Contacts of the helix formed by residues 414 - 443 (chain A) in PDB entry 1ZDT
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 414 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LEU* 5.2 3.2 - - - +
406A LEU* 5.8 4.8 - - - +
413A GLY* 1.3 68.2 - - - -
415A LYS* 1.3 59.6 + - - +
416A PHE* 3.3 14.3 + - - +
417A GLN* 3.1 31.1 + - + +
418A GLN* 3.0 33.5 + - + +
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Residues in contact with LYS 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A LEU* 2.7 36.1 + - + +
362A GLN* 3.2 10.5 + - - +
363A LEU 4.8 0.2 - - - +
364A ASP* 5.3 0.6 + - - -
367A GLU* 2.9 42.4 + - - +
405A THR* 4.0 17.3 - - + +
409A TYR* 3.3 51.9 - - + +
413A GLY 3.3 4.0 + - - -
414A ASP* 1.3 70.6 + - - +
416A PHE* 1.3 65.4 + - - +
418A GLN* 3.4 12.5 - - - +
419A LEU* 3.0 34.8 + - + +
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Residues in contact with PHE 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ASN* 3.3 41.7 - - + -
401A LEU* 3.8 19.4 - - + +
402A LEU* 3.6 39.9 - - + -
405A THR* 3.7 21.5 + - - +
414A ASP* 3.3 11.9 + - - +
415A LYS* 1.3 78.4 - - - +
417A GLN* 1.3 73.1 + - + +
419A LEU* 3.4 4.7 + - - +
420A LEU* 3.1 51.0 + - + +
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Residues in contact with GLN 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ASP* 3.1 28.9 + - + +
416A PHE* 1.3 86.3 - - + +
418A GLN* 1.3 60.7 + - + +
420A LEU* 3.2 22.4 + - - +
421A LEU* 3.0 42.4 + - + +
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Residues in contact with GLN 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A GLN* 5.7 0.2 + - - -
361A LEU* 3.0 37.1 - - + +
409A TYR* 4.9 1.7 + - - -
412A SER 4.9 2.3 + - - +
413A GLY* 4.0 19.8 - - - -
414A ASP 3.0 20.3 + - - +
415A LYS* 3.4 18.9 - - - +
417A GLN* 1.3 76.1 - - + +
419A LEU* 1.3 61.7 + - - +
421A LEU* 3.2 13.9 + - + +
422A CYS* 3.1 27.0 + - - -
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Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A LEU* 3.9 26.7 - - + -
361A LEU* 3.9 14.8 - - + -
363A LEU* 4.4 6.7 - - + -
367A GLU* 4.2 6.7 - - - -
371A LEU* 4.1 27.3 - - + +
401A LEU* 4.0 26.9 - - + -
405A THR* 4.1 6.3 - - + -
415A LYS* 3.0 46.6 + - + +
416A PHE 3.7 3.8 - - - +
418A GLN* 1.3 74.7 - - - +
420A LEU* 1.3 65.4 + - - +
422A CYS* 3.1 7.4 - - - +
423A LEU* 3.1 25.6 + - - +
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Residues in contact with LEU 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ILE* 5.2 3.4 - - + -
398A ASN* 4.4 17.5 - - - +
401A LEU* 4.3 17.9 - - + -
416A PHE* 3.1 45.4 + - + +
417A GLN* 3.2 24.0 + - - +
419A LEU* 1.3 73.4 - - - +
421A LEU* 1.3 66.5 + - - +
423A LEU* 3.1 31.3 + - + +
424A VAL* 3.2 16.1 + - - +
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Residues in contact with LEU 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A GLN* 6.2 2.0 - - - +
417A GLN* 3.0 26.7 + - + +
418A GLN* 3.2 17.9 + - + +
420A LEU* 1.3 76.1 - - - +
422A CYS* 1.3 61.6 + - - +
424A VAL* 3.3 24.2 + - + +
425A GLU* 3.3 11.4 + - - +
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Residues in contact with CYS 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A PHE* 6.6 0.4 - - + -
354A LEU* 4.1 18.2 - - + +
357A GLN* 4.3 15.9 - - - +
358A LEU* 3.5 33.2 - - + -
361A LEU* 4.2 13.7 - - - -
418A GLN 3.1 17.2 + - - -
419A LEU* 3.1 12.8 + - - +
421A LEU* 1.3 74.7 - - - +
423A LEU* 1.3 64.1 + - + +
425A GLU* 3.1 10.3 + - - +
426A VAL* 2.9 29.6 + - + +
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A PHE* 4.7 6.5 - - + -
371A LEU* 3.9 39.5 - - + +
374A ILE* 3.9 27.4 - - + -
375A ILE* 4.2 27.6 - - + -
419A LEU 3.1 7.9 + - - +
420A LEU* 3.1 24.2 + - + +
422A CYS* 1.3 79.6 - - + +
424A VAL* 1.3 64.7 + - - +
426A VAL* 3.2 13.4 + - + +
427A ARG* 3.0 22.5 + - - +
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Residues in contact with VAL 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A LEU 3.2 13.3 + - - +
421A LEU* 3.4 21.1 - - + +
422A CYS 3.2 0.6 - - - -
423A LEU* 1.3 75.7 - - + +
425A GLU* 1.3 61.3 + - - +
427A ARG* 3.3 9.4 + - - +
428A ALA* 3.1 21.8 + - + +
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Residues in contact with GLU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ARG* 3.0 54.9 + - - +
354A LEU* 3.7 33.2 - - + -
421A LEU 3.3 8.7 + - - +
422A CYS* 3.1 10.0 + - - +
424A VAL* 1.3 78.0 - - - +
426A VAL* 1.3 63.6 + - - +
428A ALA* 3.2 3.0 + - - +
429A LEU* 3.0 28.6 + - + +
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Residues in contact with VAL 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU* 3.8 35.0 - - + +
307A VAL* 4.2 10.1 - - + +
308A PHE* 4.0 28.7 - - + -
311A ILE* 5.1 0.4 - - + -
354A LEU* 3.7 21.1 - - + -
358A LEU* 6.0 0.9 - - + -
375A ILE* 4.7 7.6 - - + -
422A CYS* 2.9 17.8 + - + +
423A LEU* 3.5 17.0 - - + +
425A GLU* 1.3 75.1 - - - +
427A ARG* 1.3 59.4 + - - +
429A LEU* 3.6 5.5 - - - +
430A SER* 3.0 26.2 + - - -
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Residues in contact with ARG 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU* 4.1 24.9 + - + +
423A LEU 3.0 11.8 + - - +
424A VAL* 3.5 11.7 - - + +
425A GLU 3.2 0.2 - - - -
426A VAL* 1.3 79.3 - - - +
428A ALA* 1.3 61.7 + - - +
430A SER* 3.1 19.0 + - - -
431A MET* 3.1 19.3 + - - +
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Residues in contact with ALA 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ARG* 3.8 27.3 + - - +
424A VAL* 3.1 14.3 + - + +
425A GLU* 3.2 10.1 + - - +
427A ARG* 1.3 77.8 - - - +
429A LEU* 1.3 62.8 + - - +
431A MET* 3.4 10.5 + - - +
432A GLN* 3.2 24.4 + - - +
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Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A VAL* 4.1 19.5 - - + +
311A ILE* 4.4 1.1 - - + -
347A LEU* 3.6 20.7 - - + +
350A ARG* 3.5 45.8 - - + +
351A ALA* 3.8 28.9 - - + +
354A LEU* 3.9 26.5 - - + -
425A GLU* 3.0 19.6 + - - +
426A VAL 3.6 5.2 - - - +
428A ALA* 1.3 76.7 - - - +
430A SER* 1.3 57.9 + - - +
432A GLN* 3.3 7.5 + - - +
433A ALA* 2.9 25.8 + - - +
1001A PEF 4.7 1.3 - - + -
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Residues in contact with SER 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A SER* 3.3 40.5 + - - -
304A GLU* 3.4 19.9 + - - +
307A VAL* 3.8 11.7 - - - -
426A VAL 3.0 16.1 + - - -
427A ARG 3.1 12.3 + - - -
428A ALA 3.3 0.4 - - - -
429A LEU* 1.3 76.1 - - - +
431A MET* 1.3 56.4 + - - +
433A ALA* 3.3 4.3 + - - +
434A LYS* 3.1 31.8 + - - +
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Residues in contact with MET 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ARG* 3.1 20.1 + - - +
428A ALA* 3.4 13.9 - - - +
430A SER* 1.3 74.6 + - - +
432A GLN* 1.3 65.2 + - - +
433A ALA 3.3 0.2 + - - -
434A LYS* 3.3 13.6 + - + +
435A GLU* 3.2 49.2 + - + +
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Residues in contact with GLN 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A SER* 5.0 7.3 - - - -
347A LEU* 3.8 28.1 + - + +
350A ARG* 3.3 37.9 - - - +
428A ALA 3.2 16.3 + - - +
429A LEU* 3.6 6.7 - - - +
431A MET* 1.3 76.2 - - + +
433A ALA* 1.3 56.8 + - - +
435A GLU* 3.4 16.9 + - - +
436A TYR* 3.1 25.6 + - - +
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Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A VAL* 4.4 7.0 - - + -
347A LEU* 3.6 20.4 - - + +
429A LEU 2.9 13.9 + - - +
430A SER* 3.4 13.0 - - - +
431A MET 3.1 0.2 - - - -
432A GLN* 1.3 74.8 - - - +
434A LYS* 1.3 59.9 + - - +
436A TYR* 3.3 6.1 + - - +
437A LEU* 2.9 32.3 + - - +
1001A PEF 3.7 30.5 - - + +
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Residues in contact with LYS 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A GLN 5.5 0.4 + - - -
302A TRP* 3.9 22.9 - - + +
303A SER* 3.5 25.6 - - - +
304A GLU* 5.6 0.7 - - - -
430A SER 3.1 17.7 + - - +
431A MET* 3.7 13.9 - - + +
433A ALA* 1.3 77.1 - - - +
435A GLU* 1.3 59.2 + - + +
437A LEU* 3.4 5.9 - - + +
438A TYR* 2.8 29.0 + - - +
456A LEU* 3.6 25.4 - - + +
460A GLN* 3.3 35.5 - - - +
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Residues in contact with GLU 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LEU* 4.6 6.6 - - + +
431A MET* 3.2 48.7 + - + +
432A GLN* 3.6 15.9 + - - +
434A LYS* 1.3 74.8 - - + +
436A TYR* 1.3 61.4 + - - +
438A TYR* 3.7 8.5 - - - +
439A HIS* 2.9 28.8 + - - +
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Residues in contact with TYR 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PHE* 3.7 16.5 - + - -
343A LEU* 4.2 19.2 - - + +
344A LEU* 3.7 36.4 - - + +
347A LEU* 4.2 12.3 - - + -
432A GLN 3.1 13.5 + - - +
433A ALA 3.4 6.7 - - - +
435A GLU* 1.3 74.6 - - - +
437A LEU* 1.3 68.4 + - + +
439A HIS* 3.2 11.9 + + - +
440A LYS* 3.1 42.8 + - + +
446A MET* 5.7 0.2 - - - -
1001A PEF 2.6 84.0 + - + +
----------------------------------------------------------
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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
----------------------------------------------------------
302A TRP* 4.5 9.0 - - + -
433A ALA 2.9 16.9 + - - +
434A LYS* 3.4 14.4 - - - +
436A TYR* 1.3 83.6 - - + +
438A TYR* 1.3 56.8 + - - +
440A LYS* 3.3 5.5 + - - +
441A HIS* 3.0 27.4 + - - +
446A MET* 3.9 26.0 - - + -
452A LEU* 4.2 21.1 - - + +
453A ILE* 3.8 14.1 - - + +
456A LEU* 4.1 11.7 - - + -
1001A PEF 3.7 53.2 - - + -
----------------------------------------------------------
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Residues in contact with TYR 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A LYS 2.8 21.7 + - - +
435A GLU* 3.7 8.7 - - - +
436A TYR 3.3 0.4 - - - -
437A LEU* 1.3 70.1 - - - +
439A HIS* 1.3 66.9 + - - +
441A HIS* 3.3 14.3 + + - +
442A LEU* 3.0 63.0 + - + +
456A LEU* 3.9 19.3 - - + +
457A GLN* 4.7 5.8 - - - -
----------------------------------------------------------
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Residues in contact with HIS 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LEU* 4.0 26.5 - - + +
435A GLU 2.9 13.7 + - - +
436A TYR* 3.3 12.1 - + - +
438A TYR* 1.3 80.6 - - - +
440A LYS* 1.3 78.1 + - + +
442A LEU* 3.3 13.3 + - - +
443A GLY* 3.3 9.5 + - - -
445A GLU* 4.8 6.4 + - - +
----------------------------------------------------------
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Residues in contact with LYS 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PHE* 3.7 21.4 - - - -
436A TYR* 3.1 43.0 + - + +
437A LEU* 3.3 3.8 + - - +
439A HIS* 1.3 82.5 - - + +
441A HIS* 1.3 60.7 + - - +
443A GLY 3.4 1.9 + - - -
444A ASN 3.3 3.3 + - - -
445A GLU* 2.9 60.7 + - + +
446A MET* 3.4 27.6 - - + -
1001A PEF 2.7 41.0 + - - -
----------------------------------------------------------
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Residues in contact with HIS 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LEU 3.0 16.5 + - - +
438A TYR* 3.6 16.2 - + - +
440A LYS* 1.3 78.4 - - - +
442A LEU* 1.3 80.1 + - + +
444A ASN* 3.1 15.4 + - - +
445A GLU 5.0 0.2 - - - +
446A MET* 4.0 8.4 - - + +
453A ILE* 3.7 29.5 - - + +
456A LEU* 5.2 0.4 - - + -
457A GLN* 3.2 36.7 + - - -
----------------------------------------------------------
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Residues in contact with LEU 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A TYR* 3.0 58.5 + - + +
439A HIS* 3.3 6.7 + - - +
441A HIS* 1.3 92.7 - - + +
443A GLY* 1.3 57.5 + - - +
444A ASN* 3.2 3.7 + - - +
----------------------------------------------------------
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Residues in contact with GLY 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A HIS 3.3 9.9 + - - -
440A LYS 3.4 2.2 + - - -
441A HIS 3.2 0.8 - - - -
442A LEU* 1.3 76.3 - - - +
444A ASN* 1.3 69.3 + - - +
445A GLU* 3.1 25.1 + - - +
----------------------------------------------------------
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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