Contacts of the helix formed by residues 429 - 452 (chain A) in PDB entry 2CT8
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 LYS 429 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LEU* 3.0 36.1 + - + +
425A ASN* 5.9 0.2 - - - -
427A GLU* 3.7 28.5 + - - +
428A ARG* 1.3 101.0 - - - +
430A LYS* 1.3 54.6 + - - +
431A GLU 2.9 7.4 + - - +
432A GLU* 4.1 28.1 + - + +
433A LEU* 2.9 28.4 + - - +
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Residues in contact with LYS 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A LEU* 5.3 2.9 - - + +
428A ARG* 2.7 36.1 + - + +
429A LYS* 1.3 70.5 - - - +
431A GLU* 1.3 61.2 + - + +
433A LEU* 4.2 12.4 - - + +
434A GLN* 2.9 32.5 + - - +
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Residues in contact with GLU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ALA 5.7 0.9 + - - -
429A LYS* 3.0 1.4 - - - -
430A LYS* 1.3 80.7 - - + +
432A GLU* 1.3 65.8 + - - +
433A LEU 3.1 1.6 - - - -
434A GLN* 3.2 15.1 + - - +
435A LYS* 3.2 19.2 + - - +
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Residues in contact with GLU 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A LYS* 6.1 0.5 - - - +
424A LEU* 3.7 28.5 - - + +
429A LYS* 3.3 29.4 + - + +
431A GLU* 1.3 76.8 - - - +
433A LEU* 1.3 68.4 + - - +
435A LYS* 3.4 16.5 + - + +
436A VAL* 3.2 25.2 + - + +
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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
----------------------------------------------------------
365A PHE* 4.2 8.3 - - + +
366A LEU* 3.5 31.4 - - + -
421A PRO* 3.7 38.6 - - + +
424A LEU* 4.0 14.1 - - + +
425A ASN* 3.9 31.4 - - + +
429A LYS 2.9 19.8 + - - +
430A LYS* 4.3 10.8 - - + +
432A GLU* 1.3 77.2 - - - +
434A GLN* 1.3 57.9 + - - +
436A VAL* 2.8 21.8 + - - +
437A LEU* 3.0 21.2 + - + +
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Residues in contact with GLN 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A LEU* 3.6 34.8 - - + +
371A SER* 3.1 27.9 + - - +
372A GLY* 4.3 7.0 - - - -
430A LYS* 2.9 22.4 + - - +
431A GLU* 3.2 15.5 + - - +
433A LEU* 1.3 76.9 - - - +
435A LYS* 1.3 66.0 + - - +
436A VAL 2.9 1.2 + - - -
438A TYR* 2.9 28.7 + - - +
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Residues in contact with LYS 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ALA* 3.9 42.6 - - + +
374A ARG 3.5 23.8 - - - +
375A ASP* 4.3 20.6 + - + +
415A TYR* 4.2 2.3 + - - +
419A LYS* 5.4 4.6 - - - +
431A GLU 3.2 10.0 + - - +
432A GLU* 3.7 20.5 - - + +
433A LEU 3.3 0.2 - - - -
434A GLN* 1.3 78.6 - - - +
436A VAL* 1.3 59.6 + - + +
439A ALA* 3.3 24.1 + - - +
478A TYR* 4.8 0.2 + - - -
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Residues in contact with VAL 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A TYR* 3.6 17.1 - - + +
419A LYS* 3.5 39.9 - - + +
421A PRO* 3.9 30.3 - - + -
424A LEU* 4.2 10.1 - - + -
432A GLU* 3.2 16.8 + - + +
433A LEU 2.8 12.0 + - - +
435A LYS* 1.3 83.3 - - + +
437A LEU* 1.3 60.5 + - + +
439A ALA 4.0 0.2 - - - -
440A LEU* 3.2 26.7 + - + +
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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
----------------------------------------------------------
358A VAL* 5.3 4.7 - - + +
361A MET* 4.3 15.9 - - + +
362A ALA* 3.9 30.1 - - + +
365A PHE* 4.5 2.7 - - + -
366A LEU* 3.5 40.8 - - + -
370A VAL* 4.6 6.3 - - + -
421A PRO* 4.2 16.8 - - + -
433A LEU* 3.0 18.3 + - + +
436A VAL* 1.3 83.6 - - + +
438A TYR* 1.3 60.9 + - - +
439A ALA 3.0 1.3 - - - -
440A LEU* 2.7 20.2 + - + +
441A VAL* 2.6 38.7 + - + +
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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
----------------------------------------------------------
370A VAL* 4.0 15.7 - - - +
371A SER* 3.9 13.9 - - - +
372A GLY 3.4 29.8 - - - -
373A ALA 3.6 7.9 - - - +
374A ARG* 4.8 6.3 + - + -
434A GLN 2.9 17.4 + - - +
435A LYS 4.5 2.0 - - - +
437A LEU* 1.3 75.3 - - - +
439A ALA* 1.3 64.4 + - - +
441A VAL* 3.3 6.6 - - + +
442A ASP* 3.0 29.3 + - - +
478A TYR* 3.2 39.1 + + - +
480A LYS 2.7 21.4 + - - -
481A ASN* 2.8 22.3 - - + +
482A THR* 3.7 9.6 - - - -
483A TYR* 3.6 28.7 - + - -
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Residues in contact with ALA 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ASP* 4.4 2.5 - - + -
378A TYR* 3.6 26.5 - - + -
412A LEU* 4.8 0.6 - - - +
415A TYR* 3.5 24.7 - - + +
435A LYS 3.3 19.6 + - - +
436A VAL 3.8 3.6 - - - +
437A LEU 3.0 0.4 - - - -
438A TYR* 1.3 80.6 - - - +
440A LEU* 1.3 58.0 + - - +
443A GLY* 3.0 22.7 + - - -
478A TYR* 3.6 20.4 + - - +
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Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LEU* 5.8 0.2 - - + -
358A VAL* 4.0 27.8 - - + -
361A MET* 5.3 2.9 - - - -
412A LEU* 4.2 23.8 - - + +
415A TYR* 3.2 40.2 - - + -
416A VAL* 4.0 19.3 - - + -
421A PRO* 4.9 4.5 - - + -
436A VAL* 3.2 21.6 + - + +
437A LEU* 2.7 30.7 + - + +
439A ALA* 1.3 71.8 - - - +
441A VAL* 1.3 59.6 - - - +
443A GLY* 2.9 17.8 + - - -
444A LEU* 3.0 13.9 + - - +
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Residues in contact with VAL 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A VAL* 4.1 9.3 - - + +
362A ALA* 5.7 2.0 - - + -
370A VAL* 3.3 30.7 - - + -
437A LEU* 2.6 24.5 + - + +
438A TYR* 3.3 7.6 - - - +
440A LEU* 1.3 72.8 - - - +
442A ASP* 1.3 63.8 + - - +
444A LEU* 2.8 30.1 + - + +
445A PHE* 2.9 11.1 + - - +
466A LEU* 4.2 19.5 - - + +
483A TYR* 4.0 27.8 - - + -
485A LEU* 4.5 15.7 - - + -
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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
----------------------------------------------------------
378A TYR* 2.6 23.0 + - - -
438A TYR* 3.0 21.9 + - + +
439A ALA 3.9 2.0 - - - +
441A VAL* 1.3 78.4 - - - +
443A GLY* 1.3 62.8 + - - +
445A PHE* 3.0 4.1 + - - +
446A VAL* 3.0 22.2 + - - +
476A LYS 5.0 0.2 - - - +
477A PRO 2.3 31.3 - - - +
478A TYR* 3.3 25.2 - - + -
479A SER* 3.8 1.7 + - - +
483A TYR* 2.7 38.0 + - + -
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Residues in contact with GLY 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A TYR* 3.0 19.5 + - - -
408A PHE* 3.6 7.9 - - - -
412A LEU* 4.1 17.0 - - - -
439A ALA 3.0 10.3 + - - -
440A LEU 2.9 10.9 + - - -
442A ASP* 1.3 76.9 - - - +
444A LEU* 1.3 57.4 + - - +
446A VAL* 3.2 3.7 + - - +
447A LEU* 2.8 28.6 + - - +
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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
----------------------------------------------------------
354A LEU* 3.8 34.5 - - + -
355A TYR* 3.5 40.3 + - + +
358A VAL* 3.7 32.3 - - + -
359A VAL* 4.4 4.0 - - + -
412A LEU* 5.1 1.1 - - + -
440A LEU 3.0 13.6 + - - +
441A VAL* 2.8 12.9 + - + +
443A GLY* 1.3 76.8 - - - +
445A PHE* 1.3 57.3 + - - +
447A LEU* 4.2 5.2 - - + -
448A THR* 2.7 35.1 + - - -
466A LEU* 3.7 24.0 - - + -
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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
----------------------------------------------------------
441A VAL 2.9 7.1 + - - +
442A ASP* 3.2 10.5 - - - +
444A LEU* 1.3 79.7 - - - +
446A VAL* 1.3 67.3 + - + +
448A THR* 3.2 6.6 + - - -
449A HIS* 2.9 40.1 - + - -
463A LEU* 4.0 9.2 - - + -
466A LEU* 3.6 19.9 - - + +
468A GLU* 3.4 39.0 - - + -
470A GLU 4.5 7.0 - - - -
472A LEU* 3.4 36.1 - - + -
476A LYS 5.5 0.4 - - - -
479A SER* 3.5 14.4 - - - -
480A LYS* 4.5 8.3 - - + -
483A TYR* 3.6 31.0 - + + +
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Residues in contact with VAL 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A TYR* 4.0 11.7 - - - +
382A ALA* 5.2 3.8 - - + +
385A SER* 6.5 0.4 - - - -
386A ILE* 4.7 16.2 - - + +
408A PHE* 3.9 19.3 - - + -
442A ASP* 3.0 19.7 + - - +
443A GLY 3.5 6.1 - - - +
445A PHE* 1.3 78.5 - - + +
447A LEU* 1.3 64.3 + - - +
449A HIS* 2.8 22.3 + - - +
450A LEU* 3.1 27.6 + - + +
475A LEU* 5.1 7.4 - - + -
476A LYS 3.7 23.8 - - - +
477A PRO* 4.4 5.4 - - + -
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Residues in contact with LEU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ILE* 4.4 6.7 - - + -
354A LEU* 4.3 21.1 - - + -
355A TYR* 3.8 22.0 - - + +
405A ILE* 3.5 32.8 - - + +
408A PHE* 4.3 8.2 - - + -
409A THR* 3.3 25.1 - - + +
412A LEU* 4.4 4.5 - - + -
443A GLY 2.8 20.3 + - - +
444A LEU* 3.8 8.5 - - + +
445A PHE 3.4 0.2 - - - -
446A VAL* 1.3 72.6 - - - +
448A THR* 1.3 61.0 + - - +
450A LEU* 3.5 14.5 + - + -
451A LEU* 3.1 29.9 + - + +
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Residues in contact with THR 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A TYR* 2.6 26.0 + - - -
444A LEU 2.7 14.3 + - - -
445A PHE* 3.4 9.6 - - - -
446A VAL 3.0 0.2 + - - -
447A LEU* 1.3 77.1 - - - +
449A HIS* 1.3 58.0 + - - +
452A TYR* 3.0 26.3 + - - +
459A MET* 3.3 38.8 - - + +
462A ALA* 4.2 0.7 - - + +
463A LEU* 4.2 16.2 - - + +
466A LEU* 3.6 11.9 - - - +
471A PHE* 3.7 16.2 - - + -
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Residues in contact with HIS 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.3 9.3 - - + +
41A ARG* 5.3 1.0 + - - -
389A TYR* 4.3 1.0 + - - -
445A PHE* 2.9 55.8 - + - -
446A VAL* 2.8 9.0 + - - +
448A THR* 1.3 76.3 - - + +
450A LEU* 1.3 68.2 + - - +
452A TYR* 3.3 7.1 + - - +
453A PRO* 3.1 20.8 - - - +
463A LEU* 5.1 0.4 - - - +
471A PHE* 3.8 21.0 - + + -
472A LEU* 2.9 52.5 + - + -
475A LEU* 3.5 33.4 - - + +
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Residues in contact with LEU 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A SER* 5.6 1.6 - - - -
386A ILE* 4.3 18.6 - - + +
389A TYR* 2.6 55.5 + - + -
404A GLU* 5.5 1.3 - - + +
405A ILE* 3.2 28.0 - - + +
408A PHE* 4.1 32.8 - - + -
446A VAL* 3.1 17.5 + - + +
447A LEU* 3.6 13.7 - - + +
449A HIS* 1.3 78.5 - - - +
451A LEU* 1.3 60.0 + - - +
453A PRO* 3.3 1.9 - - - +
454A ILE* 4.3 3.6 - - - +
475A LEU* 3.5 22.4 - - + -
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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
----------------------------------------------------------
320A TYR* 4.7 19.3 - - + -
347A LEU* 5.7 2.5 - - + -
351A ILE* 3.7 32.3 - - + -
355A TYR* 4.9 0.2 - - - +
402A ILE* 5.8 0.7 - - + -
405A ILE* 3.5 31.0 - - + -
447A LEU* 3.1 18.8 + - + +
450A LEU* 1.3 76.3 - - - +
452A TYR* 1.3 65.2 + - - +
453A PRO 3.2 2.9 - - - -
454A ILE* 2.9 16.4 + - + +
455A THR* 2.8 40.9 + - + -
459A MET* 3.6 30.1 - - + -
492A PHE* 6.0 1.6 - - + -
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Residues in contact with TYR 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 2.9 53.4 + - + +
39A ARG* 5.9 3.7 - - + +
40A LEU* 3.6 25.6 - - + -
90A GLU* 4.6 1.6 + - - -
448A THR 3.0 18.9 + - - +
449A HIS* 3.6 4.5 - - - +
451A LEU* 1.3 74.6 - - - +
453A PRO* 1.3 72.4 - - + +
456A PRO* 3.1 53.2 - - + +
459A MET* 3.5 8.9 - - + +
460A LYS* 4.6 10.2 - - - -
471A PHE* 3.8 35.9 - + + -
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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