Contacts of the helix formed by residues 291 - 319 (chain A) in PDB entry 5CRV
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 PRO 291 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PRO* 5.7 3.4 - - + -
289A GLY 4.6 0.9 - - - +
290A GLN* 1.4 97.9 - - + +
292A ASP* 1.3 65.2 + - - +
293A THR* 3.6 19.5 - - + +
294A VAL* 3.1 19.8 + - + +
295A GLN* 3.2 8.1 + - - +
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Residues in contact with ASP 292 (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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290A GLN 5.0 0.7 - - - +
291A PRO* 1.3 73.6 - - - +
293A THR* 1.3 52.8 + - + +
295A GLN* 4.0 13.4 - - + +
296A ASP* 2.6 53.7 + - - +
57B ARG* 6.1 1.2 - - - -
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Residues in contact with THR 293 (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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5A PRO* 4.8 2.0 - - - +
6A ARG 4.2 13.7 - - - +
8A PRO* 3.9 24.9 - - + +
291A PRO* 3.6 17.1 - - + +
292A ASP* 1.3 78.7 - - + +
294A VAL* 1.3 66.2 + - - -
296A ASP* 3.5 7.4 + - - +
297A ALA* 3.3 22.5 + - - +
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Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET* 4.0 9.4 - - - +
8A PRO* 3.7 29.2 - - + -
240A LEU* 4.0 7.4 - - + -
243A MET* 3.7 20.9 - - + -
287A ALA* 3.9 24.9 - - + -
290A GLN* 3.7 25.8 - - + +
291A PRO* 3.1 13.8 + - + +
293A THR* 1.3 83.3 + - - +
295A GLN* 1.3 64.1 + - - +
297A ALA* 3.3 4.0 + - - +
298A LEU* 3.1 26.3 + - + +
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Residues in contact with GLN 295 (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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284A ILE* 5.3 5.0 - - - +
287A ALA* 2.7 39.8 + - - +
288A LYS* 4.6 0.6 - - - +
289A GLY 4.2 3.8 - - - +
290A GLN* 2.9 24.7 + - - +
291A PRO 3.3 11.2 - - - +
292A ASP* 3.1 17.0 + - + +
294A VAL* 1.3 78.1 - - - +
296A ASP* 1.3 59.7 + - - +
298A LEU* 3.4 8.4 + - - +
299A ARG* 2.9 41.1 + - + +
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Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 3.6 19.3 - - + +
292A ASP* 2.6 36.6 + - - +
293A THR* 3.9 7.2 + - - +
295A GLN* 1.3 77.5 - - - +
297A ALA* 1.3 59.6 + - - +
299A ARG* 3.6 17.3 + - - +
300A PHE* 3.1 24.4 + - - +
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Residues in contact with ALA 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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4A VAL* 3.5 9.2 - - + +
5A PRO* 3.2 32.0 - - - +
6A ARG 4.8 0.7 - - - -
7A MET* 3.8 24.2 - - + -
247A TYR* 4.5 3.4 - - - +
293A THR 3.3 11.5 + - - +
294A VAL 3.7 7.4 - - - +
295A GLN 3.3 0.2 - - - -
296A ASP* 1.3 77.4 - - - +
298A LEU* 1.3 62.4 + - - +
300A PHE 3.5 0.5 + - - -
301A THR* 2.9 29.3 + - - -
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Residues in contact with LEU 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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7A MET* 4.0 9.0 - - + -
243A MET* 4.3 2.9 - - - -
247A TYR* 3.5 30.5 - - + -
280A LEU* 3.6 17.3 - - + +
283A ALA* 4.2 11.0 - - + +
284A ILE* 4.0 27.2 - - + +
287A ALA* 3.5 32.3 - - + -
294A VAL* 3.1 21.7 + - + +
295A GLN* 3.8 11.2 - - - +
297A ALA* 1.3 73.0 - - - +
299A ARG* 1.3 60.8 + - - +
301A THR* 3.3 4.3 + - - +
302A MET* 2.9 31.1 + - - +
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Residues in contact with ARG 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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284A ILE* 6.1 0.2 - - - -
295A GLN* 2.9 26.0 + - + +
296A ASP* 3.6 19.9 + - - +
298A LEU* 1.3 75.8 - - - +
300A PHE* 1.3 62.9 + - - +
302A MET* 3.1 12.3 + - - +
303A ASP* 3.1 28.1 + - - +
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Residues in contact with PHE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.4 34.1 - - + -
3A ALA* 3.6 33.0 - - + -
4A VAL* 3.5 22.4 - - + -
5A PRO* 3.6 19.7 - - + -
296A ASP 3.1 15.7 + - - +
297A ALA 3.6 2.9 - - - +
299A ARG* 1.3 78.5 - - - +
301A THR* 1.3 64.3 + - - +
303A ASP* 3.3 14.1 + - + +
304A VAL* 3.3 27.3 + - + +
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Residues in contact with THR 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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1A MET 5.9 3.0 + - - +
4A VAL* 3.5 8.1 - - - +
247A TYR* 3.3 31.9 + - + +
250A ALA* 5.7 0.4 - - + -
251A VAL* 4.9 9.4 - - + -
254A LEU* 5.4 4.0 - - + -
280A LEU* 3.6 9.6 - - + -
297A ALA 2.9 17.4 + - - -
298A LEU 3.8 3.6 - - - -
299A ARG 3.3 0.2 - - - -
300A PHE* 1.3 78.3 - - - +
302A MET* 1.3 59.8 + - - +
304A VAL* 3.8 5.8 - - + +
305A ILE* 3.0 55.7 + - + +
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Residues in contact with MET 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 5.1 9.0 - - + +
280A LEU* 3.4 14.8 - - + +
281A ASN* 3.6 24.0 - - - +
284A ILE* 3.7 19.3 - - + -
298A LEU 2.9 19.2 + - - +
299A ARG* 3.4 11.0 - - - +
301A THR* 1.3 78.3 - - - +
303A ASP* 1.3 59.6 + - - +
305A ILE* 5.0 0.2 - - - -
306A GLY* 2.8 30.2 + - - +
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Residues in contact with ASP 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 ARG* 3.1 15.1 + - - +
300A PHE* 3.4 13.2 - - + +
301A THR 3.2 0.2 - - - -
302A MET* 1.3 82.1 - - - +
304A VAL* 1.3 63.1 + - + +
307A GLY* 3.0 21.1 + - - -
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Residues in contact with VAL 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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1A MET* 4.0 25.4 - - + +
254A LEU* 4.3 19.1 - - + -
300A PHE* 3.3 37.1 + - + +
301A THR* 3.4 8.3 + - + +
303A ASP* 1.3 77.8 - - + +
305A ILE* 1.3 59.2 + - + +
307A GLY* 3.8 0.5 - - - -
308A LYS* 3.0 57.5 + - + +
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Residues in contact with ILE 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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250A ALA* 4.2 14.6 - - + +
254A LEU* 4.3 23.6 - - + -
273A PHE* 3.8 13.5 - - + +
276A ALA* 3.9 28.9 - - + +
277A LEU* 3.7 34.5 - - + +
280A LEU* 4.2 8.3 - - + -
301A THR* 3.0 39.8 + - + +
302A MET 4.6 0.7 - - - +
304A VAL* 1.3 72.4 - - + +
306A GLY* 1.3 57.6 + - - +
308A LYS* 4.1 4.4 - - - +
309A TYR* 2.9 29.1 + - - +
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Residues in contact with GLY 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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277A LEU* 4.4 16.0 - - - +
302A MET* 2.8 20.4 + - - -
305A ILE* 1.3 78.1 - - - +
307A GLY* 1.3 60.6 + - - +
309A TYR* 3.9 3.5 - - - +
310A ASN* 3.2 31.8 + - - +
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Residues in contact with GLY 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 ASP 3.0 18.4 + - - -
304A VAL 3.8 0.4 - - - -
306A GLY* 1.3 74.4 - - - +
308A LYS* 1.3 57.6 + - - +
310A ASN* 3.4 8.3 + - - +
311A SER* 3.1 32.6 + - - -
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Residues in contact with LYS 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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1A MET* 5.1 10.1 - - - +
254A LEU* 4.0 21.5 - - + -
258A LYS* 4.5 23.8 - - + +
261A GLU* 5.7 5.4 - - - +
269A ARG* 5.4 0.5 + - - -
273A PHE* 3.3 26.8 - - + -
304A VAL* 3.0 33.5 + - + +
305A ILE* 4.1 3.8 - - - +
307A GLY* 1.3 73.0 - - - +
309A TYR* 1.3 65.3 - - - +
311A SER* 4.0 4.7 - - - -
312A ALA* 3.0 27.0 + - - +
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Residues in contact with TYR 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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270A VAL* 4.4 15.3 - - + +
273A PHE* 3.9 16.1 - - + +
274A GLN* 3.6 59.3 + - + -
277A LEU* 4.0 24.5 - - + -
305A ILE 2.9 20.2 + - - +
306A GLY 3.9 2.9 - - - +
308A LYS* 1.3 76.7 - - - +
310A ASN* 1.3 73.5 + - - +
312A ALA* 3.3 2.1 + - - +
313A LYS* 2.9 62.4 + - + +
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Residues in contact with ASN 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 GLY 3.2 18.5 + - - +
307A GLY* 3.6 6.6 - - - +
308A LYS 3.4 0.2 - - - -
309A TYR* 1.3 97.1 - - - +
311A SER* 1.3 57.7 + - - +
313A LYS* 3.5 3.1 + - - +
314A LYS* 2.9 31.2 + - - +
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Residues in contact with SER 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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269A ARG* 5.1 5.6 - - - -
307A GLY 3.1 17.9 + - - -
308A LYS* 4.1 5.2 - - - -
310A ASN* 1.3 75.4 - - - +
312A ALA* 1.3 58.9 + - - +
314A LYS* 3.3 10.2 + - - +
315A ASP* 2.9 42.5 + - - -
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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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266A PHE 5.0 0.5 - - - +
269A ARG* 3.6 36.0 + - + +
270A VAL* 3.4 20.1 - - + +
273A PHE* 3.6 18.6 - - + -
308A LYS 3.0 21.0 + - - +
309A TYR* 3.7 2.7 - - - +
311A SER* 1.3 77.5 - - - +
313A LYS* 1.3 57.9 + - - +
315A ASP* 3.5 2.1 + - - +
316A ASN* 3.1 23.2 + - - +
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Residues in contact with LYS 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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270A VAL* 3.6 21.1 - - + +
309A TYR* 2.9 55.6 + - + +
310A ASN* 4.1 2.9 - - - +
312A ALA* 1.3 71.1 - - - +
314A LYS* 1.3 59.9 + - - +
316A ASN* 3.8 1.1 - - - +
317A ASP* 2.9 62.8 + - - +
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Residues in contact with LYS 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 ASN 2.9 19.3 + - - +
311A SER* 3.4 9.2 - - - +
313A LYS* 1.3 76.7 - - - +
315A ASP* 1.3 70.8 + - - +
317A ASP* 3.3 2.8 + - - -
318A PHE* 3.0 54.8 + - + +
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Residues in contact with ASP 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ARG* 3.7 21.6 + - - +
311A SER* 2.9 23.6 + - - +
312A ALA 3.9 3.8 - - - +
314A LYS* 1.3 86.9 - - - +
316A ASN* 1.3 56.9 + - - +
318A PHE* 5.1 0.2 - - - -
319A ILE* 2.8 43.7 + - + +
320A TYR* 3.2 29.7 + - + -
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Residues in contact with ASN 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PHE* 4.4 12.5 - - + +
267A GLY* 4.5 1.9 + - - -
270A VAL* 4.1 11.2 - - + +
312A ALA 3.1 18.4 + - - +
313A LYS* 4.0 3.1 - - - +
315A ASP* 1.3 78.9 - - - +
317A ASP* 1.3 68.5 + - - +
318A PHE 3.6 0.3 + - - -
320A TYR* 3.8 6.5 + - - +
321A HIS* 2.7 35.1 + - - +
322A GLU* 2.7 54.5 + - - +
324A VAL* 3.8 19.4 - - - +
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Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LYS* 2.9 58.8 + - - +
314A LYS* 4.0 4.4 - - - +
316A ASN* 1.3 87.3 + - - +
318A PHE* 1.3 67.1 + - + +
321A HIS* 3.3 18.8 + - - -
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Residues in contact with PHE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LYS* 3.0 49.3 + - + +
315A ASP* 5.1 0.2 - - - -
317A ASP* 1.3 86.6 - - + +
319A ILE* 1.3 69.7 + - + +
321A HIS* 3.3 17.1 + - - -
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Residues in contact with ILE 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ASP* 2.8 36.1 + - + +
317A ASP 3.8 0.2 - - - -
318A PHE* 1.3 84.0 - - + +
320A TYR* 1.3 89.1 + - + +
321A HIS* 3.0 20.6 + - - -
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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