Contacts of the helix formed by residues 447 - 482 (chain A) in PDB entry 1YY4
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 447 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A ILE* 1.3 81.5 - - - +
448A SER* 1.3 62.2 + - - +
449A GLN* 3.2 17.5 + - - +
450A GLN* 3.4 22.8 + - - +
451A GLN* 2.9 25.3 + - - +
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Residues in contact with SER 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ILE 3.7 0.4 + - - -
447A SER* 1.3 71.4 + - - +
449A GLN* 1.3 67.0 + - - +
451A GLN* 2.9 29.8 + - - +
452A SER* 3.1 16.0 + - - -
448B SER* 4.5 12.6 + - - -
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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
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447A SER* 3.2 8.8 + - - +
448A SER* 1.3 79.8 - - - +
450A GLN* 1.3 69.1 + - - +
452A SER* 3.4 3.9 + - - -
453A MET* 3.0 41.0 + - + +
435B ASP* 2.8 28.7 + - - +
438B VAL* 3.7 29.0 - - - +
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Residues in contact with GLN 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ILE* 3.5 15.9 - - + +
447A SER* 3.4 28.7 + - - +
448A SER 3.1 0.6 - - - -
449A GLN* 1.3 91.8 + - - +
451A GLN* 1.3 58.5 + - - +
452A SER 3.2 0.4 - - - -
453A MET* 3.7 20.0 - - - +
454A ARG* 2.9 30.7 + - - +
435B ASP* 6.0 0.4 + - - -
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Residues in contact with GLN 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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438A VAL* 5.3 1.7 - - - +
441A ILE* 3.6 28.4 + - + +
442A ALA* 3.6 34.9 + - - +
445A GLY 4.9 0.4 - - - -
446A ILE* 3.0 33.7 + - + +
447A SER 2.9 16.0 + - - +
448A SER* 2.9 21.0 + - - +
450A GLN* 1.3 77.5 - - - +
452A SER* 1.3 56.7 + - - +
455A LEU* 3.2 27.8 + - - +
452B SER* 6.1 1.3 - - - +
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Residues in contact with SER 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A SER* 3.1 11.0 + - - -
449A GLN* 3.5 10.1 - - - -
451A GLN* 1.3 76.8 - - - +
453A MET* 1.3 60.8 + - - +
455A LEU* 3.5 5.2 + - - +
456A ALA* 3.0 29.5 + - - +
438B VAL* 3.8 33.6 - - - +
451B GLN* 6.1 1.0 - - - +
452B SER* 4.8 11.4 + - - -
455B LEU* 3.6 15.6 - - - +
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Residues in contact with MET 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A GLN* 3.0 42.7 + - + +
450A GLN* 3.8 24.0 - - - +
451A GLN 3.4 0.2 - - - -
452A SER* 1.3 78.2 - - - +
454A ARG* 1.3 53.6 + - - +
456A ALA* 3.3 4.8 + - - +
457A ASN* 2.6 43.3 + - - +
431B ASN* 3.7 39.7 - - - +
434B THR* 3.6 26.7 - - + -
435B ASP* 3.4 23.1 - - - +
438B VAL* 4.5 2.5 - - + -
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Residues in contact with ARG 454 (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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390A LEU* 2.7 47.2 + - + +
391A LYS* 3.0 14.7 + - - +
392A LEU* 3.9 1.0 - - - +
393A GLN* 4.6 2.8 - - - +
396A GLU* 2.8 42.4 + - - -
441A ILE* 4.2 18.4 - - + +
444A SER* 5.2 5.2 - - - -
446A ILE* 4.2 12.6 - - + -
450A GLN 2.9 19.0 + - - +
451A GLN 4.1 3.6 - - - +
453A MET* 1.3 74.9 - - - +
455A LEU* 1.3 65.8 + - - +
456A ALA 3.1 0.2 + - - -
457A ASN* 3.2 8.6 + - - +
458A LEU* 3.0 40.3 + - + +
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Residues in contact with LEU 455 (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 THR* 5.9 1.1 - - + +
437A LEU* 4.1 16.6 - - + -
438A VAL* 4.1 13.7 - - + -
441A ILE* 3.6 23.1 - - + +
451A GLN 3.2 16.9 + - - +
452A SER* 3.7 5.4 - - - +
454A ARG* 1.3 78.2 - - - +
456A ALA* 1.3 58.7 + - - +
458A LEU* 3.5 3.8 + - - +
459A LEU* 3.1 47.7 + - + +
452B SER* 3.5 41.7 - - - +
455B LEU* 4.4 12.3 - - + -
456B ALA* 4.2 7.0 - - + -
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Residues in contact with ALA 456 (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 SER 3.0 18.2 + - - +
453A MET 3.5 2.5 - - - +
454A ARG 3.0 0.2 - - - -
455A LEU* 1.3 75.4 - - - +
457A ASN* 1.3 65.9 + - - +
459A LEU* 3.3 1.2 + - - -
460A MET* 3.0 35.2 + - + +
403B MET* 5.1 0.2 - - + -
434B THR* 3.4 30.5 - - + -
455B LEU* 4.4 6.1 - - + -
459B LEU* 3.8 22.4 - - + +
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Residues in contact with ASN 457 (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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386A ARG* 4.2 16.1 + - - +
390A LEU* 3.9 30.1 - - + +
453A MET* 2.6 36.0 + - - +
454A ARG* 3.8 6.3 - - - +
456A ALA* 1.3 75.5 - - - +
458A LEU* 1.3 60.9 + - - +
460A MET* 3.6 20.0 + - - +
461A LEU* 3.5 27.4 + - - +
430B LEU* 5.4 2.4 - - - +
431B ASN* 3.5 24.4 + - - +
434B THR* 5.2 0.3 + - - -
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Residues in contact with LEU 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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387A PHE* 4.2 12.5 - - + -
390A LEU* 3.9 24.9 - - + -
392A LEU* 4.1 22.9 - - + -
396A GLU* 3.9 29.6 - - + +
400A VAL* 5.1 12.3 - - + +
437A LEU* 4.7 12.3 - - + -
441A ILE* 4.3 14.8 - - + -
454A ARG* 3.0 33.0 + - + +
455A LEU 3.7 4.0 - - - +
457A ASN* 1.3 75.8 - - - +
459A LEU* 1.3 68.8 + - + +
461A LEU* 3.2 18.4 + - - +
462A LEU* 3.8 10.4 + - - +
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Residues in contact with LEU 459 (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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400A VAL* 5.6 2.7 - - + -
403A MET* 3.4 28.5 - - + -
437A LEU* 4.1 14.6 - - + -
455A LEU* 3.1 25.2 + - + +
456A ALA 3.3 2.2 + - - +
458A LEU* 1.3 77.8 - - - +
460A MET* 1.3 61.3 + - - +
462A LEU* 3.3 34.1 + - + +
463A SER* 4.2 3.3 + - - -
456B ALA* 3.5 47.6 - - + +
459B LEU* 4.0 28.5 - - + +
460B MET* 4.2 6.4 - - + +
462B LEU* 6.0 0.5 - - - +
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Residues in contact with MET 460 (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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386A ARG* 5.4 2.2 - - - +
456A ALA* 3.0 36.8 + - + +
457A ASN* 3.8 23.3 - - - +
458A LEU 3.2 0.2 - - - -
459A LEU* 1.3 80.0 - - - +
461A LEU* 1.3 60.9 + - + +
463A SER* 3.3 15.9 + - - -
464A HIS* 3.6 3.5 - - - -
403B MET* 3.8 20.4 - - + -
407B ASN* 2.9 38.3 - - - +
430B LEU* 3.7 31.4 - - + -
434B THR* 3.3 25.1 - - - +
459B LEU* 4.4 11.4 - - + -
462B LEU* 4.8 10.3 - - + -
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Residues in contact with LEU 461 (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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383A THR* 4.6 3.6 - - + -
386A ARG* 3.4 53.8 - - + +
387A PHE* 3.4 48.7 - - + -
390A LEU* 4.0 14.6 - - + -
457A ASN 3.5 9.8 + - - +
458A LEU 3.2 6.1 + - - +
459A LEU 3.2 0.6 - - - -
460A MET* 1.3 73.0 - - - +
462A LEU* 1.3 66.3 + - - +
463A SER 3.0 2.5 - - - -
464A HIS* 2.9 35.8 + - + +
465A VAL* 3.0 17.2 + - - +
407B ASN* 5.1 0.7 - - - +
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Residues in contact with LEU 462 (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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337A GLU* 4.4 3.1 - - - +
341A MET* 5.4 0.2 - - - -
387A PHE* 5.4 2.0 - - + -
400A VAL* 3.4 33.7 - - + -
403A MET* 4.7 13.7 - - + -
404A ILE* 4.1 24.5 - - + +
407A ASN* 5.6 4.5 - - + +
458A LEU 4.0 9.6 - - - +
459A LEU* 3.3 37.9 - - + +
460A MET 3.2 0.4 - - - -
461A LEU* 1.3 79.0 - - - +
463A SER* 1.3 57.9 + - - +
465A VAL* 3.3 9.6 + - + +
466A ARG* 2.8 31.7 + - - +
460B MET* 5.2 9.4 - - + -
463B SER* 4.1 14.0 + - - +
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Residues in contact with SER 463 (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 LEU 4.5 2.8 + - - -
460A MET* 3.3 16.6 + - - -
461A LEU 3.0 0.2 - - - -
462A LEU* 1.3 79.0 - - - +
464A HIS* 1.3 57.6 + - - +
466A ARG* 3.5 7.1 + - - +
467A HIS* 3.0 26.5 + - - +
337B GLU* 5.8 0.2 - - - -
407B ASN* 3.8 9.1 + - - -
462B LEU* 4.0 23.4 - - - +
463B SER* 4.1 8.3 + - - -
466B ARG* 3.5 35.7 + - - +
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Residues in contact with HIS 464 (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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383A THR* 3.7 24.8 + - + +
386A ARG* 4.6 6.7 - - - +
460A MET 3.6 15.7 - - - -
461A LEU* 2.9 23.8 + - + +
463A SER* 1.3 77.3 - - - +
465A VAL* 1.3 59.7 + - - +
466A ARG 3.1 0.2 - - - -
467A HIS* 3.1 2.6 + - - +
468A ALA* 3.0 29.6 + - - +
407B ASN* 2.5 44.0 + - - -
409B SER* 4.0 23.6 + - - -
410B MET* 3.3 33.5 - - + +
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Residues in contact with VAL 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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337A GLU* 3.8 31.1 - - + +
340A MET* 3.6 10.1 - - + +
341A MET* 4.3 22.0 - - + +
344A MET* 3.8 30.1 - - + -
383A THR* 3.9 6.3 - - + -
387A PHE* 4.1 9.0 - - + -
404A ILE* 4.6 6.3 - - + -
461A LEU 3.0 15.6 + - - +
462A LEU* 3.7 10.3 - - + +
464A HIS* 1.3 76.9 - - - +
466A ARG* 1.3 61.6 + - - +
468A ALA* 3.7 2.3 + - - +
469A SER* 3.2 21.8 + - - -
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Residues in contact with ARG 466 (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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333A SER* 5.1 7.3 + - - -
337A GLU* 3.3 33.7 + - - +
407A ASN 4.2 8.9 + - - -
408A SER* 4.3 10.1 + - - +
410A MET* 3.2 29.4 - - - +
462A LEU 2.8 18.9 + - - +
463A SER* 3.6 6.1 - - - +
465A VAL* 1.3 78.2 - - - +
467A HIS* 1.3 58.2 + - - +
469A SER* 3.2 18.2 - - - -
470A ASN* 3.2 26.4 + - - +
463B SER* 3.7 34.4 + - - +
466B ARG* 3.8 24.0 - - + -
467B HIS* 3.9 26.9 + - - -
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Residues in contact with HIS 467 (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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375A GLU* 5.8 0.2 - - - -
379A MET* 3.2 29.6 - - + -
463A SER 3.0 14.5 + - - +
464A HIS 3.1 8.7 + - - +
466A ARG* 1.3 75.4 - - - +
468A ALA* 1.3 59.9 + - - +
469A SER 2.9 5.4 + - - -
470A ASN* 3.4 7.4 + - + +
471A LYS* 3.1 57.0 + - - +
333B SER* 5.8 2.9 - - - -
410B MET* 3.5 36.1 + - + +
466B ARG* 3.8 26.7 - - - +
470B ASN* 5.4 7.6 - - - -
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Residues in contact with ALA 468 (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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340A MET* 3.3 13.0 - - - +
344A MET* 5.4 2.0 - - + -
376A ILE* 4.5 5.8 - - + +
379A MET* 3.9 37.2 - - + +
380A LEU* 4.0 22.7 - - + -
383A THR* 5.6 0.4 - - - +
464A HIS 3.0 15.4 + - - +
465A VAL* 4.2 4.0 - - - +
467A HIS* 1.3 77.0 + - - +
469A SER* 1.3 57.3 + - - +
471A LYS* 4.1 1.6 - - - +
472A GLY* 3.0 21.7 + - - -
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Residues in contact with SER 469 (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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333A SER 5.2 2.8 + - - -
336A MET* 3.6 9.0 - - - +
337A GLU* 3.2 32.2 + - - +
340A MET* 3.0 14.8 - - - -
465A VAL 3.2 15.6 + - - -
466A ARG* 3.2 12.6 - - - -
468A ALA* 1.3 75.4 - - - +
470A ASN* 1.3 71.7 + - - +
471A LYS 3.1 0.9 - - - -
472A GLY* 2.9 2.8 + - - -
473A MET* 2.9 29.1 + - - +
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Residues in contact with ASN 470 (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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466A ARG* 3.2 28.5 + - - +
467A HIS* 3.4 6.7 + - + +
469A SER* 1.3 81.8 + - - +
471A LYS* 1.3 69.0 + - + +
473A MET* 3.5 9.1 + - - +
474A GLU* 3.1 23.0 + - - +
467B HIS* 4.5 17.9 + - - -
470B ASN* 2.4 38.1 - - + +
471B LYS* 6.2 1.0 - - - +
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Residues in contact with LYS 471 (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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375A GLU* 4.5 11.7 - - - +
376A ILE* 3.9 7.9 - - + +
379A MET* 4.0 21.5 - - + -
467A HIS* 3.1 53.0 + - + +
468A ALA 4.1 3.6 - - - +
469A SER 3.1 0.8 - - - -
470A ASN* 1.3 79.7 - - + +
472A GLY* 1.3 65.4 + - - +
474A GLU* 3.2 23.9 + - - +
475A HIS* 3.0 23.9 + - - +
470B ASN* 6.0 5.0 - - - +
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Residues in contact with GLY 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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201A 4NA 4.0 10.5 - - - +
336A MET* 4.3 13.7 - - - -
340A MET* 5.3 0.7 - - - -
376A ILE* 3.7 17.5 - - - +
468A ALA 3.0 14.6 + - - -
469A SER* 2.9 7.6 + - - -
471A LYS* 1.3 78.0 - - - +
473A MET* 1.3 55.8 + - - +
475A HIS* 3.4 2.4 + - - +
476A LEU* 2.9 28.9 + - - +
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Residues in contact with MET 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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332A GLU 4.9 5.2 - - - +
333A SER* 5.8 3.1 - - - +
335A TRP* 3.2 49.8 - - + +
336A MET* 3.9 16.1 - - + +
469A SER* 2.9 21.9 + - - +
470A ASN* 3.8 9.0 - - - +
472A GLY* 1.3 71.3 - - - +
474A GLU* 1.3 58.8 + - - +
476A LEU* 3.0 6.3 + - - +
477A LEU* 2.5 39.6 + - + +
494A MET 4.4 6.7 - - - +
495A LEU* 4.1 20.0 - - + +
497A ALA 6.2 1.6 - - - -
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Residues in contact with GLU 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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375A GLU* 5.7 0.5 - - - +
470A ASN 3.1 11.5 + - - +
471A LYS* 3.4 28.9 + - - +
473A MET* 1.3 78.4 - - - +
475A HIS* 1.3 59.2 + - - +
477A LEU* 3.9 8.3 - - - +
478A ASN* 3.0 29.0 + - + +
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Residues in contact with HIS 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A 4NA 2.7 31.3 + - + -
295A MET* 4.5 0.9 - - + -
370A VAL* 3.7 12.8 - - + -
371A GLU 2.8 27.1 + - - -
372A GLY* 3.8 7.9 - - - -
373A ILE* 3.4 33.8 - - + +
376A ILE* 3.8 7.4 - - + -
471A LYS 3.0 11.9 + - - +
472A GLY 3.6 7.6 - - - +
474A GLU* 1.3 77.9 + - - +
476A LEU* 1.3 58.1 + - - +
478A ASN* 3.2 7.2 + - - +
479A MET* 2.9 44.8 + - + +
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Residues in contact with LEU 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A 4NA 3.5 35.1 + - + -
299A THR* 4.3 15.0 - - + -
335A TRP* 3.8 23.3 - - + -
336A MET* 4.1 9.9 - - + -
472A GLY 2.9 17.9 + - - +
473A MET 3.5 3.1 - - - +
475A HIS* 1.3 73.6 - - - +
477A LEU* 1.3 55.4 + - - +
479A MET* 2.9 11.4 + - + +
480A LYS* 2.7 32.9 + - - +
485A VAL* 5.0 7.0 - - + -
491A LEU* 4.4 18.4 - - + -
495A LEU* 3.5 31.2 - - + -
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Residues in contact with LEU 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A MET 2.5 22.3 + - - +
474A GLU* 3.9 7.4 - - - +
476A LEU* 1.3 73.4 - - - +
478A ASN* 1.3 60.9 - - - +
480A LYS* 3.3 32.0 + - + +
481A CYS* 3.0 29.5 + - - +
495A LEU* 3.9 27.8 - - + +
496A ASN* 5.3 2.0 - - - +
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Residues in contact with ASN 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A GLU* 3.0 19.7 + - + +
475A HIS* 3.4 8.3 - - + +
476A LEU 3.1 0.2 - - - -
477A LEU* 1.3 77.6 - - - +
479A MET* 1.3 71.4 + - + +
481A CYS* 3.5 8.4 + - - +
482A LYS* 3.3 45.9 + - - +
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Residues in contact with MET 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A 4NA 4.1 0.2 - - - +
295A MET* 3.3 31.2 - - + +
370A VAL* 5.1 4.5 - - + -
371A GLU 5.6 2.0 - - - +
475A HIS* 2.9 37.1 + - + +
476A LEU* 2.9 9.7 + - - +
478A ASN* 1.3 88.3 - - - +
480A LYS* 1.3 64.4 + - - +
482A LYS* 3.2 26.9 + - + +
483A ASN 3.4 7.1 + - - -
484A VAL* 3.5 26.1 + - - +
485A VAL* 3.4 24.2 - - + +
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Residues in contact with LYS 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A LEU* 2.7 16.3 + - + +
477A LEU* 3.5 25.6 - - - +
478A ASN 3.2 0.2 - - - -
479A MET* 1.3 68.7 - - - +
481A CYS* 1.3 77.0 + - - +
482A LYS 2.9 4.5 - - - -
483A ASN* 2.7 30.7 + - - +
485A VAL* 3.8 14.6 - - + +
492A LEU* 3.5 33.4 - - + -
495A LEU* 3.7 22.9 - - + -
496A ASN* 3.5 18.7 + - - +
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Residues in contact with CYS 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A LEU* 3.0 23.4 + - - +
478A ASN* 3.8 10.5 - - - +
480A LYS* 1.3 98.0 - - - +
482A LYS* 1.3 59.5 + - + +
483A ASN* 3.4 8.9 - - - +
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Residues in contact with LYS 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A ASN* 3.3 37.3 - - - +
479A MET* 3.2 21.7 + - + +
480A LYS 2.9 1.6 - - - -
481A CYS* 1.3 79.4 - - + +
483A ASN* 1.3 69.3 + - - +
484A VAL* 2.8 28.3 + - + +
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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