Contacts of the helix formed by residues 405 - 427 (chain B) in PDB entry 5UFL
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 405 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403B ASN 3.8 3.2 + - - -
404B LEU* 1.3 73.9 - - - +
406B GLU* 1.3 64.1 + - - +
407B ALA* 3.4 16.9 + - - +
408B LEU* 3.1 20.1 + - + +
409B THR* 2.7 40.3 + - - -
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Residues in contact with GLU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B LEU 3.9 1.2 + - - -
405B ASP* 1.3 79.9 + - - +
407B ALA* 1.3 61.6 + - - +
409B THR* 3.4 6.9 + - - -
410B ARG* 3.2 35.9 + - - +
457B LYS* 4.8 11.8 + - - +
471B LEU* 3.7 32.1 - - - +
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Residues in contact with ALA 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ASP* 3.4 11.8 + - - +
406B GLU* 1.3 78.7 - - - +
408B LEU* 1.3 58.2 + - - +
410B ARG* 3.5 30.1 + - - +
411B LYS* 3.1 24.9 + - - +
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Residues in contact with LEU 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B LEU* 3.5 40.1 - - + +
353B ASP* 3.7 32.5 - - - +
403B ASN 5.9 0.4 - - - +
404B LEU* 4.0 21.8 - - + -
405B ASP* 3.1 26.6 + - + +
407B ALA* 1.3 76.7 - - - +
409B THR* 1.3 64.1 + - - +
411B LYS* 3.5 5.6 + - + +
412B LYS 3.2 17.2 + - - -
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Residues in contact with THR 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B PHE* 4.1 23.1 - - + -
404B LEU* 3.5 27.7 + - + +
405B ASP 2.7 28.7 + - - -
406B GLU* 3.7 7.9 - - - -
407B ALA 3.4 0.2 - - - -
408B LEU* 1.3 71.2 - - - +
410B ARG* 1.3 64.0 + - - +
412B LYS* 3.4 2.8 + - - +
413B CYS* 3.1 23.2 + - - -
455B TYR* 4.6 12.1 - - + +
471B LEU* 3.9 25.4 - - + -
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Residues in contact with ARG 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B GLU* 3.2 24.9 + - - +
407B ALA* 3.6 33.6 - - - +
408B LEU 3.3 0.2 - - - -
409B THR* 1.3 74.8 - - - +
411B LYS* 1.3 58.8 + - - +
413B CYS* 3.2 5.8 + - - +
414B GLU* 2.9 30.9 + - - +
470B GLU* 3.9 32.4 - - - +
471B LEU* 3.9 22.4 - - + +
474B LEU* 3.8 22.6 - - + +
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Residues in contact with LYS 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B PRO 5.6 0.4 - - - -
352B LEU* 3.6 19.1 - - + -
353B ASP* 3.2 33.0 - - - +
357B ASN* 3.8 31.7 + - - +
359B SER* 5.4 2.2 - - - -
360B VAL* 4.0 17.3 - - + +
407B ALA 3.1 11.7 + - - +
408B LEU* 3.7 11.9 - - + +
409B THR 3.4 0.2 - - - -
410B ARG* 1.3 78.3 - - - +
412B LYS* 1.3 56.7 + - - +
414B GLU* 3.6 15.9 + - - +
415B ARG* 3.0 37.8 + - - +
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Residues in contact with LYS 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B LEU* 3.9 15.6 - - + +
395B ASP 5.1 1.8 + - - -
396B GLN* 4.2 16.3 + - - +
398B GLN 3.0 29.9 + - - -
399B PHE* 3.6 29.2 - - + +
400B THR* 5.0 1.6 + - - -
401B GLU* 3.4 34.5 + - - +
404B LEU* 4.5 0.2 - - + -
408B LEU 3.2 14.9 + - - +
409B THR* 3.6 9.2 - - - +
410B ARG 3.2 0.4 - - - -
411B LYS* 1.3 75.7 - - - +
413B CYS* 1.3 58.1 + - - +
415B ARG* 3.2 13.6 + - + +
416B ILE* 2.8 51.2 + - + +
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Residues in contact with CYS 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B PHE* 4.1 15.5 - - - -
409B THR* 3.1 19.0 + - - +
410B ARG* 3.2 7.6 + - - +
412B LYS* 1.3 74.0 - - - +
414B GLU* 1.3 61.4 + - - +
416B ILE* 4.4 5.8 - - - -
417B ALA* 3.0 30.0 + - - +
452B GLN* 3.4 24.9 - - - +
456B GLY* 5.7 1.8 - - - -
471B LEU* 4.2 17.7 - - - -
474B LEU* 4.0 20.6 - - + +
475B ALA* 4.5 5.6 - - - -
478B VAL* 3.4 11.0 - - + +
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Residues in contact with GLU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B VAL* 4.3 28.8 - - + +
410B ARG 2.9 15.7 + - - +
411B LYS* 3.7 14.6 - - - +
413B CYS* 1.3 77.5 - - - +
415B ARG* 1.3 57.1 + - - +
417B ALA* 3.4 6.8 + - - +
418B LYS* 3.1 41.7 + - + +
474B LEU* 4.6 18.7 - - + +
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Residues in contact with ARG 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B LEU 2.8 20.4 + - - -
349B SER 4.6 0.2 - - - -
350B GLN 2.6 29.7 + - - -
351B PRO* 3.8 4.0 + - - +
352B LEU* 3.7 35.4 - - - +
359B SER* 3.1 28.3 + - - -
360B VAL* 4.7 15.0 - - + +
363B LEU* 3.4 24.5 - - + +
396B GLN* 3.0 26.5 + - + +
401B GLU* 6.2 0.2 - - - -
411B LYS* 3.0 27.7 + - - +
412B LYS* 3.2 14.4 + - + +
414B GLU* 1.3 75.4 - - - +
416B ILE* 1.3 64.8 + - - +
418B LYS* 3.5 1.4 + - - -
419B ALA* 3.2 18.7 + - - +
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Residues in contact with ILE 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B GLN 3.3 23.6 - - - +
397B LEU* 3.7 9.1 - - + +
398B GLN 4.7 2.2 - - - +
399B PHE* 3.7 21.1 - - + -
412B LYS* 2.8 40.7 + - + +
413B CYS* 3.9 4.3 - - - +
415B ARG* 1.3 71.6 - - - +
417B ALA* 1.3 62.5 + - - +
419B ALA* 3.3 6.0 + - - +
420B ILE* 3.1 22.0 + - + +
448B LEU* 4.0 24.5 - - + -
452B GLN* 3.4 21.3 - - - +
478B VAL* 3.6 24.5 - - + -
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Residues in contact with ALA 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B CYS 3.0 18.6 + - - +
414B GLU* 3.5 8.3 - - - +
415B ARG 3.3 0.2 - - - -
416B ILE* 1.3 77.8 - - - +
418B LYS* 1.3 57.4 + - + +
420B ILE* 3.3 10.2 + - - +
421B GLU* 3.1 34.8 + - - +
474B LEU* 6.0 3.6 - - + -
477B ASP* 4.6 7.2 - - - +
478B VAL* 4.0 15.5 - - + -
481B LYS* 4.1 16.6 - - + +
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Residues in contact with LYS 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B VAL* 3.7 23.8 - - + +
363B LEU* 3.8 26.9 - - + +
364B GLU* 3.6 42.0 + - + +
367B LYS* 5.6 0.4 - - + +
414B GLU* 3.1 28.8 + - - +
415B ARG 3.9 0.2 - - - +
416B ILE 3.4 0.4 - - - -
417B ALA* 1.3 72.8 - - + +
419B ALA* 1.3 65.4 + - - +
421B GLU* 3.3 32.6 + - - +
422B VAL* 3.1 25.5 + - - +
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Residues in contact with ALA 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B LEU* 3.8 14.9 - - + +
393B ILE* 3.7 13.5 - - + +
396B GLN* 3.8 19.5 - - + -
397B LEU* 3.5 18.8 - - + -
415B ARG 3.2 11.9 + - - +
416B ILE 3.3 8.7 + - - +
418B LYS* 1.3 79.8 - - - +
420B ILE* 1.3 60.8 + - - +
422B VAL* 3.5 5.2 + - - +
423B LEU* 3.3 25.1 + - - +
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Residues in contact with ILE 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B LEU* 3.5 31.2 - - + -
416B ILE* 3.1 21.3 + - + +
417B ALA* 3.3 8.9 + - - +
419B ALA* 1.3 73.0 - - - +
421B GLU* 1.3 61.6 + - - +
423B LEU* 3.1 6.5 + - - +
424B LEU* 2.8 33.5 + - + +
448B LEU* 4.0 6.7 - - + -
478B VAL* 5.1 1.6 - - + -
481B LYS* 3.7 40.4 - - + +
482B THR* 3.8 22.9 - - + +
485B LEU* 4.1 18.4 - - + -
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Residues in contact with GLU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B LYS* 3.1 39.7 + - + +
417B ALA* 3.1 21.1 + - - +
418B LYS* 3.3 39.8 + - + +
420B ILE* 1.3 73.6 - - - +
422B VAL* 1.3 63.3 + - - +
424B LEU* 3.4 14.0 + - + +
425B THR* 3.1 28.8 + - - +
481B LYS* 3.4 31.2 + - - -
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Residues in contact with VAL 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B LEU* 3.2 38.1 - - + +
366B PHE* 4.1 6.1 - - + -
367B LYS* 3.9 13.5 - - + +
370B PHE* 4.3 22.2 - - + -
393B ILE* 3.4 26.9 - - + -
418B LYS 3.1 13.6 + - - +
419B ALA 3.7 8.1 - - - +
420B ILE 3.2 0.2 - - - -
421B GLU* 1.3 74.6 - - - +
423B LEU* 1.3 62.4 + - + +
425B THR* 3.0 22.2 + - - +
426B LEU* 3.1 16.7 + - + +
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B LEU* 3.4 33.7 - - + -
393B ILE* 4.0 14.1 - - + -
394B LEU* 3.7 25.1 - - + -
397B LEU* 3.7 20.6 - - + -
419B ALA 3.3 12.5 + - - +
420B ILE* 3.1 8.8 + - - +
422B VAL* 1.3 76.2 - - + +
424B LEU* 1.3 61.5 + - - +
426B LEU* 4.3 4.0 - - + -
427B CYS* 3.2 26.9 + - - -
436B ILE* 3.6 19.1 - - + +
440B LEU* 4.5 4.9 - - + -
485B LEU* 3.9 26.5 - - + -
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Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B ILE* 2.8 37.4 + - + +
421B GLU* 3.6 15.3 - - + +
422B VAL 3.2 0.2 - - - -
423B LEU* 1.3 71.8 - - - +
425B THR* 1.3 64.7 + - + +
427B CYS* 3.4 17.3 + - - +
428B GLY* 3.8 2.6 + - - -
481B LYS* 4.2 17.5 - - + +
484B ASP* 3.8 23.1 - - - +
485B LEU* 3.6 37.9 - - + +
488B LYS* 3.9 23.4 - - + +
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Residues in contact with THR 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B LYS* 3.6 37.0 + - + +
370B PHE* 4.0 9.7 - - - +
371B GLU* 4.1 22.0 - - + +
374B ILE* 3.1 16.4 - - - +
421B GLU 3.1 14.8 + - - +
422B VAL* 3.0 16.0 + - - -
424B LEU* 1.3 73.7 - - + +
426B LEU* 1.3 66.7 + - - +
427B CYS 3.1 0.2 - - - -
428B GLY* 2.9 19.8 + - - -
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Residues in contact with LEU 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B PHE* 3.4 48.0 - - + -
374B ILE* 4.1 4.7 - - + -
386B VAL* 4.2 15.9 - - + -
389B LEU* 5.6 2.9 - - + -
390B LEU* 3.8 28.7 - - + -
393B ILE* 5.6 0.2 - - + -
422B VAL* 3.1 21.1 + - + +
423B LEU* 3.7 7.0 - - + +
425B THR* 1.3 83.1 + - - +
427B CYS* 1.3 58.1 + - - +
428B GLY 3.3 0.5 + - - -
429B ASP* 3.2 21.8 + - - +
432B LEU* 3.4 27.3 - - + +
433B LYS 3.7 0.7 + - - -
436B ILE* 3.5 21.1 - - + -
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Residues in contact with CYS 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B LEU 3.2 20.7 + - - -
424B LEU 3.5 11.0 - - - +
425B THR 3.1 1.0 - - - -
426B LEU* 1.3 72.9 - - - +
428B GLY* 1.3 63.1 + - - +
429B ASP 3.2 7.4 + - - +
430B ASP* 5.4 0.5 - - - +
433B LYS* 3.8 44.2 + - + +
436B ILE* 4.1 8.5 - - - -
485B LEU* 3.8 21.1 - - - -
488B LYS* 3.8 23.9 - - + -
489B LEU* 4.2 6.7 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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