Contacts of the helix formed by residues 364 - 392 (chain E) in PDB entry 6CP3
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 364 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E ALA* 3.3 20.9 + - - -
361E ALA 4.8 0.2 - - - -
362E VAL 3.2 5.7 + - - -
363E VAL* 1.3 94.2 - - - +
365E GLN* 1.3 65.5 + - - -
366E GLU 3.4 2.2 - - - -
367E HIS 4.3 0.7 - - - -
368E TYR 3.4 5.4 + - - -
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Residues in contact with GLN 365 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360E ALA* 3.9 17.9 + - - +
364E GLY* 1.3 70.1 - - - -
366E GLU* 1.3 60.7 + - - +
368E TYR* 3.3 11.8 + - - +
369E ASP* 2.9 66.0 + - - +
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Residues in contact with GLU 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364E GLY 3.4 0.4 - - - -
365E GLN* 1.3 79.6 - - - +
367E HIS* 1.3 56.6 + - - +
369E ASP* 3.4 7.4 + - - +
370E VAL* 3.0 36.4 + - + +
435E LYS* 5.8 1.4 + - - -
438E VAL* 4.3 16.9 - - + +
439E ALA* 5.3 3.6 + - - +
442E LYS* 2.6 46.4 + - + +
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Residues in contact with HIS 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E ILE* 6.2 1.0 - - + +
142E ASP 3.1 23.1 + - - -
143E LEU* 3.1 31.2 + - + +
146E PRO* 4.8 6.3 - - + +
358E LEU* 4.1 14.5 - - + +
363E VAL* 3.4 47.7 + - + +
364E GLY 3.9 0.8 + - - -
365E GLN 3.4 0.4 - - - -
366E GLU* 1.3 77.9 - - - +
368E TYR* 1.3 57.8 + - - +
370E VAL* 3.4 2.4 + - - +
371E ALA* 3.0 26.3 + - - +
434E LEU* 4.3 10.9 - - + +
435E LYS* 6.2 1.8 - - - +
438E VAL* 3.5 40.2 - - + +
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Residues in contact with TYR 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ARG* 4.9 13.0 + - - -
358E LEU* 3.6 40.4 - - + -
359E ASP* 4.5 4.9 - - - -
360E ALA* 3.7 31.6 - - + +
363E VAL* 3.9 6.0 - - + +
364E GLY 3.4 16.3 + - - +
365E GLN* 3.3 10.2 + - - +
366E GLU 3.3 0.6 - - - -
367E HIS* 1.3 76.4 + - - +
369E ASP* 1.3 66.0 + - - +
371E ALA* 3.5 2.6 + - - +
372E SER* 2.9 54.8 + - - -
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Residues in contact with ASP 369 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365E GLN* 2.9 50.4 + - - +
366E GLU* 3.7 7.6 - - - +
367E HIS 3.3 0.2 - - - -
368E TYR* 1.3 81.1 - - - +
370E VAL* 1.3 63.7 + - + +
372E SER* 3.3 5.3 + - - -
373E LYS* 3.0 42.9 + - + +
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Residues in contact with VAL 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E LEU* 4.3 11.4 - - + -
366E GLU* 3.0 23.3 + - + +
367E HIS* 3.9 5.2 - - - +
369E ASP* 1.3 75.9 - - + +
371E ALA* 1.3 58.4 + - - +
373E LYS* 4.8 0.7 - - - -
374E VAL* 3.0 28.7 + - + +
438E VAL* 4.3 10.8 - - + +
441E PHE* 3.8 25.4 - - + -
442E LYS* 3.8 36.6 - - + +
445E LEU* 3.4 22.9 - - + +
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Residues in contact with ALA 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E LEU* 3.9 17.0 - - + +
144E LEU* 4.3 8.2 - - + +
358E LEU* 3.8 33.0 - - + -
367E HIS* 3.0 17.5 + - + +
368E TYR 4.0 2.5 - - - +
370E VAL* 1.3 79.1 - - - +
372E SER* 1.3 57.3 + - - +
374E VAL* 3.6 6.9 - - - +
375E GLN* 2.9 34.1 + - - +
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Residues in contact with SER 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358E LEU* 5.8 1.0 - - - +
368E TYR* 2.9 54.1 + - - -
369E ASP* 3.3 6.3 + - - -
371E ALA* 1.3 76.5 - - - +
373E LYS* 1.3 64.9 + - - +
375E GLN* 3.4 8.2 + - - +
376E GLU* 3.0 38.8 + - - +
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Residues in contact with LYS 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369E ASP* 3.0 33.4 + - + +
372E SER* 1.3 81.2 - - - +
374E VAL* 1.3 53.2 + - - +
376E GLU* 3.5 15.5 + - - +
377E THR* 2.4 40.1 + - - +
445E LEU* 3.7 23.6 - - + -
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Residues in contact with VAL 374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E LEU* 4.4 16.4 - - + -
144E LEU* 3.8 22.9 - - + -
370E VAL* 3.0 23.4 + - + +
371E ALA* 3.6 7.0 - - - +
373E LYS* 1.3 77.5 - - - +
375E GLN* 1.3 57.8 + - - +
377E THR* 3.2 5.9 + - - -
378E LEU* 2.9 47.1 + - + +
410E ILE* 4.5 14.8 - - + -
414E LEU* 5.7 1.8 - - + -
441E PHE* 4.4 11.7 - - + -
445E LEU* 3.7 21.8 - - + -
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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
----------------------------------------------------------
144E LEU* 4.3 19.2 + - + +
350E PRO* 4.8 16.0 + - + +
351E LEU* 4.0 13.2 - - + +
353E SER 4.9 7.1 + - - -
354E LYS* 5.0 16.2 - - - +
358E LEU* 3.4 30.5 - - - +
371E ALA 2.9 18.3 + - - +
372E SER* 3.8 6.8 - - - +
373E LYS 3.4 0.2 - - - -
374E VAL* 1.3 75.3 - - - +
376E GLU* 1.3 59.6 + - + +
378E LEU* 3.8 2.9 - - - -
379E GLN* 2.9 29.7 + - - +
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Residues in contact with GLU 376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372E SER* 3.0 24.5 + - - +
373E LYS* 4.0 17.2 - - - +
375E GLN* 1.3 77.1 - - + +
377E THR* 1.3 57.2 + - - +
379E GLN* 3.5 7.4 - - + +
380E THR* 2.9 37.6 + - + +
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Residues in contact with THR 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 LYS* 2.4 25.5 + - - +
374E VAL* 3.2 8.0 + - - -
376E GLU* 1.3 76.7 - - - +
378E LEU* 1.3 58.8 + - + +
380E THR* 2.6 22.8 + - - +
381E TYR* 2.9 14.9 + - - +
403E THR* 4.4 9.4 - - + +
406E ARG* 4.8 6.7 - - + -
407E ALA* 3.8 25.6 - - + +
410E ILE* 4.0 18.8 - - + -
445E LEU* 4.0 9.7 - - + +
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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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350E PRO* 3.7 33.2 - - + -
351E LEU* 4.2 16.2 - - + +
374E VAL* 2.9 32.0 + - + +
375E GLN* 4.2 3.6 - - - +
377E THR* 1.3 74.7 - - + +
379E GLN* 1.3 59.9 + - - +
381E TYR* 3.4 12.6 + - + +
382E LYS* 2.9 30.3 + - - +
407E ALA* 4.1 28.5 - - + +
410E ILE* 4.3 15.7 - - + -
411E GLN* 4.6 13.7 - - + +
414E LEU* 4.4 5.6 - - + -
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Residues in contact with GLN 379 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B TYR* 5.0 9.4 + - - -
351E LEU* 3.3 27.2 - - + +
375E GLN 2.9 20.3 + - - +
376E GLU* 3.5 10.3 - - + +
377E THR 3.2 0.2 - - - -
378E LEU* 1.3 74.9 - - - +
380E THR* 1.3 61.9 + - + +
382E LYS* 3.3 7.2 + - - +
383E SER* 2.9 35.4 + - - +
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Residues in contact with THR 380 (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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376E GLU* 2.9 19.8 + - + +
377E THR* 2.6 25.6 + - - +
379E GLN* 1.3 73.4 - - + +
381E TYR* 1.3 58.3 + - - +
383E SER* 2.9 21.5 + - - +
384E LEU* 2.9 30.8 + - - +
403E THR* 4.9 12.8 - - - +
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Residues in contact with TYR 381 (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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377E THR 2.9 18.3 + - - +
378E LEU* 3.5 15.7 - - + +
379E GLN 3.2 0.2 - - - -
380E THR* 1.3 77.3 + - - +
382E LYS* 1.3 62.4 + - + +
384E LEU* 3.1 9.3 + - + +
385E GLN* 2.9 68.1 + - + +
403E THR 6.4 0.4 - - - -
404E VAL* 4.0 22.9 - - + +
407E ALA* 3.5 24.0 - - + -
408E ARG* 3.2 45.7 + - + +
411E GLN* 3.4 26.4 + - - -
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Residues in contact with LYS 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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339E ILE* 6.4 0.2 - - - +
349E ASP* 5.2 7.7 + - - -
351E LEU* 3.5 29.9 - - + +
378E LEU 2.9 17.4 + - - +
379E GLN* 3.7 8.5 - - - +
381E TYR* 1.3 79.3 - - - +
383E SER* 1.3 62.4 + - - +
384E LEU 3.4 0.3 + - - -
385E GLN* 3.4 25.1 + - + +
386E ASP* 4.6 5.5 + - - +
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Residues in contact with SER 383 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379E GLN* 2.9 21.9 + - - +
380E THR* 2.9 24.6 + - - +
382E LYS* 1.3 75.7 - - - +
384E LEU* 1.3 65.2 + - - +
386E ASP* 4.7 7.3 + - - +
387E ILE* 5.1 5.0 - - - +
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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
----------------------------------------------------------
380E THR* 2.9 26.6 + - - +
381E TYR* 3.7 6.5 - - + +
383E SER* 1.3 83.8 - - - +
385E GLN* 1.3 57.1 + - - +
386E ASP 2.9 6.6 + - - -
387E ILE* 3.0 30.9 + - + +
388E ILE* 2.9 36.5 + - + +
396E LEU* 4.4 15.0 - - + -
400E ASP* 4.7 8.1 - - + +
403E THR* 4.4 11.0 - - - +
404E VAL* 3.8 26.2 - - + -
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Residues in contact with GLN 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 TYR* 2.9 68.0 + - + +
382E LYS* 3.4 20.7 + - + +
384E LEU* 1.3 74.5 - - - +
386E ASP* 1.3 65.7 + - - +
388E ILE* 4.0 19.7 - - - +
389E ALA* 3.9 13.2 + - - +
408E ARG* 4.3 9.2 + - - +
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Residues in contact with ASP 386 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382E LYS 4.6 5.5 + - - +
383E SER 4.7 5.3 + - - +
384E LEU 2.9 1.2 + - - -
385E GLN* 1.3 80.2 - - - +
387E ILE* 1.3 65.4 + - + +
389E ALA* 3.1 9.5 + - - +
390E ILE* 3.0 37.1 + - + +
21G LYS* 5.8 1.9 + - - -
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Residues in contact with ILE 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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383E SER 5.3 3.8 - - - +
384E LEU* 3.0 41.2 + - + +
386E ASP* 1.3 78.0 - - + +
388E ILE* 1.3 62.3 + - + +
390E ILE* 3.6 19.3 - - + -
391E LEU* 2.9 48.0 + - + +
392E GLY 3.5 6.2 + - - +
395E GLU* 5.7 5.8 - - + -
396E LEU* 5.6 5.8 - - + -
234G ARG* 6.0 2.2 - - - +
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Residues in contact with ILE 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381E TYR* 6.4 0.2 - - + -
384E LEU* 2.9 32.0 + - + +
385E GLN* 4.1 21.5 - - - +
386E ASP 3.2 0.2 - - - -
387E ILE* 1.3 79.4 - - + +
389E ALA* 1.3 60.9 + - - +
392E GLY* 3.3 25.0 + - - +
393E MET* 4.8 13.0 - - + -
396E LEU* 4.0 33.7 - - + -
404E VAL* 4.2 18.6 - - + -
408E ARG* 4.2 20.0 - - - +
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Residues in contact with ALA 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385E GLN 3.9 7.3 + - - +
386E ASP* 3.1 10.9 + - - +
388E ILE* 1.3 79.0 - - + +
390E ILE* 1.3 68.7 + - + +
392E GLY 4.8 0.5 + - - -
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Residues in contact with ILE 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 ASP* 3.0 31.2 + - + +
387E ILE* 3.5 16.1 + - + -
389E ALA* 1.3 80.6 - - + +
391E LEU* 1.3 81.8 + - + +
24G LYS* 4.7 13.7 - - - +
25G ILE* 6.2 3.4 - - + -
28G SER* 4.0 21.8 - - - +
234G ARG* 4.7 16.8 - - - +
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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
----------------------------------------------------------
387E ILE* 2.9 33.9 + - + +
390E ILE* 1.3 93.6 - - + +
392E GLY* 1.3 61.5 + - - +
394E ASP* 2.9 20.1 - - - +
395E GLU* 3.7 36.3 - - + +
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Residues in contact with GLY 392 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387E ILE 3.5 4.0 + - - +
388E ILE* 3.3 24.8 + - - +
389E ALA 4.7 0.4 + - - -
390E ILE 3.7 0.8 - - - -
391E LEU* 1.3 84.3 - - - +
393E MET* 1.3 60.4 + - - -
394E ASP* 3.1 13.1 + - - +
395E GLU* 3.7 7.6 + - - +
396E LEU* 4.7 4.2 - - - +
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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