Contacts of the helix formed by residues 283 - 313 (chain A) in PDB entry 1JQI
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 LEU 283 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ALA* 5.1 10.5 - - + +
276A PHE* 5.4 4.9 - - + -
279A PRO 4.7 2.7 - - - +
280A LEU* 3.0 34.4 + - + +
282A LYS* 1.3 79.5 - - + +
284A GLN* 1.3 66.6 + - - +
285A ASN* 4.5 1.6 - - + +
286A ILE* 3.1 23.3 + - + +
287A GLN* 3.3 13.5 + - - +
799B FAD 3.6 57.7 - - + +
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Residues in contact with GLN 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LYS 3.5 4.6 + - - -
283A LEU* 1.3 70.5 - - - +
285A ASN* 1.3 64.0 + - - +
287A GLN* 3.0 19.5 + - - +
288A PHE* 3.0 51.3 + - + -
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Residues in contact with ASN 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 3.2 1.7 - - + +
284A GLN* 1.3 78.5 - - - +
286A ILE* 1.3 87.1 + - + +
288A PHE* 3.3 9.9 + - - +
289A LYS* 3.1 45.8 + - - +
772B GLU* 3.4 20.0 - - - +
775B ARG* 6.4 0.2 - - - +
799B FAD 4.1 11.5 + - + -
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Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ALA* 4.4 9.4 - - + -
280A LEU* 3.4 40.4 - - + +
281A THR* 4.1 6.7 - - - +
283A LEU* 3.1 11.3 + - + +
285A ASN* 1.3 99.8 - - - +
287A GLN* 1.3 63.5 + - - +
289A LYS* 3.3 11.9 + - - +
290A LEU* 3.1 40.6 + - + +
342A ILE* 4.6 18.8 - - + -
799B FAD 4.0 35.4 - - - +
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Residues in contact with GLN 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A THR* 3.2 28.7 + - - +
282A LYS* 3.6 19.4 + - - +
283A LEU 3.3 8.9 + - - +
284A GLN* 3.0 15.0 + - - +
286A ILE* 1.3 78.7 - - - +
288A PHE* 1.3 62.0 + - + +
290A LEU* 3.2 9.9 + - + +
291A ALA* 2.9 29.6 + - - +
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Residues in contact with PHE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLN* 3.0 46.3 + - + +
285A ASN* 3.3 12.3 + - - +
287A GLN* 1.3 80.0 - - + +
289A LYS* 1.3 62.9 + - + +
291A ALA* 3.3 8.3 + - - +
292A ASP* 3.0 31.5 + - - +
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Residues in contact with LYS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ASN* 3.1 45.6 + - - +
286A ILE* 3.5 13.2 - - + +
288A PHE* 1.3 75.3 - - - +
290A LEU* 1.3 58.6 + - - +
292A ASP* 3.0 9.1 + - - +
293A MET* 2.8 40.8 + - - +
338A GLN* 2.5 38.6 + - + +
341A GLN* 4.5 4.4 - - - +
342A ILE* 4.2 22.2 - - + -
772B GLU* 3.0 29.3 + - - -
799B FAD 5.3 1.1 - - - -
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 4.1 14.7 - - + +
266A ALA* 4.3 7.6 - - + +
267A VAL* 3.9 35.9 - - + +
270A ALA* 5.0 1.8 - - + -
281A THR* 4.6 15.0 - - + -
286A ILE* 3.1 30.4 + - + +
287A GLN* 3.6 10.1 - - + +
289A LYS* 1.3 78.7 - - - +
291A ALA* 1.3 56.6 + - - +
293A MET* 3.8 8.5 - - - +
294A ALA* 3.0 29.6 + - - +
342A ILE* 4.0 20.9 - - + -
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLN 2.9 13.5 + - - +
288A PHE* 3.4 13.0 - - - +
289A LYS 3.1 0.2 - - - -
290A LEU* 1.3 77.6 - - - +
292A ASP* 1.3 66.5 + - - +
294A ALA* 3.5 4.9 + - - +
295A LEU* 3.0 25.2 + - - +
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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
----------------------------------------------------------
288A PHE* 3.0 19.8 + - - +
289A LYS* 3.0 10.3 + - - +
291A ALA* 1.3 78.8 - - - +
293A MET* 1.3 63.1 + - + +
295A LEU* 3.7 12.7 - - - +
296A ALA* 3.1 25.3 + - - +
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Residues in contact with MET 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A SER 4.7 0.4 - - - +
263A LEU* 4.2 22.9 - - + -
266A ALA* 4.2 19.1 - - + -
289A LYS* 2.8 28.5 + - - +
290A LEU* 3.8 16.2 - - - +
292A ASP* 1.3 76.4 - - + +
294A ALA* 1.3 65.6 + - - +
296A ALA* 4.6 0.2 - - - -
297A LEU* 3.1 19.8 + - - +
335A ILE* 3.3 61.4 - - + +
338A GLN* 3.8 28.5 - - + -
339A ALA* 4.3 2.5 - - - +
342A ILE* 4.2 6.5 - - - -
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 4.1 21.7 - - + +
290A LEU 3.0 17.9 + - - +
291A ALA* 3.9 5.2 - - - +
293A MET* 1.3 76.2 - - - +
295A LEU* 1.3 63.2 + - - +
297A LEU* 3.2 2.3 + - - +
298A GLU* 2.9 42.4 + - - +
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ALA 3.0 17.7 + - - +
292A ASP* 3.7 13.7 - - - +
293A MET 3.3 0.2 - - - -
294A ALA* 1.3 76.9 - - - +
296A ALA* 1.3 63.9 + - - +
298A GLU* 3.4 4.0 + - + +
299A SER* 3.0 38.5 + - - +
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Residues in contact with ALA 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ASP 3.1 15.3 + - - +
293A MET 3.7 4.0 - - - +
294A ALA 3.3 0.2 - - - -
295A LEU* 1.3 79.9 - - - +
297A LEU* 1.3 57.4 + - - +
299A SER* 3.7 5.6 - - - -
300A ALA* 3.1 28.8 + - - +
331A ALA* 4.2 16.1 - - + +
335A ILE* 4.2 13.7 - - + -
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 6.0 0.2 - - + -
256A LEU* 3.8 32.8 - - + +
259A ALA* 3.9 13.0 - - + -
260A GLN* 3.3 43.3 - - - +
263A LEU* 4.1 17.5 - - + -
293A MET 3.1 16.8 + - - +
294A ALA* 3.7 3.6 - - - +
296A ALA* 1.3 74.3 - - - +
298A GLU* 1.3 62.7 + - + +
300A ALA* 3.1 5.0 + - - +
301A ARG* 3.0 45.1 + - - +
331A ALA* 5.1 1.8 - - + -
335A ILE* 3.9 8.2 - - + +
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL 4.0 15.1 - - - +
5A TYR* 4.0 17.2 - - + +
6A GLN 5.0 4.3 + - - +
294A ALA* 2.9 34.3 + - - +
295A LEU* 4.2 4.0 - - + +
297A LEU* 1.3 74.8 - - + +
299A SER* 1.3 61.7 + - - +
301A ARG* 3.5 22.3 + - - +
302A LEU* 3.2 31.8 + - + +
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Residues in contact with SER 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 3.0 32.7 + - - +
296A ALA* 3.7 6.3 - - - -
298A GLU* 1.3 76.7 - - - +
300A ALA* 1.3 63.5 + - - +
302A LEU* 3.3 11.3 + - - +
303A LEU* 3.2 30.9 + - - +
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 3.5 21.1 - - + -
296A ALA 3.1 19.0 + - - +
297A LEU* 3.1 3.3 + - - +
299A SER* 1.3 78.1 - - - +
301A ARG* 1.3 56.2 + - - +
303A LEU* 3.5 12.2 + - - +
304A THR* 2.8 31.7 + - - -
324A ALA* 4.9 1.4 - - - +
327A ALA* 4.2 7.2 - - + +
328A ALA* 3.8 25.1 - - - +
331A ALA* 4.6 2.7 - - + -
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Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 3.3 53.9 - - - +
79A GLU* 3.0 37.4 + - - +
256A LEU* 3.6 16.5 - - + +
260A GLN* 3.1 23.4 + - - +
297A LEU* 3.0 30.0 + - - +
298A GLU* 3.8 22.6 - - - +
299A SER 3.2 0.2 - - - -
300A ALA* 1.3 74.8 - - - +
302A LEU* 1.3 62.6 + - + +
304A THR* 3.2 0.7 + - - -
305A TRP* 2.8 55.1 + - + +
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLN 6.2 0.4 - - - +
7A SER* 6.5 1.6 - - - -
298A GLU* 3.2 18.9 + - + +
299A SER* 3.3 10.1 + - - +
301A ARG* 1.3 79.9 - - + +
303A LEU* 1.3 56.9 + - + +
305A TRP* 3.3 16.7 + - + +
306A ARG* 2.9 29.9 + - - +
309A MET* 5.6 0.2 - - - +
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A SER* 3.2 20.4 + - - +
300A ALA* 3.7 7.0 - - - +
301A ARG 3.3 0.2 - - - -
302A LEU* 1.3 78.2 - - + +
304A THR* 1.3 62.3 + - - +
306A ARG* 3.3 37.1 + - - +
307A ALA* 3.1 23.6 + - - +
320A GLU 4.4 2.1 - - - +
323A MET* 4.2 19.7 - - + +
324A ALA* 3.8 13.6 - - + +
327A ALA* 3.6 30.1 - - + -
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Residues in contact with THR 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A SER* 3.3 26.0 - - - +
249A ILE* 4.2 14.7 - - + +
252A ALA* 3.6 20.4 - - + +
253A SER* 3.6 11.0 - - - +
256A LEU* 3.7 17.5 - - + +
300A ALA 2.8 21.8 + - - -
301A ARG 3.2 4.9 + - - -
303A LEU* 1.3 77.0 - - - +
305A TRP* 1.3 56.3 + - + +
307A ALA* 3.2 4.7 + - - +
308A ALA* 3.0 26.3 + - - +
324A ALA* 3.5 13.1 + - - +
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Residues in contact with TRP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 3.8 32.5 - + - -
7A SER* 3.8 20.9 - - - -
8A VAL* 6.5 0.4 - - + -
10A LEU* 3.8 33.0 - - + -
72A LEU* 4.1 15.9 - - + -
75A SER* 4.0 18.9 + - - -
76A ILE* 3.8 28.0 - - + +
79A GLU* 4.9 4.0 + - - -
256A LEU* 5.3 0.8 - - + +
301A ARG* 2.8 43.6 + - + +
302A LEU* 3.8 16.2 - - + +
304A THR* 1.3 75.0 - - + +
306A ARG* 1.3 62.5 + - - +
308A ALA* 3.7 6.0 - - - +
309A MET* 2.9 45.3 + - + +
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Residues in contact with ARG 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU 2.9 17.8 + - - +
303A LEU* 3.5 27.1 + - - +
305A TRP* 1.3 75.9 - - - +
307A ALA* 1.3 57.5 + - - +
309A MET* 3.4 12.5 + - + +
310A LEU* 3.0 46.3 + - + +
319A LYS* 5.1 4.9 - - - +
320A GLU* 3.7 33.9 + - - +
323A MET* 3.5 31.1 - - - +
----------------------------------------------------------
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Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ILE* 3.6 24.7 - - + +
303A LEU 3.1 10.2 + - - +
304A THR 3.2 8.5 + - - +
306A ARG* 1.3 77.4 - - - +
308A ALA* 1.3 65.3 + - - +
310A LEU* 3.3 4.6 + - - +
311A LYS* 3.1 19.1 + - - +
317A PHE* 4.1 4.0 - - - +
320A GLU* 3.8 35.6 - - - +
321A SER* 4.0 6.1 - - - +
324A ALA* 4.6 3.4 - - + -
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A TYR* 3.6 30.9 - - - +
72A LEU* 3.9 7.9 - - - -
75A SER* 4.4 5.4 - - - -
249A ILE* 3.8 20.3 - - + +
304A THR 3.0 16.4 + - - +
305A TRP* 3.7 7.6 - - - +
307A ALA* 1.3 76.0 - - - +
309A MET* 1.3 58.7 + - - +
311A LYS* 3.4 4.3 + - - +
312A ASP* 3.1 32.5 + - - +
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Residues in contact with MET 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 3.8 28.0 - - + -
305A TRP* 2.9 50.0 + - + +
306A ARG* 3.8 9.6 - - + +
308A ALA* 1.3 76.3 - - - +
310A LEU* 1.3 60.8 + - + +
312A ASP* 3.2 8.9 + - - +
313A ASN* 2.9 37.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ARG* 3.0 33.4 + - + +
307A ALA 3.3 4.2 + - - +
309A MET* 1.3 76.6 - - + +
311A LYS* 1.3 61.2 + - - +
313A ASN* 3.3 5.6 + - + +
314A LYS 3.1 4.5 + - - -
315A LYS* 2.9 48.2 + - + +
316A PRO 4.1 9.2 - - - +
317A PHE* 3.9 10.5 - - + -
320A GLU* 3.4 42.0 - - + +
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Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 3.5 15.8 + - - -
71A TYR* 3.4 49.4 - - + -
246A MET* 4.1 18.6 - - + -
249A ILE* 4.5 4.3 - - + -
307A ALA 3.1 12.2 + - - +
308A ALA* 3.5 8.7 - - - +
310A LEU* 1.3 78.0 - - - +
312A ASP* 1.3 64.2 + - - +
314A LYS* 2.8 47.0 + - - +
315A LYS 4.6 0.4 - - - +
317A PHE* 3.6 41.0 - - + -
----------------------------------------------------------
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Residues in contact with ASP 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 5.0 1.2 - - - +
70A ASP* 3.3 20.6 - - + +
71A TYR* 2.8 27.8 + - - +
72A LEU* 3.1 28.2 + - - +
308A ALA 3.1 12.2 + - - +
309A MET* 3.2 10.7 + - - +
311A LYS* 1.3 82.4 - - - +
313A ASN* 1.3 65.1 + - - +
314A LYS* 3.1 14.4 + - - +
----------------------------------------------------------
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Residues in contact with ASN 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A MET* 2.9 21.4 + - - +
310A LEU* 3.3 7.7 + - + +
312A ASP* 1.3 83.8 + - - +
314A LYS* 1.3 71.0 + - - +
315A LYS* 3.3 22.0 + - + +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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