Contacts of the helix formed by residues 440 - 465 (chain A) in PDB entry 2X1L
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 ALA 440 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A SER* 3.4 3.5 + - - +
439A ASP* 1.3 80.7 - - - +
441A ALA* 1.3 63.6 + - - +
442A GLU* 3.4 13.7 - - + +
443A ASP* 3.5 25.5 + - - +
444A GLN* 3.4 21.8 + - - +
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Residues in contact with ALA 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ASP 3.6 2.7 + - - -
440A ALA* 1.3 71.1 - - - +
442A GLU* 1.3 64.2 + - - +
444A GLN* 3.4 7.0 + - - +
445A GLN* 3.3 22.7 + - - +
448A ARG* 5.6 0.2 + - - -
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Residues in contact with GLU 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ALA* 4.4 14.2 - - + +
441A ALA* 1.3 78.5 - - - +
443A ASP* 1.3 69.6 + - - +
445A GLN* 3.6 9.0 + - - +
446A ARG* 3.0 28.1 + - - +
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Residues in contact with ASP 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A LEU* 3.5 29.0 - - + +
438A SER* 2.9 35.8 + - - +
440A ALA* 3.5 15.3 + - - +
441A ALA 3.3 0.6 - - - -
442A GLU* 1.3 85.2 - - - +
444A GLN* 1.3 60.5 + - - +
446A ARG* 3.6 7.4 - - - +
447A PHE* 2.9 28.8 + - - +
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Residues in contact with GLN 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LEU* 6.0 1.6 - - - +
435A LEU 3.3 15.8 + - - -
436A ARG* 3.0 30.5 + - - +
438A SER 3.7 13.4 + - - +
439A ASP 5.2 1.6 - - - +
440A ALA 3.4 13.4 + - - +
441A ALA* 3.8 10.5 - - - +
442A GLU 3.4 0.2 - - - -
443A ASP* 1.3 76.4 - - - +
445A GLN* 1.3 63.4 + - - +
447A PHE* 3.6 13.8 - - - +
448A ARG* 3.4 28.2 + - - +
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Residues in contact with GLN 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A GLY* 3.9 25.8 - - - -
381A GLU 5.0 1.8 - - - +
441A ALA 3.3 14.1 + - - +
442A GLU* 3.9 7.6 - - - +
444A GLN* 1.3 74.8 - - - +
446A ARG* 1.3 65.0 + - - +
447A PHE 3.2 0.2 - - - -
448A ARG* 3.2 38.9 + - - +
449A THR* 3.1 25.5 + - - +
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Residues in contact with ARG 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A GLU 4.6 2.4 + - - -
383A THR* 3.0 29.4 + - - +
386A ASP* 2.8 40.2 + - - -
430A GLN* 2.9 32.9 + - - +
435A LEU* 4.2 17.5 - - + -
442A GLU 3.0 19.7 + - - +
443A ASP* 3.6 10.3 - - - +
444A GLN 3.4 0.2 - - - -
445A GLN* 1.3 76.8 - - - +
447A PHE* 1.3 61.0 + - - +
449A THR* 3.3 28.4 + - - +
450A VAL* 3.0 35.9 + - + +
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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
----------------------------------------------------------
367A MET* 4.1 14.8 - - + -
371A ASN* 4.3 16.6 - - + -
372A LEU* 3.7 38.8 - - + -
432A PRO* 3.3 39.9 - - + -
435A LEU* 3.8 15.4 - - + +
436A ARG* 3.7 24.2 - - + -
443A ASP 2.9 18.3 + - - +
444A GLN* 3.6 18.2 - - - +
445A GLN 3.2 0.2 - - - -
446A ARG* 1.3 76.8 - - - +
448A ARG* 1.3 61.5 + - - +
450A VAL* 4.0 1.9 - - - +
451A LEU* 3.3 46.8 + - + +
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Residues in contact with ARG 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LEU* 3.9 25.4 - - + -
377A PRO* 3.6 18.6 - - + +
378A ASP* 2.7 50.4 + - - +
379A PRO* 4.5 6.5 + - - +
444A GLN* 3.4 11.5 + - - +
445A GLN* 3.2 53.1 + - - +
447A PHE* 1.3 80.6 - - + +
449A THR* 1.3 57.8 - - - +
451A LEU* 3.7 0.8 + - - -
452A TYR* 3.1 27.2 + - - +
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Residues in contact with THR 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A PRO* 4.3 7.9 - - + -
380A GLY* 3.0 28.1 + - - +
381A GLU 3.9 12.6 + - - +
382A PHE* 3.9 21.3 - - + -
386A ASP* 3.5 24.2 - - - +
445A GLN* 3.1 12.4 + - - +
446A ARG* 3.3 15.9 + - - +
448A ARG* 1.3 75.0 - - - +
450A VAL* 1.3 55.6 + - - +
452A TYR* 3.2 1.7 + - - +
453A THR* 2.7 37.5 + - - +
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Residues in contact with VAL 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A TYR* 3.4 30.0 - - + +
427A PHE* 4.8 4.9 - - + -
430A GLN* 3.4 42.4 - - + +
432A PRO* 4.6 20.0 - - + -
435A LEU* 4.6 3.8 - - + -
446A ARG* 3.0 27.8 + - + +
447A PHE* 4.0 5.4 - - - +
448A ARG 3.5 0.2 - - - -
449A THR* 1.3 74.8 - - - +
451A LEU* 1.3 55.8 + - + +
453A THR* 3.4 1.9 + - - -
454A THR* 2.7 40.7 + - - +
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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
----------------------------------------------------------
364A SER* 3.3 43.5 - - - +
367A MET* 4.0 11.0 - - + -
368A VAL* 4.1 6.7 - - + -
372A LEU* 4.2 14.1 - - + -
377A PRO* 4.1 12.3 - - + -
427A PHE* 4.5 6.5 - - + -
432A PRO* 3.8 18.6 - - + -
447A PHE* 3.3 45.6 + - + +
448A ARG 4.0 3.8 - - - +
449A THR 3.3 0.6 - - - -
450A VAL* 1.3 78.5 - - + +
452A TYR* 1.3 60.6 + - - +
454A THR* 3.8 2.9 - - - -
455A LEU* 3.0 36.3 + - - +
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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
----------------------------------------------------------
376A VAL* 3.9 10.8 - - + -
377A PRO* 3.4 26.6 - - - +
379A PRO* 3.8 25.6 - - + -
382A PHE* 4.1 23.8 - + - -
390A LEU* 5.9 1.6 - - + -
448A ARG 3.1 19.0 + - - +
449A THR 3.2 4.0 + - - +
451A LEU* 1.3 77.7 - - - +
453A THR* 1.3 64.7 + - - +
455A LEU* 3.4 5.2 + - - +
456A GLU* 3.0 24.7 + - + +
495A ARG* 3.5 32.6 - - - +
496A ILE* 2.7 42.0 + - + +
498A PRO* 4.0 16.9 - - + +
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Residues in contact with THR 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A PHE* 3.9 19.1 - - - -
386A ASP* 3.9 10.9 - - - +
389A LEU* 3.9 19.3 - - + -
390A LEU* 3.8 29.7 - - + +
426A TYR* 3.5 24.6 + - + +
449A THR* 2.7 22.8 + - - +
450A VAL 3.7 0.4 - - - -
452A TYR* 1.3 78.9 - - - +
454A THR* 1.3 61.6 + - - +
456A GLU* 3.6 2.3 + - - +
457A VAL* 3.3 23.6 + - - +
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Residues in contact with THR 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU* 4.0 22.4 - - + -
364A SER* 3.8 26.2 - - - +
389A LEU* 5.4 1.3 - - - -
423A ALA* 5.2 4.9 - - + +
426A TYR* 3.8 13.9 - - - -
427A PHE* 3.6 27.3 - - + -
450A VAL 2.7 22.3 + - - -
451A LEU* 3.8 7.0 - - - -
453A THR* 1.3 77.6 - - - +
455A LEU* 1.3 60.9 + - - +
457A VAL* 3.4 7.9 + - - +
458A VAL* 3.1 23.4 + - + +
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Residues in contact with LEU 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A SER* 3.6 32.5 - - - +
365A LEU* 3.8 21.3 - - + -
368A VAL* 3.8 23.3 - - + -
376A VAL* 4.7 10.3 - - + -
377A PRO* 4.2 14.6 - - + -
451A LEU* 3.0 24.8 + - - +
452A TYR* 3.9 3.8 - - - +
454A THR* 1.3 76.6 - - - +
456A GLU* 1.3 58.2 + - - +
458A VAL* 3.7 6.5 - - + +
459A ARG* 2.9 28.8 + - - +
480A LEU* 3.9 16.6 - - + +
496A ILE* 4.6 10.2 - - + +
502A LEU* 4.4 15.9 - - + -
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Residues in contact with GLU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU* 3.7 24.0 - - + -
452A TYR* 3.0 21.6 + - + +
453A THR 3.9 4.5 - - - +
454A THR 3.3 0.4 - - - -
455A LEU* 1.3 74.1 - - - +
457A VAL* 1.3 59.8 + - - +
459A ARG* 2.8 46.1 + - - +
460A ILE* 3.0 42.4 + - + +
492A ILE 4.4 0.7 - - - +
495A ARG* 3.1 37.7 + - - +
496A ILE* 3.1 24.4 + - + +
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Residues in contact with VAL 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A LEU* 3.8 28.5 - - + +
390A LEU* 4.5 8.3 - - + -
393A ALA* 4.0 21.3 - - + +
419A VAL* 3.8 25.8 - - + +
420A LEU* 5.0 8.7 - - + -
423A ALA* 3.9 21.3 - - + -
453A THR 3.3 15.5 + - - +
454A THR* 3.7 6.7 - - - +
456A GLU* 1.3 77.4 - - - +
458A VAL* 1.3 59.4 + - + +
460A ILE* 3.3 3.0 + - - +
461A ALA* 3.0 28.5 + - + +
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Residues in contact with VAL 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 5.4 4.7 - - + +
360A LEU* 4.1 30.3 - - + -
361A ALA* 4.2 28.0 - - + -
364A SER* 4.7 3.1 - - - +
365A LEU* 5.9 1.1 - - + -
420A LEU* 5.3 3.8 - - + -
454A THR* 3.1 21.3 + - + +
455A LEU* 3.7 8.7 - - + +
456A GLU 3.3 0.2 - - - -
457A VAL* 1.3 75.8 - - + +
459A ARG* 1.3 55.1 + - - +
461A ALA* 3.5 5.6 + - - +
462A SER* 2.7 43.5 + - - +
476A LEU* 4.5 6.1 - - + -
480A LEU* 3.9 20.2 - - + -
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Residues in contact with ARG 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A LEU 2.9 18.7 + - - +
456A GLU* 2.8 44.4 + - - +
457A VAL 3.3 0.2 - - - -
458A VAL* 1.3 76.1 - - - +
460A ILE* 1.3 63.2 + - - +
462A SER* 3.4 2.9 + - - -
463A LEU* 3.0 55.1 + - + +
477A LEU* 4.2 5.1 - - + +
480A LEU* 3.7 21.3 - - + +
482A GLN* 3.4 29.5 + - - +
491A ALA 2.9 22.0 + - - -
492A ILE 3.0 19.2 + - - -
494A ASN 2.9 23.1 + - - -
496A ILE* 3.8 21.2 - - + +
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Residues in contact with ILE 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU* 5.3 0.9 - - + +
393A ALA* 3.5 37.5 - - + +
394A ASP* 3.7 21.1 - - - +
396A LEU* 4.6 3.8 - - + -
397A LEU 5.9 0.4 - - - +
456A GLU* 3.0 47.7 + - + +
457A VAL* 3.7 3.8 - - - +
459A ARG* 1.3 84.3 - - - +
461A ALA* 1.3 62.3 + - - +
463A LEU* 3.4 9.6 + - - +
464A LEU* 3.1 40.1 + - + +
492A ILE* 3.9 21.5 - - + +
495A ARG* 4.4 0.4 - - - +
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Residues in contact with ALA 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 5.0 2.9 - - + -
396A LEU* 5.5 4.2 - - + +
416A ILE* 4.0 20.0 - - + +
419A VAL* 6.4 0.9 - - + -
420A LEU* 3.9 25.8 - - + -
457A VAL* 3.0 19.2 + - + +
458A VAL* 3.8 4.3 - - - +
460A ILE* 1.3 76.5 - - - +
462A SER* 1.3 57.9 + - - +
464A LEU* 3.3 7.4 + - - +
465A LEU* 3.0 39.7 + - + +
----------------------------------------------------------
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Residues in contact with SER 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 5.3 1.2 - - - +
458A VAL* 2.7 26.8 + - - +
459A ARG* 3.7 5.8 - - - -
461A ALA* 1.3 75.6 - - - +
463A LEU* 1.3 60.8 + - - +
465A LEU* 3.5 4.8 + - - -
466A GLN* 3.5 4.5 - - - +
473A THR* 3.4 33.5 - - - +
476A LEU* 3.3 36.4 - - - +
477A LEU* 4.1 21.1 - - - -
480A LEU* 4.1 1.9 - - - +
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Residues in contact with LEU 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ARG* 3.0 54.0 + - + +
460A ILE* 3.7 4.5 - - - +
462A SER* 1.3 76.3 - - - +
464A LEU* 1.3 62.6 + - - +
466A GLN* 3.0 29.6 + - - +
477A LEU* 3.8 19.7 - - + -
482A GLN* 4.8 1.8 - - + +
486A GLU 4.4 4.5 - - - +
487A ARG* 3.7 37.2 - - + +
488A ASP 4.4 3.6 - - - +
489A PHE* 3.3 14.0 - - + -
491A ALA* 4.5 2.2 - - + -
492A ILE* 3.8 31.0 - - + +
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Residues in contact with LEU 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 5.0 3.7 - - + -
396A LEU* 3.7 35.2 - - + -
397A LEU* 3.8 38.1 - - + +
400A VAL* 4.4 19.5 - - + +
404A PHE* 5.5 2.8 - - - -
416A ILE* 4.0 20.8 - - + +
460A ILE* 3.1 35.3 + - + +
461A ALA* 3.3 4.5 + - - +
463A LEU* 1.3 76.9 - - - +
465A LEU* 1.3 58.4 + - - +
466A GLN 3.3 1.1 - - - -
467A PRO* 3.2 17.0 - - - +
468A VAL* 5.4 1.7 - - - +
489A PHE* 4.0 11.6 - - + -
492A ILE* 3.9 11.2 - - + -
----------------------------------------------------------
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Residues in contact with LEU 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 4.0 19.1 - - + -
413A LEU* 3.6 21.5 - - + -
416A ILE* 3.8 24.7 - - + -
417A TRP* 3.6 39.7 - - + -
461A ALA* 3.0 28.9 + - + +
462A SER* 3.5 2.2 + - - +
463A LEU 3.3 0.2 - - - -
464A LEU* 1.3 74.8 - - - +
466A GLN* 1.3 59.8 + - - +
467A PRO* 3.3 3.6 - - - -
468A VAL* 3.0 9.5 + - + +
469A MET* 2.8 37.8 + - + -
473A THR* 3.6 16.9 - - + +
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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