Contacts of the helix formed by residues 295 - 329 (chain A) in PDB entry 3X0X
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 ASP 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A TRP* 4.9 3.3 + - - +
289A ILE* 3.5 20.1 - - + +
291A GLN 3.4 2.4 + - - -
292A ALA* 3.4 10.0 + - - +
293A THR 3.6 0.4 - - - -
294A GLU* 1.3 77.3 - - - +
296A PRO* 1.3 68.8 - - - +
297A TYR* 2.7 34.7 + - - +
298A THR* 3.0 25.8 + - - +
299A ILE* 2.9 27.0 + - - +
395B SER* 4.9 0.6 + - - -
396B TYR* 2.7 36.6 + - - -
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Residues in contact with PRO 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ILE* 4.1 10.3 - - + -
294A GLU 3.3 7.4 - - - +
295A ASP* 1.3 88.6 - - - +
297A TYR* 1.3 71.4 + - + +
299A ILE* 3.7 6.2 + - + +
300A ARG 3.0 15.9 + - - -
396B TYR* 4.0 7.4 - - - +
296C PRO* 3.9 34.8 - - + -
297C TYR* 2.8 34.0 + - + +
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Residues in contact with TYR 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A ASP* 2.7 12.9 + - - +
296A PRO* 1.3 79.6 - - + +
298A THR* 1.3 56.7 + - - +
300A ARG* 3.4 5.0 + - - +
301A SER* 3.0 32.5 + - - -
365A GLU* 5.8 0.2 - - - +
395B SER* 3.8 31.0 - - - +
396B TYR* 3.8 37.9 - + - -
399B ALA* 3.8 22.5 - - + +
403B LYS* 5.4 1.1 + - - -
296C PRO* 2.5 48.7 + - + +
297C TYR* 4.1 9.4 - + - -
299C ILE* 4.2 3.5 - - - +
300C ARG* 3.7 38.4 + - + +
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Residues in contact with THR 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A THR* 4.0 12.1 - - + -
292A ALA 4.0 13.7 + - - +
295A ASP* 3.0 30.4 + - - +
297A TYR* 1.3 73.6 - - - +
299A ILE* 1.3 63.9 + - - +
301A SER* 3.5 2.9 + - - -
302A TYR* 3.1 54.1 + - + -
366A VAL* 3.9 22.5 + - + +
406D LEU* 4.2 6.1 - - + -
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Residues in contact with ILE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A THR 3.8 24.2 - - - +
294A GLU* 4.1 12.1 - - - +
295A ASP 2.9 21.9 + - - +
296A PRO* 3.8 6.7 - - + +
298A THR* 1.3 76.7 - - - +
300A ARG* 1.3 62.5 + - - +
302A TYR* 3.5 3.7 + - - -
303A GLY* 3.1 16.8 + - - -
297C TYR* 4.5 0.9 - - - +
399D ALA* 3.3 38.7 - - + +
402D GLY* 3.4 8.4 - - - -
403D LYS* 3.7 38.6 - - + +
406D LEU* 4.5 9.4 - - + -
407D ASN* 5.0 2.7 - - - +
409D GLN* 5.7 0.2 - - - +
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Residues in contact with ARG 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A PRO 3.0 19.0 + - - +
297A TYR* 3.6 7.4 - - - +
298A THR 3.3 0.2 - - - -
299A ILE* 1.3 75.3 - - - +
301A SER* 1.3 58.8 + - - +
303A GLY* 3.0 3.3 + - - -
304A GLU* 2.9 58.7 + - - +
297C TYR* 3.9 23.3 + - + +
300C ARG* 3.5 39.2 - - - +
301C SER* 5.9 1.2 + - - -
304C GLU* 5.3 6.3 + - - -
365C GLU* 5.1 7.5 + - - -
395D SER* 4.0 27.0 + - - +
398D ILE* 3.6 30.5 - - + +
399D ALA* 5.0 3.1 - - - +
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Residues in contact with SER 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A TYR 3.0 17.5 + - - -
298A THR 3.7 4.7 - - - -
300A ARG* 1.3 74.8 - - - +
302A TYR* 1.3 58.9 + - - +
304A GLU* 3.2 15.4 + - - +
305A PHE* 2.9 47.1 + - - -
365A GLU* 4.4 17.0 + - - -
366A VAL* 3.8 20.3 - - - +
300C ARG* 5.9 0.7 + - - -
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Residues in contact with TYR 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A LEU* 3.8 28.7 - - + -
273A ALA* 3.0 26.4 + - + +
274A ARG* 3.2 17.3 + - + -
277A THR* 2.6 26.2 + - - -
298A THR* 3.1 37.6 + - + +
299A ILE 3.8 4.3 - - - +
301A SER* 1.3 76.1 - - - +
303A GLY* 1.3 59.2 + - - +
305A PHE* 3.9 7.7 - + - +
306A THR* 2.6 34.8 + - - -
366A VAL* 3.5 20.1 - - + +
402D GLY* 4.1 15.9 - - - +
405D THR* 4.0 12.6 - - + +
406D LEU* 3.6 30.3 - - + -
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Residues in contact with GLY 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A ILE 3.1 6.9 + - - -
300A ARG 3.0 8.6 + - - -
302A TYR* 1.3 75.6 - - - +
304A GLU* 1.3 58.3 + - - +
306A THR* 3.3 1.7 + - - -
307A ILE* 2.8 40.3 + - - +
398D ILE* 3.6 10.1 - - - -
401D VAL* 3.9 4.7 - - - -
402D GLY* 3.4 24.6 - - - -
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A ARG* 2.9 50.9 + - - +
301A SER* 3.2 18.1 + - - +
303A GLY* 1.3 76.8 - - - +
305A PHE* 1.3 64.8 + - + +
307A ILE* 4.0 5.8 - - + +
308A ALA* 3.0 24.8 + - - +
300C ARG* 5.4 4.3 + - - -
398D ILE* 3.8 18.9 - - + +
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Residues in contact with PHE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A LEU* 3.8 32.3 - - + -
301A SER* 2.9 44.0 + - - +
302A TYR* 3.9 7.4 - + - +
303A GLY 3.3 0.4 - - - -
304A GLU* 1.3 79.3 - - + +
306A THR* 1.3 63.6 + - - +
308A ALA* 3.4 1.6 + - - -
309A LEU* 3.2 18.2 + - - +
358A ASN* 3.9 16.6 - - - -
359A ILE* 3.4 38.9 - - + +
362A GLY* 3.5 35.2 - - - -
363A VAL* 3.7 18.8 - - + -
365A GLU* 6.1 0.4 - - - -
366A VAL* 4.6 8.5 - - + -
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Residues in contact with THR 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A LEU* 4.2 12.2 - - + +
302A TYR 2.6 22.3 + - - -
303A GLY 3.6 3.8 - - - -
305A PHE* 1.3 78.7 - - - +
307A ILE* 1.3 63.3 + - - +
309A LEU* 3.2 6.2 + - + +
310A GLN* 3.0 26.4 + - + +
343D VAL* 6.1 2.0 - - + -
344D LYS* 6.4 0.2 - - - +
401D VAL* 3.7 14.6 - - + -
405D THR* 2.6 33.4 + - + +
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Residues in contact with ILE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A GLY 2.8 26.6 + - - +
304A GLU* 4.0 5.2 - - - +
306A THR* 1.3 73.1 - - - +
308A ALA* 1.3 64.8 + - - +
310A GLN* 3.1 21.6 + - - +
311A GLY 3.3 5.5 + - - -
347D GLY* 3.7 20.9 - - - +
350D ALA* 3.9 15.7 - - + -
351D LEU* 3.5 33.1 - - + +
398D ILE* 3.9 32.3 - - + +
401D VAL* 3.9 25.6 - - + -
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A GLU 3.0 17.9 + - - +
305A PHE* 3.9 4.7 - - - +
307A ILE* 1.3 79.2 - - - +
309A LEU* 1.3 60.9 + - - +
311A GLY* 3.7 1.0 + - - -
312A ALA* 3.2 21.8 + - - +
351A LEU* 6.1 0.3 - - - +
355A ALA* 4.3 20.7 - - + +
358A ASN* 5.7 6.3 - - - +
359A ILE* 5.0 3.6 - - + -
351D LEU* 4.8 5.4 - - - -
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A LEU* 3.8 22.7 - - + -
266A ALA* 3.8 22.2 - - + -
267A HIS* 3.7 43.1 - - + +
270A LEU* 3.7 29.2 - - + -
305A PHE 3.2 6.0 + - - +
306A THR* 3.6 9.4 - - + +
308A ALA* 1.3 74.6 - - - +
310A GLN* 1.3 60.6 + - - +
311A GLY 3.4 0.2 - - - -
312A ALA* 3.8 2.7 - - - -
313A ASP* 2.8 42.3 + - - +
355A ALA* 4.6 3.6 - - + -
359A ILE* 3.4 19.5 - - + -
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Residues in contact with GLN 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A THR* 3.0 17.3 + - + +
307A ILE* 3.1 16.6 + - - +
309A LEU* 1.3 77.1 - - - +
311A GLY* 1.3 62.6 + - - +
313A ASP* 4.0 3.6 - - - +
314A ALA* 3.0 26.5 + - - +
317A ARG* 4.5 2.7 + - - +
315D ALA* 4.5 8.2 + - + +
318D GLU* 4.7 12.2 + - - +
319D ALA* 5.6 0.2 - - - +
343D VAL 4.9 0.7 - - - +
344D LYS* 2.9 53.7 + - + +
347D GLY* 3.4 24.3 - - - -
348D VAL* 3.9 12.5 - - - +
351D LEU* 4.7 4.4 - - + +
401D VAL* 5.5 1.4 - - - +
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Residues in contact with GLY 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ILE 3.3 8.0 + - - -
308A ALA 4.1 2.0 - - - -
310A GLN* 1.3 78.9 - - - +
312A ALA* 1.3 62.8 + - - +
314A ALA* 3.8 0.3 - - - +
315A ALA* 2.9 23.4 + - - +
351A LEU* 5.5 0.7 - - - -
311D GLY* 3.5 31.8 - - - +
315D ALA* 4.2 1.1 - - - -
351D LEU* 3.8 16.8 - - - +
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A LEU* 3.6 28.2 - - + +
308A ALA 3.2 17.6 + - - +
309A LEU 4.0 1.8 - - - +
310A GLN 3.4 0.2 - - - -
311A GLY* 1.3 75.6 - - - +
313A ASP* 1.3 57.8 + - - +
315A ALA* 3.4 3.6 + - - +
316A ALA* 2.9 28.1 + - - +
348A VAL* 4.7 2.9 - - - +
351A LEU* 4.0 38.5 - - + +
352A ALA 4.5 0.2 - - - +
355A ALA* 4.4 3.4 - - + -
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Residues in contact with ASP 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ARG* 2.9 34.3 + - - +
263A LEU* 3.4 18.5 - - - +
267A HIS* 2.7 28.9 + - - -
309A LEU* 2.8 31.8 + - - +
310A GLN* 4.0 2.2 - - - +
312A ALA* 1.3 70.3 - - - +
314A ALA* 1.3 61.1 + - - +
316A ALA* 3.3 2.0 + - - +
317A ARG* 2.9 55.4 + - - +
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Residues in contact with ALA 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A GLN 3.0 19.4 + - - +
311A GLY 3.8 1.1 - - - +
313A ASP* 1.3 76.3 - - - +
315A ALA* 1.4 64.0 + - - +
317A ARG* 3.4 12.4 + - - +
318A GLU* 3.2 26.0 + - - +
314D ALA* 3.5 10.8 - - + +
315D ALA* 3.5 31.4 - - - +
318D GLU* 4.0 13.2 - - + +
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A GLY 2.9 17.5 + - - +
312A ALA 3.8 4.0 - - - +
314A ALA* 1.4 74.9 - - - +
316A ALA* 1.3 64.3 + - - +
318A GLU* 3.5 5.0 + - - +
319A ALA* 3.0 17.7 + - - +
348A VAL* 3.4 17.0 - - + +
351A LEU* 3.8 23.6 - - + -
310D GLN* 4.1 24.3 + - + +
314D ALA* 3.4 10.1 - - - +
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Residues in contact with ALA 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ILE* 6.1 0.8 - - - +
81A ARG* 5.1 0.4 - - - +
256A LEU* 4.2 3.2 - - + +
260A ASN* 3.9 28.4 + - - +
263A LEU* 4.0 8.7 - - + -
312A ALA 2.9 14.8 + - - +
313A ASP* 3.7 4.3 - - - +
314A ALA 3.2 0.2 - - - -
315A ALA* 1.3 75.1 - - - +
317A ARG* 1.3 67.3 + - + +
319A ALA* 3.0 4.3 + - - +
320A ALA* 3.0 21.4 + - - +
348A VAL* 3.6 28.0 - - + +
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Residues in contact with ARG 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ILE* 6.5 0.7 - - - -
78A GLU* 4.0 27.9 + - - +
81A ARG* 4.8 11.1 - - - +
260A ASN* 6.1 0.7 - - - +
310A GLN* 4.5 2.8 + - - +
313A ASP* 2.9 40.0 + - - +
314A ALA* 3.4 22.1 + - - +
316A ALA* 1.3 71.9 - - + +
318A GLU* 1.3 62.1 + - + +
320A ALA* 3.0 17.4 + - - +
321A HIS* 3.2 27.2 + - + +
318D GLU* 2.7 36.7 + - - -
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Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A ALA 3.2 13.0 + - - +
315A ALA* 3.7 8.7 - - - +
317A ARG* 1.3 76.4 - - + +
319A ALA* 1.3 61.8 + - - +
321A HIS* 3.5 10.6 + - + +
322A LEU* 3.1 22.3 + - - +
344A LYS* 5.3 11.5 - - + -
314D ALA* 3.7 19.7 - - + +
317D ARG* 2.8 51.3 + - - +
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LEU* 3.8 21.1 - - + +
315A ALA 3.0 15.4 + - - +
316A ALA 3.0 6.9 + - - +
318A GLU* 1.3 77.0 - - - +
320A ALA* 1.3 57.5 + - - +
322A LEU* 3.5 7.8 + - - +
323A LEU* 2.9 27.5 + - - +
341A LEU* 3.9 2.8 - - - +
344A LYS* 4.6 14.5 - - + +
345A VAL* 4.3 13.0 - - + -
348A VAL* 4.0 11.0 - - + -
310D GLN* 5.7 0.2 - - - +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TRP* 4.2 1.6 - - - +
74A PRO* 4.0 26.2 - - + +
77A ILE* 3.7 28.9 - - + -
256A LEU* 3.8 9.3 - - + +
316A ALA 3.0 12.2 + - - +
317A ARG* 3.0 12.7 + - - +
319A ALA* 1.3 75.5 - - - +
321A HIS* 1.3 59.9 + - - +
323A LEU* 3.3 4.8 + - - +
324A GLN* 2.9 27.7 + - - +
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Residues in contact with HIS 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PRO* 3.6 28.4 - - + +
317A ARG* 3.2 29.7 + - + +
318A GLU* 3.9 9.2 - - + +
320A ALA* 1.3 74.0 - - - +
322A LEU* 1.3 64.6 + - - +
324A GLN* 3.1 9.5 + - - +
325A THR* 3.0 25.9 + - - -
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Residues in contact with LEU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A GLU 3.1 17.1 + - - +
319A ALA* 3.7 6.3 - - - +
321A HIS* 1.3 78.3 - - - +
323A LEU* 1.3 56.3 + - - +
325A THR* 3.4 11.6 + - + -
326A VAL* 3.0 38.4 + - + +
337A ASP 5.9 0.4 - - - +
340A GLU* 4.4 5.6 - - + +
341A LEU* 3.8 36.6 - - + +
344A LYS* 4.0 27.8 - - + -
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TRP* 3.7 41.7 - - + +
77A ILE* 5.1 2.7 - - + -
249A LEU* 5.1 5.4 - - + -
252A PRO* 5.1 1.3 - - + +
253A ILE* 3.9 36.1 - - + +
256A LEU* 4.1 19.1 - - + -
319A ALA 2.9 18.3 + - - +
320A ALA* 3.6 4.0 - - - +
321A HIS 3.2 0.4 - - - -
322A LEU* 1.3 75.8 - - - +
324A GLN* 1.3 59.8 + - - +
326A VAL* 3.4 0.3 + - - +
327A TRP* 2.8 36.2 + - + +
341A LEU* 3.7 30.1 - - + -
345A VAL* 5.8 0.2 - - + -
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Residues in contact with GLN 324 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ASP* 3.1 18.4 - - + +
73A TRP* 2.7 37.4 + - - +
74A PRO* 3.4 6.6 - - + +
320A ALA 2.9 14.3 + - - +
321A HIS* 3.3 13.0 - - - +
323A LEU* 1.3 77.1 - - - +
325A THR* 1.3 56.7 + - - +
327A TRP* 3.0 20.0 + - - +
328A ASP* 2.8 63.9 + - - +
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Residues in contact with THR 325 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A HIS* 3.0 15.2 + - - +
322A LEU* 3.6 19.3 - - + +
324A GLN* 1.3 75.0 - - - +
326A VAL* 1.3 66.7 + - + +
328A ASP* 3.2 15.9 + - - +
329A LYS* 3.3 34.6 + - - +
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Residues in contact with VAL 326 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 3.9 29.1 - - + +
322A LEU* 3.0 34.4 + - + +
323A LEU 4.0 2.9 - - - +
325A THR* 1.3 79.3 - - + +
327A TRP* 1.3 64.6 + - - +
328A ASP 3.3 0.3 + - - -
329A LYS* 3.3 21.7 + - + +
330A GLY 4.2 2.3 + - - +
333A LEU* 4.2 22.3 - - + +
337A ASP* 4.1 34.8 - - + +
338A ARG 5.0 0.9 - - - +
341A LEU* 4.2 12.1 - - + -
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Residues in contact with TRP 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TRP* 3.4 30.1 - + - +
102A PRO* 4.0 22.9 - - + -
105A GLU* 3.4 32.7 + - + -
106A LEU* 3.6 30.3 - - + -
246A ARG* 2.7 36.8 + - - +
249A LEU* 3.8 24.0 - - + +
253A ILE* 3.7 21.1 - - + -
323A LEU* 2.8 22.4 + - + +
324A GLN* 3.0 24.4 + - - +
326A VAL* 1.3 78.5 - - - +
328A ASP* 1.3 67.1 + - - +
330A GLY 3.2 6.4 + - - -
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Residues in contact with ASP 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLN* 2.8 45.1 + - - +
325A THR* 3.7 7.3 - - - +
326A VAL 3.2 0.4 - - - -
327A TRP* 1.3 80.8 - - - +
329A LYS* 1.3 58.9 - - - +
330A GLY* 3.1 7.6 + - - -
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Residues in contact with LYS 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A THR* 3.3 32.3 + - - +
326A VAL* 3.6 15.3 - - - +
327A TRP 3.3 0.6 - - - -
328A ASP* 1.3 75.2 - - + +
330A GLY* 1.3 62.8 + - - +
331A ASP 3.3 0.2 + - - -
332A ALA* 3.0 26.0 + - + +
333A LEU* 4.0 16.4 - - - +
337A ASP* 3.3 38.0 + - - +
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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) + - + + + + + -
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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