Contacts of the helix formed by residues 346 - 377 (chain B) in PDB entry 2BAP
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 ASN 346 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ILE* 3.9 20.1 - - + +
303B VAL* 4.8 4.1 - - - +
344B ILE* 3.3 17.6 - - + +
345B GLU* 1.3 80.1 - - - +
347B GLU* 1.3 78.1 + - - +
348B ASP* 2.9 26.8 + - - +
349B MET* 3.4 22.1 - - + +
350B LYS* 3.5 24.3 + - - +
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Residues in contact with GLU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B GLU 4.7 4.3 - - - +
346B ASN* 1.3 80.8 - - - +
348B ASP* 1.3 66.1 + - - +
350B LYS* 3.7 8.9 + - - +
351B VAL* 3.3 25.3 + - - +
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Residues in contact with ASP 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B VAL* 4.0 15.4 - - + +
346B ASN* 2.9 11.7 + - - +
347B GLU* 1.3 79.8 - - - +
349B MET* 1.3 64.3 + - - +
350B LYS 3.1 2.0 - - - -
351B VAL* 3.3 9.8 + - - +
352B GLN* 3.2 23.9 + - - +
1190D GLN* 2.9 45.3 - - + +
1191D SER* 5.0 4.0 + - - -
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Residues in contact with MET 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ILE* 4.8 3.6 - - + +
302B LYS* 3.3 50.3 - - + +
303B VAL* 4.0 16.0 - - + +
306B LEU* 4.7 5.4 - - - -
341B LEU* 3.6 48.7 - - + +
344B ILE* 4.5 19.7 - - + +
346B ASN* 3.4 24.8 - - + +
348B ASP* 1.3 78.5 - - - +
350B LYS* 1.3 62.7 + - - +
352B GLN* 3.4 4.1 + - - +
353B LEU* 3.2 27.8 + - + +
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Residues in contact with LYS 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ARG* 5.4 9.4 - - - +
344B ILE 4.6 5.6 - - - +
345B GLU* 3.5 53.8 + - - +
346B ASN 3.5 14.0 + - - +
347B GLU* 3.7 10.1 - - - +
348B ASP 3.1 1.0 - - - -
349B MET* 1.3 77.6 - - - +
351B VAL* 1.3 60.5 + - + +
353B LEU* 3.3 12.6 + - + +
354B CYS* 2.8 36.4 + - - +
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Residues in contact with VAL 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B GLU 3.3 18.4 - - - +
348B ASP* 3.3 6.0 + - - +
350B LYS* 1.3 74.5 - - + +
352B GLN* 1.3 63.4 + - - +
354B CYS* 3.6 8.9 - - + +
355B VAL* 3.1 23.9 + - + +
1190D GLN 3.3 17.0 - - - +
1191D SER* 4.3 4.9 - - - -
1192D GLY* 3.4 36.0 - - - +
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Residues in contact with GLN 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B VAL* 3.8 23.8 - - + +
306B LEU* 3.5 20.4 - - + -
307B GLN* 3.1 33.4 + - - +
310B ASN* 2.8 44.1 + - - +
348B ASP 3.2 11.5 + - - +
349B MET* 3.5 9.0 - - - +
350B LYS 3.2 0.6 - - - -
351B VAL* 1.3 75.7 - - - +
353B LEU* 1.3 65.7 + - - +
354B CYS 3.2 0.3 + - - -
355B VAL* 3.2 1.9 + - - +
356B PHE* 3.1 13.0 + - - +
1189D LEU 2.9 28.1 + - - +
1190D GLN* 3.7 11.9 + - - +
1192D GLY* 5.3 0.6 - - - +
1195D PHE* 4.8 3.9 - - - -
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Residues in contact with LEU 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LEU* 3.4 19.7 - - + +
338B LEU* 3.8 26.9 - - + -
341B LEU* 3.2 35.2 - - + +
342B ARG* 3.7 21.1 - - + +
344B ILE 5.7 0.7 - - - +
349B MET* 3.2 22.9 + - + +
350B LYS* 3.8 11.9 - - + +
352B GLN* 1.3 77.5 - - - +
354B CYS* 1.3 63.4 + - - +
356B PHE* 3.4 5.1 + - + +
357B ASP* 3.1 36.9 + - - +
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Residues in contact with CYS 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LYS* 2.8 24.6 + - - +
351B VAL* 3.6 11.7 - - + +
352B GLN 3.1 0.2 - - - -
353B LEU* 1.3 75.3 - - - +
355B VAL* 1.3 57.6 + - - +
357B ASP* 3.4 4.0 + - - +
358B GLU* 3.0 40.6 + - - +
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Residues in contact with VAL 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ASN* 3.0 35.4 - - + +
314B THR* 5.1 5.2 + - - +
351B VAL* 3.1 13.2 + - + +
352B GLN* 3.2 1.8 + - - +
354B CYS* 1.3 76.1 - - - +
356B PHE* 1.3 62.4 + - - +
358B GLU* 3.4 23.9 + - + +
359B GLN* 3.6 20.1 + - - +
1192D GLY* 5.4 6.1 - - - +
1195D PHE* 3.1 52.5 - - + -
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Residues in contact with PHE 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LEU* 3.9 12.6 - - + -
309B ILE* 3.9 20.2 - - + -
310B ASN* 3.2 24.2 - - - +
313B ILE* 4.0 16.2 - - + -
326B ARG* 4.5 23.7 + - + -
329B LEU* 5.5 1.1 - - + -
330B MET* 5.0 4.9 - - + -
334B LEU* 4.0 22.0 - - + -
338B LEU* 4.3 31.6 - - + -
352B GLN 3.1 15.3 + - - +
353B LEU* 3.6 7.9 - - + +
354B CYS 3.2 0.2 - - - -
355B VAL* 1.3 77.8 - - - +
357B ASP* 1.3 65.2 + - - +
359B GLN* 3.3 4.7 + - + +
360B GLY* 2.7 34.2 + - - -
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Residues in contact with ASP 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B LEU* 4.9 8.5 - - - +
353B LEU* 3.1 25.1 + - - +
354B CYS* 4.1 4.0 - - - +
356B PHE* 1.3 85.8 - - - +
358B GLU* 1.3 64.0 + - - +
359B GLN 3.1 1.8 - - - -
360B GLY* 4.1 3.5 - - - +
361B ASP* 3.1 37.4 + - - +
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Residues in contact with GLU 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B CYS* 3.0 40.9 + - - +
355B VAL* 3.4 25.2 + - + +
357B ASP* 1.3 76.0 - - - +
359B GLN* 1.3 61.5 + - + +
361B ASP* 4.3 1.9 - - - +
362B GLU* 3.3 26.5 + - - +
1195D PHE 5.7 1.4 - - - +
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Residues in contact with GLN 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ILE* 4.6 14.4 - - + -
314B THR* 4.7 25.6 - - - +
322B ARG* 4.2 21.1 + - - -
326B ARG* 3.6 12.3 - - - +
355B VAL 3.6 14.5 + - - +
356B PHE* 3.3 4.9 + - + +
358B GLU* 1.3 82.6 + - + +
360B GLY* 1.3 63.9 + - - +
361B ASP 3.2 1.3 - - - -
362B GLU* 3.0 27.3 + - - +
363B ASP* 3.2 40.8 + - - +
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Residues in contact with GLY 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ARG* 3.6 23.7 + - - +
356B PHE* 2.7 23.6 + - - -
357B ASP* 3.5 4.6 + - - -
359B GLN* 1.3 74.0 - - - +
361B ASP* 1.3 63.7 + - - +
363B ASP* 3.8 3.8 - - - +
364B PHE* 3.3 18.9 + - - +
434B LEU 5.6 1.2 - - - +
435B HIS* 5.9 1.9 - - - -
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Residues in contact with ASP 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ASP* 3.1 25.4 + - - +
358B GLU* 4.3 2.5 - - - +
360B GLY* 1.3 76.3 - - - +
362B GLU* 1.3 60.4 + - - +
363B ASP 3.1 2.0 - - - -
364B PHE* 2.8 25.1 + - - +
365B PHE* 2.9 16.1 + - - +
435B HIS* 4.7 13.9 + - - -
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Residues in contact with GLU 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B GLU 3.3 18.0 + - - +
359B GLN* 3.0 27.5 + - - +
361B ASP* 1.3 78.5 - - - +
363B ASP* 1.3 61.0 + - - +
365B PHE* 4.1 9.9 - - + +
366B ASP* 3.0 36.8 + - - +
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Residues in contact with ASP 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 3.7 20.5 - - + +
322B ARG* 3.3 42.3 + - - +
323B VAL* 5.5 3.8 - - + -
326B ARG* 2.4 36.3 + - - +
359B GLN* 3.2 20.0 + - - +
360B GLY 3.8 2.7 - - - +
361B ASP 3.1 0.6 - - - -
362B GLU* 1.3 75.9 - - - +
364B PHE* 1.3 54.4 + - - +
366B ASP* 2.9 5.0 + - - +
367B LEU* 2.6 38.0 + - + +
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Residues in contact with PHE 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B GLY 3.3 11.9 + - - +
361B ASP* 2.8 18.5 + - - +
363B ASP* 1.3 73.3 - - - +
365B PHE* 1.3 66.2 + - - +
367B LEU* 4.4 4.9 - - - +
368B LYS* 2.9 49.8 + - + +
434B LEU* 3.7 51.6 - - + +
435B HIS* 4.3 26.0 - + + -
----------------------------------------------------------
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Residues in contact with PHE 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ASP 2.9 16.3 + - - +
362B GLU* 4.1 10.3 - - + +
364B PHE* 1.3 78.7 - - + +
366B ASP* 1.3 72.0 + - - +
368B LYS* 4.0 2.2 - - - +
369B GLY* 3.0 28.6 + - - -
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Residues in contact with ASP 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 3.7 22.7 - - + +
322B ARG* 5.3 5.7 + - - -
362B GLU* 3.0 25.2 + - - +
363B ASP* 2.9 10.2 + - - +
365B PHE* 1.3 92.3 - - - +
367B LEU* 1.3 60.1 + - - +
369B GLY* 3.7 2.2 + - - -
370B ARG* 3.4 20.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 4.1 18.8 - - + +
320B ASP* 5.2 0.4 - - - +
323B VAL* 4.0 23.1 - - + -
363B ASP* 2.6 20.7 + - + +
364B PHE* 4.1 3.1 - - - +
366B ASP* 1.3 71.8 - - - +
368B LYS* 1.3 61.9 + - - +
370B ARG* 3.2 35.0 + - + +
371B LEU* 3.1 23.4 + - - +
433B VAL* 3.3 38.1 - - + +
434B LEU* 4.0 17.8 - - + +
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Residues in contact with LYS 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B PHE* 2.9 39.0 + - + +
365B PHE* 4.1 2.2 - - - +
367B LEU* 1.3 72.2 - - - +
369B GLY* 1.3 60.2 + - - +
370B ARG 3.1 1.8 - - - -
371B LEU* 3.1 18.1 + - + +
372B ASP* 2.8 64.2 + - - +
375B ARG* 5.5 4.3 - - - +
434B LEU* 4.0 20.7 - - + +
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Residues in contact with GLY 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 3.0 17.9 + - - -
366B ASP* 4.0 3.8 - - - -
367B LEU 3.3 0.4 - - - -
368B LYS* 1.3 77.0 - - - +
370B ARG* 1.3 57.1 + - - +
372B ASP* 3.7 14.8 + - - +
373B ASP* 3.1 22.9 - - - +
----------------------------------------------------------
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Residues in contact with ARG 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 3.5 29.4 - - - +
320B ASP* 3.1 36.9 + - - -
366B ASP 3.4 13.9 + - - +
367B LEU* 3.2 27.0 + - + +
368B LYS 3.1 0.6 - - - -
369B GLY* 1.3 76.3 - - - +
371B LEU* 1.3 64.2 + - - +
372B ASP 3.2 0.4 + - - -
373B ASP* 3.5 5.0 + - - +
374B ILE* 3.3 37.7 + - + +
----------------------------------------------------------
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Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B LEU 3.1 11.5 + - - +
368B LYS* 3.1 16.5 + - + +
370B ARG* 1.3 76.1 - - - +
372B ASP* 1.3 57.9 + - - +
374B ILE* 3.3 20.2 + - + -
375B ARG* 3.0 67.1 + - + +
434B LEU* 4.3 24.0 - - + -
----------------------------------------------------------
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Residues in contact with ASP 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LYS* 2.8 45.2 + - - +
369B GLY* 3.7 12.6 - - - +
370B ARG 3.2 0.2 - - - -
371B LEU* 1.3 77.0 - - - +
373B ASP* 1.3 64.2 + - - +
375B ARG* 3.4 28.2 + - - +
376B MET* 3.6 12.3 + - - +
----------------------------------------------------------
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Residues in contact with ASP 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B GLY 3.1 20.8 - - - +
370B ARG* 3.5 6.0 + - - +
371B LEU 3.3 0.4 - - - -
372B ASP* 1.3 74.0 - - - +
374B ILE* 1.3 56.4 + - + +
375B ARG 2.6 16.4 + - - -
376B MET* 2.8 6.6 + - - +
377B GLU* 2.7 49.7 + - + +
----------------------------------------------------------
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Residues in contact with ILE 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ARG* 3.3 33.6 + - + +
371B LEU* 3.3 25.5 + - + +
373B ASP* 1.3 80.1 - - + +
375B ARG* 1.3 56.1 + - + +
377B GLU* 4.5 4.9 - - + -
378B MET* 3.4 57.5 + - + +
----------------------------------------------------------
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Residues in contact with ARG 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LYS* 5.5 4.6 - - - +
371B LEU* 3.0 48.9 + - + +
372B ASP* 3.4 22.5 + - - +
373B ASP 2.6 6.3 + - - -
374B ILE* 1.3 76.2 - - - +
376B MET* 1.3 77.4 + - + +
377B GLU 3.4 0.4 - - - -
378B MET 4.4 1.3 - - - -
379B ASP* 3.7 20.3 - - - +
426B GLU* 4.8 11.5 + - - -
----------------------------------------------------------
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Residues in contact with MET 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ASP 3.6 8.7 + - - +
373B ASP* 2.8 11.7 + - - +
375B ARG* 1.3 92.6 - - + +
377B GLU* 1.3 72.5 + - - +
379B ASP* 3.8 15.9 - - - +
----------------------------------------------------------
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Residues in contact with GLU 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ASP* 2.7 40.5 + - + +
374B ILE* 4.5 6.7 - - + -
376B MET* 1.3 89.2 - - - +
378B MET* 1.3 58.4 + - + +
379B ASP* 3.8 1.9 - - - +
383B GLU* 3.4 21.5 - - - +
387B ILE* 6.3 0.2 - - - -
----------------------------------------------------------
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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