Contacts of the helix formed by residues 477 - 502 (chain A) in PDB entry 4H3T
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 LEU 477 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A ALA* 3.5 34.8 - - + +
395A ALA* 3.6 22.2 - - + +
398A VAL* 4.2 16.9 - - + +
471A LEU* 4.0 30.5 - - + +
474A ILE* 4.1 22.0 - - + +
475A ASP 3.2 12.6 + - - +
476A ASP* 1.3 69.8 + - - +
478A GLU* 1.3 64.2 + - - +
479A ARG 3.2 1.4 + - - -
480A PRO* 3.4 14.7 - - - +
481A ARG* 3.5 14.6 + - - +
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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
----------------------------------------------------------
476A ASP* 3.0 18.9 + - - +
477A LEU* 1.3 79.3 - - - +
479A ARG* 1.3 56.7 + - - +
481A ARG* 3.5 25.2 + - - +
482A ALA* 3.1 28.2 + - - +
530A SER* 5.1 0.5 + - - -
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Residues in contact with ARG 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ILE* 5.5 3.1 - - + -
476A ASP* 3.4 23.7 + - - +
478A GLU* 1.3 75.0 - - - +
480A PRO* 1.3 68.4 - - + +
482A ALA* 3.1 8.1 + - - +
483A GLU* 2.9 47.5 + - + +
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Residues in contact with PRO 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A VAL* 5.2 1.1 - - + -
467A PHE* 3.8 16.4 - - + +
471A LEU* 3.9 25.4 - - + -
474A ILE* 3.7 29.8 - - + -
476A ASP 3.6 8.3 - - - +
477A LEU* 3.4 19.5 - - + +
479A ARG* 1.3 95.2 - - + +
481A ARG* 1.3 54.3 + - - +
483A GLU* 3.6 17.1 - - - +
484A TRP* 2.8 32.2 + - - +
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Residues in contact with ARG 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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394A ALA 5.4 0.2 + - - -
397A THR* 4.0 7.5 - - - +
398A VAL* 3.7 37.6 - - + +
401A ASP* 2.9 28.5 + - - +
477A LEU* 3.5 12.7 + - - +
478A GLU* 3.5 31.1 + - - +
480A PRO* 1.3 77.0 - - - +
482A ALA* 1.4 62.5 + - - +
484A TRP* 4.8 0.2 - - - -
485A ALA* 3.1 19.4 + - - +
528A GLU 5.0 1.6 + - - -
529A PHE* 2.8 77.0 + - + +
530A SER* 3.8 10.1 - - - +
531A PRO* 5.4 2.5 - - - -
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Residues in contact with ALA 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A GLU 3.1 12.9 + - - +
479A ARG* 3.1 9.9 + - - +
481A ARG* 1.4 73.2 - - - +
483A GLU* 1.3 64.3 + - + +
485A ALA* 3.3 4.5 + - - +
486A ALA* 3.2 22.5 + - - +
526A ARG* 4.9 5.0 + - - +
530A SER* 3.3 17.6 + - - +
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Residues in contact with GLU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A PHE* 6.2 0.7 - - + -
474A ILE* 5.8 1.4 - - - +
479A ARG* 2.9 38.8 + - + +
480A PRO* 3.6 19.2 - - - +
482A ALA* 1.3 76.7 - - + +
484A TRP* 1.3 65.0 + - - +
486A ALA* 3.4 5.1 + - - +
487A LEU* 3.0 23.8 + - - +
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Residues in contact with TRP 484 (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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324A TRP* 5.3 0.4 - + - -
402A ALA* 2.9 45.3 + - + +
405A PHE* 4.4 2.8 - + - -
406A ALA* 4.5 4.7 - - + +
460A LEU* 4.0 22.0 - - + -
463A PRO* 3.6 15.9 - - + -
464A TYR* 3.5 50.0 - + + -
467A PHE* 4.0 26.7 - + + -
480A PRO 2.8 20.9 + - - +
481A ARG 3.9 3.4 - - - +
483A GLU* 1.3 72.6 - - - +
485A ALA* 1.3 63.1 + - - +
487A LEU* 3.2 16.3 + - + +
488A VAL* 2.9 49.1 + - + +
529A PHE* 3.6 18.6 - + + -
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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
----------------------------------------------------------
405A PHE* 3.6 15.3 - - + -
481A ARG 3.1 14.5 + - - +
482A ALA 3.5 8.7 - - - +
483A GLU 3.3 0.2 - - - -
484A TRP* 1.3 76.1 - - - +
486A ALA* 1.3 61.9 + - - +
489A GLU* 3.1 28.1 + - - +
526A ARG* 3.8 27.1 - - - +
529A PHE* 3.8 8.7 - - + -
530A SER* 3.9 17.3 - - - -
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Residues in contact with ALA 486 (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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482A ALA 3.2 12.6 + - - +
483A GLU* 3.9 5.2 - - - +
485A ALA* 1.3 77.5 - - - +
487A LEU* 1.3 64.8 + - - +
489A GLU* 3.5 5.2 + - - +
490A ALA* 3.1 24.6 + - - +
526A ARG* 3.9 14.8 - - - +
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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
----------------------------------------------------------
460A LEU* 3.6 25.4 - - + -
463A PRO* 3.8 31.0 - - + +
483A GLU 3.0 17.8 + - - +
484A TRP* 3.7 18.6 - - + +
486A ALA* 1.3 74.3 - - - +
488A VAL* 1.3 66.4 + - - +
490A ALA* 3.2 7.0 + - - +
491A VAL* 3.0 29.9 + - + +
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Residues in contact with VAL 488 (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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405A PHE* 3.7 20.2 - - + -
406A ALA* 4.4 4.3 - - - -
409A ALA* 3.5 30.3 - - + -
456A ILE* 4.5 1.2 - - + +
460A LEU* 4.0 24.7 - - + -
484A TRP* 2.9 61.7 + - + +
487A LEU* 1.3 77.7 - - - +
489A GLU* 1.3 58.5 + - - +
491A VAL* 3.3 2.4 + - - +
492A ALA* 2.9 27.9 + - - +
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Residues in contact with GLU 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A PHE* 4.4 2.9 - - + -
485A ALA 3.1 19.1 + - - +
486A ALA* 3.8 5.2 - - - +
488A VAL* 1.3 78.4 - - - +
490A ALA* 1.3 52.9 + - - +
492A ALA* 3.3 1.9 + - - +
493A ARG* 2.8 51.9 + - - +
522A LEU* 3.9 31.6 - - + +
523A ALA* 6.0 1.2 - - - -
526A ARG* 2.6 51.4 + - + +
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Residues in contact with ALA 490 (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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486A ALA 3.1 16.2 + - - +
487A LEU* 3.2 6.0 + - - +
489A GLU* 1.3 75.8 - - - +
491A VAL* 1.3 66.4 + - + +
493A ARG* 4.0 5.5 - - - +
494A ASP* 3.1 23.7 + - - +
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Residues in contact with VAL 491 (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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456A ILE* 3.8 23.6 - - + -
459A ARG* 3.9 35.4 - - + +
460A LEU* 4.1 9.9 - - + -
463A PRO* 5.8 1.1 - - + -
487A LEU* 3.0 33.0 + - + +
488A VAL 3.8 3.4 - - - +
490A ALA* 1.3 75.9 - - + +
492A ALA* 1.3 64.4 + - - +
494A ASP* 3.2 8.5 + - + +
495A LEU* 3.1 22.7 + - + +
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Residues in contact with ALA 492 (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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409A ALA* 4.4 12.1 - - + -
413A LEU* 3.5 12.8 - - + +
456A ILE* 3.9 20.1 - - + +
488A VAL 2.9 17.6 + - - +
489A GLU* 3.7 6.7 - - - +
491A VAL* 1.3 76.1 - - - +
493A ARG* 1.3 56.1 + - - +
495A LEU* 3.4 1.6 + - - +
496A ALA* 2.9 27.7 + - - +
518A PHE* 3.8 23.1 - - + -
522A LEU* 4.6 2.9 - - + -
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Residues in contact with ARG 493 (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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489A GLU* 2.8 42.2 + - - +
490A ALA* 4.1 5.2 - - - +
492A ALA* 1.3 70.1 - - - +
494A ASP* 1.3 61.6 + - - +
496A ALA* 3.8 6.3 - - - +
497A SER* 2.9 35.0 + - - +
515A GLU* 5.5 8.4 + - - -
518A PHE* 4.2 18.0 - - + -
519A ARG* 4.4 26.0 - - - +
522A LEU* 4.8 5.5 - - + +
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Residues in contact with ASP 494 (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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459A ARG* 3.2 26.0 + - - +
490A ALA 3.1 14.7 + - - +
491A VAL* 3.2 11.0 + - - +
493A ARG* 1.3 77.6 - - - +
495A LEU* 1.4 60.6 + - - +
497A SER* 3.4 5.2 + - - -
498A ARG* 3.1 23.2 + - - +
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Residues in contact with LEU 495 (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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413A LEU* 4.1 14.6 - - + -
452A LEU* 4.3 9.2 - - + -
455A GLU* 3.8 21.5 - - + +
456A ILE* 3.6 48.0 - - + +
459A ARG* 3.6 37.9 - - - +
491A VAL* 3.1 14.0 + - + +
492A ALA 3.8 6.5 - - - +
494A ASP* 1.4 76.3 - - - +
496A ALA* 1.3 63.8 + - - +
498A ARG* 3.3 20.2 + - - +
499A GLU* 3.1 28.2 + - - +
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Residues in contact with ALA 496 (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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413A LEU* 3.8 12.5 - - + +
416A VAL* 4.1 15.5 - - + -
492A ALA 2.9 18.6 + - - +
493A ARG* 3.8 4.5 - - - +
494A ASP 3.3 0.2 - - - -
495A LEU* 1.3 75.9 - - - +
497A SER* 1.4 57.0 + - - +
499A GLU* 3.3 2.4 + - - +
500A LEU* 2.9 40.7 + - + +
515A GLU* 5.9 0.7 - - + +
518A PHE* 3.6 28.7 - - + -
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Residues in contact with SER 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A ARG* 2.9 20.8 + - - +
494A ASP* 3.8 7.0 - - - -
496A ALA* 1.4 76.1 - - - +
498A ARG* 1.3 63.1 + - - +
500A LEU* 3.9 9.1 - - - +
501A ALA* 3.0 25.3 + - - +
515A GLU* 5.7 1.4 + - - -
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Residues in contact with ARG 498 (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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452A LEU* 3.9 8.3 - - - +
455A GLU* 2.7 42.6 + - - -
459A ARG* 3.6 16.3 - - - +
494A ASP* 3.1 17.7 + - - +
495A LEU* 3.7 10.4 - - - +
497A SER* 1.3 76.7 - - - +
499A GLU* 1.3 93.5 + - - +
501A ALA* 3.3 11.9 + - - +
502A GLN* 3.4 27.1 + - + +
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Residues in contact with GLU 499 (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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416A VAL* 3.4 25.6 - - + +
417A ALA* 5.1 0.6 - - - -
420A ARG* 3.4 29.0 + - - -
452A LEU* 4.0 28.0 - - + +
495A LEU 3.1 14.4 + - - +
498A ARG* 1.3 107.0 + - - +
500A LEU* 1.3 62.6 + - - +
502A GLN* 3.2 22.4 + - - +
503A LEU* 3.7 11.7 + - - +
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Residues in contact with LEU 500 (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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416A VAL* 4.2 20.0 - - + -
419A ALA* 5.2 1.6 - - + -
496A ALA* 2.9 31.1 + - + +
497A SER* 3.9 8.5 - - - +
499A GLU* 1.3 75.2 - - - +
501A ALA* 1.3 62.0 + - - +
502A GLN 3.2 1.2 + - - -
503A LEU* 3.2 27.7 + - + +
511A GLY* 3.5 39.3 - - - +
515A GLU* 3.4 40.4 - - + +
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Residues in contact with ALA 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A SER 3.0 18.6 + - - +
498A ARG* 3.7 6.5 - - - +
499A GLU 3.3 0.4 - - - -
500A LEU* 1.3 76.2 - - - +
502A GLN* 1.3 61.9 + - + +
503A LEU 3.4 4.1 + - - +
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Residues in contact with GLN 502 (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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498A ARG* 3.4 26.7 - - + +
499A GLU* 3.2 16.1 + - - +
500A LEU 3.2 1.4 - - - -
501A ALA* 1.3 76.5 - - + +
503A LEU* 1.3 64.5 + - - +
504A ALA 3.5 2.1 + - - -
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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
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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