Contacts of the helix formed by residues 371 - 394 (chain E) in PDB entry 5KRA
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 THR 371 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369E ASP 5.6 0.2 - - - +
370E LEU* 1.3 78.6 - - - +
372E LEU* 1.3 65.8 + - - +
373E HIS* 3.8 6.9 + - - +
374E ASP* 3.2 32.1 + - - +
375E GLN* 3.0 21.4 + - - +
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Residues in contact with LEU 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370E LEU 3.9 0.2 + - - -
371E THR* 1.3 74.9 - - - +
373E HIS* 1.3 68.4 + - + +
375E GLN* 3.3 13.7 + - - +
376E VAL* 3.0 34.3 + - + +
691G HIS* 4.0 24.7 - - + +
694G LEU* 3.7 34.3 - - + +
695G GLN* 3.3 40.2 - - + +
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Residues in contact with HIS 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371E THR* 3.2 7.0 + - - +
372E LEU* 1.3 90.5 - - + +
374E ASP* 1.3 62.0 + - - +
376E VAL* 3.5 8.3 + - - +
377E HIS* 3.1 26.0 + - - +
691G HIS* 4.7 17.1 - + - -
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Residues in contact with ASP 374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370E LEU* 4.3 18.5 - - + +
371E THR* 3.2 26.7 + - - +
373E HIS* 1.3 81.6 - - - +
375E GLN* 1.3 64.8 + - - +
377E HIS* 3.4 1.2 + - - +
378E LEU* 3.1 30.7 + - - +
461E PHE* 3.2 38.1 - - + -
475E ILE* 5.5 1.8 - - + +
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Residues in contact with GLN 375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362E LYS* 5.7 1.7 - - - +
367E PHE* 3.1 57.6 + - + +
368E VAL* 3.4 20.0 + - - +
370E LEU* 3.0 25.4 + - + +
371E THR 3.0 16.7 + - - +
372E LEU* 3.6 20.8 - - - +
374E ASP* 1.3 75.7 - - - +
376E VAL* 1.3 63.8 + - - +
378E LEU 3.5 0.2 + - - -
379E LEU* 3.2 24.4 + - - +
694G LEU* 3.8 27.4 - - + +
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Residues in contact with VAL 376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372E LEU* 3.0 19.7 + - + +
373E HIS* 3.6 10.1 - - - +
374E ASP 3.2 0.2 - - - -
375E GLN* 1.3 76.3 - - - +
377E HIS* 1.3 57.1 + - - +
379E LEU 3.3 1.7 + - - -
380E GLU* 2.8 55.5 + - - +
688G LYS* 3.6 15.9 - - - +
690G LEU* 3.6 19.8 - - + +
691G HIS* 3.7 30.3 - - + +
694G LEU* 3.7 17.3 - - + -
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Residues in contact with HIS 377 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373E HIS 3.1 14.2 + - - +
374E ASP 3.8 0.4 - - - +
375E GLN 3.4 0.2 - - - -
376E VAL* 1.3 81.1 - - - +
378E LEU* 1.3 62.3 + - - +
380E GLU* 3.2 12.7 + - - +
381E CYS* 3.0 26.9 + - + +
457E GLY* 2.9 24.5 + - - -
460E THR* 2.6 45.3 + - - -
461E PHE* 3.3 30.3 - + + -
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Residues in contact with LEU 378 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367E PHE* 3.9 13.2 - - + -
370E LEU* 3.7 30.1 - - + -
374E ASP 3.1 17.2 + - - +
375E GLN 3.9 3.4 - - - +
377E HIS* 1.3 76.2 - - - +
379E LEU* 1.3 58.2 + - - +
381E CYS* 3.3 4.6 + - - +
382E ALA* 3.0 32.7 + - - +
453E LEU* 3.4 27.5 - - + +
454E LEU* 3.9 25.6 - - + +
457E GLY* 3.9 30.0 + - - +
458E VAL 4.0 0.7 - - - +
461E PHE* 3.9 13.7 - - + -
475E ILE* 4.3 6.7 - - + -
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Residues in contact with LEU 379 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357E MET* 4.1 28.3 - - + +
358E ILE* 4.3 11.2 - - + -
361E ALA* 4.0 16.4 - - + -
367E PHE* 4.0 11.0 - - + -
375E GLN 3.2 16.8 + - - +
376E VAL 3.8 2.7 - - - +
378E LEU* 1.3 75.9 - - - +
380E GLU* 1.3 66.1 + - - +
382E ALA* 5.2 0.2 - - - -
383E TRP* 3.1 31.9 + - - +
386E ILE* 4.7 1.3 - - + -
453E LEU* 3.7 19.5 - - + -
543E MET* 3.3 6.4 - - + +
690G LEU* 4.1 18.8 - - + -
694G LEU* 3.8 34.3 - - + -
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Residues in contact with GLU 380 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376E VAL* 2.8 31.3 + - - +
377E HIS* 3.6 12.6 + - - +
379E LEU* 1.3 76.9 - - - +
381E CYS* 1.3 50.9 + - - +
383E TRP* 3.2 8.5 - - - -
542E GLU 4.8 3.3 - - - +
543E MET* 3.8 14.9 - - - +
546E ALA* 3.6 28.9 - - + +
547E HIS* 2.7 34.1 + - - -
688G LYS* 2.9 34.5 + - - -
690G LEU* 3.7 13.8 - - + +
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Residues in contact with CYS 381 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377E HIS* 3.0 21.4 + - + +
378E LEU 3.8 3.4 - - - +
380E GLU* 1.3 79.6 - - - +
382E ALA* 1.3 57.5 + - - +
383E TRP 3.7 0.4 - - - -
384E LEU 5.3 0.5 + - - -
385E GLU* 4.1 8.8 - - - +
456E SER* 3.3 29.2 - - - -
457E GLY* 3.8 14.8 - - - +
460E THR* 5.0 5.8 - - - -
515E ARG* 4.1 10.9 + - - -
518E SER* 5.0 2.8 + - - -
522E MET* 5.6 0.2 - - - +
547E HIS* 3.4 24.8 + - - -
516F HIS* 5.3 7.9 - - - -
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Residues in contact with ALA 382 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378E LEU 3.0 16.2 + - - +
381E CYS* 1.3 79.4 - - - +
383E TRP* 1.3 64.3 + - - +
384E LEU 3.3 2.7 - - - -
385E GLU* 3.2 10.8 + - - +
386E ILE* 3.0 29.4 + - + +
452E ILE* 3.7 30.3 - - + +
453E LEU* 4.2 8.7 - - - +
456E SER* 3.8 9.4 - - - -
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Residues in contact with TRP 383 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354E LEU* 4.0 20.0 - - + -
357E MET* 3.2 24.1 - - - +
379E LEU 3.1 15.8 + - - +
380E GLU 3.2 24.8 + - - -
382E ALA* 1.3 77.2 - - - +
384E LEU* 1.3 78.3 + - + +
386E ILE* 3.4 0.6 + - - -
387E LEU* 3.0 52.7 + - + +
522E MET* 3.7 34.1 - - + +
525E LEU* 3.7 21.5 - - + -
540E LEU* 3.6 27.8 - - + -
543E MET* 3.3 53.5 + - + -
544E LEU* 4.6 2.9 - - - -
547E HIS* 4.2 1.8 - - - -
601E 6WS 4.5 2.7 - - + -
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Residues in contact with LEU 384 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381E CYS 5.3 0.6 + - - -
382E ALA 3.3 0.4 - - - -
383E TRP* 1.3 102.3 - - + +
385E GLU* 1.3 61.1 + - - +
387E LEU* 3.3 3.3 + - + +
388E MET* 2.9 57.8 + - + +
518E SER* 3.3 39.9 + - - +
521E GLY 3.8 6.5 - - - +
522E MET* 3.6 35.4 - - + +
525E LEU* 4.9 2.7 - - + -
601E 6WS 4.4 25.1 - - + -
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Residues in contact with GLU 385 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381E CYS 4.1 7.6 - - - +
382E ALA* 3.2 11.2 + - - +
384E LEU* 1.3 77.2 - - - +
386E ILE* 1.3 57.8 + - - +
388E MET* 3.2 4.1 + - - +
389E ILE* 2.8 33.5 + - - +
452E ILE* 3.6 17.6 - - + +
456E SER* 2.7 34.0 + - - -
511E LEU* 4.1 3.8 - - - +
514E ILE* 4.0 18.2 - - + +
515E ARG* 3.4 42.2 + - - +
518E SER* 3.5 25.1 + - - +
512F SER* 4.8 1.4 + - - -
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Residues in contact with ILE 386 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357E MET* 3.7 33.4 - - + -
360E TRP* 3.7 26.2 - - + -
379E LEU* 4.7 0.7 - - + -
382E ALA* 3.0 25.4 + - + +
383E TRP* 3.7 4.9 - - - +
385E GLU* 1.3 73.2 - - - +
387E LEU* 1.3 65.9 + - + +
389E ILE* 3.3 8.6 - - - +
390E GLY* 3.1 19.4 + - - -
449E LYS* 3.9 28.2 - - + +
452E ILE* 4.2 12.3 - - + -
453E LEU* 4.2 22.0 - - + -
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Residues in contact with LEU 387 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350E ALA* 4.3 24.2 - - + +
353E GLU* 3.6 43.8 - - + +
354E LEU* 4.7 2.0 - - + +
357E MET* 3.7 16.8 - - + -
383E TRP* 3.0 49.4 + - + +
384E LEU* 3.3 9.6 + - + +
386E ILE* 1.3 75.9 - - + +
388E MET* 1.3 58.0 + - - +
390E GLY* 3.5 1.2 + - - -
391E LEU* 3.0 28.1 + - - +
394E ARG* 5.2 0.3 + - - -
601E 6WS 3.8 25.6 - - + +
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Residues in contact with MET 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384E LEU* 2.9 41.1 + - + +
385E GLU* 3.6 4.5 - - - +
387E LEU* 1.3 74.8 - - - +
389E ILE* 1.3 60.5 + - - +
391E LEU* 3.1 6.8 + - - +
392E VAL* 2.8 34.8 + - - +
424E ILE* 4.2 9.2 - - + -
428E LEU* 4.1 18.8 - - + +
514E ILE* 4.7 3.6 - - + +
517E MET* 3.6 35.7 - - + +
518E SER* 3.7 23.6 - - - -
521E GLY* 4.2 2.7 - - - -
601E 6WS 4.0 34.8 - - + -
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Residues in contact with ILE 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385E GLU 2.8 23.4 + - - +
386E ILE* 3.3 15.3 - - - +
388E MET* 1.3 73.9 - - - +
390E GLY* 1.3 60.9 + - - +
392E VAL* 3.9 5.9 - - - +
393E TRP* 3.0 27.4 + - - +
435E PHE* 4.2 15.2 - - + -
445E PHE* 3.4 13.4 - - + -
448E LEU* 4.0 24.7 - - + -
449E LYS* 4.1 21.1 - - + +
452E ILE* 3.7 24.2 - - + -
511E LEU* 4.7 1.1 - - + -
514E ILE* 3.8 26.2 - - + +
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Residues in contact with GLY 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386E ILE 3.1 14.1 + - - -
387E LEU 3.8 3.4 - - - -
389E ILE* 1.3 77.7 - - - +
391E LEU* 1.3 63.7 - - - +
393E TRP* 3.3 4.6 + - - +
394E ARG* 3.2 38.4 + - - +
445E PHE* 3.9 16.6 - - - -
449E LYS* 5.4 2.2 - - - -
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Residues in contact with LEU 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387E LEU 3.0 14.9 + - - +
388E MET* 3.4 8.1 - - + +
390E GLY* 1.3 76.3 - - - +
392E VAL* 1.3 58.4 + - - +
394E ARG* 3.6 16.3 + - - +
395E SER* 2.5 38.0 + - - +
402E LEU* 4.3 9.4 - - + -
403E LEU 3.4 33.7 - - - +
404E PHE* 3.6 42.0 - - + +
428E LEU* 3.7 31.0 - - + -
601E 6WS 4.4 13.2 - - + -
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Residues in contact with VAL 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388E MET 2.8 20.2 + - - +
389E ILE* 3.9 7.0 - - - +
391E LEU* 1.3 77.7 - - + +
393E TRP* 1.3 60.1 + - - +
395E SER* 3.2 12.9 + - - -
396E MET* 3.4 3.6 + - - +
402E LEU* 5.3 1.1 - - + -
428E LEU* 3.7 39.3 - - + +
431E THR* 3.8 14.1 - - + -
432E SER* 3.3 35.5 + - - +
435E PHE* 3.5 31.2 - - + -
514E ILE* 6.2 0.2 - - + -
517E MET* 4.8 2.2 - - + -
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Residues in contact with TRP 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323E GLU* 5.4 2.1 + - - -
389E ILE 3.0 19.5 + - - +
390E GLY* 3.3 5.4 + - - +
392E VAL* 1.3 78.4 - - - +
394E ARG* 1.3 67.6 + - + +
395E SER 3.2 3.6 + - - -
396E MET* 3.3 50.4 + - + +
435E PHE* 4.9 2.9 - - + -
440E LEU* 3.2 40.2 - - + -
441E GLN* 4.1 4.5 - - - -
442E GLY* 3.4 32.1 - - - -
445E PHE* 3.4 40.8 - + + -
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Residues in contact with ARG 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326E ILE* 4.4 37.8 - - + +
353E GLU* 3.1 32.6 + - - -
387E LEU 5.2 0.6 + - - -
390E GLY* 3.2 30.2 + - - +
391E LEU* 3.7 14.5 - - - +
393E TRP* 1.3 86.6 - - + +
395E SER* 1.3 57.4 + - - +
396E MET 3.3 2.2 - - - -
397E GLU* 4.9 0.9 + - - +
398E HIS* 4.0 7.3 + - - -
403E LEU* 2.8 55.3 + - + +
404E PHE 3.2 18.5 + - - -
601E 6WS 3.5 15.8 - - - +
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il