Contacts of the helix formed by residues 494 - 521 (chain D) in PDB entry 2NPP
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 ASN 494 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492D ASP* 3.1 8.1 + - - +
493D PRO* 1.3 79.7 - - + +
495D TYR* 1.3 69.1 + - - +
496D LEU* 2.7 52.6 + - - +
497D HIS* 2.9 29.4 + - + +
498D ARG* 2.9 20.6 + - - +
277F GLU* 5.2 4.9 + - - +
279F ASP* 4.2 23.0 + - + +
280F ASP* 3.6 3.1 - - - -
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Residues in contact with TYR 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494D ASN* 1.3 76.8 + - - +
496D LEU* 1.3 93.0 + - + +
498D ARG* 3.3 30.3 - - - +
499D MET* 2.7 47.8 + - + +
533D VAL* 3.8 10.1 - - + -
535D ASN* 3.1 44.9 - - + -
536D VAL* 3.9 7.4 - - + -
51F PRO* 3.5 36.6 + - + -
52F VAL* 4.7 1.7 - - - -
53F THR* 5.2 2.4 + - - -
77F ASP 4.0 0.2 - - - -
78F THR* 3.5 8.5 - - - -
79F ASN* 3.2 31.2 + - - +
279F ASP* 5.5 1.6 - - - -
280F ASP* 2.6 12.7 + - - +
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Residues in contact with LEU 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454D HIS 6.1 0.4 - - - +
459D ARG* 4.0 25.4 + - - +
494D ASN* 2.7 33.3 + - - +
495D TYR* 1.3 110.0 - - + +
497D HIS* 1.3 66.6 + - + +
499D MET* 3.4 11.8 + - + +
500D THR* 3.4 17.9 + - - -
503D PHE* 5.3 0.9 - - - -
53F THR* 5.4 1.8 - - - +
72F GLY 4.6 4.0 - - - +
78F THR* 3.8 24.0 - - + -
277F GLU* 3.1 38.8 - - + +
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Residues in contact with HIS 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451D LEU 5.1 0.2 - - - -
452D VAL* 3.3 51.8 + - + +
453D ASP 4.5 7.3 + - - -
454D HIS* 5.8 2.9 - - - -
459D ARG* 4.9 9.6 - - - +
489D MET* 3.8 15.8 - - + +
492D ASP* 3.0 29.4 - - + +
494D ASN* 2.9 29.0 + - + +
496D LEU* 1.3 80.0 - - + +
498D ARG* 1.3 67.0 + - - +
499D MET 3.1 1.8 - - - -
500D THR* 3.0 24.7 + - - -
501D THR 3.6 2.9 + - - -
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Residues in contact with ARG 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489D MET 4.2 8.7 - - - -
490D SER 3.5 26.7 - - - +
492D ASP* 2.7 34.8 + - - +
493D PRO* 2.8 22.0 + - - +
494D ASN 2.9 13.9 + - - +
495D TYR* 3.3 16.9 - - - +
497D HIS* 1.3 77.4 - - - +
499D MET* 1.3 61.2 + - - +
501D THR* 3.3 11.1 + - - -
502D LEU 4.1 0.3 + - - -
528D MET* 3.3 34.4 - - + +
531D ASP* 2.6 38.0 + - - +
532D PRO* 4.8 4.3 - - - +
533D VAL* 3.2 8.3 - - - +
536D VAL* 4.0 3.9 - - + +
280F ASP* 2.9 30.6 + - - -
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Residues in contact with MET 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459D ARG* 5.8 1.8 - - - +
495D TYR* 2.7 39.7 + - + +
496D LEU* 3.5 21.3 - - + +
497D HIS 3.1 0.2 - - - -
498D ARG* 1.3 73.3 - - - +
500D THR* 1.3 66.1 + - - +
501D THR 2.8 3.7 + - - -
502D LEU* 3.0 20.9 + - + +
503D PHE* 3.0 31.2 + - + -
535D ASN* 4.1 13.0 - - - -
536D VAL* 3.9 22.2 - - + -
539D ASN* 3.6 24.2 - - + +
77F ASP* 3.2 30.1 - - + +
78F THR* 4.5 2.7 - - + -
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Residues in contact with THR 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451D LEU* 3.7 38.3 + - + +
459D ARG* 3.3 31.3 + - + +
463D THR* 4.3 6.7 - - - +
489D MET* 3.9 13.5 - - - -
496D LEU 3.4 6.7 + - - -
497D HIS* 3.0 14.8 + - - -
499D MET* 1.3 78.1 - - - +
501D THR* 1.3 60.8 + - - +
503D PHE* 3.2 15.7 - - + +
504D CYS* 3.0 23.1 + - - -
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Residues in contact with THR 501 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486D VAL* 3.2 23.2 + - - +
487D LEU* 4.3 5.2 - - + -
489D MET* 3.0 32.2 - - - +
490D SER* 3.1 16.7 + - - -
497D HIS 3.6 0.4 + - - -
498D ARG 3.3 13.0 + - - -
499D MET 2.8 1.6 + - - -
500D THR* 1.3 75.6 - - - +
502D LEU* 1.3 66.8 + - - +
504D CYS* 3.1 4.4 + - - +
505D ILE* 3.0 39.5 + - + +
524D THR* 4.8 0.4 - - + -
528D MET* 4.1 15.3 - - - -
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Residues in contact with LEU 502 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499D MET* 3.0 11.4 + - - +
501D THR* 1.3 80.5 - - + +
503D PHE* 1.3 60.9 + - + +
505D ILE* 3.2 8.3 + - + +
506D ASN* 2.8 36.3 + - - +
525D VAL* 4.3 17.3 - - + -
528D MET* 3.4 31.2 - - + -
536D VAL* 3.6 21.8 - - + +
539D ASN* 3.7 9.4 - - + +
540D VAL* 3.4 49.4 - - + +
543D SER* 3.3 16.2 - - - +
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Residues in contact with PHE 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456D TYR* 4.6 22.4 - + - -
459D ARG* 5.7 2.9 - - - -
463D THR* 3.6 13.1 - - + +
496D LEU 5.3 1.1 - - - -
499D MET* 3.0 37.1 + - + -
500D THR* 3.2 22.0 - - + +
502D LEU* 1.3 80.0 - - + +
504D CYS* 1.3 62.1 + - - +
506D ASN* 3.1 28.1 - - - +
507D VAL* 3.2 12.5 - - - +
539D ASN* 3.5 40.8 - - + -
77F ASP* 4.1 17.5 - - + -
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Residues in contact with CYS 504 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451D LEU* 3.7 29.8 - - - -
463D THR* 3.5 22.2 - - - -
466D LEU* 3.8 12.8 - - - -
486D VAL* 3.5 25.8 - - + -
489D MET* 5.8 0.4 - - - -
500D THR* 3.0 18.6 + - - -
501D THR 3.7 1.8 - - - +
503D PHE* 1.3 70.7 - - - +
505D ILE* 1.3 59.3 + - - +
506D ASN 2.9 1.6 - - - -
507D VAL* 2.4 26.2 + - - -
508D LEU* 2.8 26.0 + - + +
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Residues in contact with ILE 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486D VAL* 4.7 5.6 - - + -
487D LEU* 4.0 26.5 - - + -
501D THR* 3.0 23.7 + - + +
502D LEU* 3.5 11.9 - - + +
504D CYS* 1.3 77.6 - - - +
506D ASN* 1.3 63.7 + - - +
507D VAL 3.0 0.7 + - - -
508D LEU* 4.1 2.0 - - - +
509D SER* 3.1 24.6 + - - -
521D MET* 4.0 42.6 - - + +
524D THR* 4.5 3.8 - - - -
525D VAL* 3.9 33.2 - - + +
547D ILE* 4.2 14.8 - - + -
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Residues in contact with ASN 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502D LEU 2.8 23.7 + - - +
503D PHE* 3.1 31.1 - - - +
505D ILE* 1.3 76.3 - - - +
507D VAL* 1.3 57.9 + - + +
509D SER* 3.4 11.8 + - - -
510D GLU* 3.9 9.4 - - - +
539D ASN* 5.4 1.2 - - - +
542D LYS* 4.8 0.4 - - - +
543D SER* 3.1 47.6 + - - +
546D LYS* 3.8 26.3 - - + +
547D ILE* 4.7 2.7 - - - +
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Residues in contact with VAL 507 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463D THR* 3.5 25.6 - - + +
464D SER* 4.8 5.2 - - - +
467D LYS* 3.1 42.1 - - + +
503D PHE 3.2 17.5 - - - +
504D CYS 2.4 17.6 + - - +
506D ASN* 1.3 74.3 - - + +
508D LEU* 1.3 71.0 + - + +
509D SER 3.2 1.1 - - - -
510D GLU* 3.1 36.4 + - - +
511D VAL 4.1 0.5 + - - -
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Residues in contact with LEU 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466D LEU* 4.0 29.6 - - + -
467D LYS* 4.4 1.6 - - - +
470D VAL* 3.5 31.9 - - + -
478D ALA* 5.3 1.3 - - + -
482D ILE* 5.1 7.9 - - + -
483D ILE* 4.3 12.1 - - + -
486D VAL* 5.0 4.7 - - + -
504D CYS* 2.8 54.5 + - + +
505D ILE* 4.1 0.7 - - - +
507D VAL* 1.3 75.9 - - + +
509D SER* 1.3 65.4 + - - +
511D VAL* 2.8 17.6 + - - +
512D CYS* 3.0 27.2 + - - -
521D MET* 4.3 13.7 - - - -
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Residues in contact with SER 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505D ILE 3.1 19.8 + - - -
506D ASN 3.4 11.1 + - - -
508D LEU* 1.3 76.4 - - - +
510D GLU* 1.3 75.1 + - - +
511D VAL 2.8 1.9 + - - -
512D CYS 3.0 10.1 + - - +
513D GLY 3.8 3.1 + - - -
517D THR* 3.8 10.9 + - - -
521D MET* 3.5 22.2 - - - +
546D LYS* 5.1 1.6 - - - +
547D ILE* 3.5 24.6 - - - +
550D ILE* 3.5 22.5 - - - +
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Residues in contact with GLU 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467D LYS* 3.4 34.2 + - - +
506D ASN 3.9 13.0 - - - +
507D VAL* 3.2 25.2 - - - +
509D SER* 1.3 84.2 + - - +
511D VAL* 1.3 68.7 + - + +
513D GLY 5.2 0.7 + - - -
546D LYS* 4.3 22.6 + - - -
550D ILE* 3.9 11.8 - - + +
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Residues in contact with VAL 511 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467D LYS* 4.3 30.7 - - + +
470D VAL* 3.6 34.5 - - + +
471D GLU* 4.4 15.0 - - + +
475D LYS* 4.1 12.7 - - - +
507D VAL 4.8 0.2 - - - +
508D LEU* 2.8 17.1 + - - +
509D SER 2.8 3.4 + - - -
510D GLU* 1.3 86.6 - - + +
512D CYS* 1.3 57.8 + - - -
513D GLY 3.5 2.0 - - - -
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Residues in contact with CYS 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470D VAL* 4.1 8.3 - - - -
475D LYS* 3.9 15.9 - - - +
478D ALA* 4.0 26.0 - - - -
483D ILE* 4.4 8.5 - - - -
508D LEU* 3.0 34.5 + - - +
509D SER* 3.0 2.8 + - - +
511D VAL* 1.3 81.8 - - - +
513D GLY* 1.3 61.6 + - - +
516D ILE* 3.1 43.2 - - + +
517D THR* 4.5 5.4 - - - +
521D MET* 4.7 3.6 - - + -
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Residues in contact with GLY 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475D LYS* 4.6 10.5 - - - +
509D SER 3.8 5.8 + - - -
510D GLU 5.2 0.6 + - - -
511D VAL* 3.5 2.4 - - - +
512D CYS* 1.3 78.6 - - - +
514D GLN* 1.3 65.1 + - - -
515D ASP* 3.0 4.4 + - - -
516D ILE 3.4 0.7 + - - -
517D THR* 2.5 34.8 + - - -
550D ILE* 4.5 3.1 - - - -
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Residues in contact with GLN 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513D GLY* 1.3 70.7 - - - -
515D ASP* 1.3 64.6 + - - +
518D THR* 3.0 32.3 + - - +
550D ILE* 3.1 36.3 + - + +
551D LEU* 4.1 2.5 + - - -
552D ASP* 3.9 39.9 - - - +
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Residues in contact with ASP 515 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513D GLY* 3.0 2.5 + - - -
514D GLN* 1.3 81.7 - - - +
516D ILE* 1.3 62.0 + - + +
517D THR 3.1 0.7 + - - -
518D THR* 3.9 0.6 - - - -
519D LYS* 2.7 66.5 + - - +
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Residues in contact with ILE 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475D LYS* 3.7 40.4 - - + +
476D GLU* 4.9 1.6 - - - +
479D HIS* 3.9 36.1 - - + +
483D ILE* 4.5 14.6 - - + -
512D CYS* 3.1 36.6 - - + +
513D GLY 3.4 1.0 + - - -
515D ASP* 1.3 77.9 - - + +
517D THR* 1.3 59.5 + - - +
519D LYS* 4.5 5.1 - - - +
520D HIS* 2.8 35.2 + - + +
521D MET* 3.8 2.2 + - + +
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Residues in contact with THR 517 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509D SER* 3.8 21.7 + - - -
512D CYS 4.3 0.7 - - - -
513D GLY 2.5 27.7 + - - -
514D GLN 3.9 3.1 - - - -
516D ILE* 1.3 76.9 - - - +
518D THR* 1.3 59.0 + - - +
521D MET* 2.9 55.9 + - + +
522D LEU 3.1 9.8 + - - +
547D ILE* 4.5 14.8 - - + -
550D ILE* 3.8 20.0 - - + +
551D LEU* 4.4 11.2 - - + -
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Residues in contact with THR 518 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514D GLN* 3.0 21.1 + - - +
515D ASP* 3.9 1.1 - - - -
517D THR* 1.3 76.8 - - - +
519D LYS* 1.3 65.3 + - + +
520D HIS 3.5 0.2 - - - -
522D LEU* 4.1 6.8 - - + +
523D PRO* 3.7 14.9 - - - +
551D LEU* 2.8 32.4 - - - +
552D ASP* 4.9 4.4 + - - +
555D THR* 4.0 31.7 + - + +
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Residues in contact with LYS 519 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515D ASP* 2.7 47.7 + - - +
516D ILE* 4.7 1.1 - - - +
518D THR* 1.3 79.8 - - + +
520D HIS* 1.3 83.7 + - + +
521D MET 4.0 0.2 - - - -
523D PRO* 4.4 8.9 - - - +
----------------------------------------------------------
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Residues in contact with HIS 520 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479D HIS* 3.2 37.8 + + - +
483D ILE* 3.9 15.8 - - + +
487D LEU* 3.3 25.5 - - - +
516D ILE* 2.8 23.2 + - + +
519D LYS* 1.3 100.7 + - + +
521D MET* 1.3 65.6 + - + +
523D PRO* 4.0 5.8 - - - -
524D THR* 4.3 2.1 + - - -
----------------------------------------------------------
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Residues in contact with MET 521 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D ILE* 3.6 34.8 - - + -
487D LEU* 5.2 1.1 - - + -
505D ILE* 4.0 35.8 - - + +
508D LEU* 4.3 11.2 - - - -
509D SER* 3.5 32.8 - - - +
512D CYS* 4.7 4.3 - - + -
516D ILE 4.2 4.5 - - - +
517D THR* 2.9 37.2 + - + +
520D HIS* 1.3 85.5 - - - +
522D LEU* 1.3 69.0 + - - +
523D PRO* 2.7 4.9 - - - +
524D THR* 2.8 18.0 + - - -
525D VAL* 3.1 12.8 + - - +
----------------------------------------------------------
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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