Contacts of the helix formed by residues 431 - 458 (chain A) in PDB entry 2W8D
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 431 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A PHE 3.4 0.2 - - - -
430A GLY* 1.3 81.3 - - - +
432A SER* 1.3 53.1 + - - +
433A VAL* 2.9 23.0 + - - +
434A VAL* 3.3 12.3 + - - +
435A ASP* 2.8 40.4 + - - +
478A ASN 4.9 1.0 - - - +
479A HIS* 3.0 33.0 + - - +
482A ALA* 3.5 21.0 + - + +
348B THR* 4.4 13.8 - - - +
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Residues in contact with SER 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ASP* 1.3 71.6 + - - +
433A VAL* 1.3 71.1 + - - +
435A ASP* 3.8 10.8 - - - -
436A ASN* 3.0 39.0 + - - +
345B ASN* 5.3 0.5 + - - -
346B THR* 3.5 29.5 - - - +
348B THR* 4.3 5.2 + - - -
349B PHE* 4.8 5.5 - - - -
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Residues in contact with VAL 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A PHE* 3.6 29.6 - - + -
414A PRO* 4.0 16.6 - - + +
415A PHE* 3.5 25.6 - - + -
431A ASP* 2.9 9.7 + - - +
432A SER* 1.3 80.5 + - - +
434A VAL* 1.3 57.1 + - - +
436A ASN 3.9 0.5 - - - -
437A TYR* 3.1 21.5 + - - +
475A ILE* 4.5 4.7 - - + -
479A HIS* 3.7 26.0 - - + +
349B PHE* 3.6 33.7 - - + -
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Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A PHE* 4.0 11.0 - - + -
431A ASP* 3.3 11.0 + - - +
433A VAL* 1.3 74.5 - - - +
435A ASP* 1.3 66.3 + - - +
437A TYR* 3.3 16.8 - - + +
438A PHE* 3.3 16.5 - - + -
475A ILE* 4.0 17.9 - - + -
479A HIS* 3.7 31.6 - - + +
482A ALA* 3.9 21.5 - - + -
483A MSE 4.5 6.7 - - + -
486A VAL* 3.6 30.7 - - + -
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Residues in contact with ASP 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ALA* 3.5 14.2 - - + +
427A GLY* 3.1 42.0 + - - +
428A ASP* 4.4 4.0 - - - +
429A PHE* 2.9 32.5 + - - +
430A GLY 4.2 1.7 + - - -
431A ASP 2.8 36.1 + - - +
432A SER* 3.9 10.8 - - - +
433A VAL 3.4 0.2 - - - -
434A VAL* 1.3 72.4 - - - +
436A ASN* 1.3 61.7 + - - +
438A PHE* 3.7 9.2 + - - +
439A GLN 4.5 0.7 + - - -
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Residues in contact with ASN 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A PRO 4.2 3.3 + - - +
415A PHE* 3.1 31.4 - - + +
416A GLY* 4.2 15.8 - - - +
417A MSE 5.6 0.4 - - - -
426A ALA* 4.2 11.8 - - - +
432A SER* 3.0 30.5 + - - +
433A VAL 4.1 2.0 - - - +
434A VAL 3.2 0.2 - - - -
435A ASP* 1.3 77.3 - - - +
437A TYR* 1.3 66.3 + - - +
438A PHE 3.1 2.0 + - - -
439A GLN* 3.2 16.5 + - + +
440A SER* 3.2 13.7 + - - -
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Residues in contact with TYR 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A SER 2.6 29.3 + - - -
255A LEU* 3.5 5.7 - - + +
256A GLN* 3.1 25.0 + - - +
258A PHE* 3.8 16.8 - + - -
259A ILE* 3.4 33.2 - - + -
411A ASN* 3.6 16.8 - - - +
415A PHE* 3.6 39.0 - + - +
433A VAL 3.1 12.5 + - - +
434A VAL* 3.3 14.6 - - + +
436A ASN* 1.3 79.0 - - - +
438A PHE* 1.3 63.1 + + - +
440A SER* 3.3 1.9 + - - -
441A ALA* 2.9 31.3 + - + +
474A GLY* 4.4 0.7 - - - -
475A ILE* 3.7 19.7 - - + -
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Residues in contact with PHE 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PHE* 4.2 7.2 - + - -
259A ILE* 3.6 32.3 - - + -
262A TYR* 4.0 17.7 - + - -
264A ILE* 4.3 7.0 - - + -
269A VAL* 3.4 23.0 - - + +
424A PHE* 3.9 18.5 - - + -
425A PRO 4.7 3.4 - - - +
427A GLY* 4.1 9.4 - - - -
429A PHE* 3.3 33.0 - + - -
434A VAL* 3.3 30.3 - - + -
435A ASP 3.7 10.5 - - - +
436A ASN 3.1 1.2 - - - -
437A TYR* 1.3 81.4 - + - +
439A GLN* 1.3 57.2 + - - +
441A ALA* 4.3 1.3 - - - -
442A HIS* 3.1 27.7 + - - +
486A VAL* 3.8 20.4 - - + -
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Residues in contact with GLN 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A PHE 5.2 0.7 - - - +
417A MSE 4.8 21.9 + - + +
422A THR* 3.6 18.4 - - + +
424A PHE* 2.8 28.8 + - - +
425A PRO* 3.6 14.1 - - - +
426A ALA* 3.2 30.8 - - + +
435A ASP 4.6 1.3 - - - +
436A ASN* 3.2 18.2 + - + +
438A PHE* 1.3 74.5 - - - +
440A SER* 1.3 61.0 + - - +
442A HIS* 3.3 7.7 + - - +
443A TYR* 3.0 22.3 + - - +
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Residues in contact with SER 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A SER 4.1 10.5 - - - -
411A ASN* 2.8 24.8 + - - +
415A PHE* 3.2 30.8 + - - +
417A MSE 3.8 23.7 - - - +
436A ASN 3.2 7.0 + - - -
437A TYR 3.5 1.0 + - - -
439A GLN* 1.3 76.2 - - - +
441A ALA* 1.3 60.0 + - - +
443A TYR* 3.3 8.9 + - - +
444A LEU* 2.9 27.4 + - - +
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Residues in contact with ALA 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU* 4.2 22.5 - - + +
259A ILE* 4.6 7.2 - - + -
269A VAL* 3.9 13.7 - - + -
270A THR* 4.0 7.7 - - + +
411A ASN* 3.4 10.2 + - - +
437A TYR* 2.9 20.5 + - + +
438A PHE* 3.8 6.7 - - - +
440A SER* 1.3 75.0 - - - +
442A HIS* 1.3 58.7 + - - +
444A LEU* 3.2 8.8 + - - +
445A ASP* 2.9 28.2 + - - +
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Residues in contact with HIS 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLU 3.8 5.3 + - - -
269A VAL 3.0 27.3 + - - +
271A PRO* 4.1 16.3 - - + +
422A THR* 3.8 16.4 - - + -
423A ASP* 4.1 9.2 + - - -
424A PHE* 3.3 48.4 - + + -
438A PHE 3.1 19.0 + - - +
439A GLN 3.6 4.5 - - - +
440A SER 3.3 0.4 - - - -
441A ALA* 1.3 75.1 - - - +
443A TYR* 1.3 62.3 + - - +
445A ASP* 3.2 5.1 + - - +
446A GLN* 3.1 45.9 + - + +
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Residues in contact with TYR 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LYS* 3.6 16.0 - - + +
384A ASP* 4.0 0.9 - - + -
385A LYS* 3.1 56.9 + - + +
386A PRO* 3.8 1.6 - - - +
410A SER* 3.5 33.7 - - - -
417A MSE 4.0 18.6 - - + -
421A ASP* 3.4 40.9 + - + -
422A THR* 3.8 12.9 + - - +
439A GLN 3.0 14.9 + - - +
440A SER* 3.6 10.3 - - - +
442A HIS* 1.3 73.4 - - - +
444A LEU* 1.3 67.6 + - - +
446A GLN* 3.2 6.6 + - - +
447A SER* 3.0 35.3 + - - -
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Residues in contact with LEU 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU* 4.1 19.1 - - + -
253A GLU 4.0 31.2 - - - +
255A LEU* 4.5 15.0 - - + -
273A LEU* 5.6 2.2 - - + -
384A ASP* 3.4 23.6 - - - +
408A THR* 4.1 19.7 - - + +
410A SER* 6.0 0.2 - - - -
411A ASN* 4.1 13.0 - - + +
440A SER 2.9 14.7 + - - +
441A ALA* 3.4 10.3 - - - +
443A TYR* 1.3 77.3 - - - +
445A ASP* 1.3 64.3 + - - +
447A SER* 3.1 11.0 + - - -
448A ILE* 3.0 37.7 + - + +
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Residues in contact with ASP 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A VAL 4.2 0.9 - - - +
270A THR* 3.3 23.2 - - + -
271A PRO* 3.2 15.0 - - + +
272A PHE* 2.8 26.3 + - - +
273A LEU* 2.9 40.5 + - + +
441A ALA 2.9 13.8 + - - +
442A HIS* 3.2 10.0 + - - +
444A LEU* 1.3 77.3 - - - +
446A GLN* 1.3 63.7 + - - +
448A ILE* 3.4 7.6 + - - +
449A GLU* 3.1 22.2 + - - +
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Residues in contact with GLN 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PRO* 6.2 0.9 - - + -
385A LYS* 3.1 29.1 + - - -
421A ASP 4.5 0.2 - - - +
422A THR* 2.9 24.4 + - - -
423A ASP* 4.1 10.3 + - - -
442A HIS* 3.1 37.6 + - + +
443A TYR* 3.2 6.4 + - - +
445A ASP* 1.3 77.8 - - - +
447A SER* 1.3 57.8 + - - +
449A GLU* 3.4 18.8 + - - +
450A GLN* 2.9 28.6 + - - +
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Residues in contact with SER 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASP* 3.3 32.1 - - - +
385A LYS* 3.6 22.3 - - - +
388A PHE* 3.7 16.6 - - - -
443A TYR* 3.0 17.8 + - - -
444A LEU* 3.1 10.5 + - - -
446A GLN* 1.3 72.1 - - - +
448A ILE* 1.3 61.4 + - - +
450A GLN* 3.5 5.8 + - - +
451A PHE* 3.0 27.9 + - - +
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Residues in contact with ILE 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A VAL* 4.1 6.5 - - + -
252A LEU* 3.8 31.2 - - + -
272A PHE* 3.9 13.5 - - + -
273A LEU* 4.1 13.0 - - + -
388A PHE* 3.9 27.8 - - + -
444A LEU* 3.0 22.6 + - + +
445A ASP* 3.8 6.5 - - - +
446A GLN 3.3 0.2 - - - -
447A SER* 1.3 72.8 - - - +
449A GLU* 1.3 57.3 + - - +
451A PHE* 3.2 7.0 + - + +
452A PHE* 2.8 45.8 + - + -
468A MSE 3.7 27.6 - - + -
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Residues in contact with GLU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PRO* 6.2 0.2 - - - +
272A PHE* 3.8 39.1 - - + +
445A ASP* 3.1 14.0 + - - +
446A GLN* 3.4 22.2 - - - +
448A ILE* 1.3 76.4 - - - +
450A GLN* 1.3 57.7 + - - +
452A PHE* 3.3 3.6 + - - +
453A ASN* 2.9 46.8 + - - +
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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
----------------------------------------------------------
385A LYS* 3.3 35.5 + - + +
388A PHE* 3.4 14.8 - - - +
389A LYS* 3.3 57.6 - - - +
392A MSE 6.1 0.2 - - - -
446A GLN 2.9 16.6 + - - +
447A SER 3.9 2.9 - - - +
449A GLU* 1.3 75.1 - - - +
451A PHE* 1.3 66.8 + - - +
453A ASN* 3.0 13.5 + - + +
454A ASP* 2.9 27.3 + - - +
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Residues in contact with PHE 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ILE* 3.9 10.8 - - + -
250A VAL* 3.8 27.8 - - + -
388A PHE* 3.5 35.0 - + + -
392A MSE 3.7 28.5 - - + -
395A LEU* 4.8 0.9 - - + -
406A PHE* 3.7 35.4 - + - -
447A SER 3.0 14.7 + - - +
448A ILE* 3.4 12.6 - - + +
450A GLN* 1.3 81.7 - - - +
452A PHE* 1.3 64.9 + + - +
454A ASP* 3.4 3.9 + - - +
455A LEU* 2.8 59.3 + - + +
466A ILE* 5.6 1.6 - - + -
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Residues in contact with PHE 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A PHE* 3.6 29.4 - + + -
276A LEU* 4.1 15.3 - - + -
282A THR* 6.6 0.4 - - + -
448A ILE* 2.8 39.2 + - + +
449A GLU 3.5 4.3 - - - +
451A PHE* 1.3 79.1 - + - +
453A ASN* 1.3 68.2 + - - +
455A LEU* 3.2 10.8 + - + +
456A LYS* 3.1 35.7 + - - +
461A TYR* 3.6 34.5 - + - -
466A ILE* 4.0 26.5 - - + -
468A MSE 3.9 26.9 - - + -
508A HIS* 5.3 6.7 - - + -
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Residues in contact with ASN 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A PHE* 5.6 3.6 - - - -
449A GLU* 2.9 44.2 + - - +
450A GLN* 3.5 10.2 - - - +
452A PHE* 1.3 71.8 - - - +
454A ASP* 1.3 63.6 + - - +
456A LYS* 3.1 17.3 + - - +
457A LYS* 3.1 41.6 + - - +
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Residues in contact with ASP 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A LYS* 2.8 33.8 + - - -
392A MSE 3.8 33.5 - - + +
450A GLN* 2.9 25.8 + - - +
451A PHE* 3.8 4.5 - - - +
453A ASN* 1.3 79.0 - - - +
455A LEU* 1.3 62.9 + - - +
456A LYS 3.2 0.7 + - - -
457A LYS* 3.3 16.0 + - - +
458A ASP* 3.1 26.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ILE* 3.9 23.1 - - + -
392A MSE 3.7 18.8 - - + -
395A LEU* 4.0 12.3 - - + -
451A PHE* 2.8 53.9 + - + +
452A PHE* 3.2 11.2 + - + +
454A ASP* 1.3 72.7 - - - +
456A LYS* 1.3 57.7 + - - +
458A ASP* 3.2 4.2 - - - +
459A GLY 3.8 0.2 - - - -
460A LEU* 3.1 23.0 + - + -
461A TYR* 3.0 35.5 + - + +
466A ILE* 3.6 29.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A PHE* 5.0 7.3 - - - -
275A LYS* 5.4 7.1 - - - +
452A PHE* 3.3 26.6 - - - +
453A ASN* 3.1 15.5 + - - +
455A LEU* 1.3 77.6 - - - +
457A LYS* 1.3 66.8 + - - +
458A ASP 3.4 0.2 - - - -
459A GLY* 3.6 8.1 + - - -
461A TYR* 3.7 55.0 + - + -
----------------------------------------------------------
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Residues in contact with LYS 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ASN* 3.1 28.9 + - - +
454A ASP* 3.3 18.8 + - - +
456A LYS* 1.3 78.9 - - - +
458A ASP* 1.3 62.6 + - + +
459A GLY* 3.3 0.7 + - - -
----------------------------------------------------------
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Residues in contact with ASP 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A MSE 3.0 22.7 - - - +
396A GLU* 2.5 39.2 - - + +
454A ASP 3.1 6.8 + - - +
455A LEU* 3.2 7.8 - - - +
457A LYS* 1.3 78.7 - - + +
459A GLY* 1.3 58.2 + - - +
460A LEU* 3.1 35.7 + - + +
463A LYS* 4.8 5.0 + - - -
----------------------------------------------------------
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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