Contacts of the helix formed by residues 440 - 465 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B SER* 3.4 2.7 + - - +
439B ASP* 1.3 80.6 - - - +
441B ALA* 1.3 63.7 + - - +
442B GLU* 4.2 10.1 - - + +
443B ASP* 3.4 24.7 + - - +
444B GLN* 3.3 23.0 + - - +
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Residues in contact with ALA 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B ASP 3.7 2.4 + - - -
440B ALA* 1.3 70.4 - - - +
442B GLU* 1.3 65.6 + - - +
444B GLN* 3.9 8.2 - - - +
445B GLN* 3.1 25.6 + - - +
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Residues in contact with GLU 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B ALA* 3.3 6.7 - - + -
441B ALA* 1.3 80.2 - - - +
443B ASP* 1.3 64.0 + - - +
445B GLN* 3.6 13.4 + - - +
446B ARG* 3.1 27.4 + - + +
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Residues in contact with ASP 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B LEU* 3.7 28.5 - - + +
438B SER* 2.7 38.1 + - - +
440B ALA* 3.4 14.5 + - - +
441B ALA 3.3 0.6 - - - -
442B GLU* 1.3 82.5 - - - +
444B GLN* 1.3 60.6 + - - +
446B ARG* 3.3 6.8 + - - +
447B PHE* 2.9 28.6 + - - +
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Residues in contact with GLN 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B LEU 3.2 11.1 + - - -
436B ARG* 2.9 28.5 + - - +
438B SER 3.0 21.8 + - - +
439B ASP 5.2 1.8 - - - +
440B ALA 3.3 17.3 + - - +
441B ALA* 3.9 7.9 - - - +
442B GLU 3.4 0.2 - - - -
443B ASP* 1.3 75.5 - - - +
445B GLN* 1.3 63.6 + - - +
447B PHE* 3.6 10.1 - - - +
448B ARG* 2.9 56.2 + - - +
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Residues in contact with GLN 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ASP 5.6 2.9 - - - +
379B PRO 5.4 0.2 - - - -
380B GLY* 4.0 28.8 - - - +
381B GLU* 4.9 4.7 + - - +
441B ALA 3.1 17.3 + - - +
442B GLU* 3.9 13.1 - - - +
444B GLN* 1.3 74.1 - - - +
446B ARG* 1.3 60.9 + - - +
448B ARG* 3.3 10.3 + - - +
449B THR* 2.9 31.3 + - - +
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Residues in contact with ARG 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLU 4.2 3.2 + - - -
383B THR* 3.0 30.2 + - - +
386B ASP* 2.7 40.3 + - - -
430B GLN* 3.2 29.9 + - - +
435B LEU* 4.0 20.9 - - + -
442B GLU* 3.1 20.2 + - + +
443B ASP* 3.6 10.1 - - - +
445B GLN* 1.3 73.9 - - - +
447B PHE* 1.3 59.5 + - - +
449B THR* 3.5 27.9 - - - +
450B VAL* 3.0 43.9 + - + +
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Residues in contact with PHE 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B MET* 4.1 16.6 - - + -
371B ASN* 4.0 22.2 - - + -
372B LEU* 3.8 35.2 - - + -
432B PRO* 3.2 36.1 - - + -
435B LEU* 3.9 17.2 - - + +
436B ARG* 3.7 21.5 - - + -
443B ASP 2.9 16.4 + - - +
444B GLN* 3.6 10.3 - - - +
445B GLN 3.3 0.2 - - - -
446B ARG* 1.3 77.1 - - - +
448B ARG* 1.3 71.4 + - - +
450B VAL* 4.1 1.5 - - - +
451B LEU* 3.3 45.9 + - + +
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Residues in contact with ARG 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ASN 5.0 3.6 + - - -
372B LEU* 3.7 32.3 - - + +
377B PRO* 3.6 20.0 - - + +
378B ASP* 3.8 21.8 - - - +
379B PRO* 4.6 2.0 - - - +
444B GLN* 2.9 50.2 + - - +
445B GLN* 3.3 12.0 + - - +
446B ARG 3.3 0.6 - - - -
447B PHE* 1.3 81.7 - - - +
449B THR* 1.3 61.0 + - - +
451B LEU* 4.7 0.7 - - - -
452B TYR* 3.0 28.9 + - - +
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Residues in contact with THR 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B PRO* 4.1 10.3 - - + -
380B GLY* 2.9 25.9 + - - +
381B GLU 3.7 13.6 + - - +
382B PHE* 4.2 15.7 - - + -
386B ASP* 3.6 12.1 - - - +
445B GLN* 2.9 18.6 + - - +
446B ARG* 3.4 26.1 + - - +
448B ARG* 1.3 75.2 - - - +
450B VAL* 1.3 60.1 + - - +
452B TYR* 3.4 2.1 + - - +
453B THR* 2.9 34.5 + - - +
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Residues in contact with VAL 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B TYR* 3.5 26.5 - - + +
427B PHE* 4.9 4.0 - - + -
430B GLN* 3.4 47.3 - - + +
432B PRO* 4.5 19.7 - - + -
435B LEU* 4.7 3.1 - - + -
446B ARG* 3.0 33.4 + - + +
447B PHE* 4.1 5.2 - - - +
449B THR* 1.3 74.6 - - - +
451B LEU* 1.3 54.8 + - + +
453B THR* 3.5 2.3 + - - -
454B THR* 2.7 40.4 + - - +
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Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B SER* 3.3 45.5 - - - +
367B MET* 4.3 9.9 - - + -
368B VAL* 4.1 7.4 - - + -
372B LEU* 4.4 11.7 - - + -
377B PRO* 4.1 13.5 - - + -
427B PHE* 4.4 7.6 - - + -
432B PRO* 3.7 20.4 - - + -
447B PHE* 3.3 48.5 + - + +
448B ARG 4.0 3.6 - - - +
450B VAL* 1.3 79.3 - - - +
452B TYR* 1.3 62.8 + - - +
454B THR* 3.8 2.2 - - - -
455B LEU* 3.0 29.6 + - - +
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Residues in contact with TYR 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B VAL* 4.0 9.2 - - + -
377B PRO* 3.5 28.4 - - - +
379B PRO* 3.8 26.0 - - + -
382B PHE* 4.0 25.4 - + - -
390B LEU* 5.7 1.1 - - + -
448B ARG 3.0 17.9 + - - +
449B THR 3.6 3.8 - - - +
451B LEU* 1.3 75.7 - - - +
453B THR* 1.3 60.6 + - - +
455B LEU* 3.4 5.8 + - - +
456B GLU* 3.0 29.3 + - + +
495B ARG* 3.5 33.2 - - - +
496B ILE* 2.8 42.1 + - + +
498B PRO* 4.0 15.1 - - + +
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Residues in contact with THR 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B PHE* 3.8 21.0 - - - -
386B ASP* 4.0 13.4 - - - +
389B LEU* 4.0 17.7 - - + -
390B LEU* 3.9 26.2 - - + +
426B TYR* 3.6 22.0 + - + +
449B THR 2.9 19.0 + - - -
450B VAL 3.8 0.7 - - - -
452B TYR* 1.3 79.2 - - - +
454B THR* 1.3 63.0 + - - +
456B GLU* 3.4 5.3 + - - +
457B VAL* 3.2 23.6 + - - +
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Residues in contact with THR 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU* 4.0 20.0 - - + -
364B SER* 3.9 25.6 - - - +
389B LEU* 5.4 1.3 - - - -
423B ALA* 5.2 5.2 - - + +
426B TYR* 3.8 13.6 - - - -
427B PHE* 3.7 27.8 - - + -
450B VAL* 2.7 22.9 + - - +
451B LEU* 3.8 7.0 - - - -
453B THR* 1.3 76.7 - - - +
455B LEU* 1.3 61.7 + - - +
457B VAL* 3.3 8.4 + - - +
458B VAL* 3.1 29.5 + - + +
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Residues in contact with LEU 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B SER* 3.8 24.9 - - - +
365B LEU* 3.8 28.3 - - + +
368B VAL* 3.8 22.9 - - + -
376B VAL* 4.7 9.6 - - + -
377B PRO* 4.2 15.5 - - + -
451B LEU 3.0 20.8 + - - +
452B TYR* 3.8 4.3 - - - +
454B THR* 1.3 76.2 - - - +
456B GLU* 1.3 57.0 + - - +
458B VAL* 3.3 6.8 + - + +
459B ARG* 2.8 30.2 + - - +
480B LEU* 3.9 17.5 - - + +
496B ILE* 4.5 9.9 - - + -
502B LEU* 4.4 14.4 - - + -
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Residues in contact with GLU 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B LEU* 3.7 24.7 - - + -
452B TYR* 3.0 21.3 + - + +
453B THR* 3.7 5.6 - - - +
454B THR 3.3 0.2 - - - -
455B LEU* 1.3 74.3 - - - +
457B VAL* 1.3 63.5 + - - +
459B ARG* 2.8 46.1 + - - +
460B ILE* 3.1 31.7 + - + +
495B ARG* 2.9 38.9 + - - +
496B ILE* 3.1 22.5 + - + +
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Residues in contact with VAL 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B LEU* 3.8 30.7 - - + +
390B LEU* 4.7 7.4 - - + -
393B ALA* 4.1 20.8 - - + +
396B LEU* 6.1 0.2 - - - +
419B VAL* 4.0 21.8 - - + +
420B LEU* 4.9 9.6 - - + -
423B ALA* 3.8 24.7 - - + -
453B THR 3.2 15.6 + - - +
454B THR* 3.6 8.1 - - - +
456B GLU* 1.3 77.2 - - - +
458B VAL* 1.3 58.4 + - + +
460B ILE* 3.3 3.3 + - - +
461B ALA* 3.0 27.4 + - + +
----------------------------------------------------------
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Residues in contact with VAL 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LEU* 5.3 5.4 - - + -
360B LEU* 4.1 31.2 - - + -
361B ALA* 4.1 28.7 - - + -
364B SER* 4.8 2.2 - - - +
365B LEU* 5.9 0.9 - - + -
420B LEU* 5.3 3.1 - - + -
454B THR* 3.1 20.3 + - + +
455B LEU* 3.7 11.7 - - + +
457B VAL* 1.3 76.8 - - + +
459B ARG* 1.3 54.3 + - - +
461B ALA* 3.5 6.3 + - - +
462B SER* 2.6 46.2 + - - +
476B LEU* 4.6 6.7 - - + -
480B LEU* 4.0 15.9 - - + -
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Residues in contact with ARG 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B LEU 2.8 17.8 + - - +
456B GLU* 2.8 42.6 + - - +
457B VAL 3.3 0.2 - - - -
458B VAL* 1.3 76.1 - - - +
460B ILE* 1.3 68.0 + - - +
462B SER* 3.3 2.3 + - - -
463B LEU* 3.0 47.0 + - + +
477B LEU* 4.2 7.4 - - + +
480B LEU* 3.7 19.9 - - + +
482B GLN* 3.4 28.4 + - - +
491B ALA 2.8 23.8 + - - -
492B ILE* 3.0 18.3 + - - -
494B ASN 2.9 23.1 + - - -
496B ILE* 3.8 24.0 - - + +
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Residues in contact with ILE 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B LEU* 5.7 0.4 - - + -
393B ALA* 3.6 36.1 - - + +
394B ASP* 3.5 21.8 - - - +
396B LEU* 4.5 4.9 - - + -
397B LEU 5.8 0.4 - - - +
456B GLU* 3.1 44.6 + - + +
457B VAL 3.3 4.2 + - - +
459B ARG* 1.3 85.6 - - - +
461B ALA* 1.3 63.2 + - - +
463B LEU* 3.5 8.5 + - - +
464B LEU* 3.2 39.3 + - + +
492B ILE* 3.9 22.6 - - + +
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Residues in contact with ALA 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LEU* 5.1 2.9 - - + -
396B LEU* 5.4 4.6 - - + +
416B ILE* 4.1 19.1 - - + -
419B VAL* 6.5 0.9 - - + -
420B LEU* 3.9 26.2 - - + -
457B VAL* 3.0 17.5 + - + +
458B VAL* 3.7 4.5 - - - +
460B ILE* 1.3 76.9 - - - +
462B SER* 1.3 55.6 + - - +
464B LEU* 3.2 6.3 + - - +
465B LEU* 2.9 41.4 + - + +
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Residues in contact with SER 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LEU* 5.6 0.6 - - - +
458B VAL* 2.6 24.4 + - - +
459B ARG 3.3 5.1 + - - -
461B ALA* 1.3 77.4 - - - +
463B LEU* 1.3 61.9 + - - +
465B LEU* 3.4 10.6 + - - -
466B GLN* 3.4 17.1 + - - +
473B THR* 3.4 15.4 - - - +
476B LEU* 3.2 35.9 - - - +
477B LEU* 3.9 22.2 - - - -
480B LEU* 3.9 3.5 - - - +
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Residues in contact with LEU 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ARG* 3.0 54.6 + - + +
460B ILE* 3.8 4.9 - - - +
462B SER* 1.3 76.0 - - - +
464B LEU* 1.3 60.0 + - - +
466B GLN* 2.8 29.0 + - - +
477B LEU* 3.8 19.7 - - + -
482B GLN* 4.7 2.9 - - + +
486B GLU 4.4 4.0 - - - +
487B ARG* 3.8 37.5 - - + +
488B ASP 4.4 2.5 - - - +
489B PHE* 3.2 14.5 - - + -
491B ALA* 4.4 2.9 - - + -
492B ILE* 3.7 31.0 - - + +
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Residues in contact with LEU 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 4.8 4.3 - - + -
396B LEU* 3.7 36.1 - - + -
397B LEU* 3.8 36.3 - - + +
400B VAL* 4.4 18.1 - - + +
404B PHE* 5.5 3.1 - - - -
416B ILE* 4.0 21.6 - - + +
460B ILE* 3.2 32.6 + - + +
461B ALA* 3.2 4.5 + - - +
463B LEU* 1.3 74.6 - - - +
465B LEU* 1.3 57.7 + - - +
466B GLN 3.3 2.5 - - - -
467B PRO* 3.2 16.9 - - - +
468B VAL* 5.3 2.4 + - - +
489B PHE* 3.9 12.6 - - + -
492B ILE* 3.8 12.8 - - + -
----------------------------------------------------------
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Residues in contact with LEU 465 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LEU* 4.0 18.4 - - + -
413B LEU* 3.7 21.8 - - + -
416B ILE* 3.8 24.2 - - + -
417B TRP* 3.6 39.9 - - + -
420B LEU* 4.9 0.4 - - + -
461B ALA* 2.9 27.3 + - + +
462B SER* 3.4 2.0 + - - +
463B LEU 3.4 0.2 - - - -
464B LEU* 1.3 75.4 - - - +
466B GLN* 1.3 59.6 + - - +
467B PRO* 3.3 2.5 - - - -
468B VAL* 3.0 9.9 + - + +
469B MET* 2.9 36.9 + - + -
473B THR* 3.6 17.3 - - + +
476B LEU* 6.3 0.7 - - + -
----------------------------------------------------------
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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