Contacts of the helix formed by residues 304 - 338 (chain R) in PDB entry 5VAI
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 304 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302R ASN 2.9 8.5 + - - +
303R MET* 1.3 79.4 - - - +
305R TYR* 1.3 78.0 + - + +
306R TRP 3.7 0.7 - - - -
307R LEU* 4.6 5.2 - - - +
308R ILE* 3.3 22.6 + - - +
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Residues in contact with TYR 305 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284R TRP* 2.9 45.6 + + + +
287R VAL* 3.9 10.9 + - + +
288R LYS* 3.4 39.0 - - + -
291R TYR* 3.1 38.1 - - - +
292R GLU* 3.5 25.5 - - + +
299R ARG* 4.2 8.3 - - + -
302R ASN* 3.3 27.0 - - + +
304R ASN* 1.3 98.2 - - + +
306R TRP* 1.3 67.0 + - - +
308R ILE* 3.0 4.1 - - + +
309R ILE* 3.0 14.0 + - - +
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Residues in contact with TRP 306 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P HIS* 3.1 20.2 + + - -
11P THR* 4.0 16.5 + - + -
299R ARG* 2.8 56.8 - - + +
300R ASN* 4.7 15.3 - - - +
303R MET* 5.6 3.3 - - - +
304R ASN 3.7 1.8 - - - +
305R TYR* 1.3 77.7 - - - +
307R LEU* 1.3 61.6 + - + +
309R ILE* 3.2 1.0 - - - +
310R ARG* 2.8 39.6 + - + +
314R LEU* 6.5 1.1 - - + -
370R VAL* 3.4 37.2 - - + -
371R MET 3.6 17.0 - - - -
372R ASP* 4.9 6.5 - - - -
375R ALA* 4.4 15.9 - - + -
376R ARG* 4.6 6.3 - - + -
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Residues in contact with LEU 307 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303R MET 5.6 5.0 + - - +
304R ASN* 4.5 5.8 + - - +
305R TYR 3.3 0.8 - - - +
306R TRP* 1.3 84.1 - - + +
308R ILE* 1.3 65.2 + - - +
310R ARG* 3.0 8.5 + - + -
311R LEU* 2.9 32.7 + - + +
314R LEU* 5.3 8.3 - - + -
371R MET* 4.9 7.2 - - + -
372R ASP* 3.6 40.2 - - + +
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Residues in contact with ILE 308 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280R PHE* 4.3 3.7 - - + -
284R TRP* 3.5 19.7 - - + +
304R ASN* 3.3 21.8 + - - +
305R TYR* 3.0 22.2 - - + +
307R LEU* 1.3 80.5 - - - +
309R ILE* 1.3 57.6 + - - +
311R LEU* 3.7 10.5 + - + +
312R PRO* 3.1 22.0 - - - +
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Residues in contact with ILE 309 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P HIS* 3.2 11.2 - - + +
234R GLN* 3.2 27.1 - - - +
238R ALA* 6.2 0.7 - - + -
280R PHE* 3.7 25.9 - - + -
281R VAL* 4.8 9.4 - - + -
284R TRP* 3.3 36.6 - - + +
299R ARG* 3.1 24.5 - - - +
305R TYR 3.0 18.4 + - - +
306R TRP 3.2 0.7 - - - +
308R ILE* 1.3 76.4 - - - +
310R ARG* 1.3 63.8 + - - +
312R PRO* 2.9 17.3 - - - +
313R ILE* 3.4 16.3 + - + +
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Residues in contact with ARG 310 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P HIS* 3.1 24.2 - - + +
306R TRP* 2.8 32.1 + - + +
307R LEU* 3.0 10.7 + - + +
309R ILE* 1.3 78.6 - - - +
311R LEU* 1.3 53.7 + - - +
313R ILE* 3.0 1.8 + - - -
314R LEU* 2.4 55.4 + - + +
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Residues in contact with LEU 311 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307R LEU* 2.9 21.6 + - + +
308R ILE* 4.1 11.0 - - + +
310R ARG* 1.3 76.4 - - - +
312R PRO* 1.3 65.2 - - + +
314R LEU* 4.4 9.9 - - + -
315R PHE* 2.8 37.5 + - + +
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Residues in contact with PRO 312 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242R TYR* 3.3 20.5 + - - +
276R VAL* 6.3 0.4 - - + -
280R PHE* 3.2 34.5 - - + -
308R ILE 3.1 19.3 - - - +
309R ILE 2.9 17.7 - - - +
311R LEU* 1.3 81.9 - - + +
313R ILE* 1.3 56.6 + - - +
315R PHE* 3.1 10.2 + - + +
316R ALA* 2.8 26.3 + - - +
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Residues in contact with ILE 313 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P HIS* 4.3 23.1 - - + -
8P ALA* 5.8 0.4 - - + -
237R VAL* 5.5 0.4 - - + -
238R ALA* 3.9 26.5 - - + -
241R TYR* 3.6 32.8 - - + -
242R TYR* 3.2 29.4 - - + +
280R PHE* 4.9 4.5 - - + -
309R ILE* 3.4 25.8 - - + +
310R ARG* 3.0 8.8 + - - +
312R PRO* 1.3 74.8 - - - +
314R LEU* 1.3 67.4 + - + +
316R ALA* 3.0 15.9 + - - +
317R ILE* 3.0 18.5 + - + +
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Residues in contact with LEU 314 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P HIS* 5.8 1.8 - - + +
306R TRP* 6.5 0.9 - - + -
307R LEU* 5.3 8.1 - - + -
310R ARG* 2.4 46.0 + - + +
311R LEU* 4.0 10.1 - - + +
313R ILE* 1.3 77.2 - - + +
315R PHE* 1.3 57.0 + - - +
317R ILE* 3.1 10.3 + - + +
318R GLY* 2.8 25.6 + - - -
367R PHE 4.8 2.7 - - - +
368R ALA* 3.5 40.2 - - + +
370R VAL 4.2 18.6 - - - +
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Residues in contact with PHE 315 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245R LEU* 5.8 4.3 - - + -
311R LEU* 2.8 28.9 + - + +
312R PRO* 3.2 11.2 - - + +
314R LEU* 1.3 77.0 - - - +
316R ALA* 1.3 64.2 + - - +
318R GLY* 3.2 3.4 + - - +
319R VAL* 2.9 46.2 + - + +
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Residues in contact with ALA 316 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241R TYR* 4.8 4.7 - - + +
242R TYR* 3.5 32.8 - - + -
245R LEU* 3.5 26.5 - - + +
312R PRO 2.8 5.9 + - - -
313R ILE* 3.0 10.3 + - - +
315R PHE* 1.3 78.9 - - - +
317R ILE* 1.3 69.3 + - + +
319R VAL* 3.0 8.5 + - - +
320R ASN* 3.0 23.2 + - - -
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Residues in contact with ILE 317 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241R TYR* 4.1 26.7 - - + -
244R LEU* 5.3 2.2 - - + -
313R ILE* 3.0 18.5 + - + +
314R LEU* 3.6 12.8 - - + +
316R ALA* 1.3 78.0 - - - +
318R GLY* 1.3 56.7 + - - +
320R ASN* 2.8 41.1 + - + +
321R PHE* 2.9 13.3 + - - +
361R GLY 5.0 2.9 - - - +
362R THR* 5.4 1.1 - - - -
364R GLU* 3.7 44.2 - - + +
365R VAL* 3.8 24.7 - - + +
368R ALA* 4.9 5.6 - - + -
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Residues in contact with GLY 318 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314R LEU 2.8 18.0 + - - -
315R PHE* 3.2 4.9 + - - -
317R ILE* 1.3 68.0 - - - +
319R VAL* 1.3 64.3 + - - +
321R PHE* 3.0 11.3 + - - +
322R LEU* 3.0 22.9 + - - +
365R VAL* 5.2 2.6 - - - +
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Residues in contact with VAL 319 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245R LEU* 3.4 24.5 - - + +
315R PHE* 2.9 41.1 + - + +
316R ALA 3.1 9.6 - - - +
318R GLY* 1.3 75.0 - - - +
320R ASN* 1.3 55.9 + - - +
322R LEU* 3.3 6.2 + - + +
323R ILE* 2.9 59.1 + - + +
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Residues in contact with ASN 320 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241R TYR 4.9 1.0 + - - -
244R LEU* 3.8 30.5 - - - +
245R LEU* 4.2 4.0 + - - +
248R GLY* 5.6 1.9 - - - -
316R ALA 3.0 7.8 + - - +
317R ILE* 2.8 47.6 + - + +
319R VAL* 1.3 77.8 - - - +
321R PHE* 1.3 56.6 + - - +
323R ILE* 4.6 4.7 - - - +
324R PHE* 2.8 34.8 + - - +
360R LEU* 3.7 21.4 + - + +
361R GLY 5.0 1.2 + - - -
362R THR* 3.1 22.8 + - + +
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Residues in contact with PHE 321 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317R ILE 2.9 11.1 + - - +
318R GLY* 3.3 13.5 - - - +
320R ASN* 1.3 76.8 - - - +
322R LEU* 1.3 59.8 + - + +
324R PHE* 4.1 0.4 - + - +
325R ILE* 3.0 64.9 + - + +
362R THR* 3.5 14.3 - - + +
365R VAL* 4.1 30.1 - - + -
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Residues in contact with LEU 322 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252R TYR* 6.3 4.7 - - + -
318R GLY 3.0 12.4 + - - +
319R VAL* 3.9 7.6 - - + +
321R PHE* 1.3 81.3 - - + +
323R ILE* 1.3 62.5 + - + +
325R ILE* 3.7 8.6 - - + +
326R ARG* 2.9 54.6 + - + +
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Residues in contact with ILE 323 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245R LEU* 4.8 1.6 - - - +
248R GLY* 3.4 49.8 - - - +
249R ALA* 3.8 4.9 - - + +
251R LEU* 5.1 0.9 - - + -
252R TYR* 4.2 22.4 - - + +
319R VAL* 2.9 45.9 + - + +
320R ASN* 4.2 4.5 - - - +
322R LEU* 1.3 76.4 - - + +
324R PHE* 1.3 59.0 + - - +
326R ARG* 3.2 5.8 + - - +
327R VAL* 2.7 47.2 + - + +
360R LEU* 4.7 5.4 - - + -
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Residues in contact with PHE 324 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320R ASN 2.8 24.2 + - - +
321R PHE* 4.1 0.7 - + - +
323R ILE* 1.3 73.2 - - - +
325R ILE* 1.3 72.2 + - + +
327R VAL* 3.7 2.9 - - - +
328R ILE* 3.0 54.5 + - + +
353R THR 5.3 1.3 - - - -
354R LEU* 5.5 4.9 - - + -
356R LEU* 4.4 14.8 - - + -
357R ILE* 3.3 45.5 - - + -
360R LEU* 4.2 22.8 - - + +
362R THR* 3.5 24.0 - - + +
----------------------------------------------------------
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Residues in contact with ILE 325 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321R PHE* 3.0 61.7 + - + +
322R LEU* 3.7 9.6 - - + +
324R PHE* 1.3 83.1 - - + +
326R ARG* 1.3 66.7 + - - +
328R ILE* 4.2 1.9 - - - +
329R CYS* 2.9 47.5 + - - -
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Residues in contact with ARG 326 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252R TYR* 4.8 22.6 - - + -
322R LEU* 2.9 41.7 + - + +
323R ILE* 3.8 5.6 - - - +
325R ILE* 1.3 82.3 - - - +
327R VAL* 1.3 67.5 + - + +
329R CYS* 4.4 11.7 - - - +
330R ILE* 2.9 55.0 + - + +
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Residues in contact with VAL 327 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU* 5.1 8.7 - - + -
393A LEU* 5.7 0.9 - - + -
251R LEU* 4.5 24.5 - - + -
252R TYR* 5.4 2.7 - - + +
255R LEU* 4.9 13.2 - - + +
323R ILE* 2.7 40.9 + - + +
324R PHE* 3.7 7.2 - - - +
326R ARG* 1.3 79.5 - - + +
328R ILE* 1.3 59.2 + - - +
330R ILE* 3.2 6.6 + - - +
331R VAL* 2.8 43.2 + - + +
356R LEU* 3.7 26.7 - - + -
360R LEU* 4.9 2.9 - - + -
----------------------------------------------------------
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Residues in contact with ILE 328 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324R PHE* 3.0 53.3 + - + +
325R ILE* 4.4 2.2 - - - +
327R VAL* 1.3 79.8 - - + +
329R CYS* 1.3 65.6 + - - +
331R VAL* 3.1 5.6 + - + -
332R VAL* 2.9 39.3 + - + +
353R THR* 3.4 33.2 - - + +
354R LEU* 5.9 1.8 - - + -
356R LEU* 5.0 1.3 - - + -
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Residues in contact with CYS 329 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325R ILE* 2.9 42.4 + - - +
326R ARG* 4.0 17.0 - - - +
328R ILE* 1.3 77.4 - - - +
330R ILE* 1.3 53.5 + - + +
332R VAL* 4.0 5.1 - - - +
333R SER* 2.4 40.0 + - - +
----------------------------------------------------------
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Residues in contact with ILE 330 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLN* 5.1 8.1 - - + +
388A LEU* 6.2 1.6 - - + -
252R TYR* 5.9 6.1 - - + -
255R LEU* 4.5 33.4 - - + -
326R ARG* 2.9 50.9 + - + +
327R VAL* 3.6 4.3 - - - +
329R CYS* 1.3 75.3 - - + +
331R VAL* 1.3 62.9 + - + +
333R SER* 3.5 6.0 - - - -
334R LYS* 2.9 51.8 + - + +
----------------------------------------------------------
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Residues in contact with VAL 331 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU* 3.5 43.3 - - + -
393A LEU* 4.7 8.1 - - + -
394A LEU* 4.7 14.5 - - + +
255R LEU* 6.5 0.9 - - + -
327R VAL* 2.8 30.6 + - + +
328R ILE* 3.6 7.6 - - - +
330R ILE* 1.3 76.9 - - + +
332R VAL* 1.3 62.3 + - + +
334R LYS* 3.4 3.6 + - - +
335R LEU* 2.9 32.9 + - + +
353R THR* 3.9 24.2 - - + +
----------------------------------------------------------
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Residues in contact with VAL 332 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328R ILE* 2.9 33.2 + - + +
329R CYS* 4.0 4.7 - - - +
331R VAL* 1.3 75.7 - - + +
333R SER* 1.3 67.6 + - - +
335R LEU* 3.0 12.1 + - + +
336R LYS* 2.9 43.5 + - + +
346R LYS* 4.5 16.2 - - + +
350R ALA* 6.1 5.4 - - + -
353R THR* 6.1 0.4 - - - +
----------------------------------------------------------
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Residues in contact with SER 333 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329R CYS* 2.4 27.6 + - - +
330R ILE* 3.5 8.2 - - - -
332R VAL* 1.3 79.0 - - - +
334R LYS* 1.3 71.6 + - - +
336R LYS* 3.5 6.5 + - - +
337R ALA* 3.4 19.1 + - - +
----------------------------------------------------------
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Residues in contact with LYS 334 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ASP* 2.9 51.0 + - + +
384A GLN* 4.6 7.0 - - + +
385A ARG* 3.1 42.8 + - + +
388A LEU* 5.9 5.8 - - + -
394A LEU* 6.5 1.1 - - + -
330R ILE* 2.9 34.4 + - + +
331R VAL* 3.8 5.4 - - - +
333R SER* 1.3 83.6 - - - +
335R LEU* 1.3 66.5 + - - +
336R LYS 3.3 0.7 + - - -
337R ALA* 3.4 15.5 + - - +
338R ASN 4.0 0.2 + - - -
339R LEU* 3.8 5.3 + - + +
----------------------------------------------------------
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Residues in contact with LEU 335 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LEU* 5.0 4.0 - - + -
331R VAL* 2.9 23.8 + - + +
332R VAL* 3.0 14.6 + - + +
334R LYS* 1.3 78.3 - - - +
336R LYS* 1.3 53.5 + - - +
339R LEU* 3.2 41.1 - - + +
340R MET* 2.4 40.6 + - + +
344R ASP* 5.4 4.7 - - + +
346R LYS* 4.1 35.0 - - + +
349R LEU* 3.8 34.1 - - + -
350R ALA* 5.6 1.8 - - + +
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Residues in contact with LYS 336 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332R VAL* 2.9 30.1 + - + +
333R SER* 3.9 6.1 - - - +
334R LYS 3.2 0.2 - - - -
335R LEU* 1.3 76.9 - - + +
337R ALA* 1.3 68.6 + - - +
340R MET* 3.1 35.4 - - + +
341R CYS* 4.9 0.5 - - - -
346R LYS* 3.6 42.7 - - + +
----------------------------------------------------------
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Residues in contact with ALA 337 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ARG* 5.0 3.4 - - - +
333R SER 3.4 12.7 + - - +
334R LYS* 3.4 14.2 + - - +
336R LYS* 1.3 82.8 - - - +
338R ASN* 1.3 68.1 + - + +
341R CYS* 3.1 16.5 - - - -
----------------------------------------------------------
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Residues in contact with ASN 338 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ARG* 4.9 8.7 + - - -
346A LEU* 6.1 3.0 - - - +
358A TYR* 5.1 8.6 - - + -
359A CYS 4.0 7.5 + - - +
360A TYR* 3.2 44.9 - - + +
361A PRO* 4.6 7.3 - - - +
385A ARG* 4.5 6.9 - - - +
334R LYS 4.0 1.8 + - - -
337R ALA* 1.3 88.3 - - + +
339R LEU* 1.3 68.1 + - - +
340R MET 3.2 1.3 - - - -
341R CYS* 3.0 30.2 + - + +
342R LYS* 3.7 2.9 + - - +
----------------------------------------------------------
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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