Contacts of the helix formed by residues 439 - 468 (chain B) in PDB entry 1LV5
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 439 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B PRO* 1.3 78.1 - - - +
440B GLU* 1.3 66.9 + - - +
441B PRO* 3.3 12.3 - - + -
442B VAL* 3.2 18.2 + - + +
443B LEU* 2.9 19.4 + - - +
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Residues in contact with GLU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LEU* 4.0 20.5 - - + +
345B PHE* 4.2 25.0 - - + -
347B ARG* 3.5 36.1 + - - +
438B PRO 3.8 1.0 + - - -
439B ASP* 1.3 69.6 - - - +
441B PRO* 1.3 65.2 - - + +
443B LEU* 3.0 10.2 + - + +
444B ALA* 2.6 36.5 + - + +
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Residues in contact with PRO 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PHE* 5.0 2.8 - - + -
303B LEU* 5.9 3.1 - - + -
439B ASP* 3.4 12.8 - - + -
440B GLU* 1.3 96.7 - - + +
442B VAL* 1.3 64.0 + - + +
444B ALA* 3.6 6.2 + - + +
445B GLU* 3.5 22.8 + - - +
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Residues in contact with VAL 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B ARG* 5.8 5.4 - - - +
428B VAL* 4.6 10.8 - - + +
438B PRO* 3.9 20.2 - - + -
439B ASP* 3.2 27.2 + - + +
441B PRO* 1.3 77.8 - - + +
443B LEU* 1.3 61.7 + - - +
445B GLU* 3.6 12.0 - - + +
446B HIS* 3.3 21.0 + - - +
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Residues in contact with LEU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B VAL* 3.2 29.8 - - + +
345B PHE* 4.6 9.6 - - + -
429B TYR* 3.6 29.8 - - + +
437B VAL* 3.9 19.3 - - + -
438B PRO* 3.9 14.6 - - + +
439B ASP 2.9 16.0 + - - +
440B GLU* 3.6 6.1 - - + +
442B VAL* 1.3 75.3 - - - +
444B ALA* 1.3 68.2 + - - +
446B HIS* 3.3 5.8 + - + +
447B LEU* 3.0 48.6 + - + +
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Residues in contact with ALA 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PHE* 3.4 26.2 - - + -
303B LEU* 4.4 6.1 - - + -
345B PHE* 3.5 32.2 - - + -
440B GLU 2.6 22.6 + - - +
441B PRO* 3.8 4.3 - - + +
442B VAL 3.4 0.4 - - - -
443B LEU* 1.3 74.5 - - - +
445B GLU* 1.3 57.1 + - - +
447B LEU* 4.0 2.1 - - - +
448B VAL* 3.1 31.7 + - - +
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Residues in contact with GLU 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ALA 3.7 7.4 - - - +
298B LYS* 3.6 31.6 - - + +
299B MET* 3.8 9.3 + - + +
301B PHE* 3.7 22.4 - - + -
441B PRO 3.5 11.5 + - - +
442B VAL* 3.6 15.0 - - - +
444B ALA* 1.3 78.0 - - - +
446B HIS* 1.3 65.6 + - + +
448B VAL* 3.7 4.2 - - - +
449B ARG* 2.8 47.1 + - + +
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Residues in contact with HIS 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B VAL* 5.1 1.0 - - - +
423B ARG* 3.4 32.7 + - + +
425B ASP* 2.6 31.4 + - - -
428B VAL* 3.3 46.2 - - + +
429B TYR* 3.9 15.4 - - - -
442B VAL 3.3 15.2 + - - +
443B LEU* 3.3 6.2 + - + +
444B ALA 3.3 0.6 - - - -
445B GLU* 1.3 83.7 - - + +
447B LEU* 1.3 63.4 + - + +
449B ARG* 3.5 5.5 + - - +
450B LYS* 3.1 50.6 + - + +
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Residues in contact with LEU 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B VAL* 3.8 7.0 - - + +
321B GLU* 3.2 29.4 - - + +
333B VAL 4.5 0.2 - - - +
334B GLY* 3.5 37.7 - - - +
336B ALA* 3.3 23.3 - - + +
345B PHE* 4.4 7.6 - - + -
429B TYR* 3.9 1.3 - - - +
443B LEU* 3.0 43.4 + - + +
444B ALA* 4.0 2.9 - - - +
446B HIS* 1.3 77.0 - - + +
448B VAL* 1.3 62.2 + - - +
450B LYS* 2.9 36.9 + - - +
451B ALA* 3.2 15.9 + - - +
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Residues in contact with VAL 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B MET* 4.0 17.3 - - + -
300B ALA 4.6 0.2 - - - +
301B PHE* 3.6 42.6 - - + -
336B ALA* 4.1 7.6 - - + -
337B VAL 5.5 0.7 - - - +
338B VAL* 4.0 1.6 - - + +
343B ARG* 3.9 17.5 - - + -
344B PHE 4.1 20.0 - - - +
345B PHE* 4.5 2.9 - - + +
444B ALA 3.1 22.2 + - - +
445B GLU* 3.7 7.0 - - - +
446B HIS 3.3 0.2 - - - -
447B LEU* 1.3 75.4 - - - +
449B ARG* 1.3 65.0 + - - +
451B ALA* 3.0 6.5 + - - +
452B ALA* 3.0 20.3 + - - +
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Residues in contact with ARG 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ALA* 3.9 25.6 + - - +
298B LYS 4.0 3.0 + - - -
299B MET* 3.6 54.3 - - + +
419B TYR* 4.5 0.3 + - - -
421B ALA* 2.7 57.2 + - - +
422B VAL* 3.9 16.1 - - + +
423B ARG* 5.5 2.9 - - - +
445B GLU* 2.8 40.5 + - - +
446B HIS* 3.9 6.3 - - - +
448B VAL* 1.3 72.7 - - - +
450B LYS* 1.3 62.1 + - - +
452B ALA* 3.4 2.8 + - - +
453B ALA* 3.1 22.5 + - - +
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Residues in contact with LYS 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B VAL* 4.6 10.7 - - + +
321B GLU* 3.2 19.0 + - - -
410B VAL* 3.9 36.2 - - + +
422B VAL* 3.6 18.2 - - + -
423B ARG 4.8 1.8 - - - +
425B ASP* 3.6 23.6 - - - +
446B HIS* 3.1 27.3 + - + +
447B LEU* 2.9 44.0 - - - +
448B VAL 3.2 0.6 - - - -
449B ARG* 1.3 76.0 - - - +
451B ALA* 1.3 64.0 + - - +
453B ALA* 3.4 2.9 + - - +
454B ILE* 3.0 30.7 + - - +
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Residues in contact with ALA 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ALA* 3.4 17.9 - - + +
319B VAL* 3.9 17.0 - - + +
336B ALA* 4.6 5.2 - - + +
337B VAL 4.7 0.2 - - - -
338B VAL* 3.2 34.3 - - + +
447B LEU 3.2 10.6 + - - +
448B VAL* 3.0 7.7 + - - +
450B LYS* 1.3 76.4 - - - +
452B ALA* 1.3 59.7 + - - +
454B ILE* 3.2 3.2 + - - +
455B TRP* 2.9 25.6 + - - +
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Residues in contact with ALA 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B MET* 3.8 28.7 - - + -
338B VAL* 4.0 6.8 - - - +
343B ARG* 4.4 14.4 - - - +
419B TYR* 4.1 5.6 - - - +
448B VAL 3.0 11.2 + - - +
449B ARG 3.7 7.6 - - - +
450B LYS 3.4 0.2 - - - -
451B ALA* 1.3 75.7 - - - +
453B ALA* 1.3 58.5 + - - +
455B TRP* 3.3 4.7 + - - +
456B GLU* 2.7 44.5 + - - +
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Residues in contact with ALA 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B VAL* 4.0 17.9 - - + -
419B TYR* 3.6 37.8 + - + -
422B VAL* 4.3 4.0 - - + -
449B ARG 3.1 12.5 + - - +
450B LYS 3.6 7.6 - - - +
451B ALA 3.2 0.2 - - - -
452B ALA* 1.3 76.9 - - - +
454B ILE* 1.3 53.5 + - - +
456B GLU 3.0 1.2 + - - -
457B LEU* 2.5 48.4 + - + +
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Residues in contact with ILE 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ALA* 4.3 3.1 - - + -
318B LEU 4.6 1.3 - - - +
319B VAL* 4.2 21.1 - - + -
369B SER* 3.6 35.7 - - - +
370B MET* 3.9 10.5 - - - +
371B PHE* 3.9 28.9 - - + +
392B PHE* 5.1 3.7 - - + -
394B LEU* 4.2 27.6 - - + -
410B VAL* 4.3 8.0 - - + +
450B LYS 3.0 17.1 + - - +
451B ALA* 3.6 7.2 - - - +
453B ALA* 1.3 74.5 - - - +
455B TRP* 1.3 61.6 + - - +
457B LEU* 4.5 0.7 - - - +
458B GLU* 3.1 25.5 + - - +
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Residues in contact with TRP 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LYS* 3.6 30.5 - - + -
316B ALA* 3.4 22.2 - - - -
317B ALA* 3.5 13.5 - - + -
338B VAL* 3.2 37.7 - - + -
339B ASN* 3.7 11.0 - - - -
340B GLU* 4.1 20.0 - - + -
369B SER* 5.5 3.1 - - - -
451B ALA 2.9 16.9 + - - +
452B ALA 3.4 5.2 - - - +
454B ILE* 1.3 79.3 - - - +
456B GLU* 1.3 83.3 + - - +
458B GLU* 4.1 8.0 + - - +
459B ARG* 4.9 2.3 + - - +
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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
----------------------------------------------------------
338B VAL* 5.8 0.2 - - - +
343B ARG* 5.8 1.9 + - - -
419B TYR* 4.1 24.0 + - + +
452B ALA* 2.7 39.1 + - - +
453B ALA 3.7 2.2 - - - +
455B TRP* 1.3 100.3 + - - +
457B LEU* 1.3 58.5 + - - +
458B GLU 3.7 0.2 + - - -
459B ARG* 4.0 5.7 + - - +
460B PRO* 3.2 17.8 - - - +
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Residues in contact with LEU 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B LEU* 4.3 16.6 - - + -
413B ALA 4.4 2.7 - - - +
414B ALA* 3.2 38.6 - - + +
417B LYS* 3.4 34.3 - - + +
419B TYR* 4.2 20.9 - - + -
453B ALA* 2.5 32.4 + - + +
454B ILE 4.5 0.2 - - - +
456B GLU* 1.3 70.6 - - - +
458B GLU* 1.3 64.4 + - - +
459B ARG 3.1 3.1 - - - -
460B PRO* 2.9 23.1 - - + +
461B PHE* 3.1 25.3 + - + -
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Residues in contact with GLU 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LYS* 3.2 20.8 + - - -
369B SER* 2.6 26.4 + - - -
391B SER* 4.4 6.8 + - - +
392B PHE* 3.2 57.4 - - + +
454B ILE 3.1 18.0 + - - +
455B TRP* 4.5 5.7 - - - +
456B GLU 3.5 1.2 - - - -
457B LEU* 1.3 76.7 - - - +
459B ARG* 1.3 69.3 + - - +
461B PHE 3.6 0.2 + - - -
462B LEU* 3.3 35.9 + - + +
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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
----------------------------------------------------------
315B LYS* 5.4 4.6 - - - +
455B TRP 4.9 2.8 + - - +
456B GLU 4.0 6.1 + - - +
458B GLU* 1.3 88.3 + - - +
460B PRO* 1.3 68.2 - - + +
462B LEU* 3.3 37.4 + - - +
463B ASP* 2.6 46.6 + - - +
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Residues in contact with PRO 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B LYS* 3.5 31.8 + - + +
456B GLU 3.2 15.7 - - - +
457B LEU* 2.9 46.2 - - + +
459B ARG* 1.3 86.5 - - + +
461B PHE* 1.3 60.0 + - + +
463B ASP* 3.8 13.3 - - + +
464B GLU 3.4 14.4 + - - -
467B ARG* 4.9 0.7 + - - +
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Residues in contact with PHE 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B PHE* 3.7 16.2 - - + -
394B LEU* 4.1 12.8 - - + -
397B ALA* 3.4 22.4 - - + -
398B ALA* 3.6 23.1 - - + -
401B LEU* 3.3 30.9 - - + +
413B ALA* 3.4 26.0 - - + -
416B MET* 4.5 6.1 - - + -
417B LYS* 3.4 28.3 - - + -
457B LEU* 3.1 44.4 + - + +
459B ARG 3.1 0.8 - - - -
460B PRO* 1.3 77.2 - - - +
462B LEU* 1.3 60.8 + - - +
464B GLU* 3.4 1.7 + - - +
465B LEU* 2.8 36.0 + - - +
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Residues in contact with LEU 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B PHE* 3.5 23.8 - - + -
458B GLU* 3.3 29.8 + - - +
459B ARG* 3.3 44.2 + - - +
461B PHE* 1.3 74.7 - - - +
463B ASP* 1.3 67.5 + - - +
465B LEU* 4.0 7.5 - - + +
466B ARG* 3.0 26.0 + - - +
471B ASP* 4.9 9.1 - - + +
474B LEU* 4.2 13.5 - - + -
475B VAL* 5.1 10.1 - - + -
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Residues in contact with ASP 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ARG* 2.6 45.2 + - - +
460B PRO* 3.8 9.6 - - + +
462B LEU* 1.3 78.9 - - - +
464B GLU* 1.3 58.5 + - - +
466B ARG* 3.9 4.1 - - - +
467B ARG* 3.1 54.3 + - - +
----------------------------------------------------------
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Residues in contact with GLU 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B LEU* 3.9 24.7 - - + +
417B LYS* 2.3 46.8 + - - +
460B PRO 3.4 6.3 + - - +
461B PHE 4.0 2.0 - - - +
462B LEU 3.3 0.4 - - - -
463B ASP* 1.3 76.2 - - - +
465B LEU* 1.3 67.8 + - - +
466B ARG 3.1 1.8 - - - -
467B ARG* 2.8 20.7 + - + +
468B ASN* 2.8 41.1 + - - +
772B TYR* 5.1 4.5 + - - -
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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
----------------------------------------------------------
397B ALA* 4.0 22.7 - - + +
400B LEU* 4.3 11.9 - - + -
401B LEU* 3.2 31.0 - - + -
461B PHE 2.8 33.0 + - - +
462B LEU* 4.0 11.0 - - + +
464B GLU* 1.3 72.6 - - - +
466B ARG* 1.3 53.6 + - - +
468B ASN* 3.2 1.4 + - - +
469B GLU 2.9 7.3 + - - -
470B GLN* 2.6 50.7 + - + +
471B ASP* 3.7 12.8 - - - +
474B LEU* 3.6 36.3 - - + -
----------------------------------------------------------
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Residues in contact with ARG 466 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B LEU 3.0 19.2 + - - +
463B ASP* 3.9 4.3 - - - +
465B LEU* 1.3 74.7 - - - +
467B ARG* 1.3 59.0 + - - +
469B GLU* 2.5 28.8 + - - +
471B ASP* 3.4 40.6 + - + +
----------------------------------------------------------
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Residues in contact with ARG 467 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B LYS* 5.0 4.6 - - - +
460B PRO* 4.9 1.8 + - - +
463B ASP* 3.1 41.9 + - - +
464B GLU* 2.8 24.8 + - + +
466B ARG* 1.3 81.0 - - + +
468B ASN* 1.3 65.6 + - - +
469B GLU* 3.7 8.1 - - - +
----------------------------------------------------------
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Residues in contact with ASN 468 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B LEU* 4.4 8.9 + - - +
464B GLU* 2.8 34.2 + - - +
465B LEU 3.5 4.3 - - - +
467B ARG* 1.3 75.8 - - - +
469B GLU* 1.3 74.5 + - - +
470B GLN* 2.9 34.6 + - + +
768B HIS* 4.1 5.4 - - - +
770B ARG* 3.4 47.6 + - - +
772B TYR* 4.2 5.7 + - - -
----------------------------------------------------------
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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