Contacts of the helix formed by residues 431 - 457 (chain B) in PDB entry 4Z2C
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 GLY 431 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A ARG 4.1 8.7 + - - -
397A SER 3.8 8.0 + - - -
398A GLU* 5.7 1.6 - - - -
430B THR* 1.3 75.9 - - - +
432B LEU* 1.3 60.9 + - - +
433B GLU 3.1 5.6 + - - -
434B ARG* 3.6 14.7 + - - +
435B ASP* 4.5 2.1 + - - +
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Residues in contact with LEU 432 (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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398A GLU* 4.8 19.8 + - + +
430B THR* 4.2 2.7 + - - +
431B GLY* 1.3 73.0 - - - +
433B GLU* 1.3 63.4 + - - +
434B ARG 3.4 0.7 - - - -
435B ASP* 3.6 9.8 + - + +
436B LYS* 3.5 18.9 + - - +
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Residues in contact with GLU 433 (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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384B LEU* 4.9 0.4 - - + -
427B ARG 5.2 1.0 - - - +
428B ARG* 3.3 68.6 + - + +
430B THR* 3.5 22.7 + - - +
431B GLY 3.1 1.2 - - - -
432B LEU* 1.3 76.6 - - - +
434B ARG* 1.3 65.2 + - - +
436B LYS* 3.3 14.7 + - - +
437B ILE* 3.1 39.4 + - + +
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Residues in contact with ARG 434 (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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381B LEU* 3.8 27.9 + - - +
384B LEU* 3.8 27.9 - - + +
385B ASP* 2.5 49.4 + - - -
430B THR 4.6 3.5 + - - +
431B GLY 3.6 10.4 + - - +
432B LEU 3.4 0.2 - - - -
433B GLU* 1.3 78.9 - - - +
435B ASP* 1.3 60.4 + - + +
437B ILE* 3.2 7.0 + - - +
438B GLN* 3.0 65.8 + - - +
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Residues in contact with ASP 435 (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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431B GLY 4.5 1.7 + - - +
432B LEU* 3.6 13.1 + - - +
433B GLU 3.3 0.4 - - - -
434B ARG* 1.3 80.0 - - + +
436B LYS* 1.3 60.3 - - - +
438B GLN* 3.1 10.3 + - - +
439B SER* 2.9 28.8 + - - -
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Residues in contact with LYS 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B LEU 3.5 10.0 + - - +
433B GLU* 3.3 21.2 + - - +
435B ASP* 1.3 77.7 - - - +
437B ILE* 1.3 58.7 + - + +
439B SER* 2.4 27.0 + - - +
440B GLU* 2.9 17.9 + - + +
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Residues in contact with ILE 437 (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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377B LEU* 3.6 30.8 - - + +
380B LEU* 4.5 20.0 - - + -
381B LEU* 3.6 20.6 - - + -
384B LEU* 3.7 28.0 - - + -
424B MET* 5.7 2.7 - - + -
428B ARG* 5.0 10.1 - - - +
433B GLU* 3.1 28.4 + - + +
434B ARG 3.4 7.2 - - - +
435B ASP 3.2 0.2 - - - -
436B LYS* 1.3 76.0 - - + +
438B GLN* 1.3 58.3 + - - +
440B GLU* 3.4 11.8 + - - +
441B TYR* 2.9 27.7 + - - +
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Residues in contact with GLN 438 (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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381B LEU* 4.1 15.5 - - + +
434B ARG* 3.0 51.3 + - - +
435B ASP* 3.1 12.8 + - - +
437B ILE* 1.3 75.7 - - - +
439B SER* 1.3 56.5 + - - +
441B TYR* 3.1 14.5 + - - +
442B ASP* 2.9 53.9 + - - +
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Residues in contact with SER 439 (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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435B ASP 2.9 9.9 + - - -
436B LYS* 2.4 31.6 + - - +
438B GLN* 1.3 73.4 - - - +
440B GLU* 1.3 65.3 + - - +
442B ASP* 3.2 10.2 + - - +
443B ASP* 3.0 34.1 + - - +
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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
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373B ARG* 3.1 37.7 + - - +
377B LEU* 3.6 19.8 - - + +
436B LYS* 2.9 14.4 + - + +
437B ILE* 3.7 10.7 - - - +
439B SER* 1.3 82.6 + - - +
441B TYR* 1.3 57.2 + - - +
443B ASP* 3.6 7.8 + - - +
444B LEU* 2.9 34.7 + - + +
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Residues in contact with TYR 441 (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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374B ALA* 3.5 28.0 - - + -
377B LEU* 4.1 16.1 - - + +
378B GLU* 2.8 44.7 + - + +
381B LEU* 4.5 12.6 - - + -
437B ILE 2.9 18.4 + - - +
438B GLN* 3.3 17.0 - - - +
440B GLU* 1.3 73.8 - - - +
442B ASP* 1.3 70.0 + - - +
444B LEU* 3.2 7.4 + - - +
445B LEU* 2.9 55.9 + - + +
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Residues in contact with ASP 442 (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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438B GLN* 2.9 41.0 + - - +
439B SER* 3.2 9.0 + - - +
441B TYR* 1.3 82.3 - - - +
443B ASP* 1.3 66.6 + - - +
445B LEU* 2.9 23.4 + - - +
446B ALA* 3.0 13.3 + - - +
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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
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439B SER* 3.0 25.7 + - - +
440B GLU* 3.7 7.3 - - - +
442B ASP* 1.3 75.4 - - - +
444B LEU* 1.3 57.3 + - - +
446B ALA* 3.3 8.2 + - - +
447B LEU* 2.9 29.5 + - - +
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Residues in contact with LEU 444 (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 ALA* 3.7 33.0 - - + +
373B ARG* 3.5 31.2 - - + -
374B ALA* 3.5 29.8 - - + +
377B LEU* 4.0 9.0 - - + -
440B GLU* 2.9 21.4 + - + +
441B TYR* 3.2 10.8 - - - +
442B ASP 3.1 0.2 - - - -
443B ASP* 1.3 77.8 - - - +
445B LEU* 1.3 57.4 + - - +
447B LEU* 3.3 15.6 + - + +
448B ILE* 2.9 36.7 + - + +
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Residues in contact with LEU 445 (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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374B ALA* 5.4 2.5 - - + -
441B TYR* 2.9 58.1 + - + +
442B ASP* 2.9 15.1 + - - +
444B LEU* 1.3 78.6 - - - +
446B ALA* 1.3 62.5 + - - +
448B ILE* 3.3 17.5 + - + +
449B ALA* 2.9 23.5 + - - +
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Residues in contact with ALA 446 (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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442B ASP 3.0 10.3 + - - +
443B ASP* 3.6 11.2 - - - +
445B LEU* 1.3 75.7 - - - +
447B LEU* 1.3 63.5 + - - +
449B ALA* 3.2 9.3 + - - +
450B ASP* 3.0 23.1 + - - +
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Residues in contact with LEU 447 (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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366B ASP* 5.5 2.7 - - + +
370B ALA* 4.1 9.9 - - + -
443B ASP 2.9 14.7 + - - +
444B LEU* 3.4 28.5 - - + +
446B ALA* 1.3 75.8 - - - +
448B ILE* 1.3 57.3 + - - +
450B ASP* 3.0 11.6 + - + +
451B LEU* 2.9 59.7 + - + +
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Residues in contact with ILE 448 (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* 4.1 10.4 - - + +
370B ALA* 3.7 23.3 - - + +
371B GLU* 3.6 51.8 - - + +
374B ALA* 4.2 13.2 - - + -
444B LEU 2.9 26.2 + - - +
445B LEU* 3.7 14.6 - - + +
447B LEU* 1.3 71.5 - - - +
449B ALA* 1.3 64.8 + - - +
451B LEU* 3.3 8.4 + - - +
452B ALA* 2.9 26.0 + - + +
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Residues in contact with ALA 449 (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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445B LEU 2.9 14.0 + - - +
446B ALA* 3.2 12.3 + - - +
448B ILE* 1.3 77.9 - - - +
450B ASP* 1.3 56.5 + - - +
452B ALA* 3.4 5.8 + - - +
453B ASP* 2.9 29.5 + - - +
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Residues in contact with ASP 450 (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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446B ALA 3.0 12.6 + - - +
447B LEU* 3.0 13.2 + - + +
449B ALA* 1.3 78.2 - - - +
451B LEU* 1.3 59.1 + - + +
453B ASP* 3.3 5.3 + - - +
454B ILE* 2.9 32.2 + - - +
460B ARG* 2.7 39.8 + - - -
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Residues in contact with LEU 451 (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 THR* 3.7 20.9 - - + +
366B ASP* 3.7 19.1 - - + +
367B LYS* 3.5 40.2 - - + +
370B ALA* 4.8 0.7 - - + -
447B LEU* 2.9 48.4 + - + +
448B ILE* 3.8 5.8 - - - +
450B ASP* 1.3 75.0 - - + +
452B ALA* 1.3 60.5 + - - +
454B ILE* 3.2 17.9 + - + +
455B LEU* 2.9 32.8 + - - +
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Residues in contact with ALA 452 (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* 3.8 23.2 - - - +
448B ILE* 2.9 19.1 + - + +
449B ALA* 3.7 6.5 - - - +
451B LEU* 1.3 75.6 - - - +
453B ASP* 1.3 58.0 + - - +
455B LEU* 3.2 5.7 + - - +
456B ALA* 2.9 29.5 + - - +
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Residues in contact with ASP 453 (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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449B ALA 2.9 14.5 + - - +
450B ASP* 3.4 10.8 - - - +
452B ALA* 1.3 76.8 - - - +
454B ILE* 1.3 61.1 + - - +
456B ALA* 3.2 8.8 + - - +
457B LYS* 3.1 26.5 + - - +
460B ARG* 2.7 28.0 + - - +
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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
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363B THR* 3.8 23.1 - - + +
450B ASP* 2.9 22.2 + - - +
451B LEU* 3.2 25.3 + - + +
453B ASP* 1.3 77.0 - - - +
455B LEU* 1.3 59.4 + - + +
457B LYS 2.9 24.4 - - - +
460B ARG* 3.4 35.9 - - + +
461B VAL* 3.8 25.5 - - + +
464B ILE* 3.7 26.5 - - + -
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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
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360B VAL* 4.0 23.8 - - + +
363B THR* 3.7 20.4 - - + -
364B ARG* 3.8 39.9 - - + +
367B LYS* 4.5 22.2 - - + +
451B LEU 2.9 19.4 + - - +
452B ALA* 3.2 6.3 + - - +
454B ILE* 1.3 77.3 - - + +
456B ALA* 1.3 58.6 + - - +
457B LYS 3.3 1.3 + - - -
458B PRO* 5.6 0.7 - - - +
461B VAL* 5.6 0.9 - - + -
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Residues in contact with ALA 456 (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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452B ALA 2.9 16.5 + - - +
453B ASP* 3.2 11.4 + - - +
455B LEU* 1.3 77.1 - - - +
457B LYS* 1.3 58.8 + - - +
458B PRO* 3.9 6.9 - - - +
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Residues in contact with LYS 457 (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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453B ASP* 3.1 17.5 + - - +
454B ILE 2.9 17.7 + - - +
455B LEU 3.3 1.0 - - - -
456B ALA* 1.3 82.0 - - - +
458B PRO* 1.3 67.6 - - - +
459B GLU* 4.6 4.7 - - + +
460B ARG* 3.3 26.2 + - + +
461B VAL* 3.6 5.0 + - - +
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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