Contacts of the helix formed by residues 431 - 455 (chain A) in PDB entry 4JGV
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 431 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A GLU 3.9 0.6 + - - -
430A LEU* 1.3 73.6 - - - +
432A PRO* 1.3 73.6 - - - +
433A ALA* 3.4 7.8 + - - +
434A ASP* 3.0 21.0 + - - +
435A GLN* 2.8 20.6 + - - +
519A GLN* 2.3 35.4 + - - -
520A GLU* 4.0 20.3 + - - +
523A ARG* 4.1 0.4 - - - +
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Residues in contact with PRO 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU 3.4 7.4 - - - +
431A SER* 1.3 83.8 - - - +
433A ALA* 1.3 61.7 + - - +
435A GLN* 3.3 12.9 + - + +
436A ASP* 3.1 32.0 + - - +
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Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A SER* 3.1 3.0 + - - +
432A PRO* 1.3 75.7 - - - +
434A ASP* 1.3 63.5 + - - +
436A ASP* 3.3 8.4 + - - +
437A LEU* 2.8 31.3 + - - +
519A GLN* 3.6 28.5 - - + +
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Residues in contact with ASP 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 4.3 8.9 - - + +
431A SER* 3.0 25.7 + - - +
433A ALA* 1.3 73.9 - - - +
435A GLN* 1.3 61.2 + - - +
437A LEU* 3.7 2.4 - - - +
438A LEU* 2.9 40.9 + - + +
517A GLY 4.5 1.0 - - - +
518A LEU* 3.6 23.6 - - + +
519A GLN* 2.8 30.6 + - - +
520A GLU* 2.9 34.7 + - - +
524A VAL* 4.6 3.0 - - + +
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Residues in contact with GLN 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A GLU* 2.8 27.6 - - - +
427A PHE* 3.3 35.0 + - + +
428A ALA* 2.9 35.3 + - - +
430A LEU* 3.0 20.6 + - + +
431A SER 2.8 11.6 + - - +
432A PRO* 3.4 15.2 - - + +
433A ALA 3.2 0.2 - - - -
434A ASP* 1.3 78.1 - - - +
436A ASP* 1.3 60.5 + - - +
438A LEU* 3.3 0.4 + - - -
439A LEU* 3.0 37.3 + - + +
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Residues in contact with ASP 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ARG* 4.1 15.5 + - - +
432A PRO* 3.1 18.4 + - - +
433A ALA* 3.7 8.9 - - - +
435A GLN* 1.3 75.8 - - - +
437A LEU* 1.3 62.0 + - - +
439A LEU* 3.4 7.4 + - - +
440A GLU* 2.9 43.1 + - + +
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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
----------------------------------------------------------
433A ALA 2.8 18.3 + - - +
434A ASP* 3.7 5.4 - - - +
436A ASP* 1.3 74.4 - - - +
438A LEU* 1.3 62.5 + - - +
440A GLU* 3.3 10.2 + - + +
441A SER* 2.6 42.0 + - - +
515A ARG* 3.9 11.0 - - + -
516A HIS 3.6 25.6 - - - +
517A GLY* 3.9 6.3 - - - +
518A LEU* 3.7 35.0 - - + +
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Residues in contact with LEU 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A PHE* 4.0 10.8 - - + -
430A LEU* 3.9 27.6 - - + -
434A ASP 2.9 22.3 + - - +
435A GLN 3.9 2.9 - - - +
437A LEU* 1.3 76.9 - - - +
439A LEU* 1.3 56.7 - - - +
441A SER* 3.9 4.3 - - - -
442A ALA* 3.1 32.6 + - - +
511A LEU* 3.3 30.5 - - + +
512A ILE* 4.9 4.7 - - + -
513A THR 3.3 28.7 - - - +
515A ARG* 4.0 12.7 + - + -
518A LEU* 4.1 13.2 - - + -
524A VAL* 4.2 16.4 - - + -
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Residues in contact with LEU 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU* 4.8 9.2 - - + +
417A ILE* 3.9 21.7 - - + +
418A ARG* 3.6 46.2 - - + +
421A ALA* 3.8 22.2 - - + -
422A GLU* 5.0 3.6 - - - +
427A PHE* 4.1 17.9 - - + -
435A GLN* 3.0 23.8 + - + +
436A ASP* 3.8 4.7 - - - +
438A LEU* 1.3 75.8 - - - +
440A GLU* 1.3 64.6 + - + +
442A ALA 3.8 0.7 - - - -
443A PHE* 3.1 26.5 + - - +
446A LEU* 5.3 0.6 - - + +
511A LEU* 3.8 13.5 - - + -
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Residues in contact with GLU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ARG* 6.3 1.1 - - - +
436A ASP* 2.9 28.9 + - + +
437A LEU* 3.3 10.5 + - + +
439A LEU* 1.3 75.9 - - + +
441A SER* 1.3 65.1 - - - +
442A ALA 3.4 0.3 + - - -
443A PHE 3.6 5.9 + - - -
444A LEU 5.1 0.7 + - - -
587A ILE* 6.0 1.6 - - + +
590A LYS* 3.3 29.3 + - - +
591A ILE* 3.5 50.7 - - + +
594A ASP* 2.7 33.3 - - - +
595A THR* 3.6 8.7 - - + +
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Residues in contact with SER 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LEU* 2.6 31.2 + - - +
438A LEU 3.9 1.1 - - - -
440A GLU* 1.3 78.4 - - - +
442A ALA* 1.3 59.7 + - - +
443A PHE 3.8 0.2 + - - -
444A LEU* 5.3 0.9 + - - +
445A GLU* 4.9 4.7 + - - +
515A ARG* 3.2 49.6 + - - +
595A THR* 4.2 12.9 - - - +
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Residues in contact with ALA 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A LEU 3.1 18.8 + - - +
439A LEU 3.8 0.9 - - - +
441A SER* 1.3 79.8 - - - +
443A PHE* 1.3 57.6 + - - +
444A LEU 3.6 1.3 - - - -
445A GLU* 3.6 7.0 + - - +
446A LEU* 2.8 50.1 + - + +
510A VAL* 3.8 15.3 - - + +
511A LEU* 3.8 7.2 - - + -
515A ARG* 3.7 15.3 - - - +
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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
----------------------------------------------------------
410A LEU* 3.3 39.7 - - + -
413A SER* 3.9 6.3 - - - -
414A LEU* 3.4 43.7 - - + -
417A ILE* 3.8 20.2 - - + -
439A LEU 3.1 17.9 + - - +
440A GLU 3.6 8.8 + - - +
441A SER 3.5 2.8 - - - -
442A ALA* 1.3 78.0 - - - +
444A LEU* 1.3 67.0 + - + +
446A LEU* 3.0 7.0 + - - +
447A PHE* 2.7 39.9 + - + +
588A ILE* 4.0 17.5 - - + -
591A ILE* 4.2 19.5 - - + -
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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
----------------------------------------------------------
410A LEU* 4.6 14.6 - - + -
440A GLU 5.1 0.6 + - - -
441A SER 5.3 1.0 + - - +
443A PHE* 1.3 88.5 - - + +
445A GLU* 1.3 63.4 + - - +
447A PHE* 3.2 5.6 + - + +
448A ILE* 3.0 34.1 + - + +
482A TRP* 3.9 29.2 - - + -
566A CYS* 3.7 29.8 - - + +
569A GLY* 4.3 2.2 - - - -
570A LEU* 3.8 32.8 - - + +
573A ILE* 5.0 11.9 - - + -
591A ILE* 5.7 6.7 - - + +
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Residues in contact with GLU 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A SER 4.9 3.9 + - - +
442A ALA* 3.6 8.4 + - - +
443A PHE 3.2 0.6 - - - -
444A LEU* 1.3 77.8 - - - +
446A LEU* 1.3 62.8 + - - +
448A ILE* 3.8 3.0 - - - +
449A LEU* 3.1 23.6 + - + +
510A VAL* 3.8 27.6 - - + +
515A ARG* 4.1 15.4 + - - -
559A LEU* 4.1 12.6 - - - +
562A LEU* 3.6 34.9 - - + +
563A ARG* 5.4 6.1 - - - +
566A CYS* 3.6 22.5 - - - -
601A T94 4.7 3.3 - - - +
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Residues in contact with LEU 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ILE* 4.0 22.9 - - + -
420A TRP* 3.7 29.4 - - + -
439A LEU* 5.3 1.1 - - + +
442A ALA* 2.8 38.6 + - + +
443A PHE* 3.5 4.0 - - - +
445A GLU* 1.3 74.8 - - - +
447A PHE* 1.3 63.7 + - - +
449A LEU* 4.6 4.3 - - + -
450A ARG* 2.9 39.2 + - + +
507A SER* 3.4 34.8 - - - +
510A VAL* 3.7 17.5 - - + -
511A LEU* 4.1 10.5 - - + -
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Residues in contact with PHE 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A LEU 4.2 9.2 - - - -
410A LEU* 3.7 33.2 - - + -
413A SER* 3.3 35.0 - - - -
417A ILE* 4.2 3.0 - - - +
443A PHE* 2.7 26.6 + + + +
444A LEU* 3.4 11.2 - - + +
446A LEU* 1.3 71.8 - - - +
448A ILE* 1.3 70.7 + - + +
450A ARG* 4.3 2.4 - - - +
451A LEU* 3.0 55.3 + - + +
454A ARG* 5.5 1.1 + - - -
464A PHE* 4.6 12.6 - + - -
479A PHE* 4.3 19.3 - + - -
482A TRP* 4.1 16.6 - + - -
486A ILE* 5.1 1.8 - - + -
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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
----------------------------------------------------------
444A LEU* 3.0 21.9 + - + +
445A GLU 3.8 3.4 - - - +
447A PHE* 1.3 81.0 - - + +
449A LEU* 1.3 61.0 + - - +
451A LEU* 3.7 5.3 - - - +
452A ALA* 2.8 28.9 + - - +
482A TRP* 3.8 24.2 - - + +
486A ILE* 4.4 12.9 - - + +
489A PHE* 4.6 4.0 - - + -
562A LEU* 3.6 17.7 - - + -
565A LEU* 3.7 31.2 - - + +
566A CYS* 3.6 41.1 - - - +
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Residues in contact with LEU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLU 3.1 16.3 + - - +
446A LEU* 3.4 6.9 + - + +
448A ILE* 1.3 82.6 - - - +
450A ARG* 1.3 58.5 + - + +
452A ALA* 3.4 3.7 + - - +
453A TYR* 3.0 28.1 + - - +
489A PHE* 4.1 15.7 - - + -
493A LEU* 4.0 18.6 - - + -
503A PHE* 3.6 28.7 - - + -
506A LEU* 5.2 1.1 - - + -
507A SER* 4.5 13.5 - - - +
510A VAL* 4.1 25.6 - - + -
562A LEU* 4.5 8.1 - - + -
601A T94 4.5 22.4 - - + -
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Residues in contact with ARG 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A HIS* 4.5 5.9 + - - -
375A SER* 3.2 44.2 + - - -
413A SER* 4.8 3.4 + - - -
416A VAL* 3.7 15.4 - - - +
417A ILE* 3.8 20.5 - - - +
420A TRP* 4.3 20.7 - - - +
446A LEU* 2.9 40.2 + - + +
447A PHE* 4.3 2.0 - - - +
449A LEU* 1.3 77.4 - - + +
451A LEU* 1.3 62.2 + - - +
453A TYR* 3.4 2.9 + - - +
454A ARG* 3.1 51.6 + - - +
465A CYS* 4.3 2.6 - - - +
503A PHE* 4.0 22.9 - - + -
507A SER* 5.1 6.8 - - - -
607A GOL 3.8 12.6 + - - +
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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 PHE* 3.0 47.6 + - + +
448A ILE* 3.7 2.9 - - - +
450A ARG* 1.3 76.0 - - - +
452A ALA* 1.3 59.6 + - - +
454A ARG* 3.6 11.5 - - - +
455A SER* 2.5 47.3 + - - +
462A LEU* 4.4 10.8 - - + -
463A ILE 3.0 31.6 - - - +
464A PHE* 3.7 27.8 - - + -
479A PHE* 5.4 0.4 - - + -
483A ILE* 4.7 2.7 - - + -
486A ILE* 4.1 26.9 - - + -
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Residues in contact with ALA 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A ILE 2.8 19.2 + - - +
449A LEU 3.8 3.8 - - - +
451A LEU* 1.3 78.4 - - - +
453A TYR* 1.3 62.2 + - - +
454A ARG 3.4 0.2 + - - -
455A SER* 3.7 1.7 + - - -
486A ILE* 4.3 10.7 - - + +
489A PHE* 3.6 29.8 - - + -
490A SER* 2.5 43.3 + - - +
493A LEU* 4.3 3.1 - - + -
494A HIS* 3.5 5.7 + - - -
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Residues in contact with TYR 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A HIS* 4.2 14.4 - + - -
449A LEU 3.0 18.0 + - - +
450A ARG 3.8 3.4 - - - +
452A ALA* 1.3 77.6 - - - +
454A ARG* 1.3 60.4 + - + +
493A LEU* 3.9 19.5 - - + +
494A HIS* 3.1 27.0 + + - -
498A VAL* 2.5 37.3 + - + -
499A ASP* 3.6 1.0 - - - -
500A VAL* 3.5 27.8 + - + +
503A PHE* 3.6 52.9 - + + -
607A GOL 5.7 3.8 - - - -
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Residues in contact with ARG 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A PRO* 4.3 4.9 - - + -
413A SER* 5.5 2.6 + - - -
447A PHE* 5.5 0.8 + - - -
450A ARG* 3.1 44.2 + - - +
451A LEU* 3.6 23.0 - - - +
452A ALA 3.2 0.2 - - - -
453A TYR* 1.3 79.3 - - + +
455A SER* 1.3 65.8 + - - +
456A LYS* 4.6 4.5 + - - +
463A ILE* 3.0 57.1 + - + +
464A PHE* 3.6 7.7 - - - +
465A CYS* 3.5 29.3 - - - +
607A GOL 3.0 43.4 + - - +
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Residues in contact with SER 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A LEU* 2.5 30.3 + - - +
452A ALA* 3.7 1.3 + - - -
453A TYR 3.5 0.6 - - - -
454A ARG* 1.3 81.5 - - - +
456A LYS* 1.3 64.3 + - - +
457A PRO* 3.7 2.7 - - - -
461A LYS 3.5 12.1 - - - -
462A LEU* 3.5 12.6 - - - +
463A ILE* 3.1 23.9 + - - +
486A ILE* 6.5 0.2 - - - -
487A LEU* 4.6 6.3 - - - -
490A SER* 4.3 8.5 - - - -
494A HIS* 3.0 24.0 - - - -
----------------------------------------------------------
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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