Contacts of the helix formed by residues 445 - 472 (chain A) in PDB entry 3ECP
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 SER 445 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A ARG* 3.8 5.6 - - - +
444A ALA* 1.3 77.8 - - - +
446A TRP* 1.3 67.1 + - - +
447A GLY* 3.1 5.8 + - - -
448A ALA* 2.8 28.6 + - - +
449A LEU* 3.1 12.1 + - - +
5C C 3.2 28.2 + - - -
6C T 3.0 21.2 + - - -
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Residues in contact with TRP 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A GLU* 3.4 31.8 + - + +
330A LYS* 3.9 25.3 - - + +
331A ALA* 3.6 35.4 - - + -
334A THR* 4.9 5.2 - - + -
335A GLY* 3.9 24.5 - - - -
363A LEU* 4.1 41.6 - - + +
364A LEU* 3.7 20.3 - - + +
367A ARG* 3.5 33.0 - - + +
445A SER* 1.3 73.9 - - - +
447A GLY* 1.3 80.9 + - - +
449A LEU* 3.4 1.6 + - - +
450A TRP* 2.9 30.6 + - + +
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Residues in contact with GLY 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A SER* 2.9 8.1 + - - -
446A TRP* 1.3 95.5 - - - +
448A ALA* 1.3 64.0 + - - +
450A TRP* 3.4 5.4 + - - +
451A GLU* 3.1 32.0 + - - +
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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
----------------------------------------------------------
429A ILE 4.5 0.5 - - - +
430A ALA 4.6 2.7 - - - +
433A GLY* 3.5 24.5 - - - +
435A PHE* 4.5 13.5 - - + +
444A ALA* 4.2 9.4 - - + -
445A SER* 2.8 20.6 + - - +
447A GLY* 1.3 74.3 - - - +
449A LEU* 1.3 65.5 + - + +
451A GLU* 3.1 2.7 + - - -
452A GLY* 2.9 19.8 + - - -
6C T 4.0 15.9 - - - +
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Residues in contact with LEU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A LEU* 5.6 1.3 - - + -
367A ARG* 3.7 31.0 - - + +
370A PHE* 4.4 18.2 - - + -
426A TYR* 4.0 35.7 - - + +
429A ILE* 3.7 26.1 - - + +
430A ALA* 4.2 7.4 - - + +
444A ALA* 3.3 32.5 - - + -
445A SER 3.1 12.4 + - - +
446A TRP 3.8 6.5 - - - +
448A ALA* 1.3 75.0 - - - +
450A TRP* 1.3 57.3 + - - +
452A GLY* 3.3 1.0 + - - -
453A TRP* 2.7 31.8 + - - +
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Residues in contact with TRP 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ALA 3.5 9.9 - - - -
40A LYS* 3.8 10.3 - - - -
41A TYR 4.5 0.7 - - - -
42A SER* 3.4 50.4 + - - -
44A LYS* 6.1 0.2 - - - +
362A ARG* 4.2 4.9 - - - -
363A LEU* 3.8 23.3 - - + +
366A LEU* 3.5 36.6 - - + -
446A TRP* 2.9 18.7 + - + +
447A GLY* 3.7 5.8 - - - +
448A ALA 3.2 0.2 - - - -
449A LEU* 1.3 73.9 - - - +
451A GLU* 1.3 84.7 + - - +
453A TRP* 3.3 20.9 + + - +
454A GLU* 2.9 52.7 + - + +
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Residues in contact with GLU 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A LEU 4.8 0.7 - - - +
433A GLY* 4.0 18.8 - - - +
447A GLY* 3.1 25.5 + - - +
448A ALA* 3.1 4.2 + - - +
450A TRP* 1.3 89.1 + - - +
452A GLY* 1.3 53.6 + - - +
454A GLU* 3.4 14.0 + - - +
455A ALA* 2.8 36.0 + - - +
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Residues in contact with GLY 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ILE* 3.3 31.0 - - - -
432A LEU* 3.9 8.0 - - - +
433A GLY* 3.5 10.7 - - - -
448A ALA 2.9 9.7 + - - -
449A LEU 3.6 1.8 - - - -
451A GLU* 1.3 73.9 - - - +
453A TRP* 1.3 59.3 + - - +
455A ALA* 3.2 2.3 + - - +
456A LEU* 2.8 31.0 + - - +
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Residues in contact with TRP 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A HIS* 3.6 33.8 + + + -
8A ARG* 3.4 26.0 - - - -
362A ARG* 4.5 7.1 - - - +
366A LEU* 4.2 17.9 - - + +
370A PHE* 3.6 34.5 - + + -
397A LEU* 4.0 15.5 - - + -
401A GLU* 4.0 4.5 - - - -
429A ILE* 3.3 10.5 - - + +
449A LEU 2.7 20.6 + - - +
450A TRP* 3.6 35.5 - + + +
452A GLY* 1.3 70.1 - - - +
454A GLU* 1.3 53.7 + - - +
456A LEU* 3.1 14.0 + - + +
457A GLN* 2.7 71.8 + - + +
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Residues in contact with GLU 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS 4.8 6.7 - - - +
41A TYR* 5.8 6.6 - - - -
42A SER 5.2 0.5 - - - +
44A LYS* 4.2 27.6 + - - -
450A TRP* 2.9 53.2 + - + +
451A GLU* 3.6 13.0 - - - +
453A TRP* 1.3 80.2 - - - +
455A ALA* 1.3 57.8 + - - +
457A GLN* 3.5 8.1 + - + +
458A SER* 2.9 34.1 + - - -
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Residues in contact with ALA 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A LEU* 4.2 21.8 - - + +
451A GLU 2.8 20.4 + - - +
452A GLY* 3.5 4.9 - - - +
454A GLU* 1.3 70.5 - - - +
456A LEU* 1.3 61.6 + - - +
458A SER* 3.0 6.2 + - - -
459A LYS* 2.8 48.1 + - - +
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Residues in contact with LEU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A LEU* 4.8 5.6 - - + -
401A GLU* 4.2 24.7 - - + +
404A LEU* 4.1 11.4 - - + -
405A LEU* 4.0 35.2 - - + +
408A LEU* 4.0 22.2 - - + -
429A ILE* 4.8 6.1 - - + -
432A LEU* 3.9 12.4 - - + +
452A GLY 2.8 16.5 + - - +
453A TRP* 3.5 22.2 - - + +
455A ALA* 1.3 72.6 - - - +
457A GLN* 1.3 70.7 + - - +
459A LYS* 3.6 3.5 + - - +
460A LEU* 3.0 27.0 + - + +
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Residues in contact with GLN 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 3.6 10.2 + - - -
401A GLU* 2.9 32.7 + - - +
453A TRP* 2.7 65.0 + - + +
454A GLU* 3.6 8.5 - - + +
456A LEU* 1.3 76.0 - - - +
458A SER* 1.3 59.5 + - - +
460A LEU* 3.3 27.3 + - - +
461A ASP* 3.4 13.7 + - - +
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Residues in contact with SER 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A GLU* 2.9 23.5 + - - -
455A ALA* 3.0 8.2 + - - -
457A GLN* 1.3 71.2 - - - +
459A LYS* 1.3 67.6 + - - +
460A LEU 3.1 1.3 - - - -
461A ASP* 3.1 28.5 + - - +
462A GLY 3.8 2.1 + - - -
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Residues in contact with LYS 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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404A LEU* 3.6 17.8 - - + +
408A LEU* 3.6 31.2 - - + -
432A LEU* 4.2 21.8 - - - -
455A ALA* 2.8 27.6 + - - +
456A LEU 4.0 1.3 - - - +
458A SER* 1.3 76.6 - - - +
460A LEU* 1.3 57.7 + - - +
462A GLY* 3.2 4.8 + - - +
463A PHE* 3.1 24.4 + - - +
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Residues in contact with LEU 460 (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 THR* 5.3 1.1 - - - +
400A ASP* 4.2 12.3 - - + +
401A GLU* 3.7 46.4 - - + +
404A LEU* 3.6 16.8 - - + +
456A LEU* 3.0 15.5 + - + +
457A GLN* 3.3 28.7 - - - +
458A SER 3.1 0.4 - - - -
459A LYS* 1.3 75.1 - - - +
461A ASP* 1.3 59.1 + - - +
463A PHE* 3.4 11.2 - - + +
464A LEU* 2.9 46.5 + - + +
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Residues in contact with ASP 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 5.9 1.6 + - - -
457A GLN 3.4 9.3 + - - +
458A SER* 3.1 19.2 + - - +
460A LEU* 1.3 79.7 - - - +
462A GLY* 1.3 56.3 + - - +
464A LEU* 3.8 6.2 - - - +
465A ALA* 2.9 29.7 + - - +
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Residues in contact with GLY 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A SER 3.8 3.2 + - - -
459A LYS 3.2 6.9 + - - -
460A LEU 3.2 0.4 - - - -
461A ASP* 1.3 77.0 - - - +
463A PHE* 1.3 57.3 + - - +
465A ALA* 3.3 8.3 + - - +
466A ALA* 2.9 30.3 + - - +
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Residues in contact with PHE 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ASP* 4.0 31.0 - - + -
403A GLN* 3.8 23.8 - - + -
404A LEU* 3.8 35.7 - - + -
407A TYR* 6.2 2.0 - - + -
459A LYS 3.1 12.9 + - - +
460A LEU* 3.4 26.7 - - + +
462A GLY* 1.3 76.4 - - - +
464A LEU* 1.3 62.2 + - + +
466A ALA* 3.5 5.6 + - - +
467A LYS* 3.0 29.6 + - + +
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Residues in contact with LEU 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ASP* 4.0 22.7 - - + +
460A LEU* 2.9 39.4 + - + +
461A ASP* 3.8 6.5 - - - +
463A PHE* 1.3 77.5 - - + +
465A ALA* 1.3 56.0 + - - +
467A LYS* 3.1 29.0 + - + +
468A ASP* 2.7 37.3 + - - +
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Residues in contact with ALA 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ASP 2.9 18.2 + - - +
462A GLY* 3.4 9.4 - - - +
464A LEU* 1.3 74.6 - - - +
466A ALA* 1.3 59.4 + - - +
468A ASP* 3.8 6.6 - - - +
469A LEU* 3.1 40.8 + - + +
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Residues in contact with ALA 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A GLY 2.9 16.5 + - - +
463A PHE* 3.7 6.7 - - - +
465A ALA* 1.3 72.3 - - - +
467A LYS* 1.3 57.2 + - - +
469A LEU* 3.4 2.9 + - - +
470A MET* 2.6 40.7 + - + +
476A ILE* 3.8 23.2 - - + +
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Residues in contact with LYS 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ASP* 2.9 26.0 + - - +
463A PHE* 3.0 20.4 + - + +
464A LEU* 3.2 28.8 - - + +
466A ALA* 1.3 75.2 - - - +
468A ASP* 1.3 53.3 + - - +
470A MET* 3.2 5.6 + - - +
471A ALA* 2.7 41.5 + - + +
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Residues in contact with ASP 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A LEU 2.7 19.9 + - - +
465A ALA* 3.8 8.1 - - - +
466A ALA 3.3 0.2 - - - -
467A LYS* 1.3 72.7 - - - +
469A LEU* 1.3 56.4 + - + +
471A ALA* 3.0 9.6 + - - +
472A GLN* 2.9 47.9 + - - +
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Residues in contact with LEU 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A ALA* 3.1 24.3 + - + +
466A ALA* 3.8 5.6 - - - +
468A ASP* 1.3 78.1 - - + +
470A MET* 1.3 63.2 + - - +
472A GLN* 3.1 22.9 + - - +
474A ILE* 3.0 56.1 + - + -
475A LYS 6.0 1.1 - - - +
476A ILE* 4.3 15.9 - - + -
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Residues in contact with MET 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ALA 2.6 25.2 + - - +
467A LYS* 3.6 6.5 - - - +
469A LEU* 1.3 73.7 - - - +
471A ALA* 1.3 58.9 + - - +
473A GLY* 3.4 12.3 + - - -
474A ILE 4.1 6.5 - - - +
475A LYS* 5.9 1.8 - - - -
476A ILE* 3.9 19.4 - - + +
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Residues in contact with ALA 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A LYS* 2.7 24.5 + - + +
468A ASP* 3.0 11.4 + - - +
470A MET* 1.3 74.0 - - - +
472A GLN* 1.3 55.7 + - - +
473A GLY 3.2 4.0 + - - -
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Residues in contact with GLN 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A ASP* 2.9 52.1 + - - +
469A LEU* 3.1 24.0 + - - +
471A ALA* 1.3 76.3 - - - +
473A GLY* 1.3 60.4 + - - +
474A ILE* 3.5 22.0 + - + +
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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