65.4 + - - +
479B LEU* 3.2 12.3 + - - +
480B LEU* 3.1 29.4 + - + +
650B ILE* 5.3 0.3 - - - +
654B ILE* 3.4 30.1 - - + +
657B ARG* 2.9 38.5 + - - -
665B TYR* 3.3 13.9 - - - +
668B LEU* 3.9 21.6 + - + +
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Residues in contact with ALA 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B LEU* 3.4 18.5 - - + +
460B LEU* 5.7 0.2 - - + -
473B TYR* 2.8 38.7 + - + +
474B LYS* 4.1 2.9 - - - +
476B ASP* 1.3 76.8 - - - +
478B LEU* 1.3 57.5 + - - +
480B LEU* 4.4 2.5 - - - -
481B TRP* 2.9 30.1 + - - +
550B PHE* 3.5 15.2 - - + -
668B LEU* 3.6 14.9 - - + +
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Residues in contact with LEU 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B LEU* 3.8 19.5 - - + -
457B VAL* 4.1 28.5 - - + -
460B LEU* 3.9 15.3 - - + -
466B ASP* 5.0 5.8 - - + -
474B LYS* 3.1 36.2 + - + +
475B ASP 3.9 3.8 - - - +
476B ASP 3.2 0.2 - - - -
477B ALA* 1.3 75.3 - - - +
479B LEU* 1.3 65.3 + - - +
481B TRP* 3.9 1.5 - - + +
482B ASN* 3.0 37.3 + - - +
1D GLC 4.6 6.5 - - - +
2D FRU 3.5 32.5 - - - +
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Residues in contact with LEU 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B ASP* 3.3 16.1 + - + +
476B ASP* 3.2 16.9 + - - +
478B LEU* 1.3 79.7 - - + +
480B LEU* 1.3 57.5 + - - +
482B ASN* 3.5 5.9 + - - +
483B VAL* 3.0 32.6 + - - +
650B ILE* 3.7 30.3 - - + -
653B GLN* 3.6 40.6 - - + +
654B ILE* 5.3 1.1 - - + -
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Residues in contact with LEU 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B ASP* 3.1 23.4 + - + +
477B ALA* 3.9 3.8 - - - +
479B LEU* 1.3 76.0 - - - +
481B TRP* 1.3 59.6 + - - +
483B VAL* 3.7 1.5 - - - +
484B ILE* 2.8 38.3 + - + +
550B PHE* 4.4 1.8 - - + -
554B CYS* 3.7 24.5 - - + -
623B LEU* 3.9 27.4 - - + -
647B LEU* 4.0 15.9 - - + -
650B ILE* 4.1 14.6 - - + -
668B LEU* 3.5 39.3 - - + +
670B PRO* 4.3 13.9 - - + -
673B VAL* 5.3 0.7 - - + -
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Residues in contact with TRP 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B TYR 3.6 24.5 - - - -
455B ASP* 4.4 4.2 + - - -
456B LEU* 3.8 31.2 - - + -
457B VAL* 3.9 20.6 - - + +
477B ALA 2.9 18.8 + - - +
478B LEU* 3.9 4.9 - - + +
479B LEU 3.4 0.2 - - - -
480B LEU* 1.3 76.9 - - - +
482B ASN* 1.3 72.8 + - - +
484B ILE* 3.8 2.3 - - - +
485B HIS* 2.8 39.6 + + + +
543B HIS* 4.1 20.0 - + - -
546B THR* 3.9 21.1 - - + +
547B VAL* 3.7 24.7 - - + -
550B PHE* 3.5 49.9 - + + -
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Residues in contact with ASN 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B VAL* 4.9 6.1 - - - +
478B LEU* 3.0 28.4 + - - +
479B LEU* 3.9 5.8 - - - +
481B TRP* 1.3 93.9 - - - +
483B VAL* 1.3 58.5 + - + +
485B HIS* 3.8 6.5 + - - +
486B GLN* 3.1 25.8 + - - +
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Residues in contact with VAL 483 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B LEU 3.0 20.2 + - - +
480B LEU 3.3 4.0 + - - +
482B ASN* 1.3 76.7 - - + +
484B ILE* 1.3 65.7 + - + +
486B GLN* 3.5 6.6 + - - +
487B PHE 3.2 16.3 + - - -
643B PHE* 3.4 29.7 - - + -
646B ASN* 3.7 33.0 + - + +
647B LEU* 3.7 17.9 - - + -
650B ILE* 3.5 17.7 - - + -
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Residues in contact with ILE 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU* 2.8 20.8 + - - +
481B TRP* 3.8 3.6 - - - +
483B VAL* 1.3 75.0 - - + +
485B HIS* 1.3 66.2 + - - +
487B PHE* 3.3 2.9 + - + +
488B VAL* 3.0 29.9 + - + +
546B THR* 4.3 14.1 - - + +
549B VAL* 3.6 30.7 - - + -
550B PHE* 4.0 20.9 - - + -
553B SER* 4.2 6.3 - - - +
554B CYS* 3.9 26.9 - - - -
623B LEU* 4.4 8.5 - - + -
643B PHE* 3.8 25.8 - - + -
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Residues in contact with HIS 485 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B TRP* 2.8 28.6 + - + +
482B ASN* 3.8 9.8 + - - +
483B VAL 3.3 0.2 - - - -
484B ILE* 1.3 76.3 - - - +
486B GLN* 1.3 64.9 + - - +
488B VAL* 3.6 1.6 + - - +
489B GLN* 3.0 46.3 + - - +
539B GLU 5.6 0.6 + - - -
542B VAL* 3.6 16.2 - - + +
543B HIS* 4.8 13.1 + - - +
546B THR* 3.4 33.4 - - + +
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Residues in contact with GLN 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ASN 3.1 17.9 + - - +
483B VAL* 3.6 8.5 - - - +
485B HIS* 1.3 80.2 + - - +
487B PHE* 1.3 57.1 + - - +
489B GLN* 3.3 20.2 + - - +
490B ASP* 2.9 60.5 + - - +
642B LYS* 3.4 29.3 - - - +
646B ASN* 4.8 7.6 - - - +
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Residues in contact with PHE 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B LEU* 3.6 24.2 - - + -
405B HIS* 5.1 2.2 - - - -
483B VAL 3.2 3.0 + - - +
484B ILE* 3.3 7.8 + - + +
486B GLN* 1.3 80.2 - - - +
488B VAL* 1.3 70.5 + - + +
490B ASP* 3.1 8.4 + - - +
491B ILE* 3.0 44.2 + - + +
549B VAL* 5.8 2.2 - - + -
626B TYR* 3.8 25.1 - + - -
631B PHE* 5.7 2.0 - + - -
639B ALA* 3.7 18.2 - - + -
640B MET* 3.6 38.6 - - + -
643B PHE* 3.4 41.7 - + + -
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Residues in contact with VAL 488 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B LEU* 4.4 12.1 - - + -
484B ILE* 3.0 30.5 + - + +
485B HIS 4.0 0.7 - - - +
487B PHE* 1.3 83.3 - - + +
489B GLN* 1.3 58.0 + - - +
491B ILE* 3.4 5.8 + - - +
492B ILE* 3.0 35.9 + - + +
542B VAL* 3.7 30.5 - - + +
545B LEU* 3.9 16.2 - - + -
546B THR* 4.0 18.2 - - - +
549B VAL* 4.4 14.8 - - + -
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Residues in contact with GLN 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B HIS* 3.0 40.5 + - - +
486B GLN* 3.6 24.0 + - - +
488B VAL* 1.3 74.9 - - - +
490B ASP* 1.3 66.9 + - - +
492B ILE* 3.9 0.7 - - - +
493B GLN* 3.0 57.3 + - + +
539B GLU* 5.7 7.3 + - - +
542B VAL* 3.9 22.2 - - + +
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Residues in contact with ASP 490 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B GLN* 2.9 37.9 + - - +
487B PHE* 3.1 10.0 + - - +
489B GLN* 1.3 79.6 - - - +
491B ILE* 1.3 62.9 + - - +
493B GLN* 3.4 6.8 + - - +
494B ILE* 3.2 28.2 + - + +
639B ALA* 4.0 19.7 - - + +
642B LYS* 2.9 36.7 + - - +
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Residues in contact with ILE 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B PRO* 5.0 4.3 - - + +
401B LEU* 4.1 22.2 - - + -
487B PHE* 3.0 39.2 + - + +
488B VAL* 3.8 5.8 - - - +
490B ASP* 1.3 76.6 - - - +
492B ILE* 1.3 67.1 + - + +
494B ILE* 3.1 15.4 + - + +
495B TYR* 3.1 31.7 - - + -
631B PHE* 4.1 23.3 - - + -
636B ALA* 4.1 23.6 - - + +
639B ALA* 3.6 24.7 - - + -
640B MET* 5.1 0.9 - - + -
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Residues in contact with ILE 492 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B PRO* 6.3 1.6 - - + -
398B VAL* 4.2 9.4 - - + -
401B LEU* 4.8 6.1 - - + -
488B VAL* 3.0 29.1 + - + +
489B GLN 3.9 3.4 - - - +
491B ILE* 1.3 79.1 - - + +
493B GLN* 1.3 58.1 + - + +
494B ILE 3.2 0.4 - - - -
495B TYR* 3.3 1.4 + - - -
496B TYR* 2.8 57.6 + - + +
538B ARG* 4.6 13.0 - - + -
541B LEU* 3.9 20.6 - - + -
542B VAL* 4.0 22.9 - - + -
545B LEU* 3.8 23.1 - - + -
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Residues in contact with GLN 493 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B GLN* 3.0 49.6 + - + +
490B ASP* 3.9 7.1 - - - +
491B ILE 3.3 0.2 - - - -
492B ILE* 1.3 76.8 - - + +
494B ILE* 1.3 63.6 + - - +
495B TYR 3.3 0.2 - - - -
496B TYR 3.7 14.1 - - - +
497B ASN* 5.0 3.3 - - - -
538B ARG* 3.6 36.5 + - + +
539B GLU* 5.2 5.7 + - - -
542B VAL* 6.0 1.1 - - + -
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Residues in contact with ILE 494 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B ASP* 3.2 17.4 + - + +
491B ILE* 3.1 18.0 + - + +
493B GLN* 1.3 80.8 - - - +
495B TYR* 1.3 83.1 + - + +
633B ASP* 5.7 1.8 - - + -
635B ALA* 3.4 50.0 - - + +
636B ALA* 3.8 9.2 - - + +
639B ALA* 4.5 4.7 - - + -
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Residues in contact with TYR 495 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ALA* 3.6 32.3 - - + -
121B LEU* 3.2 30.2 - - + +
397B PRO* 3.7 30.1 - - + -
491B ILE* 3.1 30.7 - - + -
492B ILE* 3.3 2.1 + - + -
494B ILE* 1.3 101.5 - - + +
496B TYR* 1.3 68.1 + - + +
497B ASN* 3.7 3.4 + - - +
501B SER* 4.9 1.2 - - - -
631B PHE* 3.5 24.0 - + - -
633B ASP* 2.7 34.8 + - - +
636B ALA* 3.9 4.2 - - + +
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Residues in contact with TYR 496 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 3.6 20.0 - - + -
396B HIS* 3.2 15.8 - - - -
397B PRO* 4.8 2.7 - - + -
398B VAL* 4.1 7.9 - - + +
492B ILE* 2.8 44.1 + - + +
493B GLN* 3.7 6.6 - - - +
495B TYR* 1.3 81.4 - + + +
497B ASN* 1.3 59.8 + - - +
498B ASP 3.3 0.9 - - - -
501B SER* 3.7 28.7 - - - -
502B VAL* 3.6 26.5 - - + -
505B ASP* 2.6 29.7 + - + -
508B ILE* 4.3 5.4 - - + +
538B ARG* 2.9 39.2 + - + -
541B LEU* 4.0 16.3 - - + +
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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