Contacts of the helix formed by residues 436 - 463 (chain A) in PDB entry 5XA0
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 436 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A ARG* 6.4 0.7 - - - +
434A PRO 3.8 2.9 + - - -
435A VAL* 1.4 72.6 - - - +
437A PRO* 1.3 62.8 - - - +
438A ALA* 3.6 6.9 + - - +
439A GLU* 2.8 40.1 + - - +
440A VAL* 2.7 31.9 + - - +
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Residues in contact with PRO 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ASP* 5.7 5.8 - - - +
384A ARG* 6.4 0.4 - - - +
435A VAL 3.9 5.8 - - - +
436A SER* 1.3 81.7 - - - +
438A ALA* 1.3 61.6 + - - +
440A VAL* 4.1 7.9 - - + -
441A ARG* 2.7 60.0 + - + +
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Residues in contact with ALA 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A SER* 3.3 6.4 + - - +
437A PRO* 1.3 78.1 - - - +
439A GLU* 1.3 57.9 + - - +
441A ARG* 4.7 2.0 - - - +
442A ASP* 2.4 46.2 + - - +
506A ARG* 5.0 7.0 - - - +
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Residues in contact with GLU 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ARG* 5.4 7.9 + - - -
275A ALA* 4.2 19.7 - - - +
435A VAL* 5.1 5.1 - - + +
436A SER* 2.8 35.2 + - - +
438A ALA* 1.3 74.3 - - - +
440A VAL* 1.4 56.4 + - + +
442A ASP* 4.2 4.7 - - - +
443A LEU* 2.9 38.2 + - + +
505A GLU* 4.1 33.0 - - + +
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Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A VAL* 4.5 9.2 - - + -
281A LEU* 5.9 4.0 - - + -
308A LEU* 6.4 1.6 - - + -
435A VAL* 3.2 34.8 - - + +
436A SER 2.7 36.5 + - - +
437A PRO* 4.1 5.6 - - + +
439A GLU* 1.4 71.6 - - - +
441A ARG* 1.3 61.2 + - + +
443A LEU* 4.5 3.8 - - + -
444A ASP* 2.8 30.4 + - + +
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Residues in contact with ARG 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.8 3.4 - - - +
126A LEU 4.9 0.6 + - - -
127A LYS 5.1 5.3 + - - -
128A SER* 3.8 12.5 + - - +
129A ASN* 2.1 57.2 + - - +
437A PRO* 2.7 38.8 + - + +
438A ALA* 4.3 1.8 - - - +
440A VAL* 1.3 72.2 - - + +
442A ASP* 1.3 67.0 + - - +
444A ASP* 3.4 6.9 - - - +
445A PHE* 2.9 26.9 + - - +
483A PHE* 4.7 1.9 - - - -
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Residues in contact with ASP 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ALA* 2.4 32.8 + - - +
439A GLU* 4.2 3.7 - - - +
441A ARG* 1.3 77.6 - - - +
443A LEU* 1.3 61.5 + - - +
445A PHE* 2.8 18.5 + - - +
446A ALA 3.0 6.2 + - - -
483A PHE* 3.5 24.0 - - + -
505A GLU* 5.1 7.3 - - + +
506A ARG* 2.5 47.7 + - - +
509A LEU* 3.0 18.3 - - + +
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Residues in contact with LEU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A SER* 4.6 21.1 - - - -
281A LEU* 4.8 17.0 - - + -
439A GLU* 2.9 30.7 + - + +
440A VAL* 4.4 3.8 - - + +
442A ASP* 1.3 67.3 - - - +
444A ASP* 1.3 66.8 + - - +
445A PHE 2.9 1.2 + - - -
446A ALA 3.0 1.6 + - - -
447A ASN* 3.0 6.5 + - - +
509A LEU* 3.1 18.2 - - + +
513A GLN* 2.3 63.9 - - + +
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Residues in contact with ASP 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 2.9 23.1 - - + +
440A VAL* 2.8 26.7 + - + +
441A ARG* 3.4 9.2 - - - +
443A LEU* 1.3 73.9 - - - +
445A PHE* 1.3 63.5 + - - +
447A ASN* 3.1 11.3 + - - +
448A ASP* 3.0 15.5 + - - +
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Residues in contact with PHE 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 2.5 35.2 - - + -
441A ARG 2.9 10.3 + - - +
442A ASP 2.8 17.7 + - - +
444A ASP* 1.3 66.6 - - - +
446A ALA* 1.3 69.4 + - - +
447A ASN 2.9 2.9 + - - -
448A ASP 3.0 1.0 + - - -
449A ALA* 2.9 37.1 + - + +
476A LEU* 4.8 9.9 - - + -
479A ASP* 4.8 14.6 - - + -
480A LEU* 4.6 14.6 - - + -
483A PHE* 3.1 59.2 - + + -
515A ILE* 5.6 0.7 - - + -
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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
----------------------------------------------------------
442A ASP 3.0 6.5 + - - -
443A LEU 3.0 0.2 + - - -
445A PHE* 1.3 76.5 - - - +
447A ASN* 1.3 50.7 + - - +
450A SER* 2.5 30.1 + - - -
483A PHE* 4.8 1.9 - - + -
509A LEU* 2.9 33.9 - - + -
513A GLN* 2.6 21.7 + - + +
514A ASN 3.4 3.1 - - - +
515A ILE* 2.8 36.3 - - + +
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Residues in contact with ASN 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU* 3.9 7.3 + - - +
444A ASP* 3.3 13.1 - - - +
445A PHE 2.9 2.4 + - - -
446A ALA* 1.3 70.5 - - - +
448A ASP* 1.3 52.2 + - - +
450A SER* 1.8 37.4 + - - -
451A LYS* 2.1 24.7 + - + +
513A GLN* 2.0 49.0 + - - +
514A ASN* 4.7 1.4 - - - +
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Residues in contact with ASP 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU 4.6 2.1 - - - +
31A GLY* 2.8 12.5 - - - -
32A LEU* 2.1 52.3 + - + +
33A VAL* 2.6 38.9 - - - +
444A ASP* 3.0 7.0 + - - +
445A PHE 3.0 2.0 + - - -
447A ASN* 1.3 73.3 - - - +
449A ALA* 1.3 73.5 + - - +
451A LYS* 2.6 30.4 + - - +
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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
----------------------------------------------------------
33A VAL* 3.6 1.6 - - - +
445A PHE* 2.9 30.9 + - + +
448A ASP* 1.3 76.1 - - - +
450A SER* 1.3 53.6 + - - +
452A VAL* 2.5 34.2 - - - +
453A LEU* 2.5 22.9 - - + +
476A LEU* 4.1 9.2 - - + -
480A LEU* 4.7 4.0 - - + -
515A ILE* 3.1 31.4 - - + -
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Residues in contact with SER 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ALA 2.5 11.2 + - - -
447A ASN* 1.8 43.1 + - - -
449A ALA* 1.3 70.7 - - - +
451A LYS* 1.3 70.4 + - - -
452A VAL 2.8 1.2 + - - -
453A LEU* 2.9 11.6 - - - +
454A GLY* 3.9 0.2 - - - -
513A GLN* 3.5 0.2 + - - -
514A ASN* 2.7 40.3 + - - +
518A GLN* 2.0 29.9 - - - +
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Residues in contact with LYS 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 2.9 22.7 - - + -
34A ASP* 5.1 1.3 - - - +
447A ASN* 2.1 37.1 + - + +
448A ASP* 2.6 50.3 + - - +
450A SER* 1.3 82.6 + - - +
452A VAL* 1.3 66.1 + - - +
454A GLY* 3.4 1.0 + - - -
455A SER* 3.0 21.1 + - - -
514A ASN* 5.3 0.4 + - - -
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Residues in contact with VAL 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 2.8 41.8 - - + +
34A ASP* 5.9 0.4 - - - +
448A ASP 3.0 2.6 + - - -
449A ALA* 2.5 45.6 + - - +
451A LYS* 1.3 78.7 - - - +
453A LEU* 1.3 53.5 + - - +
455A SER* 2.5 23.8 + - - -
456A ILE* 2.9 27.8 + - + -
472A SER* 5.2 5.8 - - - +
473A VAL* 5.7 0.2 - - - -
476A LEU* 2.9 38.4 - - + -
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Residues in contact with LEU 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A ALA* 2.5 34.1 - - + +
450A SER* 2.9 15.3 - - - +
452A VAL* 1.3 78.2 - - - +
454A GLY* 1.3 53.5 + - - +
456A ILE* 4.2 8.7 - - - -
457A ALA 2.7 17.0 + - - -
476A LEU* 3.4 27.6 - - + -
477A LEU* 5.5 2.5 - - + -
480A LEU* 4.0 10.3 - - + -
514A ASN 3.5 2.2 - - - +
515A ILE* 4.5 2.5 - - - +
518A GLN* 2.8 31.0 - - + +
519A ILE* 3.6 20.4 - - + -
522A LEU* 2.5 45.3 - - + +
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Residues in contact with GLY 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A SER 3.0 2.5 + - - -
451A LYS* 4.0 1.3 - - - -
452A VAL 2.7 4.6 + - - -
453A LEU* 1.3 64.1 - - - +
455A SER* 1.4 45.7 - - - +
458A GLY* 3.2 6.2 + - - -
459A LYS* 1.7 35.5 + - - -
518A GLN* 1.8 36.2 + - - -
521A LYS* 5.4 0.9 - - - -
522A LEU* 3.4 4.3 - - - +
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Residues in contact with SER 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ASP* 5.6 2.3 + - - -
451A LYS* 3.0 13.6 + - - -
452A VAL* 2.5 18.3 + - - -
454A GLY* 1.4 65.2 - - - -
456A ILE* 1.4 49.9 - - - +
459A LYS* 2.2 42.4 - - - +
469A GLU* 4.3 11.3 + - - +
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Residues in contact with ILE 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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452A VAL* 2.9 55.9 + - + +
453A LEU* 3.9 7.4 - - - +
455A SER* 1.4 75.4 - - - +
457A ALA* 1.4 51.1 + - - +
459A LYS* 2.5 28.9 - - + +
460A LEU* 3.1 15.4 + - - +
465A ILE* 4.0 16.9 - - + +
469A GLU* 5.0 11.9 - - + +
472A SER 5.7 0.2 - - - -
473A VAL* 3.4 48.0 - - + +
476A LEU* 4.1 4.0 - - + -
477A LEU* 5.7 0.9 - - + -
522A LEU* 5.9 0.9 - - + -
552A ILE* 6.0 1.8 - - + -
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Residues in contact with ALA 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A LEU 2.7 6.5 + - - -
456A ILE* 1.4 64.6 - - - +
458A GLY* 1.4 59.6 + - - +
459A LYS* 2.4 12.7 - - - +
460A LEU* 2.3 34.4 + - - +
461A GLU* 2.9 12.4 + - - -
521A LYS 3.9 4.7 - - - +
522A LEU* 2.7 59.5 - - + +
524A GLN 5.8 2.6 - - - -
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Residues in contact with GLY 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A GLY 3.2 3.8 + - - -
457A ALA* 1.4 67.4 - - - +
459A LYS* 1.4 84.8 + - - +
461A GLU* 3.3 7.6 + - - +
462A LYS* 2.9 35.3 + - - +
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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
----------------------------------------------------------
454A GLY 1.7 41.0 + - - -
455A SER* 2.2 36.6 - - - +
456A ILE* 2.5 30.0 - - + +
457A ALA 2.4 18.7 - - - +
458A GLY* 1.4 86.3 - - - +
460A LEU* 1.3 49.7 + - - +
462A LYS* 2.6 26.7 + - - +
463A GLY* 2.4 35.8 + - - +
464A THR 4.6 13.2 - - - +
465A ILE* 5.0 7.0 - - + -
469A GLU* 4.8 11.4 - - - +
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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
----------------------------------------------------------
456A ILE 3.1 14.6 + - - +
457A ALA* 2.3 28.3 + - - +
459A LYS* 1.3 72.6 - - - +
461A GLU* 1.3 64.1 + - - +
462A LYS 3.1 0.9 + - - -
463A GLY* 3.5 22.9 + - - +
465A ILE* 4.9 16.6 - - + +
522A LEU 5.3 2.5 - - - +
524A GLN 3.6 26.2 - - - +
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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 ALA 2.9 10.5 + - - +
458A GLY* 3.8 9.6 - - - +
460A LEU* 1.3 81.2 - - - +
462A LYS* 1.3 64.2 + - + +
524A GLN 4.6 13.0 + - - +
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Residues in contact with LYS 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A GLY* 2.9 19.0 + - - +
459A LYS* 2.6 40.1 + - - +
461A GLU* 1.3 78.1 - - + +
463A GLY* 1.3 54.3 + - - +
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Residues in contact with GLY 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A LYS* 2.4 23.4 + - - +
460A LEU* 3.5 19.9 + - - +
462A LYS* 1.3 73.2 - - - +
464A THR* 1.3 59.9 + - - -
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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