Contacts of the helix formed by residues 464 - 487 (chain A) in PDB entry 3N00
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 464 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A ASP 3.8 1.2 + - - -
463A LEU* 1.3 76.1 - - - +
465A GLN* 1.3 64.8 + - - +
466A HIS 4.2 1.1 - - - -
467A ASP* 3.1 27.2 + - - +
468A GLN* 2.9 21.7 + - - +
554A GLU* 2.9 27.6 + - - +
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Residues in contact with GLN 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A ARG* 3.2 27.2 + - - -
463A LEU 3.8 0.4 + - - -
464A SER* 1.3 73.1 - - - +
466A HIS* 1.3 57.5 + - - +
468A GLN* 3.5 11.0 + - - +
469A VAL* 2.9 39.7 + - + +
2063B PHE* 3.4 32.5 + - - +
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Residues in contact with HIS 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A SER* 3.2 1.0 + - - -
465A GLN* 1.3 79.7 - - - +
467A ASP* 1.3 68.1 + - - +
469A VAL* 3.5 4.9 + - - +
470A THR* 2.8 46.9 + - - -
552A GLY* 2.8 26.4 + - - -
554A GLU* 3.4 37.3 + - + +
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Residues in contact with ASP 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A LEU* 4.2 9.0 - - + -
464A SER* 3.1 26.6 + - - +
466A HIS* 1.3 78.0 - - - +
468A GLN* 1.3 65.8 + - - +
470A THR* 3.1 2.6 + - - -
471A LEU* 2.9 29.1 + - - +
553A MET* 3.6 20.1 - - - +
554A GLU* 2.8 31.6 + - - +
555A ASN* 2.8 37.0 + - - +
558A SER* 4.1 2.8 + - - -
559A VAL* 4.5 3.8 - - + +
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Residues in contact with GLN 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A PHE* 3.4 44.8 - - + +
461A ARG* 3.0 58.2 + - - +
463A LEU* 2.7 27.5 + - + +
464A SER 2.9 15.2 + - - +
465A GLN* 3.5 13.4 + - - +
467A ASP* 1.3 76.1 - - - +
469A VAL* 1.3 63.3 + - - +
471A LEU* 3.2 0.7 + - - +
472A LEU* 3.1 28.0 + - - +
2063B PHE* 3.6 12.6 - - + -
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Residues in contact with VAL 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A GLN* 2.9 29.4 + - - +
466A HIS* 3.8 6.1 - - - +
468A GLN* 1.3 73.4 - - - +
470A THR* 1.3 63.2 + - - +
472A LEU* 3.4 4.4 + - - +
473A LYS* 3.1 53.2 + - - +
2059B ILE* 4.0 13.0 - - + +
2060B THR* 5.4 2.0 - - - +
2063B PHE* 3.7 36.1 - - + -
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Residues in contact with THR 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A HIS* 2.8 41.8 + - - -
467A ASP* 3.6 6.7 - - - -
469A VAL* 1.3 78.6 - - - +
471A LEU* 1.3 56.2 + - - +
473A LYS* 3.6 7.7 + - - +
474A ALA* 3.0 28.0 + - + +
549A ASP 5.2 3.1 - - - +
551A SER 3.8 21.8 - - - +
552A GLY* 4.1 6.5 + - - +
553A MET* 3.5 22.7 - - + -
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Residues in contact with LEU 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A PHE* 3.9 17.3 - - + -
463A LEU* 3.8 28.7 - - + -
467A ASP 2.9 11.3 + - - +
468A GLN 3.6 4.5 - - - +
470A THR* 1.3 75.4 - - - +
472A LEU* 1.3 54.7 + - - +
474A ALA* 3.6 2.3 - - - +
475A GLY* 2.6 34.5 + - - -
545A LEU* 3.6 21.5 - - + +
546A VAL* 4.2 21.8 - - + +
548A ALA* 4.0 21.6 - - + +
549A ASP 5.1 0.7 - - - +
550A ARG* 5.2 0.2 - - + -
553A MET* 3.6 23.8 - - + -
559A VAL* 4.1 21.3 - - + -
562A LEU* 5.3 0.2 - - + -
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Residues in contact with LEU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A VAL* 4.0 11.4 - - + -
451A VAL* 4.2 19.3 - - + -
454A ALA* 4.0 8.3 - - + -
460A PHE* 3.8 19.5 - - + -
468A GLN 3.1 18.9 + - - +
469A VAL 3.9 3.8 - - - +
471A LEU* 1.3 73.4 - - - +
473A LYS* 1.3 61.6 + - - +
476A THR* 2.4 52.0 + - - +
545A LEU* 3.9 27.6 - - + -
2059B ILE* 3.5 15.6 - - + +
2063B PHE* 3.7 30.5 - - + -
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Residues in contact with LYS 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A VAL* 3.1 42.2 + - + +
470A THR* 3.8 7.6 - - - +
472A LEU* 1.3 79.7 - - - +
474A ALA* 1.3 62.6 + - - +
476A THR 4.4 1.6 + - - -
477A PHE* 5.3 1.9 + - - +
2055B ILE* 4.6 7.0 - - - +
2056B CYS* 3.5 41.3 + - + +
2059B ILE* 3.7 14.1 - - + +
2060B THR* 2.9 29.5 + - - +
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Residues in contact with ALA 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470A THR* 3.0 20.6 + - + +
471A LEU* 3.8 0.9 - - - +
473A LYS* 1.3 80.1 - - - +
475A GLY* 1.3 57.4 + - - +
476A THR 3.8 0.2 - - - -
477A PHE* 5.0 2.8 + - - +
478A GLU* 4.1 4.0 + - - +
548A ALA* 3.7 11.4 - - + +
549A ASP* 3.5 31.0 + - + +
551A SER 6.1 0.2 - - - +
599A ASN* 3.9 20.1 + - - -
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Residues in contact with GLY 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A LEU 2.6 20.2 + - - -
474A ALA* 1.3 73.6 - - - +
476A THR* 1.3 61.4 + - - +
477A PHE 3.5 2.0 - - - -
478A GLU* 3.4 13.3 + - - +
479A VAL* 3.2 24.6 + - - +
544A VAL* 4.7 1.2 - - - +
545A LEU* 4.3 12.6 - - - -
548A ALA* 3.4 16.2 - - - -
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Residues in contact with THR 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A VAL* 4.1 24.2 - - + +
450A VAL* 4.0 20.5 - - + +
451A VAL* 5.5 0.2 - - - +
472A LEU* 2.4 55.3 + - - +
473A LYS 4.4 0.4 + - - -
474A ALA 3.8 0.8 - - - -
475A GLY* 1.3 69.6 - - - +
477A PHE* 1.3 66.2 + - - +
479A VAL* 3.2 7.9 + - - +
480A LEU* 2.9 34.4 + - + +
545A LEU* 5.1 0.4 - - - -
2055B ILE* 3.8 14.4 - - + -
2059B ILE* 3.9 3.3 - - - +
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Residues in contact with PHE 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A PHE* 5.8 0.2 - + - -
473A LYS 5.3 2.1 + - - +
474A ALA 5.0 2.8 + - - +
475A GLY 3.5 0.6 - - - -
476A THR* 1.3 76.9 - - - +
478A GLU* 1.3 59.2 + - - +
480A LEU* 3.2 8.0 + - + +
481A MET* 3.0 64.4 + - + +
516A LEU* 4.1 3.1 - - + -
598A LEU 3.7 4.5 - - - -
599A ASN* 3.6 47.8 - - + +
602A HIS* 3.7 23.1 - - + -
603A SER* 3.9 17.5 - - - -
2051B LEU* 3.4 40.4 - - + -
2052B ALA* 6.3 0.2 - - - -
2055B ILE* 3.9 19.3 - - + +
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Residues in contact with GLU 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A ALA 4.1 9.1 - - - +
475A GLY* 3.4 11.0 + - - +
476A THR 3.2 0.6 - - - -
477A PHE* 1.3 75.7 - - - +
479A VAL* 1.3 62.3 + - - +
481A MET* 3.2 25.1 + - - +
482A VAL* 3.2 7.4 + - - +
544A VAL* 3.8 22.8 - - + +
547A SER 5.1 0.5 - - - +
548A ALA* 4.9 6.1 - - - -
549A ASP 5.4 0.9 + - - -
592A LEU* 4.9 3.3 - - - +
595A LEU* 3.5 47.3 - - + +
596A ARG* 3.7 27.4 + - - -
599A ASN* 2.9 31.3 + - + +
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Residues in contact with VAL 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A PHE* 5.0 2.2 - - + -
450A VAL* 3.8 29.6 - - + -
453A PHE* 5.5 2.0 - - + -
475A GLY 3.2 15.5 + - - +
476A THR* 3.2 9.1 + - - +
478A GLU* 1.3 77.7 - - - +
480A LEU* 1.3 57.8 + - - +
482A VAL* 2.9 9.8 + - - +
483A ARG* 2.9 29.3 + - + +
541A THR* 3.7 26.2 - - + +
544A VAL* 4.0 7.6 - - + -
545A LEU* 3.8 37.5 - - + +
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Residues in contact with LEU 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A PHE* 6.2 0.2 - - + -
443A PHE* 3.9 31.0 - - + -
446A ALA* 3.7 26.5 - - + +
447A VAL* 4.1 20.0 - - + -
450A VAL* 3.8 20.2 - - + -
476A THR* 2.9 23.4 + - + +
477A PHE* 3.5 9.4 - - + +
479A VAL* 1.3 76.4 - - - +
481A MET* 1.3 64.4 + - + +
483A ARG* 3.7 11.8 - - + +
484A PHE* 2.8 39.2 + - + -
2051B LEU* 5.4 0.2 - - + -
2055B ILE* 4.3 10.8 - - + -
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Residues in contact with MET 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A PHE* 5.7 5.6 - - + -
477A PHE* 3.0 63.0 + - + +
478A GLU* 3.2 13.0 + - + +
480A LEU* 1.3 84.4 - - + +
482A VAL* 1.3 59.9 + - - +
484A PHE* 4.0 5.0 - - + +
485A ALA* 3.2 17.3 + - - -
516A LEU* 4.4 3.8 - - + -
520A MET* 3.3 43.8 - - - +
523A PHE* 4.0 11.9 - - + -
524A SER* 4.5 1.2 + - - -
595A LEU* 3.5 17.7 - - + -
598A LEU* 4.3 20.9 - - + -
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Residues in contact with VAL 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A GLU 3.5 13.5 - - - +
479A VAL* 2.9 11.5 + - - +
481A MET* 1.3 75.0 - - - +
483A ARG* 1.3 65.6 + - + +
485A ALA* 3.2 13.9 + - - -
486A SER* 3.6 5.9 + - - -
523A PHE* 4.5 8.7 - - + -
527A LEU* 4.2 11.3 - - + +
537A LEU* 4.0 21.4 - - + +
540A PHE* 3.9 24.0 - - + -
541A THR* 3.5 25.8 - - + +
544A VAL* 4.2 8.3 - - + -
595A LEU* 4.0 16.8 - - + -
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Residues in contact with ARG 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A HIS* 3.6 26.2 + - - -
300A PHE* 3.4 65.7 + - + +
449A GLU* 5.5 0.4 + - - -
479A VAL* 2.9 22.0 + - + +
480A LEU* 3.7 18.2 - - + +
482A VAL* 1.3 75.0 + - - +
484A PHE* 1.3 65.7 + - + +
486A SER* 3.1 48.7 + - - -
487A LEU* 3.3 13.6 + - - +
534A GLU* 5.7 0.6 + - - -
537A LEU* 4.7 4.6 - - - +
541A THR* 5.1 6.3 - - + -
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Residues in contact with PHE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A PHE* 6.2 3.6 - + - -
480A LEU* 2.8 28.7 + - + +
481A MET* 4.0 4.9 - - + +
483A ARG* 1.3 71.8 - - + +
485A ALA* 1.3 64.1 + - - +
487A LEU* 2.8 22.4 + - - -
488A PHE* 3.1 13.8 + - - +
520A MET* 3.4 41.3 - - + -
524A SER* 4.4 1.1 - - - +
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Residues in contact with ALA 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A MET 3.2 10.7 + - - -
482A VAL 3.2 7.8 + - - -
483A ARG 3.1 1.8 - - - -
484A PHE* 1.3 79.0 - - - +
486A SER* 1.3 60.6 + - - +
488A PHE* 3.6 9.4 - - - +
523A PHE* 5.6 0.2 - - - -
524A SER* 2.9 38.9 + - - +
527A LEU* 4.8 7.0 - - - -
528A ASN* 4.0 15.2 + - - +
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Residues in contact with SER 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A VAL 3.6 6.0 + - - -
483A ARG* 3.1 37.9 + - - -
484A PHE 3.2 0.2 - - - -
485A ALA* 1.3 70.8 - - - +
487A LEU* 1.3 60.8 + - - +
488A PHE* 2.9 14.2 + - - +
527A LEU* 5.4 1.2 - - - +
528A ASN* 5.2 6.3 + - - +
537A LEU* 4.6 15.7 - - - -
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Residues in contact with LEU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ARG* 3.3 14.5 + - - +
484A PHE* 2.8 20.4 + - - +
486A SER* 1.3 73.9 + - - +
488A PHE* 1.3 60.4 + - - +
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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