Contacts of the helix formed by residues 369 - 396 (chain E) in PDB entry 6V3O
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 GLU 369 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330E LEU 5.7 0.4 - - - -
331E SER* 4.6 12.8 - - - +
332E MET 4.1 4.7 - - - +
365E ILE* 4.2 1.6 - - + +
366E PRO* 3.3 37.7 + - + +
367E PRO 3.1 1.2 - - - -
368E ASN* 1.3 90.0 + - - +
370E PRO* 1.3 67.8 - - - +
371E TYR 3.5 1.3 - - - -
372E ARG* 3.2 38.0 + - + +
373E VAL* 3.1 23.1 + - - +
183F ARG* 2.9 32.6 + - - -
232F ARG* 5.4 3.1 - - - -
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Residues in contact with PRO 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332E MET 3.2 19.7 - - - +
333E TRP* 3.7 17.9 - - - +
335E CYS* 3.9 19.7 - - + -
339E LEU* 3.5 24.2 - - + +
340E ARG* 5.6 0.9 - - + -
343E ALA* 4.2 15.2 - - + +
367E PRO 4.3 10.1 - - - +
368E ASN* 3.5 5.8 - - - +
369E GLU* 1.3 87.7 - - - +
371E TYR* 1.3 64.9 + - + +
373E VAL* 2.9 15.8 + - + +
374E ILE* 3.1 15.4 + - - +
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Residues in contact with TYR 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330E LEU* 3.9 31.9 - - + +
332E MET* 3.8 35.2 - - + -
334E ARG 3.1 26.9 + - - -
335E CYS* 3.7 7.9 - - + -
339E LEU* 3.4 24.9 - - + -
369E GLU 3.5 0.4 - - - -
370E PRO* 1.3 77.1 - - + +
372E ARG* 1.3 56.6 + - - +
374E ILE* 3.5 6.0 + - - +
375E LEU* 3.0 35.8 + - - +
419E CYS* 3.8 21.1 - - + -
422E SER* 2.9 21.6 + - - -
423E LEU* 3.6 38.3 + - + +
426E CYS* 4.8 1.4 - - - +
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Residues in contact with ARG 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327E MET* 2.7 34.2 + - + +
328E PHE* 3.1 24.0 + - - +
330E LEU* 3.5 15.4 + - + +
331E SER* 3.9 13.3 - - - +
361E PHE* 3.6 29.0 - - - -
365E ILE* 3.5 26.0 - - + +
369E GLU* 3.2 40.3 + - + +
370E PRO 3.1 0.6 - - - -
371E TYR* 1.3 78.0 - - - +
373E VAL* 1.3 57.8 + - - +
375E LEU* 4.7 3.1 - - - +
376E GLY* 3.1 20.4 + - - -
183F ARG* 3.6 18.2 - - - +
185F SER* 2.8 29.7 + - - -
1003F SO4 4.5 5.1 + - - -
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Residues in contact with VAL 373 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343E ALA* 3.5 32.5 - - + +
346E LEU* 4.0 16.2 - - + +
347E HIS* 4.8 6.3 - - + +
365E ILE* 3.8 20.4 - - + +
366E PRO 3.5 20.4 - - - +
367E PRO* 4.4 7.4 - - + -
369E GLU 3.1 16.1 + - - +
370E PRO* 2.9 9.2 + - + +
372E ARG* 1.3 73.4 - - - +
374E ILE* 1.3 64.0 + - - +
376E GLY* 3.5 1.9 + - - -
377E HIS* 3.2 20.4 + - - +
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Residues in contact with ILE 374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339E LEU* 3.9 22.0 - - + -
342E ARG* 3.5 34.3 - - + +
343E ALA* 4.0 12.3 - - + +
346E LEU* 3.6 17.9 - - + -
370E PRO 3.1 12.4 + - - +
371E TYR 4.0 4.7 - - - +
373E VAL* 1.3 76.6 - - - +
375E LEU* 1.3 58.8 + - + +
377E HIS* 2.8 22.0 + - + +
378E VAL* 2.9 13.1 + - + +
415E PRO* 4.0 28.5 - - + +
418E LEU* 5.2 5.4 - - + -
419E CYS* 4.1 19.1 - - - -
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Residues in contact with LEU 375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323E ILE* 3.5 34.8 - - + +
326E LEU* 3.9 41.3 - - + +
327E MET* 3.6 19.7 - - + +
330E LEU* 3.9 19.1 - - + -
371E TYR 3.0 22.4 + - - +
374E ILE* 1.3 78.2 - - + +
376E GLY* 1.3 57.7 + - - +
378E VAL* 3.2 7.0 + - + +
379E ARG* 2.9 24.4 + - - +
415E PRO 6.1 0.2 - - - -
416E LEU* 4.1 17.3 - - + -
419E CYS* 4.7 15.3 - - + -
436E LEU* 5.9 1.1 - - + -
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Residues in contact with GLY 376 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327E MET* 3.8 17.4 - - - +
365E ILE* 4.5 7.0 - - - -
372E ARG 3.1 20.2 + - - -
373E VAL 3.9 1.6 - - - -
374E ILE 3.2 0.2 - - - -
375E LEU* 1.3 77.9 - - - +
377E HIS* 1.3 60.3 + - - +
379E ARG* 3.4 6.9 + - - +
380E ASP* 3.1 31.2 + - - +
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Residues in contact with HIS 377 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342E ARG* 3.6 28.2 + - - -
346E LEU* 3.8 34.2 - - + +
373E VAL 3.2 5.9 + - - +
374E ILE* 2.8 12.6 + - + +
376E GLY* 1.3 75.0 - - - +
378E VAL* 1.3 66.1 + - + +
380E ASP* 3.2 16.2 + - + +
381E LYS* 3.1 50.1 + - + +
415E PRO* 6.1 4.3 - - + -
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Residues in contact with VAL 378 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323E ILE* 3.9 18.4 - - + -
374E ILE* 2.9 14.4 + - + +
375E LEU* 3.2 18.1 + - + +
377E HIS* 1.3 79.2 - - + +
379E ARG* 1.3 64.4 + - - +
381E LYS 3.3 1.4 + - - -
382E LEU* 3.0 24.5 + - + +
406E PHE* 3.7 15.0 - - + -
412E PHE* 3.7 30.7 - - + -
415E PRO* 3.6 34.3 - - + -
416E LEU* 4.7 3.6 - - + -
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Residues in contact with ARG 379 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320E ILE* 4.2 14.8 - - + +
323E ILE* 4.2 8.9 - - + +
324E GLU* 2.9 45.0 + - - +
327E MET* 4.2 16.6 - - - +
355E THR* 4.5 5.1 - - - +
358E TYR* 3.2 45.3 - - + +
360E GLU 3.0 19.8 + - - -
361E PHE* 3.2 34.7 + - - +
365E ILE* 5.4 1.6 - - - +
375E LEU 2.9 16.3 + - - +
376E GLY* 3.6 7.3 + - - +
377E HIS 3.3 0.2 - - - -
378E VAL* 1.3 77.4 - - - +
380E ASP* 1.3 62.5 + - - +
382E LEU* 3.2 11.3 + - - +
383E TYR* 3.0 22.7 + - - +
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Residues in contact with ASP 380 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350E SER 4.8 9.5 - - - +
355E THR* 4.3 15.2 + - - -
357E TYR* 5.9 1.3 - - - -
358E TYR* 3.0 31.1 + - - -
376E GLY 3.1 16.7 + - - +
377E HIS* 3.5 19.2 + - + +
378E VAL 3.2 0.6 - - - -
379E ARG* 1.3 78.0 + - - +
381E LYS* 1.3 62.2 + - + +
383E TYR* 3.2 6.1 + - - +
384E ASN* 3.1 28.9 + - - +
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Residues in contact with LYS 381 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377E HIS* 3.1 42.9 + - + +
380E ASP* 1.3 76.8 - - + +
382E LEU* 1.3 57.4 + - - +
384E ASN* 3.4 4.0 + - - +
385E THR* 2.8 32.7 + - - -
403E GLU 2.8 26.5 + - - -
404E SER* 3.8 18.6 - - - +
405E SER* 3.7 18.6 + - - -
406E PHE* 3.5 39.3 - - + -
411E GLU* 3.9 11.1 + - - -
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Residues in contact with LEU 382 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316E ALA* 3.9 15.8 - - + +
319E TYR* 3.8 34.8 - - + -
320E ILE* 3.6 22.2 - - + +
323E ILE* 4.1 20.9 - - + -
378E VAL* 3.0 27.3 + - + +
379E ARG* 3.6 5.8 - - - +
380E ASP 3.2 0.2 - - - -
381E LYS* 1.3 75.6 - - - +
383E TYR* 1.3 58.8 + - - +
385E THR* 3.2 9.0 + - + -
386E ARG* 2.9 29.5 + - - +
406E PHE* 3.9 19.7 - - + -
412E PHE* 4.3 11.2 - - + -
448E LEU* 5.1 6.7 - - + -
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Residues in contact with TYR 383 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320E ILE* 3.9 13.1 - - + +
357E TYR* 3.8 52.4 - + + +
358E TYR* 3.6 34.3 - + - +
379E ARG 3.0 7.5 + - - +
380E ASP 3.4 9.2 - - - +
382E LEU* 1.3 75.9 - - - +
384E ASN* 1.3 64.1 + - - +
386E ARG* 3.2 30.9 + - - +
387E GLU* 2.9 55.5 + - + +
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Residues in contact with ASN 384 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357E TYR* 5.7 2.1 + - - -
380E ASP* 3.1 18.3 + - - +
381E LYS* 3.6 4.2 - - - +
383E TYR* 1.3 79.9 - - - +
385E THR* 1.3 60.4 + - - +
387E GLU* 3.3 3.7 + - - +
388E ARG* 2.9 33.4 + - - +
400E ILE* 3.9 19.3 - - + +
404E SER* 3.0 45.3 + - - +
405E SER* 4.2 2.7 - - - -
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Residues in contact with THR 385 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E ARG* 5.3 12.9 - - + +
316E ALA* 4.9 9.4 - - + -
381E LYS 2.8 22.3 + - - -
382E LEU* 3.2 15.2 + - + -
384E ASN* 1.3 75.0 - - - +
386E ARG* 1.3 61.9 + - - +
388E ARG* 3.7 3.5 + - - +
389E ALA* 3.3 21.0 + - - +
405E SER* 3.7 8.9 - - - -
406E PHE* 2.8 43.1 + - + +
448E LEU* 5.7 7.4 - - + -
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Residues in contact with ARG 386 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E ARG 5.3 0.4 - - - -
313E MET* 4.0 29.9 - - + +
316E ALA* 3.8 12.3 - - + +
317E ASN* 2.8 39.1 + - - +
320E ILE* 4.7 9.4 - - + +
382E LEU 2.9 13.8 + - - +
383E TYR* 3.3 42.2 + - - +
384E ASN 3.2 0.2 - - - -
385E THR* 1.3 77.9 - - - +
387E GLU* 1.3 86.6 + - - +
389E ALA* 3.1 8.7 + - - +
390E ARG* 3.0 35.8 + - - +
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Residues in contact with GLU 387 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383E TYR* 2.9 43.3 + - + +
384E ASN* 4.0 2.2 - - - +
386E ARG* 1.3 102.7 + - - +
388E ARG* 1.3 56.8 + - - +
390E ARG* 2.7 40.5 + - - +
391E HIS* 2.9 41.9 + - - +
400E ILE* 3.5 23.3 - - + -
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Residues in contact with ARG 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384E ASN 2.9 18.0 + - - +
385E THR* 3.8 5.4 - - - +
387E GLU* 1.3 76.5 - - - +
389E ALA* 1.3 57.9 + - - +
391E HIS* 3.3 2.8 + - - +
392E LEU* 2.9 55.6 + - + +
398E SER* 3.5 32.4 + - - +
400E ILE* 2.7 39.9 + - + +
401E SER* 4.0 2.0 - - - +
402E ALA* 4.0 25.8 - - - +
405E SER* 3.8 20.6 + - - -
407E THR* 6.2 0.2 - - - +
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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
----------------------------------------------------------
309E LEU* 4.0 25.1 - - + +
312E ARG* 4.6 12.3 - - + -
313E MET* 3.6 20.4 - - + +
385E THR 3.3 9.9 + - - +
386E ARG 3.1 8.8 + - - +
388E ARG* 1.3 79.9 - - - +
390E ARG* 1.3 58.1 + - - +
392E LEU* 3.4 9.3 + - - +
393E LEU* 2.9 30.7 + - - +
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Residues in contact with ARG 390 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313E MET* 3.6 38.1 - - + +
317E ASN* 5.7 1.2 - - - +
386E ARG* 3.0 30.2 + - - +
387E GLU* 2.7 49.4 + - - +
389E ALA* 1.3 74.9 - - - +
391E HIS* 1.3 65.5 + - + +
393E LEU* 3.4 6.5 + - + +
394E ALA* 3.0 29.8 + - + +
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Residues in contact with HIS 391 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387E GLU* 2.9 28.0 + - - +
388E ARG 3.6 0.2 - - - +
390E ARG* 1.3 85.1 - - + +
392E LEU* 1.3 61.6 + - - +
394E ALA* 3.0 5.8 + - + +
395E SER* 2.8 35.3 + - - +
397E VAL 3.7 9.6 - - - +
398E SER* 3.4 20.8 + - - +
400E ILE* 4.1 19.8 - - + +
399H GLU* 2.3 37.2 + - - +
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Residues in contact with LEU 392 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305E ARG* 2.4 31.7 + - - +
309E LEU* 3.9 25.1 - - + -
388E ARG* 2.9 53.4 + - + +
389E ALA* 3.8 4.5 - - - +
391E HIS* 1.3 72.7 - - - +
393E LEU* 1.3 54.1 + - - +
396E GLY 2.9 32.0 + - - +
397E VAL* 3.9 1.6 - - - +
398E SER* 3.9 23.3 - - - +
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Residues in contact with LEU 393 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302E GLU* 5.3 1.2 - - - +
305E ARG* 4.4 5.8 + - - +
306E ASP* 3.8 31.3 - - + +
309E LEU* 3.7 18.6 - - + +
310E LEU* 3.8 37.5 - - + +
313E MET* 5.4 4.9 - - - -
389E ALA 2.9 17.9 + - - +
390E ARG* 3.7 7.4 - - + +
392E LEU* 1.3 78.7 - - - +
394E ALA* 1.3 65.3 + - + +
396E GLY 4.7 0.3 + - - -
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Residues in contact with ALA 394 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390E ARG* 3.0 20.8 + - + +
391E HIS* 3.0 6.3 + - + +
393E LEU* 1.3 82.8 - - + +
395E SER* 1.3 61.2 - - - +
----------------------------------------------------------
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Residues in contact with SER 395 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391E HIS* 2.8 10.3 + - - -
394E ALA* 1.3 76.2 - - - +
396E GLY* 1.3 59.3 + - - +
397E VAL* 2.8 43.2 + - - +
399H GLU* 4.5 10.1 - - - +
----------------------------------------------------------
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Residues in contact with GLY 396 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305E ARG* 3.5 12.5 + - - +
392E LEU* 2.9 34.6 + - - +
393E LEU 4.6 0.6 + - - -
394E ALA 3.9 0.4 - - - -
395E SER* 1.3 75.0 - - - +
397E VAL* 1.3 64.5 + - - +
----------------------------------------------------------
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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