Contacts of the helix formed by residues 410 - 446 (chain C) in PDB entry 5U07
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 ASN 410 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C ASP* 1.3 88.0 - - - +
411C GLU* 1.3 58.6 + - - +
413C ALA* 3.1 10.6 + - - +
414C ARG* 2.9 41.9 + - - +
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Residues in contact with GLU 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C ASP 3.2 4.5 - - - +
410C ASN* 1.3 78.4 - - - +
412C ASN* 1.3 68.4 + - - +
414C ARG* 3.1 12.0 + - + +
415C ILE* 3.0 28.9 + - - +
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Residues in contact with ASN 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C PRO* 6.1 3.4 - - - +
361C LEU* 5.6 7.1 - - - +
399C LEU* 3.1 36.6 + - - +
409C ASP* 3.0 22.9 + - - +
411C GLU* 1.3 82.3 + - - +
413C ALA* 1.3 66.7 + - - +
415C ILE* 3.0 12.2 - - - +
416C VAL* 2.9 32.2 + - - +
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Residues in contact with ALA 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C ASP* 2.4 32.9 + - - +
410C ASN* 3.1 15.5 + - - +
412C ASN* 1.3 70.3 - - - +
414C ARG* 1.3 66.4 + - - +
416C VAL* 3.8 6.0 - - - +
417C ARG* 2.8 29.0 + - - +
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Residues in contact with ARG 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C ASN* 2.9 33.9 + - - +
411C GLU* 3.1 11.4 + - + +
413C ALA* 1.3 81.5 - - - +
415C ILE* 1.3 65.5 + - - +
417C ARG* 3.1 23.0 + - - +
418C ARG* 2.9 24.8 + - - +
498C ALA* 6.3 2.2 - - - -
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Residues in contact with ILE 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C VAL* 5.9 5.8 - - + -
399C LEU 4.7 4.9 - - - +
411C GLU* 3.0 21.0 + - - +
412C ASN* 3.0 37.6 + - - +
414C ARG* 1.3 75.0 - - - +
416C VAL* 1.3 66.0 + - + +
418C ARG* 3.2 35.7 + - - +
419C ILE* 3.0 33.9 + - + +
485C VAL* 4.7 11.9 - - + +
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Residues in contact with VAL 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C ASP* 4.9 1.8 - - - +
342C LEU* 3.3 49.8 - - + -
343C HIS 5.1 6.1 - - - +
399C LEU 4.8 1.3 - - - +
412C ASN* 2.9 33.8 + - - +
413C ALA* 4.0 5.4 - - - +
415C ILE* 1.3 79.3 - - + +
417C ARG* 1.3 58.5 + - - +
419C ILE* 3.0 7.3 + - + +
420C THR* 2.8 43.6 + - + +
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Residues in contact with ARG 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C ALA 2.8 19.8 + - - +
414C ARG* 3.1 24.6 + - - +
416C VAL* 1.3 76.8 - - - +
418C ARG* 1.3 63.1 + - - +
420C THR* 2.9 25.0 + - - +
421C LEU* 2.9 32.1 + - + +
498C ALA* 3.5 37.8 + - - +
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Residues in contact with ARG 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C ARG 2.9 13.3 + - - +
415C ILE* 3.5 37.3 - - - +
417C ARG* 1.3 75.6 - - - +
419C ILE* 1.3 63.4 + - - +
421C LEU* 3.5 5.1 + - - +
422C ALA* 3.0 25.7 + - - +
484C ILE* 3.0 24.5 + - + -
485C VAL* 2.6 32.7 + - - +
487C ASP* 4.0 22.6 + - - +
493C TYR* 3.4 23.7 + - + +
496C GLY* 5.6 3.4 - - - -
497C MET 4.6 13.5 - - - +
498C ALA* 5.0 11.7 - - - +
499C GLY 5.8 0.9 - - - +
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Residues in contact with ILE 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C LEU* 5.2 8.3 - - + -
339C ASP* 2.9 36.5 - - + +
342C LEU* 4.6 17.3 - - + -
398C VAL* 4.7 12.1 - - + -
415C ILE* 3.0 22.1 + - + +
416C VAL* 3.0 10.8 + - + +
418C ARG* 1.3 77.8 - - + +
420C THR* 1.3 56.5 + - - +
422C ALA* 3.2 5.0 + - - +
423C ARG* 2.9 25.8 + - - +
481C PHE* 3.9 16.4 - - + -
484C ILE* 6.3 0.4 - - - -
485C VAL* 3.5 36.8 - - + -
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Residues in contact with THR 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C ASP* 3.0 23.5 - - - +
342C LEU* 6.1 1.3 - - + +
347C ASP* 4.3 17.5 - - - +
416C VAL* 2.8 29.0 + - + +
417C ARG* 2.9 16.2 + - - +
419C ILE* 1.3 68.0 - - - +
421C LEU* 1.3 68.1 + - - +
422C ALA 2.7 15.7 + - - -
423C ARG* 3.8 0.8 - - - +
424C LYS* 2.8 36.4 + - - +
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Residues in contact with LEU 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C ARG* 2.9 43.6 + - + +
418C ARG* 4.1 3.1 - - - +
420C THR* 1.3 79.4 + - - +
422C ALA* 1.3 54.9 + - - +
424C LYS* 3.9 21.0 - - + +
425C ALA* 3.2 27.2 + - - +
498C ALA 3.9 22.4 - - - +
499C GLY* 4.8 1.6 - - - -
500C PRO* 3.9 30.9 - - + +
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Residues in contact with ALA 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C ARG* 3.0 17.9 + - + +
419C ILE* 3.3 5.4 - - - +
420C THR 2.7 2.2 + - - -
421C LEU* 1.3 74.4 - - - +
423C ARG* 1.3 67.1 + - - +
424C LYS 2.9 1.4 + - - -
425C ALA* 3.1 4.1 + - - +
426C ALA* 2.8 26.0 + - - +
481C PHE* 3.8 20.0 - - + -
484C ILE* 4.2 20.0 - - + -
500C PRO* 5.5 4.5 - - + -
504C PHE* 4.1 10.0 - - + -
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Residues in contact with ARG 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C TRP* 4.0 9.4 - - + -
336C ARG* 3.4 43.6 + - + -
339C ASP* 3.0 37.1 + - + +
340C ALA* 4.9 7.1 - - - +
347C ASP* 3.2 35.6 + - - +
419C ILE 2.9 9.6 + - - +
420C THR* 4.9 1.0 + - - +
422C ALA* 1.3 71.8 - - - +
424C LYS* 1.3 79.7 + - - +
426C ALA* 4.0 6.1 - - - -
427C GLU* 2.4 76.7 + - - +
481C PHE* 3.9 4.4 - - + -
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Residues in contact with LYS 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C ASP* 5.8 7.9 - - + +
420C THR* 2.8 31.5 + - - +
421C LEU* 3.9 21.3 - - + +
422C ALA 2.9 0.4 + - - -
423C ARG* 1.3 93.5 - - - +
425C ALA* 1.3 69.2 + - - +
426C ALA 3.0 0.3 + - - -
427C GLU* 4.1 6.1 - - - +
428C ALA* 2.9 28.2 + - + +
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Residues in contact with ALA 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421C LEU 3.2 15.8 + - - +
422C ALA* 3.1 3.4 + - - +
424C LYS* 1.3 77.4 - - - +
426C ALA* 1.3 57.3 + - - +
428C ALA* 4.5 3.4 - - - -
429C LEU* 2.9 43.6 + - + +
500C PRO* 4.0 22.2 - - + -
502C ASN* 6.2 2.2 - - - -
504C PHE* 4.8 7.6 - - + -
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Residues in contact with ALA 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C TRP* 3.7 27.8 - - + -
422C ALA 2.8 20.9 + - - +
423C ARG* 3.4 5.8 - - - +
424C LYS 3.0 0.8 + - - -
425C ALA* 1.3 73.4 - - - +
427C GLU* 1.3 65.5 + - - +
429C LEU* 3.7 0.3 - - - +
430C GLY 3.0 17.0 + - - -
473C TYR* 3.1 12.2 + - - +
474C TRP* 4.6 2.2 - - + -
504C PHE* 3.8 31.5 - - + -
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Residues in contact with GLU 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C ARG* 3.1 15.9 - - + +
423C ARG* 2.4 80.4 + - - +
424C LYS* 4.1 3.8 - - - +
426C ALA* 1.3 78.4 - - - +
428C ALA* 1.3 66.8 + - - +
431C ARG* 2.8 39.2 + - - +
474C TRP* 3.7 25.5 - - + -
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Residues in contact with ALA 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C LYS* 2.9 22.0 + - + +
425C ALA* 3.8 4.5 - - - +
427C GLU* 1.3 80.3 - - - +
429C LEU* 1.3 63.4 + - - +
431C ARG* 3.2 35.7 + - - +
432C ARG* 3.0 36.5 + - - +
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Residues in contact with LEU 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C ALA* 2.9 33.3 + - + +
426C ALA 3.7 1.1 - - - +
428C ALA* 1.3 74.4 - - - +
430C GLY* 1.3 57.6 + - - +
432C ARG* 3.0 24.9 - - + +
433C LEU* 2.9 28.2 + - - +
473C TYR* 3.1 26.7 - - - +
502C ASN* 5.7 1.8 - - - -
504C PHE* 3.2 27.4 - - + +
505C ASN* 3.3 45.1 - - - +
508C ALA* 3.6 14.4 - - + -
536C LEU* 5.0 2.9 - - + +
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Residues in contact with GLY 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426C ALA 3.0 12.0 + - - -
427C GLU* 3.0 4.2 + - - -
429C LEU* 1.3 77.7 - - - +
431C ARG* 1.3 56.6 + - - +
433C LEU* 3.0 10.5 + - - +
434C GLU* 3.0 21.2 + - - -
470C MET* 3.6 12.7 - - - +
473C TYR* 3.5 31.9 - - - -
474C TRP* 5.0 2.9 - - - -
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Residues in contact with ARG 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C GLU* 2.8 26.0 + - + +
428C ALA* 3.2 47.1 + - - +
430C GLY* 1.3 69.7 - - - -
432C ARG* 1.3 66.1 + - + +
434C GLU* 2.9 25.0 + - + +
435C LYS* 3.0 14.4 + - - +
474C TRP* 5.5 1.4 - - - -
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Residues in contact with ARG 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428C ALA* 3.0 29.2 + - - +
429C LEU* 3.0 33.3 - - + +
430C GLY 3.2 0.2 - - - -
431C ARG* 1.3 82.9 - - + +
433C LEU* 1.3 57.3 - - - +
435C LYS* 3.6 18.4 + - - +
436C ALA* 2.9 27.9 + - - +
505C ASN* 5.9 0.9 - - - -
535C THR* 4.3 22.2 + - - +
536C LEU* 4.5 13.1 - - + +
538C SER* 6.2 3.7 - - - -
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Residues in contact with LEU 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429C LEU 2.9 12.1 + - - +
430C GLY* 3.0 8.7 + - - +
432C ARG* 1.3 76.0 - - - +
434C GLU* 1.3 58.4 + - - +
436C ALA* 3.9 4.0 - - + -
437C CYS* 2.8 34.4 + - - -
469C GLY* 4.9 4.9 - - - +
470C MET* 3.5 24.0 - - + -
473C TYR* 4.3 15.0 - - + -
508C ALA* 4.1 23.3 - - + +
511C ALA* 5.0 3.1 - - + -
512C TYR* 3.4 37.0 - - + +
536C LEU* 3.5 25.8 - - + -
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Residues in contact with GLU 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C GLY 3.0 8.5 + - - +
431C ARG* 2.9 17.5 + - + +
433C LEU* 1.3 76.0 - - - +
435C LYS* 1.3 67.3 + - - +
436C ALA 3.2 0.3 + - - -
437C CYS* 3.8 4.3 - - - +
438C LYS* 2.9 32.2 + - - +
466C VAL* 3.0 40.0 - - - +
469C GLY 4.8 0.5 - - - -
470C MET* 2.9 52.5 + - + +
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Residues in contact with LYS 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C ARG 3.0 13.9 + - - +
432C ARG* 4.0 14.3 + - - +
434C GLU* 1.3 74.1 - - - +
436C ALA* 1.3 71.3 + - - +
438C LYS* 3.8 8.2 - - - +
439C GLU* 2.9 45.6 + - + +
532C HIS* 5.9 3.9 + - - +
535C THR* 4.8 20.8 + - - +
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Residues in contact with ALA 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C ARG 2.9 19.9 + - - +
433C LEU* 3.3 13.0 - - + +
435C LYS* 1.3 84.3 - - + +
437C CYS* 1.3 58.8 + - - +
439C GLU* 3.9 1.4 - - - +
440C ALA* 2.8 33.8 + - - +
512C TYR* 5.0 4.3 - - + -
532C HIS* 3.9 21.7 - - - +
535C THR* 4.4 4.0 - - - +
536C LEU* 3.9 17.3 - - + -
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Residues in contact with CYS 437 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433C LEU* 2.8 33.7 + - - +
434C GLU* 3.8 6.3 - - - +
436C ALA* 1.3 72.8 - - - +
438C LYS* 1.3 63.3 + - - +
440C ALA* 3.3 6.5 - - - +
441C TRP* 2.9 24.8 + - - +
465C TRP* 3.9 24.9 - - + +
466C VAL* 3.9 16.2 - - + -
469C GLY* 5.4 3.1 - - - -
512C TYR* 3.4 33.0 - - - -
515C VAL* 4.8 9.4 - - - -
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Residues in contact with LYS 438 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434C GLU* 2.9 25.9 + - - +
435C LYS* 3.8 6.2 - - - +
437C CYS* 1.3 74.5 - - - +
439C GLU* 1.3 65.7 + - - +
441C TRP* 3.2 6.2 + - - +
442C LYS* 3.0 24.3 + - + +
463C GLY* 5.2 13.1 - - - +
466C VAL* 3.5 25.2 - - + +
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Residues in contact with GLU 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C LYS* 2.9 40.7 + - + +
436C ALA* 4.0 1.8 - - - +
438C LYS* 1.3 73.0 - - - +
440C ALA* 1.3 65.6 + - - +
442C LYS* 2.8 40.9 + - - +
443C GLU* 2.8 46.7 + - - +
532C HIS* 3.9 16.3 + - + -
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Residues in contact with ALA 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C ALA 2.8 25.3 + - - +
437C CYS* 3.3 6.3 - - - +
439C GLU* 1.3 72.0 - - - +
441C TRP* 1.3 64.9 + - - +
443C GLU 3.5 0.2 + - - -
444C SER* 2.9 25.8 + - - -
465C TRP* 4.2 10.3 - - + -
512C TYR* 4.2 18.4 - - - +
528C VAL* 3.6 5.2 - - - +
529C VAL* 4.5 6.5 - - - -
532C HIS* 3.7 25.0 - - + -
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Residues in contact with TRP 441 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C CYS 2.9 16.0 + - - +
438C LYS 3.7 7.2 - - - +
440C ALA* 1.3 72.8 - - - +
442C LYS* 1.3 67.1 + - + +
444C SER* 2.4 28.3 + - - -
445C ASN* 3.0 17.1 + - + +
463C GLY* 4.1 22.1 - - - -
464C PRO* 3.9 16.2 - - + +
465C TRP* 3.4 56.4 - + + -
519C TYR* 4.7 5.2 - + + -
199D VAL* 3.6 32.3 - - + -
201D VAL* 3.5 24.2 - - + -
225D GLN* 3.5 31.1 - - + +
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Residues in contact with LYS 442 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C LYS* 3.0 11.5 + - + +
439C GLU* 2.8 59.1 + - - +
441C TRP* 1.3 77.7 - - + +
443C GLU* 1.3 64.4 + - - +
444C SER 2.8 1.0 + - - -
445C ASN* 2.8 6.8 + - - -
446C SER* 2.4 39.9 + - - -
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Residues in contact with GLU 443 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C GLU* 2.8 41.0 + - + +
442C LYS* 1.3 85.5 + - - +
444C SER* 1.3 65.1 + - - +
446C SER* 3.1 13.8 + - - +
524C ARG* 4.3 4.0 + - - -
528C VAL* 3.5 12.7 - - + +
531C ARG* 3.5 17.3 + - - +
532C HIS* 2.4 36.1 + - - -
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Residues in contact with SER 444 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C ALA 2.9 15.5 + - - -
441C TRP* 2.4 26.4 + - - -
442C LYS 2.8 0.8 + - - -
443C GLU* 1.3 75.7 - - - +
445C ASN* 1.3 70.6 + - - +
446C SER 2.8 12.9 + - - -
465C TRP* 5.4 0.4 - - - -
524C ARG* 3.2 26.5 + - - +
525C VAL* 3.8 29.8 - - - +
528C VAL* 3.4 24.6 - - - +
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Residues in contact with ASN 445 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C TRP* 3.4 32.2 - - + +
442C LYS* 2.8 5.1 + - - +
444C SER* 1.3 82.7 + - - +
446C SER* 1.3 70.4 + - - +
524C ARG* 4.5 1.6 - - - -
201D VAL* 3.0 38.4 - - + +
203D PHE* 4.9 8.3 - - - +
223D ALA* 3.2 32.0 + - - +
225D GLN* 4.3 7.1 - - - +
21H ASP* 4.6 1.6 - - - +
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Residues in contact with SER 446 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C LYS* 2.4 27.2 + - - -
443C GLU* 3.5 12.1 - - - +
444C SER 2.8 4.9 + - - -
445C ASN* 1.3 75.6 - - - +
524C ARG* 3.3 9.0 - - - -
203D PHE* 4.9 11.0 - - - -
221D MET* 5.5 5.4 - - - +
21H ASP* 3.0 31.3 + - - +
----------------------------------------------------------
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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