Contacts of the helix formed by residues 438 - 463 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431E ALA* 5.0 1.2 - - - +
436E LYS 4.5 1.8 - - - -
437E SER* 1.3 85.0 + - - +
439E LYS* 1.3 66.7 + - + +
440E GLU* 3.3 7.0 - - + +
441E ILE* 3.0 24.4 + - + +
442E PHE* 2.6 41.6 + - - +
82F ARG* 5.5 2.2 - - - +
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Residues in contact with LYS 439 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436E LYS 5.3 8.5 - - - +
438E GLU* 1.3 80.0 - - + +
440E GLU* 1.3 62.6 + - - +
442E PHE* 3.7 10.0 - - + +
443E GLU* 3.1 39.8 + - - +
82F ARG* 5.4 11.6 - - - +
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Residues in contact with GLU 440 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E LYS* 3.5 22.3 - - - +
28E TYR* 2.2 35.7 + - - -
416E PRO* 4.6 12.3 - - + +
438E GLU* 3.3 5.5 - - + +
439E LYS* 1.3 79.9 - - - +
441E ILE* 1.3 66.7 + - + +
443E GLU* 3.9 9.7 + - - +
444E ALA* 3.3 23.7 + - - +
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Residues in contact with ILE 441 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ILE* 4.0 39.9 - - + +
21E SER* 5.3 2.5 - - - -
22E LYS* 5.4 4.0 - - + +
28E TYR* 4.9 12.3 - - + -
416E PRO* 4.6 8.1 - - + -
420E ILE* 4.5 13.7 - - + -
429E LYS* 4.4 13.0 - - - +
431E ALA* 3.7 21.8 - - + -
438E GLU* 3.0 24.7 + - + +
440E GLU* 1.3 87.8 - - + +
442E PHE* 1.3 57.7 + - - +
443E GLU 3.2 1.6 - - - -
444E ALA* 3.6 4.6 - - - -
445E SER* 2.8 32.7 + - - -
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Residues in contact with PHE 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431E ALA* 4.4 13.6 - - - +
432E LEU* 3.2 40.9 - - + +
438E GLU 2.6 26.6 + - - +
439E LYS* 3.7 7.6 - - + +
441E ILE* 1.3 73.8 - - - +
443E GLU* 1.3 70.3 + - + +
446E ALA* 3.2 8.0 + - - +
82F ARG* 3.5 59.9 - - + +
83F TYR* 3.5 40.8 - + - -
85F SER* 4.3 5.2 - - - -
86F LEU* 3.6 21.8 - - + -
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Residues in contact with GLU 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439E LYS* 3.1 25.9 + - - +
440E GLU* 4.2 8.6 - - - +
442E PHE* 1.3 83.6 - - + +
444E ALA* 1.3 60.0 + - - +
445E SER 3.1 0.2 - - - -
446E ALA* 3.0 3.8 + - - +
447E HIS* 2.9 49.4 + - + +
85F SER* 4.3 14.8 + - - +
86F LEU* 4.1 17.9 - - + -
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Residues in contact with ALA 444 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415E HIS* 5.2 3.4 - - + -
416E PRO* 4.2 20.4 - - + -
417E LEU* 3.8 15.5 - - + +
420E ILE* 3.9 13.4 - - + +
440E GLU 3.3 16.5 + - - +
441E ILE* 3.2 7.7 + - - +
443E GLU* 1.3 79.9 - - - +
445E SER* 1.3 56.9 + - - +
447E HIS* 3.4 16.6 + - - +
448E ALA* 3.0 25.1 + - - +
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Residues in contact with SER 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420E ILE* 3.8 19.9 - - - +
425E HIS* 5.9 2.1 - - - +
430E ASP* 4.5 6.8 + - - -
431E ALA* 4.3 14.2 + - - +
432E LEU* 3.8 28.1 - - - +
441E ILE 2.8 18.0 + - - -
443E GLU 3.1 0.2 - - - -
444E ALA* 1.3 75.9 - - - +
446E ALA* 1.3 62.2 - - - +
448E ALA* 3.6 4.9 + - - +
449E GLN* 3.3 21.7 + - - +
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Residues in contact with ALA 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432E LEU* 4.0 8.5 - - + +
442E PHE 3.2 8.5 + - - +
443E GLU 3.0 9.3 + - - +
445E SER* 1.3 77.1 - - - +
447E HIS* 1.3 63.2 + - - +
448E ALA 3.2 0.2 - - - -
449E GLN* 3.6 11.0 + - - +
450E ALA* 3.3 21.7 + - - +
55F GLY* 5.6 1.3 - - - -
86F LEU* 3.6 39.0 - - + -
89F MET* 3.9 11.5 - - + +
90F TYR* 4.3 5.4 + - - +
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Residues in contact with HIS 447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415E HIS* 5.5 1.5 - + - -
417E LEU* 4.0 16.4 - - + +
443E GLU* 2.9 40.6 + - + +
444E ALA* 3.5 16.4 - - + +
445E SER 3.4 0.2 - - - -
446E ALA* 1.3 77.5 - - - +
448E ALA* 1.3 55.8 + - - +
450E ALA* 3.4 3.1 + - - +
451E ILE* 3.1 35.2 + - - +
480E ILE* 4.1 13.1 - - + +
484E ASP* 3.1 42.8 + - + +
485E ALA* 4.0 14.1 - - - +
86F LEU* 5.4 2.2 - - + +
89F MET* 3.4 24.5 - - + +
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Residues in contact with ALA 448 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417E LEU* 4.2 13.9 - - + +
420E ILE* 3.6 29.4 - - + +
421E LEU* 4.6 12.1 - - + +
425E HIS* 6.0 1.8 - - + -
444E ALA 3.0 16.7 + - - +
445E SER 3.7 5.8 - - - +
446E ALA 3.2 0.4 - - - -
447E HIS* 1.3 74.9 - - - +
449E GLN* 1.3 60.9 + - - +
451E ILE* 3.4 2.5 + - - +
452E LEU* 2.9 32.0 + - - +
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Residues in contact with GLN 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432E LEU* 4.0 15.3 - - + +
445E SER 3.3 11.1 + - - +
446E ALA* 3.7 12.1 - - - +
448E ALA* 1.3 79.7 - - - +
450E ALA* 1.3 61.3 + - + +
452E LEU* 3.9 10.6 - - + +
453E HIS* 2.9 43.8 + - + +
54F ILE* 3.7 12.1 + - - +
55F GLY* 3.3 6.5 - - - -
56F ALA* 2.5 47.1 + - + +
90F TYR* 4.1 2.8 + - - +
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Residues in contact with ALA 450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446E ALA 3.3 11.6 + - - +
447E HIS 3.5 8.5 - - - +
448E ALA 3.1 0.8 - - - -
449E GLN* 1.3 79.7 - - + +
451E ILE* 1.3 64.6 + - - +
453E HIS* 3.2 4.9 + - - +
454E LEU* 3.0 27.3 + - - +
480E ILE* 3.9 9.9 - - + -
75F TRP* 3.8 27.6 - - + -
89F MET* 3.7 21.5 - - - -
90F TYR* 4.9 1.3 - - + -
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Residues in contact with ILE 451 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417E LEU* 4.1 15.9 - - + -
421E LEU* 4.1 16.2 - - + -
447E HIS 3.1 18.6 + - - +
448E ALA 3.8 3.6 - - - +
450E ALA* 1.3 74.1 - - - +
452E LEU* 1.3 52.4 + - - +
454E LEU* 3.0 10.9 + - - +
455E GLN* 2.7 46.3 + - + +
477E ILE* 3.7 26.0 - - + -
480E ILE* 4.1 18.6 - - + -
481E LEU* 3.7 31.6 - - + -
499E CYS* 3.8 15.0 - - - -
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Residues in contact with LEU 452 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365E TYR* 5.2 10.1 - - + +
421E LEU* 5.5 3.1 - - + +
425E HIS* 3.9 31.6 - - + +
448E ALA 2.9 18.5 + - - +
449E GLN* 3.9 10.5 - - + +
451E ILE* 1.3 76.9 - - - +
453E HIS* 1.3 62.2 + - + +
455E GLN* 3.8 20.1 - - + +
456E GLU* 3.1 56.8 + - + +
502E GLN* 5.7 0.4 - - - +
506E LEU* 5.8 2.9 - - + -
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Residues in contact with HIS 453 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449E GLN* 2.9 37.8 + - + +
450E ALA* 3.4 6.7 - - - +
452E LEU* 1.3 79.3 - - + +
454E LEU* 1.3 59.7 + - - +
456E GLU* 3.7 13.0 + - - +
457E GLN* 3.3 27.4 + - - +
56F ALA 3.6 24.9 - - - -
57F ALA* 4.0 1.9 - - - -
58F PHE* 3.6 45.4 + - + +
75F TRP* 4.2 12.2 - - + -
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Residues in contact with LEU 454 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450E ALA 3.0 18.0 + - - +
451E ILE 3.0 5.8 + - - +
453E HIS* 1.3 75.9 - - - +
455E GLN* 1.3 65.5 + - - +
457E GLN* 3.1 12.7 + - - +
458E ILE* 3.2 20.3 + - - +
473E TYR* 3.8 32.4 - - + +
476E GLN* 3.7 39.3 - - + +
477E ILE* 3.7 26.2 - - + +
480E ILE* 4.0 15.3 - - + -
58F PHE* 4.5 9.4 - - + -
75F TRP* 4.2 17.7 - - + -
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Residues in contact with GLN 455 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365E TYR* 5.0 1.4 + - - -
421E LEU* 4.8 3.3 - - - +
451E ILE* 2.7 29.4 + - + +
452E LEU* 3.8 27.2 - - + +
454E LEU* 1.3 72.8 - - - +
456E GLU* 1.3 63.4 + - + +
457E GLN 3.2 1.0 + - - -
458E ILE* 3.3 13.5 + - - +
459E VAL* 3.3 20.1 + - - +
477E ILE* 3.8 14.3 - - + +
499E CYS* 2.8 36.5 + - - +
502E GLN* 3.0 34.0 + - - +
503E VAL* 3.7 19.8 - - + +
506E LEU* 5.4 7.1 - - + +
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Residues in contact with GLU 456 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452E LEU* 3.1 45.0 + - + +
453E HIS* 4.0 14.4 - - - +
455E GLN* 1.3 76.6 - - + +
457E GLN* 1.3 58.1 + - - +
459E VAL* 4.1 8.8 - - - +
460E LYS* 3.2 25.8 + - - +
506E LEU* 5.1 12.0 - - + +
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Residues in contact with GLN 457 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453E HIS 3.3 15.0 + - - +
454E LEU* 3.1 8.0 + - - +
455E GLN 3.1 0.8 - - - -
456E GLU* 1.3 78.4 + - - +
458E ILE* 1.3 64.0 + - - +
460E LYS* 3.8 29.4 - - - +
461E GLU* 3.2 56.3 + - - +
473E TYR* 4.1 15.2 + - + -
58F PHE* 3.4 37.0 + - + -
59F LEU* 5.5 1.6 - - - +
60F THR* 4.5 14.6 + - - +
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Residues in contact with ILE 458 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454E LEU 3.2 15.2 + - - +
455E GLN 3.3 4.9 + - - +
457E GLN* 1.3 78.2 - - - +
459E VAL* 1.3 62.4 + - - +
461E GLU* 3.4 3.5 + - - +
462E MET* 3.1 48.0 + - + +
470E VAL* 4.1 28.4 - - + +
473E TYR* 3.5 32.5 - - + -
474E LEU* 3.7 34.1 - - + +
477E ILE* 4.5 8.1 - - + -
503E VAL* 4.0 17.0 - - + -
511E LEU* 4.7 1.3 - - + -
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Residues in contact with VAL 459 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455E GLN 3.3 18.8 + - - +
456E GLU* 4.2 7.9 - - - +
458E ILE* 1.3 77.2 - - - +
460E LYS* 1.3 63.9 + - - +
462E MET* 3.4 8.8 + - - +
463E ASN* 3.1 42.9 + - - +
503E VAL* 3.8 29.8 - - + +
506E LEU* 3.2 40.8 - - + +
507E SER* 4.0 6.5 - - - -
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Residues in contact with LYS 460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456E GLU 3.2 18.4 + - - +
457E GLN* 3.8 31.0 - - - +
458E ILE 3.3 0.2 - - - -
459E VAL* 1.3 80.9 - - - +
461E GLU* 1.3 63.2 + - + +
463E ASN* 3.8 8.2 + - - +
464E ASP* 3.7 17.0 + - - +
464G ASP* 3.6 32.0 + - - +
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Residues in contact with GLU 461 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457E GLN* 3.2 25.6 + - - +
458E ILE* 4.1 3.1 - - - +
460E LYS* 1.3 77.9 - - + +
462E MET* 1.3 57.4 + - - +
463E ASN 3.4 0.2 - - - -
464E ASP* 3.3 6.2 + - - +
465E GLY 3.1 3.8 + - - -
466E ASP* 2.7 55.2 + - + +
469E SER* 2.4 28.1 + - - -
470E VAL* 6.5 0.2 - - + -
473E TYR* 2.9 32.3 + - - -
60F THR* 5.4 0.9 + - - +
71F LYS* 3.3 27.2 + - - +
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Residues in contact with MET 462 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458E ILE* 3.1 41.3 + - + +
459E VAL* 3.4 7.6 + - - +
461E GLU* 1.3 73.4 - - - +
463E ASN* 1.3 59.7 + - - +
464E ASP 3.1 4.7 - - - -
465E GLY* 3.0 18.1 + - - +
466E ASP 4.0 3.8 - - - +
467E TYR* 3.5 48.0 + - + +
470E VAL* 4.3 10.8 - - + -
503E VAL* 4.2 3.6 - - + -
507E SER* 3.6 31.6 - - - +
510E LYS* 4.2 8.8 - - + +
511E LEU* 3.9 33.7 - - + +
514E TYR* 5.3 0.2 - - - -
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Residues in contact with ASN 463 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459E VAL* 3.1 36.5 + - - +
460E LYS* 4.0 7.9 - - - +
461E GLU 3.4 0.2 - - - -
462E MET* 1.3 76.7 - - - +
464E ASP* 1.3 59.2 + - - +
506E LEU 5.2 1.4 + - - -
507E SER* 4.6 3.7 - - - +
510E LYS* 2.7 42.0 + - - +
460G LYS* 6.1 0.2 - - - -
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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