Contacts of the helix formed by residues 438 - 463 (chain G) in PDB entry 4KYI
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 GLU 438 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431G ALA* 5.0 0.8 - - - +
436G LYS 3.3 8.3 - - - +
437G SER* 1.3 94.0 + - - +
439G LYS* 1.3 62.7 + - + +
440G GLU* 4.5 8.5 - - + +
441G ILE* 2.9 23.3 + - + +
442G PHE* 2.4 44.6 + - - +
82H ARG* 4.6 1.8 - - - +
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Residues in contact with LYS 439 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435G GLU 5.9 0.7 - - - -
438G GLU* 1.3 76.8 - - + +
440G GLU* 1.3 61.8 + - - +
442G PHE* 3.8 10.3 - - + +
443G GLU* 3.2 36.3 + - - +
82H ARG* 3.1 44.3 + - - +
85H SER* 5.3 4.0 + - - -
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Residues in contact with GLU 440 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G LYS* 3.4 25.4 - - - +
28G TYR* 2.3 42.0 + - + -
416G PRO* 4.7 6.8 - - + +
438G GLU* 3.0 6.7 + - + +
439G LYS* 1.3 79.0 - - - +
441G ILE* 1.3 71.6 + - + +
443G GLU* 3.5 5.3 + - - +
444G ALA* 3.4 19.8 + - - +
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Residues in contact with ILE 441 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ILE* 3.8 34.1 - - + +
22G LYS* 5.8 4.0 - - + +
28G TYR* 4.5 11.2 - - + -
416G PRO* 3.8 26.7 - - + -
420G ILE* 4.7 10.5 - - + -
429G LYS* 4.4 17.0 - - - +
431G ALA* 4.2 15.3 - - + -
438G GLU* 2.9 22.7 + - + +
440G GLU* 1.3 82.4 - - + +
442G PHE* 1.3 59.8 + - - +
444G ALA* 3.7 3.9 - - + -
445G SER* 2.8 29.9 + - - -
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Residues in contact with PHE 442 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431G ALA* 3.3 30.3 - - - +
432G LEU* 3.7 34.3 - - + +
438G GLU 2.4 32.3 + - - +
439G LYS* 3.8 10.1 - - + +
441G ILE* 1.3 75.4 - - - +
443G GLU* 1.3 71.1 + - + +
445G SER* 3.6 0.5 + - - -
446G ALA* 3.4 14.6 + - - +
82H ARG* 3.4 57.0 - - - +
83H TYR* 3.6 31.4 - + - -
85H SER* 4.5 3.8 - - - -
86H LEU* 3.9 21.3 - - + -
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Residues in contact with GLU 443 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439G LYS* 3.2 23.4 + - + +
440G GLU* 3.9 5.2 - - - +
441G ILE 3.2 0.6 - - - -
442G PHE* 1.3 81.3 - - + +
444G ALA* 1.3 60.1 + - - +
445G SER 3.2 1.6 - - - -
446G ALA* 3.0 15.1 + - - +
447G HIS* 3.1 38.5 + - + +
484G ASP 5.0 4.0 - - - +
85H SER* 4.0 23.9 + - - +
86H LEU* 4.1 20.9 - - + -
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Residues in contact with ALA 444 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415G HIS* 5.0 2.9 - - + -
416G PRO* 3.9 29.4 - - + -
417G LEU* 3.9 19.4 - - + +
420G ILE* 4.2 6.8 - - + +
440G GLU 3.4 13.8 + - - +
441G ILE* 3.3 5.1 + - - +
443G GLU* 1.3 78.1 - - - +
445G SER* 1.3 61.1 + - - +
446G ALA 3.4 0.3 + - - -
447G HIS* 3.5 16.4 + - + +
448G ALA* 3.4 22.2 + - - +
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Residues in contact with SER 445 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420G ILE* 4.4 23.3 - - - +
429G LYS* 5.8 0.3 + - - -
430G ASP* 4.5 3.1 + - - -
431G ALA* 3.9 24.6 + - - +
432G LEU* 3.9 20.2 - - - +
441G ILE 2.8 17.3 + - - -
442G PHE 3.8 5.8 - - - -
443G GLU 3.2 0.4 - - - -
444G ALA* 1.3 76.1 - - - +
446G ALA* 1.3 58.6 + - - +
448G ALA* 4.3 3.0 - - - +
449G GLN* 3.7 16.5 + - - +
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Residues in contact with ALA 446 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432G LEU* 4.0 9.2 - - + -
442G PHE 3.4 6.8 + - - +
443G GLU 3.0 10.0 + - - +
445G SER* 1.3 79.6 - - - +
447G HIS* 1.3 65.8 + - - +
448G ALA 3.3 0.2 - - - -
449G GLN* 3.1 11.4 + - - +
450G ALA* 3.1 20.6 + - - +
55H GLY* 5.9 0.2 - - - -
86H LEU* 3.6 38.1 - - + -
89H MET* 4.3 9.0 - - + +
90H TYR* 4.9 5.5 + - - +
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Residues in contact with HIS 447 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415G HIS* 5.6 1.1 - + - -
417G LEU* 3.7 28.3 - - + -
443G GLU* 3.1 37.2 + - + +
444G ALA* 3.5 15.3 - - + +
445G SER 3.6 0.2 - - - -
446G ALA* 1.3 75.9 - - - +
448G ALA* 1.3 51.2 + - - +
450G ALA* 3.1 4.5 + - - +
451G ILE* 2.8 39.1 + - - +
480G ILE* 3.8 16.4 - - + +
484G ASP* 3.4 39.0 + - + +
485G ALA* 4.3 7.0 - - + -
86H LEU* 5.0 3.4 - - + -
89H MET* 3.3 23.0 - - + +
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Residues in contact with ALA 448 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417G LEU* 3.9 8.0 - - + +
420G ILE* 3.6 30.3 - - + -
421G LEU* 3.8 20.1 - - + +
425G HIS* 6.0 2.0 - - + -
444G ALA 3.4 8.9 + - - +
445G SER 4.4 2.9 - - - +
446G ALA 3.3 0.2 - - - -
447G HIS* 1.3 79.2 - - - +
449G GLN* 1.3 53.3 + - - +
451G ILE* 3.7 8.2 - - - +
452G LEU* 2.8 35.9 + - - +
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Residues in contact with GLN 449 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432G LEU* 3.4 20.5 - - + +
445G SER 3.7 12.3 + - - +
446G ALA* 3.1 12.1 + - - +
448G ALA* 1.3 76.3 - - - +
450G ALA* 1.3 65.0 + - - +
452G LEU* 3.4 6.3 + - - +
453G HIS* 3.0 39.3 + - + +
54H ILE* 3.4 21.6 + - - +
55H GLY* 3.2 5.5 - - - -
56H ALA* 2.5 40.4 + - - +
90H TYR* 4.3 3.8 + - - -
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Residues in contact with ALA 450 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446G ALA 3.1 3.6 + - - +
447G HIS 3.1 8.1 + - - +
449G GLN* 1.3 79.0 - - - +
451G ILE* 1.3 63.7 + - - +
453G HIS* 3.2 6.0 + - - +
454G LEU* 3.2 24.6 + - - +
480G ILE* 3.7 19.5 - - + -
75H TRP* 3.6 31.8 - - + -
89H MET* 3.8 18.6 - - - -
90H TYR* 4.8 2.5 - - + -
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Residues in contact with ILE 451 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417G LEU* 4.2 17.5 - - + -
421G LEU* 4.2 11.7 - - + -
447G HIS 2.8 20.1 + - - +
448G ALA* 3.7 5.4 - - - +
450G ALA* 1.3 75.7 - - - +
452G LEU* 1.3 51.5 + - - +
454G LEU* 3.0 11.5 + - - +
455G GLN* 2.8 57.4 + - + +
477G ILE* 4.1 22.7 - - + -
480G ILE* 3.9 26.0 - - + -
481G LEU* 4.1 23.8 - - + -
499G CYS* 4.1 7.9 - - - -
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Residues in contact with LEU 452 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365G TYR* 4.6 11.9 - - + +
421G LEU* 6.2 3.1 - - + -
425G HIS* 4.1 27.6 - - + +
448G ALA 2.8 21.1 + - - +
449G GLN* 3.8 6.5 - - - +
450G ALA 3.3 0.2 - - - -
451G ILE* 1.3 70.9 - - - +
453G HIS* 1.3 65.0 + - - +
455G GLN* 3.3 24.9 - - + +
456G GLU* 3.1 52.9 + - + +
502G GLN* 5.6 0.2 - - - +
506G LEU* 5.5 3.4 - - + -
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Residues in contact with HIS 453 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449G GLN* 3.0 30.0 + - + +
450G ALA 3.3 8.5 - - - +
451G ILE 3.1 0.2 - - - -
452G LEU* 1.3 78.5 - - - +
454G LEU* 1.3 60.9 + - - +
456G GLU* 3.6 11.6 + - - +
457G GLN* 3.2 26.7 + - - +
56H ALA 2.9 27.7 + - - -
57H ALA* 4.5 2.0 - - - -
58H PHE* 3.5 46.9 + - + +
75H TRP* 3.9 16.4 - + + -
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Residues in contact with LEU 454 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450G ALA 3.4 13.7 - - - +
451G ILE 3.0 6.3 + - - +
453G HIS* 1.3 74.8 - - - +
455G GLN* 1.3 64.8 + - - +
457G GLN* 3.1 4.8 + - - +
458G ILE* 3.0 31.4 + - - +
473G TYR* 3.9 22.6 - - + +
476G GLN* 3.4 48.2 - - + +
477G ILE* 3.7 27.6 - - + +
480G ILE* 4.2 12.6 - - + -
58H PHE* 4.6 13.5 - - + -
75H TRP* 4.2 15.3 - - + -
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Residues in contact with GLN 455 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365G TYR* 4.4 2.9 + - - -
421G LEU* 5.0 3.8 - - - +
451G ILE* 2.8 34.2 + - + +
452G LEU* 3.3 28.1 - - + +
454G LEU* 1.3 74.6 - - - +
456G GLU* 1.3 60.7 + - - +
458G ILE* 3.4 5.0 + - - +
459G VAL* 3.2 28.4 + - - +
477G ILE* 4.1 6.5 - - + +
499G CYS* 3.4 45.9 + - - +
502G GLN* 3.5 22.2 + - - +
503G VAL* 3.9 22.4 - - + +
506G LEU* 4.8 7.9 - - + +
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Residues in contact with GLU 456 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452G LEU* 3.1 42.0 + - + +
453G HIS* 4.0 10.8 + - - +
455G GLN* 1.3 79.1 - - + +
457G GLN* 1.3 54.1 + - - +
459G VAL* 3.5 8.0 + - - +
460G LYS* 2.8 34.0 + - - +
506G LEU* 5.3 8.3 - - + -
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Residues in contact with GLN 457 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453G HIS 3.2 15.0 + - - +
454G LEU* 3.1 7.5 + - + +
456G GLU* 1.3 76.0 - - + +
458G ILE* 1.3 64.0 + - - +
459G VAL 3.2 0.2 - - - -
460G LYS* 3.8 28.0 - - + +
461G GLU* 3.1 50.1 + - - +
473G TYR* 4.3 15.2 - - + -
58H PHE* 3.4 27.7 + - + -
59H LEU* 5.3 0.4 - - - +
60H THR* 3.0 31.6 + - - +
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Residues in contact with ILE 458 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454G LEU 3.0 22.1 + - - +
455G GLN* 3.4 6.3 + - - +
457G GLN* 1.3 75.0 - - - +
459G VAL* 1.3 62.2 + - - +
461G GLU* 4.4 2.0 - - - +
462G MET* 3.2 53.4 + - + +
470G VAL* 4.1 30.2 - - + +
473G TYR* 3.5 37.5 - - + -
474G LEU* 4.2 21.1 - - + +
477G ILE* 4.8 3.1 - - + -
503G VAL* 3.7 22.7 - - + -
511G LEU* 4.9 1.6 - - + -
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Residues in contact with VAL 459 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455G GLN 3.2 16.3 + - - +
456G GLU* 3.6 9.0 - - - +
458G ILE* 1.3 75.9 - - - +
460G LYS* 1.3 66.6 + - - +
462G MET* 3.6 7.3 + - - +
463G ASN* 3.1 32.4 + - - +
503G VAL* 3.8 20.9 - - + +
506G LEU* 3.3 50.9 - - + +
507G SER* 4.1 5.2 - - - +
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Residues in contact with LYS 460 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464E ASP* 3.5 32.6 + - - +
456G GLU 2.8 22.1 + - - +
457G GLN* 3.3 33.9 + - - +
459G VAL* 1.3 74.4 - - - +
461G GLU* 1.3 61.5 + - + +
463G ASN* 3.0 23.3 + - - +
464G ASP* 3.3 11.8 + - + +
60H THR* 5.4 5.9 + - - -
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Residues in contact with GLU 461 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457G GLN* 3.1 33.6 + - - +
458G ILE* 4.5 2.5 - - - +
460G LYS* 1.3 84.3 - - + +
462G MET* 1.3 52.2 + - + +
464G ASP* 2.8 10.5 + - - +
465G GLY 2.8 31.4 + - - -
466G ASP* 3.1 36.9 + - + +
469G SER* 3.0 22.6 + - - -
470G VAL* 6.1 1.1 - - + +
473G TYR* 3.3 15.5 + - - -
60H THR* 4.9 0.9 - - - +
71H LYS* 2.7 30.5 + - - -
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Residues in contact with MET 462 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458G ILE* 3.2 34.5 + - + +
459G VAL* 4.0 3.1 - - - +
461G GLU* 1.3 76.0 - - - +
463G ASN* 1.3 61.2 + - - +
464G ASP 3.1 2.6 + - - -
465G GLY* 3.8 6.0 + - - -
466G ASP 3.8 12.6 - - - +
467G TYR* 3.6 50.7 + - + +
470G VAL* 4.1 16.4 - - + -
503G VAL* 4.4 3.1 - - + -
507G SER* 3.7 29.6 - - - +
510G LYS* 3.8 10.9 + - + +
511G LEU* 3.8 31.4 - - + +
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Residues in contact with ASN 463 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459G VAL* 3.1 27.3 + - - +
460G LYS* 3.0 10.1 + - - +
462G MET* 1.3 76.1 - - - +
464G ASP* 1.3 60.4 + - - +
506G LEU 5.0 4.0 + - - -
507G SER* 4.3 9.8 + - - +
510G LYS* 3.0 38.7 + - - +
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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