Contacts of the helix formed by residues 438 - 465 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 6.2 5.2 - - + -
436A LYS 3.6 8.0 + - - +
437A SER* 1.3 75.5 - - - +
439A LYS* 1.3 62.3 + - - +
440A GLU* 4.3 5.2 - - + +
441A ILE* 3.2 27.6 + - + +
442A PHE* 2.9 25.5 + - - +
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Residues in contact with LYS 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A SER 4.7 4.5 - - - +
438A GLU* 1.3 74.4 + - - +
440A GLU* 1.3 53.8 + - - +
442A PHE* 4.1 10.1 - - + -
443A GLU* 2.7 51.8 + - + +
82B ARG* 4.9 20.2 - - + +
85B SER* 6.1 0.4 - - - +
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Residues in contact with GLU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 3.3 20.3 - - - +
28A TYR* 2.5 39.2 + - - +
416A PRO* 4.4 12.2 - - + +
438A GLU* 3.1 3.9 - - + +
439A LYS* 1.3 79.6 - - - +
441A ILE* 1.3 63.6 + - + +
443A GLU* 4.1 8.6 - - - +
444A ALA* 3.2 26.3 + - - +
389E GLU* 3.9 11.1 - - - +
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Residues in contact with ILE 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 4.0 42.6 - - + +
22A LYS* 5.3 7.2 - - + +
28A TYR* 4.5 19.1 - - + -
416A PRO* 4.8 7.0 - - + -
420A ILE* 5.0 8.5 - - + +
431A ALA* 3.7 20.9 - - + -
437A SER* 5.2 2.2 - - - -
438A GLU* 3.2 28.3 + - + +
440A GLU* 1.3 84.3 - - + +
442A PHE* 1.3 57.7 + - - +
443A GLU 3.2 0.2 - - - -
444A ALA* 3.3 5.0 + - - +
445A SER* 2.6 41.7 + - - +
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Residues in contact with PHE 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ALA* 3.8 10.7 - - - +
432A LEU* 3.4 61.9 - - + +
437A SER* 4.0 3.6 - - - +
438A GLU 2.9 17.3 + - - +
439A LYS* 3.7 11.4 - - + +
441A ILE* 1.3 77.7 - - - +
443A GLU* 1.3 68.2 + - + +
445A SER* 4.3 2.7 - - - -
446A ALA* 3.5 7.3 + - - +
82B ARG* 3.6 60.6 - - + +
83B TYR* 3.6 32.1 - + - -
85B SER* 5.3 0.7 - - - -
86B LEU* 3.7 18.6 - - + -
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Residues in contact with GLU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A LYS* 2.7 38.3 + - + +
440A GLU* 4.1 7.7 - - - +
442A PHE* 1.3 77.3 - - + +
444A ALA* 1.3 59.3 + - - +
445A SER 3.1 2.0 - - - -
446A ALA* 3.1 4.0 + - - +
447A HIS* 3.0 44.5 + - + -
486A LYS* 5.9 0.9 + - - -
85B SER* 3.2 31.5 + - - +
86B LEU* 3.7 24.9 - - + -
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Residues in contact with ALA 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A HIS* 5.1 2.9 - - + -
416A PRO* 4.0 29.4 - - + +
417A LEU* 3.7 20.7 - - + +
420A ILE* 4.4 5.6 - - + +
440A GLU 3.2 17.6 + - - +
441A ILE* 3.3 4.7 + - - +
443A GLU* 1.3 78.4 - - - +
445A SER* 1.3 57.0 + - - +
447A HIS* 3.7 13.6 - - - +
448A ALA* 3.2 23.4 + - - +
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Residues in contact with SER 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ILE* 3.8 21.2 - - - +
430A ASP* 5.6 0.4 - - - -
431A ALA* 3.8 16.0 + - - +
432A LEU* 4.1 18.9 - - - +
441A ILE* 2.6 22.6 + - - +
442A PHE* 3.8 6.7 - - - -
443A GLU 3.1 0.2 - - - -
444A ALA* 1.3 76.7 - - - +
446A ALA* 1.3 60.3 + - - +
447A HIS 3.2 0.2 - - - -
448A ALA* 3.0 9.3 + - - +
449A GLN* 3.0 27.2 + - - +
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Residues in contact with ALA 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A LEU* 4.1 11.1 - - + +
442A PHE 3.5 5.6 + - - +
443A GLU 3.1 9.0 + - - +
445A SER* 1.3 75.1 - - - +
447A HIS* 1.3 66.3 + - - +
449A GLN* 3.4 14.1 + - - +
450A ALA* 3.2 23.4 + - - +
55B GLY* 5.3 3.1 - - - -
86B LEU* 3.6 32.8 - - + -
89B MET* 3.8 4.4 - - + +
90B TYR* 4.3 12.5 + - - +
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Residues in contact with HIS 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A HIS* 5.7 0.4 - - - -
417A LEU* 3.8 16.6 - - + +
443A GLU* 3.0 32.5 + - + -
444A ALA* 3.7 16.1 - - - +
446A ALA* 1.3 77.5 - - - +
448A ALA* 1.3 57.9 + - - +
450A ALA* 3.9 1.9 - - - +
451A ILE* 3.2 30.7 + - - +
480A ILE* 3.9 6.1 - - + +
484A ASP* 3.3 37.6 - - + +
485A ALA* 3.8 15.8 + - - +
86B LEU* 3.5 19.9 - - + +
89B MET* 3.5 27.2 - - - +
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Residues in contact with ALA 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LEU* 3.7 14.8 - - + -
420A ILE* 3.6 27.1 - - + +
421A LEU* 4.6 12.0 - - + +
425A HIS* 6.2 0.7 - - + -
444A ALA 3.2 14.2 + - - +
445A SER 3.0 10.0 + - - +
447A HIS* 1.3 77.9 - - - +
449A GLN* 1.3 59.3 + - - +
450A ALA 3.3 0.4 - - - -
451A ILE* 3.6 5.5 + - - +
452A LEU* 3.1 26.7 + - - +
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Residues in contact with GLN 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A LEU* 4.2 12.4 - - + +
445A SER 3.0 10.7 + - - +
446A ALA* 3.5 14.8 - - - +
448A ALA* 1.3 73.7 - - - +
450A ALA* 1.3 65.3 + - - +
452A LEU* 3.8 11.1 - - + +
453A HIS* 3.0 44.8 + - + +
54B ILE 3.9 7.6 + - - -
55B GLY* 3.2 12.3 - - - -
56B ALA* 2.8 44.8 + - + +
75B TRP* 6.2 0.4 - - + -
90B TYR* 4.4 3.9 + - - +
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Residues in contact with ALA 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ALA 3.2 17.2 + - - +
447A HIS 3.9 2.5 - - - +
448A ALA 3.3 0.2 - - - -
449A GLN* 1.3 76.5 - - + +
451A ILE* 1.3 64.1 + - - +
453A HIS* 3.2 5.9 + - - +
454A LEU* 3.1 27.2 + - - +
480A ILE* 3.7 21.3 - - + -
75B TRP* 3.8 28.0 - - + -
89B MET* 4.2 12.3 - - + -
90B TYR* 4.9 1.3 - - + -
303B EDO 5.1 0.7 - - - -
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Residues in contact with ILE 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LEU* 4.3 7.9 - - + -
421A LEU* 4.3 16.4 - - + -
447A HIS 3.2 20.5 + - - +
448A ALA 3.9 4.5 - - - +
450A ALA* 1.3 76.1 - - - +
452A LEU* 1.3 51.0 + - - +
454A LEU* 3.1 10.9 + - - +
455A GLN* 2.7 63.3 + - + +
477A ILE* 3.7 26.9 - - + -
480A ILE* 4.1 18.2 - - + -
481A LEU* 3.8 32.8 - - + -
499A CYS* 3.9 4.5 - - - -
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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
----------------------------------------------------------
365A TYR* 5.4 5.8 - - - +
421A LEU* 5.7 1.3 - - + +
425A HIS* 3.9 33.4 - - + +
448A ALA 3.1 18.8 + - - +
449A GLN* 3.8 10.5 - - + +
450A ALA 3.3 0.2 - - - -
451A ILE* 1.3 72.9 - - - +
453A HIS* 1.3 60.3 + - + +
455A GLN* 3.5 21.2 - - + +
456A GLU* 2.9 62.2 + - + +
506A LEU* 5.6 3.8 - - + -
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Residues in contact with HIS 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 36.9 + - + -
450A ALA 3.3 8.5 - - - +
451A ILE 3.2 0.2 - - - -
452A LEU* 1.3 78.3 - - + +
454A LEU* 1.3 60.9 + - - +
456A GLU* 3.6 12.5 + - - +
457A GLN* 3.3 26.0 + - - +
56B ALA 3.0 28.0 + - - -
57B ALA* 3.9 3.1 - - + -
58B PHE* 3.5 45.9 + - + +
75B TRP* 4.1 13.9 - + + -
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Residues in contact with LEU 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ALA 3.4 13.5 - - - +
451A ILE* 3.1 6.8 + - - +
453A HIS* 1.3 75.6 - - - +
455A GLN* 1.3 65.7 + - - +
457A GLN* 3.0 7.0 + - - +
458A ILE* 3.0 28.4 + - - +
473A TYR* 3.8 28.4 - - + +
476A GLN* 3.7 40.2 - - + +
477A ILE* 3.7 30.5 - - + +
480A ILE* 4.4 11.4 - - + -
58B PHE* 4.6 9.2 - - + -
75B TRP* 4.3 14.4 - - + -
303B EDO 4.6 3.6 - - - +
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Residues in contact with GLN 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TYR* 4.8 1.6 + - - -
421A LEU* 4.5 5.0 - - - +
451A ILE* 2.7 48.9 + - + +
452A LEU* 3.5 24.7 - - + +
454A LEU* 1.3 74.3 - - - +
456A GLU* 1.3 60.2 + - + +
458A ILE* 3.5 6.3 + - - +
459A VAL* 3.2 28.3 + - - +
477A ILE* 4.0 6.9 - - + +
499A CYS* 3.5 29.0 - - - +
502A GLN* 3.7 21.7 + - - +
503A VAL* 3.6 27.4 - - + +
506A LEU* 4.6 9.8 - - + +
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Residues in contact with GLU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LEU* 2.9 47.0 + - + +
453A HIS* 4.1 12.6 + - - +
455A GLN* 1.3 77.0 - - + +
457A GLN* 1.3 58.3 + - - +
459A VAL* 3.9 8.4 - - - +
460A LYS* 3.1 26.3 + - - +
506A LEU* 5.4 7.6 - - + -
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Residues in contact with GLN 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A HIS 3.3 9.9 + - - +
454A LEU* 3.0 11.5 + - - +
456A GLU* 1.3 76.2 - - - +
458A ILE* 1.3 60.7 + - - +
459A VAL 3.2 1.3 - - - -
460A LYS* 3.1 28.9 + - - +
461A GLU* 2.8 64.5 + - - +
473A TYR* 4.2 12.3 - - + +
58B PHE* 3.4 32.7 - - + -
59B LEU* 5.4 0.4 - - - +
60B THR* 4.1 21.8 + - - +
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Residues in contact with ILE 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A LEU 3.0 16.2 + - - +
455A GLN* 3.5 8.0 + - - +
457A GLN* 1.3 75.3 - - - +
459A VAL* 1.3 57.6 + - - +
461A GLU* 4.1 2.5 - - - +
462A MET* 3.0 55.1 + - + +
470A VAL* 3.9 27.4 - - + +
473A TYR* 3.6 36.1 - - + -
474A LEU* 3.7 31.6 - - + +
477A ILE* 4.5 8.5 - - + -
503A VAL* 4.1 13.7 - - + -
511A LEU* 5.1 1.8 - - + -
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Residues in contact with VAL 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A GLN 3.2 17.7 + - - +
456A GLU* 3.9 8.1 - - - +
457A GLN 3.2 0.2 - - - -
458A ILE* 1.3 74.8 - - - +
460A LYS* 1.3 65.2 + - - +
462A MET* 4.1 6.0 - - - -
463A ASN* 2.8 45.8 + - - +
503A VAL* 4.1 19.3 - - + +
506A LEU* 3.4 46.7 - - + +
507A SER* 4.2 3.8 - - - -
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Residues in contact with LYS 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A GLU 3.1 19.1 + - - +
457A GLN* 3.1 32.4 + - - +
459A VAL* 1.3 79.1 - - - +
461A GLU* 1.3 63.3 + - + +
463A ASN* 3.7 4.6 + - - +
464A ASP* 3.3 24.7 + - - +
60B THR* 5.8 2.6 + - - -
463C ASN 5.6 1.3 - - - +
464C ASP* 3.2 43.5 + - - +
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Residues in contact with GLU 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A GLN* 2.8 35.2 + - - +
458A ILE* 4.2 3.1 - - - +
460A LYS* 1.3 74.5 - - + +
462A MET* 1.3 56.5 + - - +
464A ASP* 3.2 9.1 + - - +
465A GLY 2.9 7.8 + - - -
466A ASP* 2.7 59.7 + - + +
469A SER* 2.8 24.6 + - - -
470A VAL* 5.3 2.3 + - + +
473A TYR* 2.8 30.7 + - - -
60B THR* 5.0 3.6 + - - +
71B LYS* 4.7 10.8 + - - +
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Residues in contact with MET 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A ILE* 3.0 43.4 + - + +
459A VAL* 4.1 3.1 - - - +
461A GLU* 1.3 75.7 - - - +
463A ASN* 1.3 62.1 + - - +
465A GLY* 3.1 16.9 + - - +
466A ASP 3.8 3.6 - - - +
467A TYR* 3.5 50.6 + - + +
470A VAL* 3.8 15.5 - - + -
503A VAL* 4.3 4.0 - - + -
507A SER* 3.7 30.7 - - - +
510A LYS* 4.1 7.6 - - + +
511A LEU* 4.0 35.4 - - + +
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Residues in contact with ASN 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A VAL* 2.8 33.6 + - - +
460A LYS* 4.0 5.2 - - - +
462A MET* 1.3 76.5 - - - +
464A ASP* 1.3 63.4 + - - +
465A GLY* 4.6 0.2 - - - -
506A LEU 5.3 0.6 + - - -
507A SER* 4.5 4.6 - - - +
510A LYS* 3.2 42.2 + - - +
460C LYS* 5.5 2.3 + - - -
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Residues in contact with ASP 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LYS* 3.3 18.9 + - - +
461A GLU* 3.2 14.2 + - - +
463A ASN* 1.3 78.0 - - - +
465A GLY* 1.3 57.4 + - - +
466A ASP* 3.6 4.9 - - + +
460C LYS* 3.5 40.3 + - - +
464C ASP* 3.2 32.6 - - - +
----------------------------------------------------------
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Residues in contact with GLY 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A GLU 2.9 2.2 + - - -
462A MET 3.1 12.0 + - - -
463A ASN 3.2 0.4 - - - -
464A ASP* 1.3 79.8 - - - +
466A ASP* 1.3 59.3 + - - +
467A TYR* 3.1 25.2 + - - -
----------------------------------------------------------
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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