Contacts of the helix formed by residues 444 - 472 (chain A) in PDB entry 3UMH
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 ASP 444 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A CD 2.3 31.4 - - - -
440A VAL* 2.7 19.2 + - + +
443A VAL* 1.3 82.7 - - + +
445A PRO* 1.3 60.5 - - - +
446A LYS* 3.7 10.0 + - - +
447A LYS* 2.9 54.3 + - + +
448A ALA 3.1 8.8 + - - -
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Residues in contact with PRO 445 (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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441A ARG* 3.4 24.1 - - + +
442A MET 4.6 2.7 - - - +
443A VAL 3.8 5.2 - - - +
444A ASP* 1.3 88.2 - - - +
446A LYS* 1.3 72.9 + - + +
448A ALA* 3.2 7.7 + - + +
449A ALA* 3.1 22.3 + - - +
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Residues in contact with LYS 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ASP* 3.2 11.0 + - - +
445A PRO* 1.3 86.8 - - + +
447A LYS* 1.3 61.6 + - - +
449A ALA* 3.5 18.7 + - - +
450A GLN* 3.6 13.5 + - - +
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Residues in contact with LYS 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A CD 4.2 5.5 - - - -
376A GLN* 4.0 23.3 - - - +
440A VAL* 4.0 19.3 - - + -
444A ASP* 2.9 37.6 + - + +
446A LYS* 1.3 76.9 - - - +
448A ALA* 1.3 60.8 + - - +
450A GLN* 3.0 45.3 + - - +
451A ILE* 3.5 11.9 + - + +
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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
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437A PHE* 3.5 17.6 - - + -
440A VAL* 3.8 8.9 - - + +
441A ARG* 3.5 44.9 - - + +
444A ASP 3.1 5.0 + - - +
445A PRO 3.5 7.9 - - - +
447A LYS* 1.3 73.5 - - - +
449A ALA* 1.3 62.2 + - - +
450A GLN 3.1 0.2 + - - -
451A ILE* 3.1 6.5 + - - +
452A ARG* 2.9 32.3 + - - +
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Residues in contact with ALA 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A PRO 3.1 12.9 + - - +
446A LYS* 3.5 14.4 - - - +
447A LYS 3.2 0.4 - - - -
448A ALA* 1.3 77.0 - - - +
450A GLN* 1.3 60.2 + - + +
452A ARG* 3.6 21.4 - - - +
453A SER* 5.0 1.6 + - - -
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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 LYS 3.6 14.3 - - - +
447A LYS* 3.0 31.4 + - - +
449A ALA* 1.3 79.5 - - + +
451A ILE* 1.3 61.4 + - + +
452A ARG 3.5 0.2 - - - -
453A SER* 5.2 2.1 + - - -
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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
----------------------------------------------------------
437A PHE* 4.0 21.5 - - + -
440A VAL* 4.4 26.2 - - + -
447A LYS* 4.0 12.1 - - + +
448A ALA* 3.5 9.9 - - - +
450A GLN* 1.3 83.8 - - + +
452A ARG* 1.3 68.0 + - - +
453A SER 3.3 3.4 - - - -
454A GLN* 3.2 22.2 + - - +
455A VAL* 3.0 31.3 + - + +
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Residues in contact with ARG 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A PHE* 3.5 36.7 - - - -
441A ARG* 4.2 20.8 - - - +
448A ALA* 2.9 18.0 + - - +
449A ALA* 3.6 17.8 - - - +
450A GLN 3.5 1.0 - - - -
451A ILE* 1.3 77.0 - - - +
453A SER* 1.3 61.5 + - - +
455A VAL* 3.2 1.9 + - - +
456A MET* 2.9 45.1 + - + +
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Residues in contact with SER 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A ALA 5.0 0.8 + - - -
450A GLN 5.2 1.9 + - - -
451A ILE 3.3 0.8 - - - -
452A ARG* 1.3 77.1 - - - +
454A GLN* 1.3 67.3 + - - +
456A MET* 3.5 4.0 + - - +
457A THR* 2.9 29.8 + - - -
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Residues in contact with GLN 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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451A ILE* 3.2 23.0 + - - +
453A SER* 1.3 79.1 - - - +
455A VAL* 1.3 65.2 + - + +
457A THR* 3.4 6.5 + - - +
458A HIS* 3.1 23.6 + - + +
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Residues in contact with VAL 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A THR* 4.0 21.1 - - + +
434A LEU* 5.4 0.7 - - - -
437A PHE* 3.8 43.7 - - + -
451A ILE* 3.0 32.2 + - + +
452A ARG 3.6 3.8 - - - +
454A GLN* 1.3 80.6 - - + +
456A MET* 1.3 67.7 + - + +
458A HIS* 3.1 7.8 + - - +
459A LEU* 3.0 33.6 + - + +
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Residues in contact with MET 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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434A LEU* 4.7 5.4 - - + -
437A PHE* 4.1 33.2 - - + -
452A ARG* 2.9 34.2 + - + +
453A SER* 4.1 4.5 - - - +
455A VAL* 1.3 77.7 - - + +
457A THR* 1.3 56.8 + - - +
459A LEU* 3.2 30.1 + - + +
460A ARG* 2.8 30.1 + - - +
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Residues in contact with THR 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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453A SER* 2.9 21.5 + - - -
454A GLN* 3.5 7.9 - - - +
456A MET* 1.3 74.6 - - - +
458A HIS* 1.3 68.0 + - + +
460A ARG* 3.4 8.0 + - - +
461A VAL* 3.1 31.7 + - + +
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Residues in contact with HIS 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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2A CD 2.5 31.0 - - - -
387A GLU* 3.4 13.0 + - - -
429A ASP* 3.4 10.1 + - - -
433A THR* 3.6 26.2 + - + -
454A GLN* 3.1 12.0 + - + +
455A VAL* 3.1 9.8 + - - +
457A THR* 1.3 80.8 - - - +
459A LEU* 1.3 63.8 + - - +
461A VAL* 3.4 11.4 + - + +
462A ILE* 3.1 38.0 + - + +
465A ARG* 5.3 2.7 - - - -
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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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430A ARG* 3.8 45.7 - - + +
433A THR* 4.2 13.0 - - + -
434A LEU* 3.9 21.5 - - + -
455A VAL* 3.0 21.2 + - + +
456A MET* 3.5 41.1 - - + +
457A THR 3.2 0.2 - - - -
458A HIS* 1.3 78.1 - - - +
460A ARG* 1.3 62.3 + - - +
462A ILE* 3.2 8.8 + - + +
463A TYR* 3.0 34.3 + - + -
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Residues in contact with ARG 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A MET 2.8 17.3 + - - +
457A THR* 3.8 7.4 - - - +
458A HIS 3.4 0.2 - - - -
459A LEU* 1.3 75.4 - - - +
461A VAL* 1.3 59.6 + - + +
463A TYR* 3.2 9.4 + - + +
464A GLU* 2.8 64.9 + - + +
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Residues in contact with VAL 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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457A THR* 3.1 24.0 + - + +
458A HIS* 3.4 18.4 - - + +
459A LEU 3.2 0.2 - - - -
460A ARG* 1.3 78.0 - - + +
462A ILE* 1.3 63.3 + - - +
464A GLU* 3.3 15.5 + - - +
465A ARG* 2.9 45.8 + - + +
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Residues in contact with ILE 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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426A GLU* 3.7 36.1 - - + +
429A ASP* 3.6 28.7 - - + +
430A ARG* 4.0 26.5 - - + +
433A THR* 4.8 0.2 - - - +
458A HIS* 3.1 36.0 + - + +
459A LEU* 3.5 11.2 - - + +
461A VAL* 1.3 77.8 - - + +
463A TYR* 1.3 58.8 + - + +
465A ARG* 3.6 24.6 - - - +
466A MET* 3.0 31.5 + - + +
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Residues in contact with TYR 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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430A ARG* 3.8 38.0 + - - -
459A LEU* 3.0 28.0 + - + +
460A ARG* 3.4 13.2 - - + +
461A VAL 3.2 0.2 - - - -
462A ILE* 1.3 77.4 - - + +
464A GLU* 1.3 62.9 + - + +
466A MET* 4.1 16.1 - - + +
467A ASN* 2.7 48.6 + - - +
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Residues in contact with GLU 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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460A ARG* 2.8 61.9 + - + +
461A VAL* 3.7 16.6 - - - +
463A TYR* 1.3 72.7 - - + +
465A ARG* 1.3 58.1 + - - +
467A ASN* 3.3 6.1 + - - +
468A GLN* 2.4 47.7 + - - +
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Residues in contact with ARG 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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394A ARG* 3.2 43.9 - - - +
398A LEU* 5.7 7.4 - - + -
422A TYR* 3.7 4.5 - - + +
426A GLU* 2.7 37.9 + - - +
429A ASP* 4.1 5.3 + - - -
458A HIS* 5.3 3.2 - - - -
461A VAL* 2.9 33.6 + - + +
462A ILE* 3.6 26.2 - - - +
464A GLU* 1.3 77.9 - - - +
466A MET* 1.3 55.8 + - - +
468A GLN* 3.4 6.1 + - - +
469A SER* 2.9 36.0 + - - +
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Residues in contact with MET 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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422A TYR* 3.4 20.3 + - + +
423A VAL* 4.2 24.0 - - + +
426A GLU* 3.9 27.3 + - + -
427A GLN* 4.4 11.7 - - + +
462A ILE* 3.0 20.5 + - - +
463A TYR* 4.1 19.3 - - + +
465A ARG* 1.3 76.0 - - - +
467A ASN* 1.3 64.4 + - - +
469A SER* 3.2 2.6 + - - -
470A LEU* 2.9 53.3 + - + +
491A LEU* 5.1 10.3 - - + -
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Residues in contact with ASN 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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463A TYR* 2.7 43.8 + - - +
464A GLU* 3.7 5.9 - - - +
466A MET* 1.3 79.2 - - - +
468A GLN* 1.3 67.1 + - - +
470A LEU* 3.2 15.6 + - - +
471A SER* 2.9 28.9 + - - -
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Residues in contact with GLN 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A GLU* 2.4 45.2 + - - +
465A ARG* 3.7 7.0 - - - +
467A ASN* 1.3 83.0 + - - +
469A SER* 1.3 62.9 + - - +
471A SER* 3.3 18.3 + - - -
472A LEU* 3.4 17.4 + - - +
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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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398A LEU* 3.6 18.7 - - - +
401A TYR* 2.8 29.1 + - - -
422A TYR* 2.9 45.5 + - - -
465A ARG* 2.9 17.5 + - - +
466A MET 3.5 0.9 - - - -
468A GLN* 1.3 77.6 - - - +
470A LEU* 1.3 58.2 + - - +
472A LEU* 3.4 17.5 + - - +
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Residues in contact with LEU 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A TYR* 4.1 1.8 - - - -
419A LEU* 3.6 36.8 - - + -
422A TYR* 5.6 0.2 - - + -
423A VAL* 4.0 11.0 - - + -
466A MET* 2.9 40.4 + - + +
467A ASN* 3.6 14.4 - - - +
468A GLN 3.2 0.2 - - - -
469A SER* 1.3 74.2 - - - +
471A SER* 1.3 66.0 + - - +
472A LEU 3.1 0.4 - - - -
473A LEU* 3.1 24.2 + - + +
474A TYR* 4.5 6.1 + - - -
487A VAL* 4.6 11.7 - - + -
491A LEU* 4.0 28.3 - - + -
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Residues in contact with SER 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ASN 2.9 16.8 + - - -
468A GLN* 3.3 13.4 + - - -
470A LEU* 1.3 76.4 - - - +
472A LEU* 1.3 65.1 + - - +
473A LEU 3.1 0.7 + - - -
474A TYR* 3.1 33.1 + - - +
475A ASN* 4.4 3.8 + - - +
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Residues in contact with LEU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LEU* 5.2 1.3 - - + -
401A TYR* 4.3 5.8 - - + -
402A ILE* 4.0 31.6 - - + -
405A LEU* 3.7 21.0 - - + +
468A GLN 3.4 10.9 + - - +
469A SER* 3.4 23.3 - - - +
470A LEU 3.1 0.4 - - - -
471A SER* 1.3 78.3 - - - +
473A LEU* 1.3 63.0 + - - +
475A ASN* 3.0 32.3 + - - +
476A VAL* 4.3 1.7 + - - +
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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