Contacts of the helix formed by residues 402 - 430 (chain B) in PDB entry 5SY1
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 PHE 402 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LYS* 4.7 10.8 - - + +
275B LEU* 3.9 25.6 - - + -
278B SER* 4.2 11.2 - - - -
367B HIS* 4.8 2.9 - + - -
398B CYS 3.7 12.3 + - - +
399B TRP 3.5 6.5 + - - +
401B GLY* 1.3 76.4 - - - +
403B THR* 1.3 67.8 + - - +
404B SER 3.2 1.8 - - - -
405B TYR* 3.2 15.6 + - + +
406B GLN* 3.2 16.5 + - - +
526B LEU* 3.6 30.1 - - + -
544B CYS* 3.9 17.9 - - + -
545B TYR* 3.8 36.8 - + - -
548B TYR* 4.0 34.1 - + + -
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Residues in contact with THR 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A PHE* 3.7 23.7 - - - -
94B TYR* 5.0 4.2 - - + -
274B LYS* 3.2 48.8 - - + +
277B ILE* 4.1 14.4 - - + -
278B SER* 3.9 26.0 - - - +
281B VAL* 5.0 5.4 - - - +
401B GLY* 4.8 4.0 - - - -
402B PHE* 1.3 76.5 + - - +
404B SER* 1.3 62.6 + - - +
406B GLN* 3.4 2.8 + - - +
407B ALA* 3.4 21.8 + - - +
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Residues in contact with SER 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A PHE* 4.0 14.4 - - - -
500A ASN* 3.3 45.3 + - - +
501A VAL* 3.7 19.9 - - - +
401B GLY* 3.5 14.4 + - - -
403B THR* 1.3 80.3 + - - +
405B TYR* 1.3 64.0 + - - +
407B ALA* 3.5 2.6 + - - +
408B ALA* 3.0 30.5 + - - +
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Residues in contact with TYR 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A GLN* 5.7 0.7 + - - -
500A ASN* 3.8 16.7 + - + -
503A ILE* 3.9 14.1 - - + +
504A GLY* 3.6 31.0 - - - -
507A LEU* 3.8 23.0 - - + +
397B VAL* 5.5 4.5 + - - +
398B CYS* 4.9 6.1 - - - -
400B MET 5.6 0.8 + - - -
401B GLY 3.2 20.9 - - - -
402B PHE* 3.2 10.8 + - + +
404B SER* 1.3 86.3 + - - +
406B GLN* 1.3 60.7 + - - +
408B ALA* 4.4 2.5 - - - -
409B PHE* 3.1 39.8 + + + -
526B LEU* 4.1 12.1 - - + -
544B CYS* 3.6 38.5 - - + -
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Residues in contact with GLN 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B SER* 3.4 37.2 - - - +
282B ALA* 4.2 6.2 - - + +
360B LEU* 3.7 27.5 - - - +
363B SER* 5.4 4.4 + - - -
367B HIS* 5.5 5.5 - - - -
402B PHE* 3.2 18.9 + - + +
403B THR 3.8 8.1 - - - +
404B SER 3.2 0.4 - - - -
405B TYR* 1.3 80.0 - - - +
407B ALA* 1.3 60.6 + - - +
408B ALA 3.5 0.3 + - - -
409B PHE* 3.6 2.2 + - - +
410B LEU* 3.5 18.9 + - - +
524B GLY 3.9 15.4 + - - -
525B ARG* 5.2 1.0 - - - +
526B LEU* 3.3 33.7 + - + +
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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
----------------------------------------------------------
497A PHE* 6.5 0.2 - - + -
501A VAL* 5.6 2.5 - - + -
98B PHE* 4.3 16.5 - - + -
278B SER 5.8 0.2 - - - +
281B VAL* 3.9 39.7 - - + +
282B ALA* 4.5 7.0 - - - +
285B ALA* 4.2 3.7 - - + +
403B THR 3.4 10.3 + - - +
404B SER* 4.3 3.1 - - - +
406B GLN* 1.3 79.3 - - - +
408B ALA* 1.3 63.0 + - - +
410B LEU* 3.9 3.3 + - - +
411B CYS* 3.4 26.2 + - - -
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Residues in contact with ALA 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A VAL* 4.1 17.2 - - + +
504A GLY* 3.5 34.5 - - - +
505A VAL* 4.4 6.4 - - + +
404B SER 3.0 18.4 + - - +
405B TYR 4.0 3.4 - - - +
406B GLN 3.3 0.2 - - - -
407B ALA* 1.3 77.9 - - - +
409B PHE* 1.3 64.9 + - - +
410B LEU 3.1 1.3 + - - -
411B CYS* 3.4 13.6 + - - +
412B LEU* 3.5 16.1 + - - +
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Residues in contact with PHE 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A GLY* 3.4 25.8 - - - -
507A LEU* 3.8 24.7 - - + -
508A GLY* 3.5 21.3 - - - -
511A ARG* 3.8 23.3 - - - -
405B TYR* 3.1 25.4 + + + +
406B GLN* 3.6 3.8 + - - +
408B ALA* 1.3 76.1 - - - +
410B LEU* 1.3 58.6 + - - +
411B CYS 3.5 0.2 - - - -
412B LEU* 4.1 7.5 - - - +
413B GLY* 3.3 15.4 + - - -
523B LEU* 4.3 10.4 - - - +
524B GLY* 3.7 18.4 - - - -
525B ARG 4.9 0.9 - - - -
526B LEU* 3.5 34.5 - - + -
540B PRO 5.2 0.9 - - - -
541B GLY* 3.7 19.3 - - - -
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ALA* 3.3 42.2 - - + +
285B ALA* 4.9 2.9 - - + -
286B LEU* 4.3 17.5 - - + +
356B ASN* 3.8 34.5 - - + +
360B LEU* 3.9 17.0 - - + -
406B GLN* 3.5 17.8 + - - +
407B ALA* 4.4 5.6 - - - +
408B ALA 3.1 1.0 - - - -
409B PHE* 1.3 78.4 - - - +
411B CYS* 1.3 59.7 + - - +
412B LEU 3.3 0.2 - - - -
413B GLY* 3.0 14.3 + - - +
414B MET* 3.0 17.4 + - + +
524B GLY* 4.7 15.7 - - - +
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Residues in contact with CYS 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 4.4 10.1 - - - -
285B ALA* 3.9 21.8 - - - -
288B GLN* 6.4 0.2 - - - -
289B MET* 3.6 44.6 - - + +
407B ALA 3.4 17.2 + - - -
408B ALA* 3.4 8.4 + - - +
410B LEU* 1.3 78.2 - - - +
412B LEU* 1.3 63.0 + - + +
414B MET* 3.6 0.9 + - - -
415B ALA* 3.3 16.8 + - - +
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Residues in contact with LEU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A GLY 5.1 0.2 - - - +
505A VAL* 4.4 23.8 - - + +
508A GLY* 3.7 37.2 - - - +
509A ILE* 4.2 11.4 - - + +
512A VAL* 6.1 1.1 - - + -
408B ALA 3.5 14.3 + - - +
409B PHE* 4.3 7.2 - - - +
410B LEU 3.3 0.6 - - - -
411B CYS* 1.3 76.2 - - + +
413B GLY* 1.3 64.1 + - - +
415B ALA* 3.7 10.1 - - + +
416B ILE* 3.3 33.9 + - + +
523B LEU* 4.8 4.7 - - + +
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Residues in contact with GLY 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B ASN* 4.4 3.6 - - - -
409B PHE 3.3 13.9 + - - -
410B LEU* 3.0 10.8 + - - -
412B LEU* 1.3 77.4 - - - +
414B MET* 1.3 56.4 + - - +
415B ALA 3.2 0.3 + - - -
416B ILE* 4.2 0.3 - - - +
417B GLN* 3.0 46.5 + - - +
523B LEU* 4.8 14.3 - - - +
524B GLY* 5.1 4.9 - - - -
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Residues in contact with MET 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 3.7 22.9 - - + -
289B MET* 4.0 24.9 - - + -
290B ALA* 4.9 10.8 - - + -
293B LEU* 4.0 9.1 - - + +
349B VAL* 4.5 9.2 - - + +
352B SER* 3.3 31.2 - - - +
353B CYS* 3.7 20.4 - - + +
356B ASN* 2.7 31.2 - - - +
410B LEU* 3.0 14.5 + - + +
411B CYS 3.6 2.0 + - - +
413B GLY* 1.3 75.7 - - - +
415B ALA* 1.3 60.5 + - - +
417B GLN* 4.2 1.8 - - - -
418B THR* 2.8 30.5 + - - +
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Residues in contact with ALA 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B MET* 4.7 10.7 - - + +
293B LEU* 5.4 6.1 - - + -
411B CYS 3.3 13.6 + - - +
412B LEU* 3.7 16.8 - - + +
413B GLY 3.2 0.8 - - - -
414B MET* 1.3 80.6 - - - +
416B ILE* 1.3 66.7 + - + +
418B THR* 3.9 2.5 - - - -
419B LEU* 3.1 23.4 + - - +
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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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512A VAL* 4.0 33.2 - - + -
412B LEU* 3.3 19.6 + - + +
413B GLY 4.4 0.9 - - - +
415B ALA* 1.3 78.9 - - + +
417B GLN* 1.3 63.2 + - + +
419B LEU* 3.1 13.1 + - + +
420B VAL* 2.9 34.2 + - + +
520B ILE* 4.1 25.4 - - + -
523B LEU* 4.2 13.5 - - + -
701B CLR 4.2 23.3 - - + -
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Residues in contact with GLN 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B SER* 3.6 19.9 - - - +
355B VAL* 4.6 7.5 - - - +
356B ASN* 3.0 40.5 + - - +
413B GLY* 3.0 22.6 + - - +
414B MET 4.7 0.2 - - - +
416B ILE* 1.3 77.8 - - + +
418B THR* 1.3 58.0 + - - +
420B VAL* 4.1 4.0 - - - +
421B PHE* 3.1 48.0 + - + -
520B ILE* 2.6 42.7 + - + +
521B VAL* 3.4 13.1 + - - +
523B LEU* 4.9 4.1 - - + +
524B GLY 5.2 1.0 - - - +
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Residues in contact with THR 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B LEU* 3.9 13.8 - - + +
345B TYR* 4.5 13.7 - - + -
348B ALA* 3.9 18.8 - - + +
349B VAL* 3.7 27.1 - - + -
352B SER* 2.8 21.0 + - - -
414B MET 2.8 20.4 + - - -
415B ALA 3.4 3.2 + - - -
416B ILE 3.2 0.6 - - - -
417B GLN* 1.3 76.9 - - - +
419B LEU* 1.3 60.7 + - - +
421B PHE* 4.7 0.4 - - - -
422B PHE* 3.0 31.9 + - - +
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B ALA 3.1 18.6 + - - +
416B ILE* 3.1 12.8 + - + +
418B THR* 1.3 76.1 - - - +
420B VAL* 1.3 61.1 + - + +
422B PHE* 4.1 8.4 - - + +
423B ILE* 3.6 29.1 + - + +
701B CLR 3.8 33.0 - - + -
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ILE* 2.9 26.3 + - + +
417B GLN 4.1 2.0 - - - +
419B LEU* 1.3 76.5 - - + +
421B PHE* 1.3 68.2 + - + +
422B PHE 3.1 1.8 - - - -
423B ILE* 3.1 15.3 + - - +
424B CYS* 3.1 28.6 + - - -
517B LEU* 6.1 1.1 - - + -
520B ILE* 3.8 32.5 - - + -
701B CLR 3.5 54.1 - - + -
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Residues in contact with PHE 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ALA* 4.3 11.9 - - + -
351B LEU* 3.6 42.0 - - + -
352B SER* 4.4 13.5 - - - -
355B VAL* 4.8 10.8 - - + -
417B GLN* 3.1 33.2 + - + +
418B THR 4.3 2.0 - - - +
420B VAL* 1.3 83.6 - - + +
422B PHE* 1.3 62.1 + - - +
424B CYS* 3.3 15.1 + - + -
425B ILE* 3.3 26.5 - - + +
517B LEU* 4.8 11.9 - - + -
520B ILE* 3.7 28.3 - - + -
521B VAL* 5.1 11.4 - - + -
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Residues in contact with PHE 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B VAL* 4.2 21.1 - - + -
344B CYS* 3.5 28.7 - - + -
345B TYR* 3.6 47.8 - + + -
348B ALA* 4.0 7.5 - - + +
418B THR 3.0 21.0 + - - +
419B LEU* 4.1 11.0 - - + +
420B VAL 3.1 0.2 - - - -
421B PHE* 1.3 78.2 - - - +
423B ILE* 1.3 68.9 - - + +
424B CYS 3.5 0.2 + - - -
426B LEU* 3.4 42.7 + - + +
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Residues in contact with ILE 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B LEU* 3.6 26.5 - - + +
420B VAL* 3.1 8.5 + - - +
422B PHE* 1.3 86.4 - - + +
424B CYS* 1.3 62.3 + - - +
425B ILE 3.4 0.7 - - - -
426B LEU* 4.4 7.3 - - + +
427B PHE* 3.6 19.6 + - + +
701B CLR 4.6 28.0 - - + -
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Residues in contact with CYS 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B VAL* 3.1 35.8 + - - +
421B PHE* 3.3 15.5 + - + +
422B PHE 3.2 0.8 - - - -
423B ILE* 1.3 82.9 - - - +
425B ILE* 1.3 62.2 + - + +
427B PHE* 4.3 9.2 - - - +
428B ALA* 4.0 13.0 + - - +
517B LEU* 6.2 4.3 - - - -
701B CLR 4.9 13.0 - - - -
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Residues in contact with ILE 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B CYS* 3.9 16.6 - - + -
347B SER* 3.9 24.7 - - - +
348B ALA* 4.7 10.8 - - - -
351B LEU* 4.8 16.4 - - + -
421B PHE* 3.3 20.8 + - - +
422B PHE 3.7 0.2 + - - -
423B ILE 3.4 0.2 - - - -
424B CYS* 1.3 82.8 - - + +
426B LEU* 1.3 54.1 + - - +
427B PHE 3.2 1.1 - - - -
428B ALA* 2.8 9.2 + - + +
429B VAL* 2.5 52.9 + - + +
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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
----------------------------------------------------------
340B CYS 4.6 7.0 - - - +
341B VAL* 5.1 9.9 - - + -
344B CYS* 3.7 24.2 - - + -
422B PHE* 3.4 43.2 + - + +
423B ILE* 4.8 6.7 - - + +
425B ILE* 1.3 77.6 - - - +
427B PHE* 1.3 56.1 + - - +
429B VAL* 4.2 7.0 - - + +
430B PHE* 2.9 61.8 + - + +
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Residues in contact with PHE 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B ILE* 3.6 19.8 + - + +
424B CYS* 4.4 8.7 - - - +
425B ILE 3.2 0.8 - - - -
426B LEU* 1.3 76.5 - - - +
428B ALA* 1.3 58.6 + - + +
431B LEU* 3.3 49.0 - - + +
432B ILE* 5.3 1.0 - - - +
443B MET* 6.3 0.4 - - + -
444B LEU* 5.0 14.1 - - + -
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Residues in contact with ALA 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B CYS 4.0 10.9 + - - +
425B ILE* 2.8 13.9 + - + +
427B PHE* 1.3 82.2 - - + +
429B VAL* 1.3 60.9 + - + +
431B LEU 3.8 0.2 - - - -
432B ILE* 2.9 42.4 + - + +
433B ILE* 3.1 16.2 + - + +
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Residues in contact with VAL 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B CYS* 4.5 20.2 - - + +
344B CYS* 5.7 2.9 - - + -
425B ILE* 2.5 40.7 + - + +
426B LEU* 4.3 8.5 - - + +
428B ALA* 1.3 74.7 - - + +
430B PHE* 1.3 67.8 + - + +
431B LEU 3.1 1.2 + - - -
433B ILE* 3.7 20.4 - - + -
434B ILE* 3.1 47.2 + - + +
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Residues in contact with PHE 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B TYR* 3.9 39.3 - + + -
340B CYS* 4.4 16.6 - - + -
341B VAL* 5.1 7.9 - - + -
426B LEU* 2.9 40.6 + - + +
429B VAL* 1.3 77.0 - - + +
431B LEU* 1.3 72.3 + - + +
434B ILE* 3.6 22.0 - - + +
435B PRO* 4.7 8.1 - - - +
441B ASN* 5.6 6.8 + - - +
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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).
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