Contacts of the helix formed by residues 429 - 452 (chain B) in PDB entry 2CSX
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 LYS 429 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B LEU* 3.3 32.7 + - + +
425B ASN* 6.0 0.7 - - - -
427B GLU* 3.2 29.8 - - + +
428B ARG* 1.3 74.5 - - - +
430B LYS* 1.3 62.5 + - - +
431B GLU* 3.0 6.2 + - - -
432B GLU* 3.1 17.1 + - + -
433B LEU* 3.1 10.9 + - - +
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Residues in contact with LYS 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ASN* 4.3 20.8 + - - +
428B ARG* 2.9 67.1 + - - +
429B LYS* 1.3 70.2 - - - +
431B GLU* 1.3 69.2 + - - +
433B LEU* 3.9 8.9 - - + +
434B GLN* 3.3 34.9 + - + +
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ALA* 6.1 0.5 - - - +
428B ARG 5.3 0.2 - - - +
429B LYS* 3.0 2.4 + - - -
430B LYS* 1.3 83.5 + - - +
432B GLU* 1.3 66.0 + - - +
433B LEU 2.8 6.1 + - - -
434B GLN* 3.2 18.5 + - - +
435B LYS* 3.7 10.2 + - - +
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Residues in contact with GLU 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B LEU* 3.2 33.9 - - + -
429B LYS* 3.1 10.4 + - + +
431B GLU* 1.3 78.0 - - - +
433B LEU* 1.3 56.4 + - - +
435B LYS* 3.8 13.4 - - - +
436B VAL* 2.8 36.0 + - - +
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Residues in contact with LEU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 3.8 13.5 - - + -
366B LEU* 3.3 27.8 - - + -
421B PRO* 3.6 27.4 - - + +
424B LEU* 3.5 22.6 - - + +
425B ASN* 3.9 21.5 - - + +
429B LYS 3.1 12.8 + - - +
430B LYS* 3.9 10.1 - - + +
431B GLU 2.8 1.8 + - - -
432B GLU* 1.3 75.0 - - - +
434B GLN* 1.3 53.8 + - - +
435B LYS 2.3 19.6 + - - -
436B VAL* 3.2 11.1 + - + -
437B LEU* 3.2 37.4 + - + +
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Residues in contact with GLN 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LEU* 4.2 26.0 - - + +
369B GLU 5.2 3.6 - - - +
370B VAL* 4.7 0.2 - - - -
371B SER* 2.4 50.7 + - - +
372B GLY* 3.7 9.0 - - - -
373B ALA 5.6 0.2 - - - +
430B LYS* 3.3 22.6 + - + +
431B GLU* 3.2 9.5 + - - +
433B LEU* 1.3 74.6 - - - +
435B LYS* 1.3 57.0 + - - +
438B TYR* 2.8 16.6 - - - +
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Residues in contact with LYS 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ALA* 2.8 37.1 - - + +
374B ARG 3.4 28.9 + - - -
375B ASP* 3.7 20.9 + - + +
377B GLU* 4.9 8.1 + - - -
431B GLU 3.7 7.1 + - - +
432B GLU* 3.8 18.4 - - - +
433B LEU 2.3 16.6 + - - -
434B GLN* 1.3 67.4 - - - +
436B VAL* 1.3 53.7 + - + +
437B LEU 2.7 5.2 + - - -
438B TYR* 2.5 25.9 + - - +
439B ALA* 2.7 17.6 + - + +
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Residues in contact with VAL 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B TYR* 3.4 28.5 - - + +
419B LYS* 3.3 37.0 - - + +
421B PRO* 4.2 11.6 - - + +
424B LEU* 3.4 20.6 - - + -
432B GLU* 2.8 31.4 - - - +
433B LEU* 3.6 7.4 - - + +
435B LYS* 1.3 73.5 - - - +
437B LEU* 1.3 54.1 + - - +
439B ALA* 3.9 1.1 - - - -
440B LEU* 2.7 37.2 + - + +
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Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B VAL* 4.9 7.0 - - + +
361B MET* 4.0 33.7 - - + -
362B ALA* 4.6 8.2 - - + +
365B PHE* 4.1 11.0 - - + -
366B LEU* 3.4 30.7 - - + -
370B VAL* 3.3 15.5 - - + +
421B PRO* 4.0 9.9 - - + -
433B LEU* 3.2 37.6 + - + +
435B LYS 2.7 4.6 + - - -
436B VAL* 1.3 74.3 - - - +
438B TYR* 1.3 53.1 + - - +
439B ALA 3.1 4.9 - - - -
440B LEU* 3.5 9.0 - - + +
441B VAL* 2.8 36.6 + - - +
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Residues in contact with TYR 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B VAL* 3.0 19.5 - - + +
371B SER* 3.5 17.5 - - - +
372B GLY 3.5 26.5 - - - -
373B ALA 3.7 10.8 - - - -
374B ARG* 4.8 2.0 - - + -
434B GLN 2.8 22.4 + - - +
435B LYS* 2.5 10.1 + - - +
437B LEU* 1.3 72.4 - - - +
439B ALA* 1.3 56.1 + - - +
441B VAL* 3.6 2.2 - - - -
442B ASP* 3.3 19.1 + - - +
478B TYR* 3.0 39.6 + + - +
480B LYS 2.6 29.2 + - - -
481B ASN* 3.1 30.0 - - - +
483B TYR* 4.3 16.8 - + - -
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Residues in contact with ALA 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ASP* 4.5 5.6 - - + -
378B TYR* 3.5 21.7 - - + -
412B LEU* 4.5 0.3 - - - +
415B TYR* 4.1 20.9 - - + +
435B LYS* 2.7 12.2 + - + +
436B VAL 4.1 2.9 - - - +
438B TYR* 1.3 77.3 - - - +
440B LEU* 1.3 61.4 + - + +
443B GLY* 2.6 31.2 + - - -
478B TYR* 3.4 25.6 - - + +
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Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B VAL* 3.5 29.2 - - + +
378B TYR* 6.4 0.7 - - + -
412B LEU* 3.9 24.3 - - + +
415B TYR* 3.3 31.9 - - + -
416B VAL* 3.2 35.9 - - + -
421B PRO* 5.8 2.9 - - + -
436B VAL* 2.7 26.9 - - + +
437B LEU* 3.1 10.9 + - + +
439B ALA* 1.3 80.8 - - + +
441B VAL* 1.3 65.7 + - - +
442B ASP 3.1 1.3 - - - -
443B GLY* 3.0 10.2 + - - -
444B LEU* 3.0 17.5 + - - +
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Residues in contact with VAL 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B VAL* 4.0 4.8 - - + +
362B ALA* 5.6 0.2 - - + -
370B VAL* 3.7 17.3 - - + -
437B LEU 2.8 24.6 + - - +
438B TYR* 3.6 14.6 - - - -
440B LEU* 1.3 73.9 - - - +
442B ASP* 1.3 64.1 + - - +
444B LEU* 3.3 14.6 - - - +
445B PHE* 3.3 17.7 + - - +
466B LEU* 4.2 9.4 - - + +
483B TYR* 3.3 33.1 - - + -
485B LEU* 3.5 35.9 - - + -
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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
----------------------------------------------------------
378B TYR* 2.3 30.6 + - - +
438B TYR 3.3 18.4 - - - +
439B ALA* 3.6 3.1 + - - +
440B LEU 3.1 0.6 - - - -
441B VAL* 1.3 76.4 - - - +
443B GLY* 1.3 63.6 + - - +
444B LEU 2.9 6.3 + - - -
445B PHE* 2.9 12.3 + - - +
446B VAL* 2.9 12.7 + - - +
477B PRO* 2.8 34.8 - - - +
478B TYR* 3.1 18.7 - - + -
480B LYS 4.5 0.2 - - - +
483B TYR* 2.7 33.9 + - + -
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Residues in contact with GLY 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B TYR* 3.2 17.2 + - - -
408B PHE* 3.6 12.8 - - - -
412B LEU* 3.6 21.6 - - - +
439B ALA 2.6 21.2 + - - -
440B LEU 3.0 5.1 + - - -
442B ASP* 1.3 72.7 - - - +
444B LEU* 1.3 56.1 + - - +
446B VAL* 4.0 0.7 - - - -
447B LEU* 3.3 23.0 + - - +
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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
----------------------------------------------------------
354B LEU* 4.3 17.9 - - + +
355B TYR* 3.6 43.0 + - + +
358B VAL* 4.0 25.6 - - + -
359B VAL* 4.2 15.3 - - + -
412B LEU* 6.0 0.9 - - + -
440B LEU 3.0 15.0 + - - +
441B VAL* 3.3 9.9 - - + +
442B ASP 2.9 0.4 - - - -
443B GLY* 1.3 76.6 - - - +
445B PHE* 1.3 57.6 + - - +
446B VAL 3.0 1.3 - - - -
447B LEU* 2.8 7.1 + - + +
448B THR* 2.6 36.6 + - - +
466B LEU* 3.4 31.0 - - + -
485B LEU* 5.8 0.7 - - + -
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Residues in contact with PHE 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B VAL 3.3 7.6 + - - +
442B ASP* 2.9 9.1 + - - +
444B LEU* 1.3 78.2 - - - +
446B VAL* 1.3 58.0 + - + +
448B THR* 2.7 14.2 - - + +
449B HIS* 2.6 55.5 - + - -
463B LEU* 3.9 10.8 - - + -
466B LEU* 3.6 17.2 - - + +
468B GLU* 3.3 42.8 - - + -
470B GLU 4.4 10.5 - - - -
472B LEU* 4.2 15.9 - - + -
479B SER* 3.4 26.2 - - - -
480B LYS* 4.5 10.1 - - + -
483B TYR* 3.8 20.2 - + + +
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Residues in contact with VAL 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B TYR* 4.2 4.3 - - - +
382B ALA* 5.0 6.3 - - + +
385B SER* 6.2 0.2 - - - -
386B ILE* 4.3 22.2 - - + -
408B PHE* 3.5 25.6 - - + -
442B ASP* 2.9 28.9 + - - +
443B GLY 3.9 4.5 - - - +
445B PHE* 1.3 79.3 - - + +
447B LEU* 1.3 63.7 + - - +
449B HIS* 3.3 9.4 + - - +
450B LEU* 2.9 36.4 + - + +
475B LEU* 4.8 2.6 - - + +
476B LYS 4.7 3.8 - - - +
477B PRO* 4.2 23.8 - - + +
479B SER* 5.8 0.9 - - - +
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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
----------------------------------------------------------
351B ILE* 4.5 5.6 - - + -
354B LEU* 4.0 17.9 - - + -
355B TYR* 3.9 26.0 - - + +
405B ILE* 3.6 25.4 - - + +
408B PHE* 4.4 4.9 - - + -
409B THR* 3.3 37.2 - - + -
412B LEU* 5.9 0.4 - - + -
443B GLY 3.3 12.2 + - - +
444B LEU* 2.8 11.7 + - + +
446B VAL* 1.3 79.3 - - - +
448B THR* 1.3 62.8 + - - +
450B LEU* 3.0 18.4 + - + +
451B LEU* 2.9 28.0 + - + +
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Residues in contact with THR 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B TYR* 3.0 21.8 + - - -
444B LEU 2.6 18.0 + - - +
445B PHE* 2.7 39.0 - - + +
447B LEU* 1.3 70.0 - - - +
449B HIS* 1.3 60.6 + - + +
451B LEU 3.3 0.5 + - - -
452B TYR* 2.9 27.2 + - - +
459B MET* 3.1 34.2 + - - +
462B ALA* 4.0 7.0 - - - +
463B LEU* 4.3 6.7 + - + +
466B LEU* 3.8 11.7 - - + -
471B PHE* 3.8 10.4 - - - -
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Residues in contact with HIS 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.6 8.4 - - + +
389B TYR* 4.4 0.7 + - - -
445B PHE* 2.6 55.7 + + - -
446B VAL* 3.5 8.1 - - - +
447B LEU 3.2 0.6 - - - -
448B THR* 1.3 81.5 - - + +
450B LEU* 1.3 67.9 + - - +
451B LEU 3.0 1.0 + - - -
452B TYR* 3.1 16.8 + - - +
453B PRO* 3.4 10.0 - - - +
463B LEU* 5.1 0.6 - - - +
471B PHE* 3.7 21.9 - + + +
472B LEU* 2.9 44.9 + - + -
474B GLU 4.9 0.9 - - - -
475B LEU* 3.7 36.3 - - + +
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Residues in contact with LEU 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B SER* 5.3 3.8 - - - +
386B ILE* 4.3 15.7 - - + +
389B TYR* 2.6 56.9 + - + -
404B GLU 5.8 0.2 - - - +
405B ILE* 3.1 27.2 - - + +
408B PHE* 3.7 20.2 - - + -
446B VAL* 2.9 37.6 + - + +
447B LEU* 3.3 15.3 - - + +
449B HIS* 1.3 75.9 - - - +
451B LEU* 1.3 58.3 + - - +
453B PRO* 3.8 1.6 - - - +
454B ILE* 4.5 4.0 - - - +
475B LEU* 3.5 22.4 - - + -
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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
----------------------------------------------------------
320B TYR* 5.0 6.3 - - + -
347B LEU* 5.5 0.7 - - + -
351B ILE* 3.8 39.7 - - + -
402B ILE* 6.1 0.7 - - + -
405B ILE* 3.8 29.6 - - + -
447B LEU* 2.9 19.8 + - + +
450B LEU* 1.3 76.7 - - - +
452B TYR* 1.3 64.5 + - - +
453B PRO* 3.3 3.4 - - - -
454B ILE* 3.1 30.2 + - + +
455B THR* 2.9 33.4 + - + +
459B MET* 3.6 33.0 - - + -
492B PHE* 5.1 2.0 - - + -
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Residues in contact with TYR 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 2.8 52.2 + - + +
39B ARG* 5.8 3.9 - - + +
40B LEU* 3.5 28.5 - - + -
90B GLU* 4.9 3.6 + - - -
448B THR 2.9 15.8 + - - +
449B HIS 3.6 7.4 - - - +
451B LEU* 1.3 71.8 - - - +
453B PRO* 1.3 70.5 - - + +
456B PRO* 2.8 57.1 - - + +
459B MET* 3.7 9.4 - - + -
460B LYS* 4.3 14.9 + - - -
471B PHE* 3.4 39.0 - + + -
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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
------------------------------------------------------------
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