Contacts of the helix formed by residues 428 - 457 (chain A) in PDB entry 3DCU
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 GLN 428 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ASN* 3.2 13.5 + - - +
427A PRO* 1.3 86.6 - - + +
429A HIS* 1.3 63.8 + - - +
430A PHE 3.4 1.1 - - - -
431A ALA* 3.3 16.9 + - + +
432A CYS* 3.0 27.9 + - - +
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Residues in contact with HIS 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU* 4.0 32.5 - - + +
376A LYS 5.4 0.4 - - - -
381A GLU* 2.9 32.5 + - - -
419A CYS* 3.6 23.6 - - + -
423A GLN* 3.7 36.5 + - + +
426A ASN* 3.1 32.8 + - - +
427A PRO 3.2 1.8 - - - +
428A GLN* 1.3 74.9 - - - +
430A PHE* 1.3 57.8 + - - +
432A CYS* 2.8 9.9 + - - +
433A LEU* 2.8 46.4 + - + +
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Residues in contact with PHE 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LEU* 3.4 25.8 - - + -
415A LEU* 3.5 20.4 - - + -
416A GLN* 3.4 56.3 - - + -
419A CYS* 3.6 27.8 - - + +
427A PRO 4.2 7.0 + - - +
428A GLN 3.4 0.2 - - - -
429A HIS* 1.3 77.2 - - - +
431A ALA* 1.3 60.3 + - - +
433A LEU* 3.0 7.3 + - - +
434A LEU* 3.0 58.4 + - + +
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Residues in contact with ALA 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A PRO 5.1 0.4 + - - -
428A GLN* 3.3 22.2 + - - +
429A HIS 3.3 0.8 - - - -
430A PHE* 1.3 80.7 - - + +
432A CYS* 1.3 57.0 + - - +
434A LEU* 3.5 13.8 + - + +
435A GLY* 3.1 22.9 + - - -
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Residues in contact with CYS 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU* 4.5 19.7 - - + -
426A ASN* 6.0 1.3 - - - -
428A GLN* 3.0 17.8 + - - +
429A HIS* 2.8 16.3 + - - +
431A ALA* 1.3 74.2 - - - +
433A LEU* 1.3 66.7 + - - +
435A GLY* 3.2 10.5 + - - +
436A ARG* 3.0 26.2 + - - +
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Residues in contact with LEU 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU* 3.5 26.7 - - + -
377A MET* 4.1 20.4 - - + -
381A GLU* 3.8 21.5 - - + +
385A LEU* 3.9 17.1 - - + +
415A LEU* 3.6 40.8 - - + -
419A CYS* 3.9 12.3 - - - -
429A HIS* 2.8 30.3 + - + +
430A PHE* 3.2 7.2 - - - +
432A CYS* 1.3 77.9 - - - +
434A LEU* 1.3 63.5 + - - +
435A GLY 3.1 1.0 + - - -
436A ARG* 3.1 22.4 + - - +
437A LEU 4.0 0.5 + - - -
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Residues in contact with LEU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A LEU* 5.0 1.8 - - + -
412A LEU* 4.1 24.9 - - + -
415A LEU* 4.4 8.3 - - + -
430A PHE* 3.0 48.6 + - + +
431A ALA* 3.7 11.7 - - + +
432A CYS 3.3 0.2 - - - -
433A LEU* 1.3 76.7 - - - +
435A GLY* 1.3 64.1 + - - +
437A LEU* 3.0 38.6 + - + +
438A THR* 3.7 5.2 + - - -
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Residues in contact with GLY 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ALA 3.1 14.0 + - - -
432A CYS* 3.2 6.2 + - - -
433A LEU 3.1 1.8 - - - -
434A LEU* 1.3 78.1 - - - +
436A ARG* 1.3 64.8 + - - +
438A THR* 2.9 21.0 + - - -
439A GLU* 3.1 15.5 + - - +
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Residues in contact with ARG 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 5.7 0.2 - - + -
368A PHE* 4.2 8.5 - - + -
371A SER* 3.1 42.8 + - - -
372A ILE* 3.4 28.4 - - + +
375A LEU* 3.4 23.0 - - + +
377A MET* 4.6 6.7 - - + -
385A LEU* 4.3 11.4 - - + -
432A CYS* 3.0 28.5 + - - +
433A LEU 3.1 13.2 + - - +
435A GLY* 1.3 75.7 - - - +
437A LEU* 1.3 55.7 + - - +
439A GLU* 2.6 39.7 + - - +
440A LEU* 2.6 43.4 + - + +
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Residues in contact with LEU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLU* 4.6 5.0 - - - +
385A LEU* 4.1 18.8 - - + +
388A ILE* 3.8 24.0 - - + -
389A VAL* 3.6 36.6 - - + -
392A SER* 4.5 8.5 - - - +
408A GLN* 5.6 1.1 - - - +
412A LEU* 5.2 2.0 - - + -
433A LEU 4.0 0.4 + - - -
434A LEU* 3.0 32.8 + - + +
436A ARG* 1.3 79.4 - - - +
438A THR* 1.3 59.7 + - - +
440A LEU* 3.6 8.9 - - + +
441A ARG* 3.1 31.0 + - - +
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Residues in contact with THR 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A LEU 4.2 5.0 + - - -
435A GLY* 2.9 13.4 + - - -
437A LEU* 1.3 76.3 - - - +
439A GLU* 1.3 67.2 + - - +
441A ARG* 2.9 27.2 + - + +
442A THR* 3.2 10.5 + - - +
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Residues in contact with GLU 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A PHE* 3.2 25.2 - - + -
371A SER* 4.0 10.6 + - - -
435A GLY 3.1 18.4 + - - +
436A ARG* 2.6 45.6 + - - +
438A THR* 1.3 75.5 - - - +
440A LEU* 1.3 62.9 + - - +
442A THR* 3.2 19.8 - - - -
443A PHE* 3.1 19.5 - - + -
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Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLU* 3.6 26.5 - - + +
329A PHE* 3.6 29.8 - - + -
330A LEU* 4.0 22.2 - - + -
368A PHE* 3.4 28.5 - - + -
385A LEU* 6.0 1.6 - - + -
389A VAL* 3.8 28.0 - - + -
436A ARG* 2.6 28.7 + - + +
437A LEU* 3.6 6.5 - - - +
439A GLU* 1.3 69.4 - - - +
441A ARG* 1.3 67.8 + - - +
443A PHE* 2.8 23.6 + - + +
444A ASN* 3.6 4.9 + - - -
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Residues in contact with ARG 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLU* 3.9 12.8 + - - +
392A SER* 3.5 23.6 + - - -
394A ASP* 2.7 55.3 + - - -
395A ARG* 3.6 20.7 - - - +
437A LEU* 3.1 19.6 + - - +
438A THR* 2.9 14.7 + - + +
440A LEU* 1.3 76.5 - - - +
442A THR* 1.3 67.0 + - - +
444A ASN* 2.8 30.4 + - - +
445A HIS* 4.1 1.0 + - - +
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Residues in contact with THR 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A THR* 3.2 10.7 + - - +
439A GLU* 3.2 16.8 + - - -
440A LEU 3.1 0.2 - - - -
441A ARG* 1.3 78.5 - - - +
443A PHE* 1.3 71.5 + - + +
444A ASN 3.2 1.2 + - - -
445A HIS* 3.3 20.4 + - - +
446A HIS* 3.8 3.1 + - - +
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Residues in contact with PHE 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A VAL* 5.1 2.9 - - + -
329A PHE* 3.4 41.2 - + + -
361A TYR 5.1 1.3 - - - -
364A PRO* 3.4 46.0 - - + -
365A MET* 3.8 8.3 - - + -
368A PHE* 3.5 34.5 - + + -
439A GLU* 3.1 26.7 - - + -
440A LEU* 2.8 23.2 + - + +
442A THR* 1.3 76.2 - - + +
444A ASN* 1.3 57.3 + - - -
445A HIS 3.2 0.2 - - - -
446A HIS* 3.2 13.7 + - + +
447A HIS* 2.8 30.5 + - - +
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Residues in contact with ASN 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLY 4.0 11.6 - - - +
325A VAL* 4.0 20.8 - - - +
326A GLU* 2.5 40.0 + - - +
395A ARG* 4.8 0.4 - - - +
440A LEU 3.6 0.2 + - - -
441A ARG* 2.8 31.3 + - - +
443A PHE* 1.3 73.2 - - - +
445A HIS* 1.3 66.5 + - - +
447A HIS* 3.2 6.1 + - - +
448A ALA* 3.0 23.0 + - - +
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Residues in contact with HIS 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ARG 4.1 1.2 + - - +
442A THR* 3.3 12.4 + - - +
443A PHE 3.2 0.6 - - - -
444A ASN* 1.3 80.5 - - - +
446A HIS* 1.3 63.4 + - - +
448A ALA* 3.3 12.2 + - - +
449A GLU* 3.3 17.7 + - - +
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Residues in contact with HIS 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A TYR* 3.9 40.1 - - + -
442A THR* 3.8 2.9 + - + +
443A PHE* 3.2 24.1 + - + +
445A HIS* 1.3 79.6 - - - +
447A HIS* 1.3 62.3 + - - +
449A GLU* 3.0 22.7 + - - +
450A MET* 3.1 6.6 + - - +
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Residues in contact with HIS 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A O62 3.5 33.2 + + + +
325A VAL* 3.8 27.3 - - + +
329A PHE* 5.6 3.6 - + + -
443A PHE 2.8 20.8 + - - +
444A ASN* 3.2 6.0 + - - +
446A HIS* 1.3 73.9 - - - +
448A ALA* 1.3 64.6 + - - +
450A MET* 3.1 8.2 + - + +
451A LEU* 3.0 52.9 + - + +
454A TRP* 5.5 1.8 - + - -
469A TRP* 3.5 40.2 - + - -
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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
----------------------------------------------------------
444A ASN 3.0 11.9 + - - +
445A HIS* 3.6 11.0 - - - +
447A HIS* 1.3 80.1 + - - +
449A GLU* 1.3 66.7 + - + +
451A LEU* 3.5 9.1 + - - +
452A MET* 3.3 26.0 + - - +
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Residues in contact with GLU 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A TYR* 3.2 29.0 + - + +
445A HIS 3.3 15.3 + - - +
446A HIS* 3.0 10.3 + - - +
448A ALA* 1.3 80.7 - - - +
450A MET* 1.3 64.9 + - - +
452A MET* 2.9 11.7 + - - +
453A SER* 2.9 21.2 + - - -
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Residues in contact with MET 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLY 3.7 13.0 - - - +
357A ILE* 3.6 12.6 - - + -
358A SER* 2.7 52.3 - - - +
361A TYR* 3.5 15.9 - - + -
446A HIS 3.1 6.1 + - - +
447A HIS* 3.1 12.8 + - + +
449A GLU* 1.3 80.1 - - - +
451A LEU* 1.3 58.2 + - - +
453A SER* 3.5 21.1 - - - +
454A TRP* 2.9 66.1 + - + -
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Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A HIS* 3.0 48.0 + - + +
448A ALA* 3.6 12.1 - - - +
449A GLU 3.1 0.2 - - - -
450A MET* 1.3 76.2 - - - +
452A MET* 1.3 67.3 + - + +
454A TRP* 3.8 16.0 - - + +
455A ARG* 2.9 35.0 + - - +
461A PHE* 3.8 24.4 - - + -
469A TRP* 3.7 37.2 - - + +
471A VAL* 4.0 16.8 - - + -
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Residues in contact with MET 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A ALA 3.3 12.5 + - - +
449A GLU* 2.9 12.4 + - - +
451A LEU* 1.3 86.7 - - + +
453A SER* 1.3 66.4 + - - +
455A ARG* 3.3 11.3 + - + +
456A VAL* 3.0 33.6 + - + +
470A ASP 5.5 2.9 - - - +
471A VAL* 4.7 16.2 - - + -
----------------------------------------------------------
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Residues in contact with SER 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLY 4.5 4.7 + - - -
449A GLU 2.9 10.9 + - - -
450A MET* 3.4 31.6 - - - +
452A MET* 1.3 75.8 - - - +
454A TRP* 1.3 63.6 + - - +
456A VAL* 2.6 29.2 - - - +
457A ASN* 2.9 15.5 + - - +
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Residues in contact with TRP 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A O62 3.4 39.0 - - + -
284A PHE* 3.3 22.2 - + - -
355A SER* 3.0 22.4 + - - -
356A GLY* 3.7 15.9 + - - -
357A ILE* 3.6 30.3 - - + -
447A HIS* 5.2 1.1 - + - -
450A MET* 2.9 52.7 + - + +
451A LEU* 3.8 11.0 - - + -
453A SER* 1.3 75.2 + - - +
455A ARG* 1.3 57.8 + - - +
457A ASN* 2.9 18.1 + - - +
459A HIS* 3.0 53.7 + + + +
461A PHE* 3.8 23.1 - + + -
----------------------------------------------------------
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Residues in contact with ARG 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A LEU 2.9 22.9 + - - +
452A MET* 3.4 20.2 - - + +
454A TRP* 1.3 76.0 - - - +
456A VAL* 1.3 60.1 + - + +
458A ASP* 2.9 21.1 + - - -
459A HIS 3.7 19.7 + - - +
461A PHE* 3.8 32.6 - - + +
466A CYS* 4.5 11.0 - - - -
471A VAL* 4.4 10.6 + - + +
472A GLN* 2.5 35.7 + - - +
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Residues in contact with VAL 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A MET* 3.0 19.5 + - + +
453A SER* 2.6 32.1 - - - +
455A ARG* 1.3 75.7 - - + +
457A ASN* 1.3 66.0 + - - +
458A ASP* 3.1 3.9 + - - +
----------------------------------------------------------
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Residues in contact with ASN 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A SER* 2.9 27.2 + - - +
454A TRP* 2.9 10.5 + - - +
456A VAL* 1.3 88.0 - - - +
458A ASP* 1.3 69.7 + - - +
459A HIS* 2.9 24.5 + - + +
----------------------------------------------------------
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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