Contacts of the helix formed by residues 433 - 463 (chain B) in PDB entry 1Z5A
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 VAL 433 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 5.3 2.0 - - + +
26A PRO* 3.8 26.2 - - + +
345B TYR* 3.5 31.2 - - + -
346B GLN* 4.0 15.5 - - + +
387B VAL* 5.1 0.5 - - - +
421B PRO* 3.9 28.9 - - + -
431B ALA 3.0 11.6 + - - +
432B GLU* 1.3 73.4 - - - +
434B GLU* 1.3 60.0 + - - +
435B ASP* 4.3 4.3 - - + +
436B ILE* 3.2 23.9 + - + +
437B GLU* 2.9 26.4 + - - +
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Residues in contact with GLU 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASN* 4.8 13.2 - - + +
28A PRO* 6.1 2.0 - - + -
182A LYS* 3.0 29.9 + - - +
432B GLU 3.8 3.2 + - - -
433B VAL* 1.3 72.5 - - - +
435B ASP* 1.3 60.6 + - - +
437B GLU* 3.2 24.7 + - - +
438B LYS* 2.9 43.4 + - + +
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Residues in contact with ASP 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B TYR* 2.8 40.7 + - - -
344B ALA 4.2 5.7 - - - +
345B TYR* 4.0 22.2 - - + +
346B GLN* 5.3 0.7 + - - +
350B PHE* 3.8 6.1 - - + -
433B VAL* 3.4 3.8 - - + +
434B GLU* 1.3 78.6 - - - +
436B ILE* 1.3 61.6 + - - +
438B LYS* 3.7 20.8 + - - +
439B GLU* 3.3 23.0 + - - +
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Residues in contact with ILE 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B TYR* 3.7 26.9 - - + -
350B PHE* 4.1 23.6 - - + -
387B VAL* 4.8 2.0 - - + -
415B LEU* 4.1 26.5 - - + -
421B PRO* 3.6 34.5 - - + -
430B ILE* 4.8 8.1 - - + -
431B ALA 5.6 0.2 - - - +
433B VAL* 3.2 21.3 + - + +
435B ASP* 1.3 74.0 - - - +
437B GLU* 1.3 60.5 + - - +
439B GLU* 3.3 1.7 + - - +
440B ILE* 2.9 51.1 + - + +
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Residues in contact with GLU 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B VAL* 3.8 26.1 - - + +
390B LYS* 3.4 36.5 + - - +
391B VAL* 3.7 18.7 - - + +
394B GLU* 4.4 6.6 - - - +
432B GLU* 4.6 9.0 - - - +
433B VAL 2.9 13.1 + - - +
434B GLU* 3.2 24.2 + - - +
436B ILE* 1.3 77.4 - - - +
438B LYS* 1.3 63.7 + - - +
440B ILE* 3.4 5.1 + - - +
441B LYS* 3.2 22.4 + - + +
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Residues in contact with LYS 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B GLU* 2.9 29.5 + - - +
435B ASP* 4.0 19.2 + - - +
437B GLU* 1.3 76.4 - - - +
439B GLU* 1.3 58.9 + - + +
441B LYS* 3.4 10.6 + - + +
442B ASN* 2.9 44.1 + - - +
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Residues in contact with GLU 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ARG* 2.8 52.6 + - - +
341B LYS 4.1 2.8 - - - +
343B LYS* 3.9 27.0 - - + +
350B PHE* 3.8 25.6 - - + -
352B VAL* 3.8 14.4 + - + +
435B ASP 3.3 17.0 + - - +
436B ILE 3.8 3.1 - - - +
438B LYS* 1.3 76.6 - - + +
440B ILE* 1.3 61.3 + - - +
442B ASN* 3.3 8.8 + - - +
443B ALA* 2.8 29.8 + - - +
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Residues in contact with ILE 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B VAL* 3.8 26.0 - - + -
387B VAL* 4.0 22.7 - - + -
388B ILE* 4.0 21.8 - - + -
391B VAL* 4.0 22.4 - - + -
413B VAL* 4.4 16.4 - - + -
415B LEU* 5.6 4.5 - - + -
430B ILE* 5.6 0.9 - - + -
436B ILE* 2.9 41.1 + - + +
437B GLU* 3.7 5.4 - - - +
439B GLU* 1.3 75.2 - - - +
441B LYS* 1.3 58.2 + - - +
443B ALA* 3.7 1.7 - - - +
444B LEU* 2.9 38.3 + - + +
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Residues in contact with LYS 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B VAL* 3.6 24.7 - - + -
394B GLU* 5.4 14.2 + - - -
395B LEU* 4.4 8.5 - - + -
437B GLU* 3.2 13.6 + - + +
438B LYS* 3.5 12.1 - - + +
440B ILE* 1.3 75.3 - - - +
442B ASN* 1.3 68.5 + - - +
444B LEU* 3.2 3.8 + - - +
445B MET* 2.9 55.6 + - + +
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Residues in contact with ASN 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ARG* 3.6 24.7 + - - +
343B LYS* 6.2 0.2 - - - +
438B LYS* 2.9 38.0 + - - +
439B GLU* 3.3 15.0 + - - +
441B LYS* 1.3 77.6 - - - +
443B ALA* 1.3 61.6 + - - +
445B MET* 3.4 15.7 + - - +
446B GLU* 3.2 20.6 + - - +
449B ARG* 5.1 1.7 + - - -
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Residues in contact with ALA 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ILE* 3.9 4.8 - - + +
340B ARG* 3.6 26.2 - - + +
352B VAL* 3.6 26.9 - - + -
354B ALA* 4.0 13.0 - - + -
439B GLU 2.8 21.0 + - - +
440B ILE 3.7 2.5 - - - +
442B ASN* 1.3 71.5 - - - +
444B LEU* 1.3 64.5 + - - +
446B GLU* 3.1 14.9 + - - +
447B VAL* 3.3 14.2 + - - +
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Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ALA* 4.4 6.7 - - + -
355B GLY 5.1 1.3 - - - +
356B VAL* 6.4 0.4 - - + -
391B VAL* 3.8 18.8 - - + -
392B VAL* 3.7 28.5 - - + -
395B LEU* 4.4 16.4 - - + +
397B TRP* 4.7 9.9 - - + -
411B VAL* 3.6 25.6 - - + -
412B MET 5.1 0.2 - - - +
413B VAL* 4.3 13.9 - - + -
440B ILE* 2.9 28.9 + - + +
441B LYS* 3.2 5.4 + - - +
443B ALA* 1.3 76.5 - - - +
445B MET* 1.3 56.3 + - - +
447B VAL* 3.3 16.5 - - + +
448B ALA* 2.9 30.9 + - - +
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Residues in contact with MET 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B LEU* 3.9 20.0 - - + -
399B ARG* 5.0 7.0 - - - +
400B TYR* 3.5 20.2 - - - +
441B LYS* 2.9 54.2 + - + +
442B ASN* 3.6 15.0 - - - +
443B ALA 3.2 0.2 - - - -
444B LEU* 1.3 73.5 - - - +
446B GLU* 1.3 64.8 + - - +
448B ALA* 3.2 7.7 + - - +
449B ARG* 3.0 48.3 + - - +
----------------------------------------------------------
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Residues in contact with GLU 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ILE* 3.3 36.2 - - + +
340B ARG* 2.8 39.1 + - - +
442B ASN 3.2 6.6 + - - +
443B ALA* 3.1 11.7 + - - +
445B MET* 1.3 76.8 - - - +
447B VAL* 1.3 63.9 + - - +
449B ARG* 3.1 41.4 + - - +
450B LYS* 3.4 19.3 + - - +
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Residues in contact with VAL 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ALA* 4.2 4.9 - - + +
337B SER* 3.7 21.1 - - - +
338B ILE* 3.7 24.9 - - + -
354B ALA* 3.7 24.5 - - + +
355B GLY 4.9 0.4 - - - +
356B VAL* 4.0 22.8 - - + +
397B TRP* 6.2 1.1 - - + -
443B ALA 3.5 8.5 - - - +
444B LEU* 3.3 27.4 - - + +
446B GLU* 1.3 78.1 - - - +
448B ALA* 1.3 61.5 + - - +
450B LYS* 3.2 12.5 + - + +
451B LEU* 3.1 21.7 + - - +
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Residues in contact with ALA 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B VAL* 5.7 0.7 - - - -
395B LEU* 4.6 1.6 - - + -
397B TRP* 4.2 17.3 - - + -
400B TYR* 3.5 42.3 - - + +
444B LEU 2.9 20.6 + - - +
445B MET* 3.5 8.5 - - - +
446B GLU 3.2 0.2 - - - -
447B VAL* 1.3 78.8 - - - +
449B ARG* 1.3 56.5 + - - +
451B LEU* 3.3 8.3 + - - +
452B LYS* 3.0 22.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ARG* 5.9 0.2 - - - +
400B TYR* 4.2 15.8 + - + -
442B ASN 5.1 1.6 + - - -
445B MET* 3.0 41.3 + - - +
446B GLU* 3.1 38.6 + - - +
448B ALA* 1.3 75.8 - - - +
450B LYS* 1.3 64.2 + - + +
452B LYS* 3.4 10.7 + - + +
453B GLN* 3.1 21.5 + - - +
----------------------------------------------------------
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Residues in contact with LYS 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B GLU* 5.4 2.6 + - - -
334B PHE* 3.6 12.0 - - + -
336B ALA* 4.0 27.4 - - + -
337B SER 3.3 24.1 + - - +
338B ILE* 4.5 14.5 - - - +
446B GLU* 3.4 19.9 + - - +
447B VAL* 3.2 14.0 + - - +
449B ARG* 1.3 76.6 - - + +
451B LEU* 1.3 61.8 + - - +
453B GLN* 3.2 12.2 + - - +
454B TYR 3.0 16.3 + - - -
----------------------------------------------------------
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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
----------------------------------------------------------
334B PHE* 3.8 24.6 - - + -
356B VAL* 4.1 13.5 - - + -
358B PHE* 3.8 28.3 - - + -
397B TRP* 4.3 10.5 - - + -
400B TYR* 4.6 3.8 - - + +
402B ILE* 3.9 18.2 - - + -
409B MET* 3.8 28.0 - - - -
447B VAL 3.1 12.9 + - - +
448B ALA* 3.5 8.7 - - - +
450B LYS* 1.3 73.6 - - - +
452B LYS* 1.3 54.7 + - - +
454B TYR* 3.1 4.7 + - + +
455B LEU* 2.8 49.1 + - + +
----------------------------------------------------------
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Residues in contact with LYS 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ARG 3.5 23.5 + - - +
400B TYR* 3.3 31.8 + - + +
401B GLY* 4.4 2.7 - - - +
448B ALA 3.0 12.6 + - - +
449B ARG* 3.5 13.5 - - + +
451B LEU* 1.3 73.8 - - - +
453B GLN* 1.3 56.1 + - - +
455B LEU* 4.1 2.0 - - - +
456B SER* 2.8 42.1 + - - -
459B ARG* 5.5 1.5 + - - +
----------------------------------------------------------
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Residues in contact with GLN 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B PHE* 6.4 0.4 - - + -
449B ARG 3.1 12.7 + - - +
450B LYS* 3.2 13.2 + - - +
452B LYS* 1.3 74.7 - - - +
454B TYR* 1.3 59.4 + - - +
456B SER* 4.0 3.9 - - - -
457B GLU* 2.9 65.8 + - - +
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Residues in contact with TYR 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ASP* 3.4 29.2 + - + +
334B PHE* 3.6 61.7 - + + -
358B PHE* 4.3 12.9 - + - -
450B LYS 3.0 6.8 + - - +
451B LEU* 3.1 9.8 + - + +
453B GLN* 1.3 79.0 - - - +
455B LEU* 1.3 76.7 + - + +
457B GLU* 3.5 7.4 + - + +
458B LYS* 3.1 61.1 + - + +
----------------------------------------------------------
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Residues in contact with LEU 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B PHE* 4.0 32.3 - - + -
400B TYR 3.6 19.7 - - - +
401B GLY* 3.9 11.0 - - - -
402B ILE* 3.8 19.5 - - + -
403B GLU* 4.4 9.6 - - - +
451B LEU* 2.8 35.0 + - + +
452B LYS 4.1 2.2 - - - +
454B TYR* 1.3 87.6 - - + +
456B SER* 1.3 60.7 + - - +
458B LYS* 4.0 13.5 - - - +
459B ARG* 3.2 47.6 + - - +
----------------------------------------------------------
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Residues in contact with SER 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B LYS* 2.8 23.5 + - - -
453B GLN* 4.0 4.0 - - - -
455B LEU* 1.3 72.8 - - - +
457B GLU* 1.3 54.2 + - - +
458B LYS 2.7 15.5 + - - -
459B ARG* 3.0 22.3 + - - +
460B LYS* 3.2 34.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B GLN* 2.9 49.5 + - - +
454B TYR* 3.6 7.3 - - + +
456B SER* 1.3 70.5 + - - +
458B LYS* 1.3 56.8 + - - +
460B LYS* 4.6 15.3 - - + +
461B GLU* 4.1 13.2 + - - +
----------------------------------------------------------
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Residues in contact with LYS 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B PHE* 4.6 19.0 - - - -
403B GLU* 5.2 5.3 + - - -
454B TYR* 3.1 49.5 + - + +
455B LEU* 4.0 13.3 - - - +
456B SER 2.7 3.0 + - - -
457B GLU* 1.3 79.5 - - - +
459B ARG* 1.3 63.7 + - - +
460B LYS 3.4 0.9 - - - -
461B GLU* 3.3 27.5 + - + +
462B GLN* 3.5 32.8 + - - +
----------------------------------------------------------
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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
----------------------------------------------------------
401B GLY* 2.6 34.4 + - - -
403B GLU* 2.6 36.7 + - - +
452B LYS* 5.5 1.8 + - - +
455B LEU* 3.2 37.8 + - - +
456B SER* 3.0 12.0 + - - +
458B LYS* 1.3 75.2 - - - +
460B LYS* 1.3 58.2 + - + +
461B GLU 2.9 5.1 + - - -
462B GLN* 3.0 19.5 + - - +
463B GLU* 2.8 31.9 + - - +
----------------------------------------------------------
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Residues in contact with LYS 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B SER* 3.2 30.3 + - - +
457B GLU* 4.9 11.6 - - + +
458B LYS 3.4 0.2 - - - -
459B ARG* 1.3 78.5 - - + +
461B GLU* 1.3 60.3 + - - +
463B GLU* 3.5 42.0 + - - +
----------------------------------------------------------
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Residues in contact with GLU 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B GLU 4.1 12.0 + - - +
458B LYS* 3.3 24.9 + - + +
459B ARG 2.9 0.2 - - - -
460B LYS* 1.3 77.0 - - - +
462B GLN* 1.3 65.4 + - + +
463B GLU 3.1 5.5 + - - -
----------------------------------------------------------
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Residues in contact with GLN 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B LYS* 3.5 33.9 + - - +
459B ARG* 3.0 20.6 + - - +
461B GLU* 1.3 79.0 - - + +
463B GLU* 1.3 61.2 + - - +
----------------------------------------------------------
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Residues in contact with GLU 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ARG* 2.8 12.8 + - - +
460B LYS* 3.5 43.3 + - - +
461B GLU 3.1 4.2 - - - -
462B GLN* 1.3 81.2 - - - +
----------------------------------------------------------
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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