Contacts of the helix formed by residues 444 - 483 (chain A) in PDB entry 3WWS
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 444 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A ASN 4.1 0.6 + - - -
443A LEU* 1.3 78.3 - - - +
445A LEU* 1.3 65.3 + - - +
446A GLU* 3.5 22.3 - - - +
447A GLU* 3.2 26.4 + - - +
448A LEU* 3.0 21.2 + - - +
453D LYS* 5.0 8.6 + - - -
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Residues in contact with LEU 445 (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 LEU 3.9 0.8 + - - -
444A SER* 1.3 72.5 - - - +
446A GLU* 1.3 63.4 + - - +
448A LEU* 3.2 10.2 + - + +
449A GLN* 3.0 28.2 + - - +
481B MSE 4.0 49.6 - - + +
484B LYS* 5.2 15.5 - - - +
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Residues in contact with GLU 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A SER* 3.5 21.8 + - - +
445A LEU* 1.3 79.0 + - - +
447A GLU* 1.3 65.6 + - + +
449A GLN* 3.4 12.8 + - - +
450A MSE 3.1 22.5 + - - +
478C LEU* 4.6 23.5 - - + +
481C MSE 4.3 24.9 - - + +
452D LEU* 3.5 30.2 - - + +
453D LYS* 5.0 6.2 + - - +
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Residues in contact with GLU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU* 3.6 24.5 - - + +
444A SER* 3.2 21.6 + - - +
446A GLU* 1.3 82.8 - - + +
448A LEU* 1.3 59.0 + - - +
450A MSE 3.4 23.2 + - + +
451A ARG* 2.9 64.5 + - + +
481C MSE 6.1 0.7 - - - -
453D LYS* 5.6 4.9 + - - +
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Residues in contact with LEU 448 (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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440A LEU* 3.3 48.9 - - + +
441A LYS* 5.3 0.2 - - - -
443A LEU* 3.3 30.7 - - + +
444A SER 3.0 15.5 + - - +
445A LEU* 3.2 9.8 + - + +
447A GLU* 1.3 75.8 - - - +
449A GLN* 1.3 64.0 + - - +
451A ARG* 3.6 2.8 + - - +
452A LEU* 3.1 19.1 + - - +
477B ILE* 3.2 23.1 - - + +
480B ALA* 3.9 26.5 - - + +
481B MSE 3.6 22.9 - - + -
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Residues in contact with GLN 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A LEU 3.0 13.1 + - - +
446A GLU* 3.7 13.4 - - - +
448A LEU* 1.3 75.6 - - - +
450A MSE 1.3 57.7 + - - +
452A LEU* 3.5 8.1 + - + +
453A LYS* 3.0 59.3 + - + +
481B MSE 3.8 19.0 - - + +
481C MSE 3.4 10.4 + - - +
482C ASP* 3.0 45.3 + - - +
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Residues in contact with MSE 450 (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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446A GLU 3.1 16.4 + - - +
447A GLU* 3.7 24.0 - - + +
448A LEU 3.2 0.2 - - - -
449A GLN* 1.3 74.3 - - - +
451A ARG* 1.3 63.0 + - + +
452A LEU 3.1 1.3 - - - -
453A LYS* 3.3 7.7 + - - +
454A ALA* 3.0 30.5 + - + +
481C MSE 4.2 10.3 - - + -
445D LEU* 3.5 48.0 - - + +
446D GLU* 4.2 12.3 - - + +
449D GLN* 3.6 23.6 - - + -
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Residues in contact with ARG 451 (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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434A ALA* 4.5 9.5 - - - +
439A PHE* 4.0 22.5 - - - -
440A LEU* 3.9 24.6 - - - +
443A LEU* 3.6 11.3 - - - +
447A GLU* 2.9 49.4 + - + +
448A LEU* 3.9 6.7 - - - +
450A MSE 1.3 78.2 - - + +
452A LEU* 1.3 61.7 + - - +
454A ALA* 3.5 14.5 + - - +
455A LEU* 3.7 18.0 + - - +
477B ILE* 4.0 15.7 - - + +
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Residues in contact with LEU 452 (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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448A LEU 3.1 19.1 + - - +
449A GLN* 3.5 10.3 - - + +
450A MSE 3.1 0.2 - - - -
451A ARG* 1.3 74.9 - - - +
453A LYS* 1.3 70.8 + - + +
455A LEU* 3.3 17.5 + - - +
456A ASP* 4.3 7.4 + - - +
474B ARG* 3.9 40.4 + - + +
477B ILE* 3.9 18.8 - - + +
478B LEU* 4.2 29.2 - - + -
481B MSE 4.4 12.3 - - + -
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Residues in contact with LYS 453 (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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449A GLN* 3.0 53.0 + - + +
450A MSE 3.3 4.0 + - - +
452A LEU* 1.3 82.8 - - + +
454A ALA* 1.3 61.1 + - - +
455A LEU 3.3 1.0 + - - -
456A ASP* 3.4 15.1 + - - +
457A PRO* 3.3 16.5 - - - +
481C MSE 3.6 14.8 - - - +
482C ASP 3.9 3.4 + - - -
484C LYS* 3.6 33.7 - - + +
445D LEU* 4.0 29.5 - - + +
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Residues in contact with ALA 454 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A MSE 3.0 18.5 + - + +
451A ARG* 3.7 9.9 - - - +
452A LEU 3.2 0.4 - - - -
453A LYS* 1.3 79.3 - - - +
455A LEU* 1.3 61.4 + - + +
456A ASP 3.3 0.2 - - - -
457A PRO* 3.2 12.1 - - - +
458A MSE 3.2 27.6 - - - +
445D LEU* 5.2 4.4 - - + +
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Residues in contact with LEU 455 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A ARG 3.7 11.2 + - - +
452A LEU* 3.3 8.5 + - - +
453A LYS 3.2 1.6 - - - -
454A ALA* 1.3 77.1 - - + +
456A ASP* 1.3 63.0 + - - +
458A MSE 3.4 24.6 + - + +
459A MSE 3.0 31.5 + - - +
470B TYR* 3.6 12.4 - - + +
473B LYS* 3.9 34.5 - - + -
474B ARG* 3.8 30.7 - - + +
477B ILE* 3.9 24.9 - - + -
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Residues in contact with ASP 456 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A LEU 4.4 7.5 - - - +
453A LYS* 3.4 14.6 + - - +
454A ALA 3.3 0.2 - - - -
455A LEU* 1.3 73.3 - - - +
457A PRO* 1.3 71.6 - - + +
459A MSE 3.3 9.6 + - + +
460A GLU* 3.0 32.2 + - + +
474B ARG* 3.2 30.1 + - - -
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Residues in contact with PRO 457 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A LYS 3.3 12.3 - - - +
454A ALA* 3.2 18.4 - - - +
456A ASP* 1.3 90.6 - - + +
458A MSE 1.3 55.3 + - + +
460A GLU* 3.3 7.9 + - + +
461A ARG* 3.0 30.2 + - - +
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Residues in contact with MSE 458 (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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454A ALA* 3.2 24.0 - - - +
455A LEU* 3.4 28.9 + - + +
456A ASP 3.2 0.6 - - - -
457A PRO* 1.3 77.8 - - + +
459A MSE 1.3 63.6 + - - +
461A ARG* 3.4 7.6 + - - +
462A GLU* 3.1 27.0 + - - +
470B TYR* 3.7 19.1 - - + +
473B LYS* 4.3 10.5 - - - +
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Residues in contact with MSE 459 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A LEU 3.0 17.5 + - - +
456A ASP* 3.3 7.8 + - - +
458A MSE 1.3 78.2 - - - +
460A GLU* 1.3 85.8 + - + +
462A GLU* 3.1 4.6 + - - +
463A ILE* 2.9 31.7 + - + +
466B LEU* 3.8 8.7 - - + -
467B ARG* 3.6 36.1 - - - +
470B TYR* 3.6 41.6 + - + -
474B ARG* 3.6 28.3 - - - +
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Residues in contact with GLU 460 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A ASP* 3.0 25.9 + - + +
457A PRO* 3.8 6.1 - - + +
459A MSE 1.3 97.7 - - - +
461A ARG* 1.3 57.3 + - - +
463A ILE* 3.8 16.9 - - - +
464A GLU* 3.0 27.5 + - - +
467A ARG* 5.5 3.6 + - - -
467B ARG* 4.5 6.3 + - - -
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Residues in contact with ARG 461 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A PRO 3.0 18.3 + - - +
458A MSE 3.6 8.5 - - - +
460A GLU* 1.3 75.4 - - - +
462A GLU* 1.3 59.9 + - + +
464A GLU* 3.3 17.6 + - - +
465A GLU* 2.9 53.9 + - - +
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Residues in contact with GLU 462 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A MSE 3.1 13.7 + - - +
459A MSE 3.1 8.6 + - - +
461A ARG* 1.3 76.2 - - + +
463A ILE* 1.3 58.5 + - - +
465A GLU* 3.3 12.2 - - - +
466A LEU* 3.0 26.9 + - - +
469A ARG* 4.9 1.7 + - - -
466B LEU* 3.8 22.4 - - + +
469B ARG* 4.6 9.7 + - - -
470B TYR* 2.3 38.0 + - - -
473B LYS* 4.9 3.3 + - - -
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Residues in contact with ILE 463 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A MSE 2.9 30.6 + - + +
460A GLU* 3.8 16.8 - - - +
461A ARG 3.2 0.2 - - - -
462A GLU* 1.3 72.6 - - - +
464A GLU* 1.3 66.2 + - - +
466A LEU* 2.9 8.6 + - - +
467A ARG* 2.9 55.9 + - - +
463B ILE* 4.1 25.4 - - + -
466B LEU* 4.0 19.3 - - + -
467B ARG* 3.6 40.6 - - + +
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Residues in contact with GLU 464 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A GLU 3.0 14.6 + - - +
461A ARG* 3.6 24.9 - - - +
463A ILE* 1.3 74.4 - - - +
465A GLU* 1.3 59.8 + - - +
467A ARG* 3.0 34.3 + - - +
468A GLN* 2.9 49.1 + - + +
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Residues in contact with GLU 465 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A ARG* 2.9 46.7 + - - +
462A GLU* 3.3 14.6 - - - +
463A ILE 3.2 0.2 - - - -
464A GLU* 1.3 75.1 - - - +
466A LEU* 1.3 66.2 + - - +
468A GLN* 3.2 8.6 + - + +
469A ARG* 3.1 40.8 + - - +
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Residues in contact with LEU 466 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A GLU 3.0 10.8 + - - +
463A ILE 2.9 11.5 + - - +
465A GLU* 1.3 74.9 - - - +
467A ARG* 1.3 63.3 + - - +
469A ARG* 3.3 27.2 + - - +
470A TYR* 3.3 30.9 + - + -
459B MSE 3.2 37.9 - - + +
462B GLU* 3.6 44.6 - - + +
463B ILE* 3.7 16.6 - - + +
466B LEU* 3.9 16.6 - - + -
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Residues in contact with ARG 467 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A GLU* 5.5 4.2 + - - -
463A ILE* 2.9 38.6 + - - +
464A GLU* 3.0 36.1 + - - +
466A LEU* 1.3 76.0 - - - +
468A GLN* 1.3 64.8 + - - +
470A TYR* 3.2 4.9 + - - +
471A THR* 3.1 24.3 + - - -
474A ARG* 4.9 1.0 + - - -
459B MSE 4.2 28.6 - - + +
463B ILE* 4.4 14.1 - - + +
467B ARG* 5.1 8.3 - - - +
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Residues in contact with GLN 468 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A GLU* 2.9 33.1 + - - +
465A GLU* 3.2 10.9 + - + +
467A ARG* 1.3 77.8 + - - +
469A ARG* 1.3 60.4 + - + +
471A THR* 3.3 35.6 + - - +
472A ALA* 3.4 11.6 + - - +
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Residues in contact with ARG 469 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A GLU 4.9 1.6 + - - -
465A GLU* 3.1 33.1 + - - +
466A LEU* 3.3 39.2 + - - +
468A GLN* 1.3 78.1 - - + +
470A TYR* 1.3 66.4 + - + +
472A ALA* 3.4 11.4 + - - +
473A LYS* 3.3 28.7 + - - +
462B GLU* 4.4 11.9 + - - -
466B LEU* 5.9 1.2 - - - +
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Residues in contact with TYR 470 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A LEU* 3.3 30.7 + - + -
467A ARG 3.2 8.7 + - - +
469A ARG* 1.3 77.7 - - + +
471A THR* 1.3 65.2 + - - +
472A ALA 3.2 0.4 - - - -
473A LYS* 3.2 37.2 + - + +
474A ARG* 3.1 34.6 + - - +
455B LEU* 3.4 44.2 - - + -
456B ASP* 6.0 0.7 - - - -
458B MSE 3.4 20.7 - - + +
459B MSE 3.8 33.0 - - + -
461B ARG* 5.2 0.3 + - - -
462B GLU* 3.4 25.5 + - - -
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Residues in contact with THR 471 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A ARG* 3.1 15.2 + - - +
468A GLN* 3.4 30.6 + - - +
469A ARG 3.3 0.4 - - - -
470A TYR* 1.3 75.3 - - - +
472A ALA* 1.3 59.8 + - - +
474A ARG* 3.2 28.9 + - - +
475A GLN* 3.0 47.6 + - + +
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Residues in contact with ALA 472 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A GLN 3.4 8.0 + - - +
469A ARG* 3.4 13.6 + - - +
470A TYR 3.2 0.2 - - - -
471A THR* 1.3 80.3 - - - +
473A LYS* 1.3 57.0 + - + +
475A GLN* 3.7 7.9 + - - +
476A PRO* 3.1 25.1 - - - +
436B ASP 5.1 4.3 + - - -
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Residues in contact with LYS 473 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ARG* 3.3 18.6 + - - +
470A TYR* 3.2 51.1 + - + +
472A ALA* 1.3 78.6 - - + +
474A ARG* 1.3 60.4 + - - +
476A PRO* 3.4 3.3 - - - +
477A ILE* 3.8 4.7 - - - +
436B ASP 6.1 0.4 - - - +
437B PHE* 3.3 39.7 - - + -
455B LEU* 4.1 22.8 - - + +
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Residues in contact with ARG 474 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ARG 4.9 1.2 + - - -
470A TYR* 3.1 29.3 + - - +
471A THR* 3.2 39.7 + - - +
473A LYS* 1.3 76.2 - - - +
475A GLN* 1.3 67.1 + - - +
477A ILE* 2.9 18.2 + - - +
478A LEU* 3.0 31.4 + - + +
452B LEU* 4.8 21.3 - - + -
455B LEU* 3.9 21.1 - - + +
456B ASP* 4.6 17.5 + - - -
459B MSE 5.0 6.5 - - - +
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Residues in contact with GLN 475 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A THR* 3.0 42.7 + - + +
472A ALA* 3.9 7.2 - - - +
474A ARG* 1.3 80.1 - - - +
476A PRO* 1.4 71.1 - - + +
478A LEU* 3.5 20.6 + - - +
479A ASP* 3.0 38.4 + - - +
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Residues in contact with PRO 476 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A ALA 3.1 20.6 - - - +
473A LYS 3.4 15.9 - - - +
475A GLN* 1.4 89.6 - - + +
477A ILE* 1.3 59.0 + - - +
479A ASP* 3.9 6.1 - - + +
480A ALA* 3.1 18.2 + - - +
436B ASP* 3.8 21.3 - - + +
437B PHE* 3.7 26.0 - - + +
440B LEU* 3.3 27.0 - - + +
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Residues in contact with ILE 477 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A LYS 3.8 15.3 - - - +
474A ARG* 2.9 9.3 + - - +
476A PRO* 1.3 71.9 - - - +
478A LEU* 1.3 68.9 + - - +
480A ALA* 3.1 6.5 + - - +
481A MSE 2.9 30.4 + - + +
437B PHE* 3.8 15.9 - - + -
440B LEU* 3.7 30.7 - - + -
448B LEU* 3.3 39.4 - - + +
451B ARG* 4.1 17.7 - - + -
452B LEU* 4.2 19.1 - - + +
455B LEU* 4.9 6.1 - - + -
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Residues in contact with LEU 478 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ARG* 3.0 38.7 + - + +
475A GLN* 3.9 20.9 - - - +
477A ILE* 1.3 75.2 - - - +
479A ASP* 1.3 63.5 + - - +
481A MSE 3.2 13.0 + - - +
482A ASP* 2.9 33.8 + - - +
452B LEU* 3.9 24.7 - - + -
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Residues in contact with ASP 479 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A GLN* 3.0 29.9 + - - +
476A PRO* 3.9 6.5 - - + +
478A LEU* 1.3 75.9 - - - +
480A ALA* 1.3 63.0 + - - +
482A ASP* 3.2 10.4 + - - +
483A ALA* 3.1 23.5 + - - +
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Residues in contact with ALA 480 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A PRO 3.1 15.7 + - - +
477A ILE 3.1 6.1 + - - +
479A ASP* 1.3 79.0 - - - +
481A MSE 1.3 61.7 + - - +
483A ALA* 3.5 11.2 + - - +
484A LYS* 3.1 27.9 - - - +
440B LEU* 3.8 30.3 - - + +
441B LYS* 4.8 5.8 - - + +
448B LEU* 3.8 13.7 - - + -
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Residues in contact with MSE 481 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ILE* 2.9 16.8 + - + +
478A LEU* 3.4 15.0 - - - +
479A ASP 3.2 0.2 - - - -
480A ALA* 1.3 77.9 - - - +
482A ASP* 1.3 62.5 + - - +
484A LYS* 3.2 20.7 + - - +
445B LEU* 3.8 24.0 - - + +
448B LEU* 3.3 25.4 - - + +
449B GLN* 3.0 57.0 - - + +
452B LEU* 4.0 24.7 - - + -
----------------------------------------------------------
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Residues in contact with ASP 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A LEU* 2.9 29.9 + - - +
479A ASP* 3.2 9.1 + - - +
481A MSE 1.3 75.7 - - - +
483A ALA* 1.3 58.1 + - - +
484A LYS 3.2 4.5 + - - +
----------------------------------------------------------
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Residues in contact with ALA 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A ASP 3.1 14.6 + - - +
480A ALA* 3.8 10.5 - - - +
481A MSE 3.1 0.8 - - - -
482A ASP* 1.3 78.9 - - - +
484A LYS* 1.3 64.7 + - - +
441B LYS* 5.7 11.9 - - + -
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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