Contacts of the helix formed by residues 225 - 277 (chain A) in PDB entry 6FPK
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 225 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ASP* 1.3 67.4 + - - +
227A LEU* 3.2 10.3 - - - +
228A PHE* 3.4 31.5 + - + +
229A GLU* 3.2 22.2 + - - +
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Residues in contact with ASP 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ASP* 1.3 73.3 - - - +
227A LEU* 1.3 59.9 + - + +
229A GLU* 3.5 15.5 + - - +
230A GLU* 3.0 30.0 + - - +
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ASP* 3.2 10.0 + - - +
226A ASP* 1.3 77.8 - - + +
228A PHE* 1.3 64.8 + - - +
230A GLU* 3.4 5.2 + - + +
231A LEU* 3.0 23.4 + - - +
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Residues in contact with PHE 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ASP* 3.4 28.3 + - + +
227A LEU* 1.3 78.1 - - - +
229A GLU* 1.3 58.7 + - - +
231A LEU* 3.4 23.0 - - + +
232A GLU* 2.9 43.2 + - + +
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Residues in contact with GLU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ASP 3.2 16.0 + - - +
226A ASP* 3.5 17.0 - - - +
228A PHE* 1.3 76.1 - - - +
230A GLU* 1.3 61.2 + - - +
232A GLU* 3.4 17.8 + - - +
233A GLU* 3.0 27.8 + - + +
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Residues in contact with GLU 230 (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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226A ASP 3.0 17.4 + - - +
227A LEU* 4.0 6.5 - - + +
229A GLU* 1.3 74.8 - - - +
231A LEU* 1.3 64.8 + - - +
233A GLU* 3.3 19.5 + - - +
234A GLN* 3.0 46.6 + - + +
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Residues in contact with LEU 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A LEU 3.0 14.2 + - - +
228A PHE* 3.4 29.8 - - + +
229A GLU 3.4 0.2 - - - -
230A GLU* 1.3 77.8 - - - +
232A GLU* 1.3 57.8 + - - +
234A GLN* 3.3 7.6 + - + +
235A LEU* 2.9 61.5 + - + +
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Residues in contact with GLU 232 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A PHE* 2.9 34.5 + - + +
229A GLU* 3.8 17.8 - - - +
230A GLU 3.2 0.6 - - - -
231A LEU* 1.3 78.6 - - - +
233A GLU* 1.3 64.3 + - - +
235A LEU* 3.4 8.9 + - - +
236A LEU* 2.9 23.8 + - + +
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Residues in contact with GLU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLU 3.0 17.9 + - - +
230A GLU* 3.8 23.3 - - - +
232A GLU* 1.3 78.8 - - - +
234A GLN* 1.3 59.2 + - - +
236A LEU* 3.2 13.2 + - + +
237A ILE* 2.9 49.3 + - + +
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Residues in contact with GLN 234 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLU* 3.0 41.8 + - + +
231A LEU* 3.6 8.3 - - + +
233A GLU* 1.3 78.1 - - - +
235A LEU* 1.3 58.8 + - + +
237A ILE* 3.4 25.1 + - - +
238A ALA* 3.0 27.2 + - - +
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Residues in contact with LEU 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU* 2.9 49.5 + - + +
232A GLU* 3.8 7.4 - - - +
234A GLN* 1.3 76.6 - - + +
236A LEU* 1.3 57.4 + - - +
238A ALA* 3.4 6.4 + - + +
239A ASP* 2.9 29.8 + - - +
302A MPD 4.6 29.8 - - + +
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Residues in contact with LEU 236 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A GLU* 2.9 16.9 + - + +
233A GLU* 3.4 16.4 - - + +
235A LEU* 1.3 74.1 - - - +
237A ILE* 1.3 63.7 + - + +
239A ASP* 3.3 10.4 + - - +
240A VAL* 3.0 50.9 + - + +
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Residues in contact with ILE 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A GLU* 2.9 37.4 + - + +
234A GLN* 3.6 31.2 - - - +
236A LEU* 1.3 74.9 - - + +
238A ALA* 1.3 67.7 + - - +
240A VAL* 3.3 5.8 + - - +
241A GLY* 3.0 20.4 + - - -
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Residues in contact with ALA 238 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A GLN 3.0 16.6 + - - +
235A LEU* 3.8 9.4 - - + +
236A LEU 3.3 0.2 - - - -
237A ILE* 1.3 78.5 - - - +
239A ASP* 1.3 58.8 + - - +
241A GLY* 3.3 1.3 + - - -
242A VAL* 2.9 37.8 + - + +
302A MPD 3.9 19.5 - - + +
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Residues in contact with ASP 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A LEU 2.9 17.5 + - - +
236A LEU* 3.6 13.3 - - + +
237A ILE 3.2 0.2 - - - -
238A ALA* 1.3 79.4 - - - +
240A VAL* 1.3 59.9 + - - +
242A VAL* 4.1 0.4 - - - +
243A GLU* 2.9 46.2 + - - +
302A MPD 3.5 35.0 + - + +
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Residues in contact with VAL 240 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A LEU* 3.0 38.4 + - + +
237A ILE* 3.8 6.3 - - - +
238A ALA 3.3 0.2 - - - -
239A ASP* 1.3 78.4 - - + +
241A GLY* 1.3 56.1 + - - +
243A GLU* 4.1 3.5 - - - +
244A THR* 2.6 46.4 + - - +
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Residues in contact with GLY 241 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ILE 3.0 14.7 + - - -
238A ALA* 3.7 2.5 - - - -
240A VAL* 1.3 79.0 - - - +
242A VAL* 1.3 57.9 + - - +
244A THR* 3.7 5.2 - - - -
245A THR* 2.8 33.2 + - - -
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Residues in contact with VAL 242 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ALA* 2.9 25.5 + - + +
239A ASP 4.1 2.0 - - - +
241A GLY* 1.3 73.2 - - - +
243A GLU* 1.3 62.6 + - + +
245A THR* 3.4 7.1 + - - -
246A ARG* 3.0 45.2 + - + +
301A MPD 4.1 16.8 - - + -
302A MPD 4.5 20.2 - - + +
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Residues in contact with GLU 243 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ASP* 2.9 37.3 + - - +
240A VAL* 4.1 3.8 - - - +
242A VAL* 1.3 76.3 - - + +
244A THR* 1.3 67.2 + - - +
246A ARG* 3.1 33.5 + - - +
247A LYS* 3.0 25.5 + - - +
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Residues in contact with THR 244 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A VAL* 2.6 34.1 + - - +
241A GLY* 3.7 6.1 - - - -
243A GLU* 1.3 76.9 - - - +
245A THR* 1.3 62.9 + - - +
247A LYS* 3.2 6.9 + - + +
248A ILE* 3.0 44.4 + - + +
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Residues in contact with THR 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A GLY 2.8 22.9 + - - -
242A VAL* 3.5 8.8 - - - -
243A GLU 3.3 0.2 - - - -
244A THR* 1.3 75.8 - - - +
246A ARG* 1.3 66.2 + - + +
248A ILE* 4.0 5.2 - - - +
249A ILE* 3.0 43.3 + - + +
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Residues in contact with ARG 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A VAL* 3.0 32.7 + - + +
243A GLU* 3.1 32.5 + - - +
245A THR* 1.3 80.4 - - + +
247A LYS* 1.3 56.5 + - - +
249A ILE* 4.2 2.6 - - - +
250A THR* 2.7 41.4 + - - +
301A MPD 2.6 60.6 + - - +
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Residues in contact with LYS 247 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A GLU 3.0 18.6 + - - +
244A THR* 3.2 6.3 + - + +
246A ARG* 1.3 78.2 - - - +
248A ILE* 1.3 75.6 + - + +
250A THR* 3.8 4.3 - - - -
251A ASN* 3.0 53.8 + - - +
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Residues in contact with ILE 248 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A THR* 3.0 35.8 + - + +
245A THR* 4.0 4.9 - - - +
247A LYS* 1.3 90.0 - - + +
249A ILE* 1.3 64.9 + - + +
251A ASN* 3.2 5.2 + - - +
252A LEU* 2.8 50.5 + - + +
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Residues in contact with ILE 249 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A THR* 3.0 35.7 + - + +
246A ARG* 4.2 2.9 - - - +
248A ILE* 1.3 83.3 - - + +
250A THR* 1.3 59.1 + - - +
252A LEU* 3.4 11.3 + - + +
253A THR* 2.8 42.0 + - - +
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Residues in contact with THR 250 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ARG* 2.7 27.9 + - - +
247A LYS* 3.8 5.2 - - - -
249A ILE* 1.3 74.8 - - - +
251A ASN* 1.3 66.5 + - - +
253A THR* 3.3 5.6 + - - -
254A GLU* 3.0 51.8 + - + +
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Residues in contact with ASN 251 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A LYS* 3.0 50.5 + - - +
248A ILE* 3.7 5.4 - - - +
250A THR* 1.3 78.2 - - - +
252A LEU* 1.3 62.9 + - + +
254A GLU* 3.7 14.5 - - - +
255A GLY* 2.9 25.1 + - - -
258A ARG* 4.9 2.8 + - - -
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Residues in contact with LEU 252 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ILE* 2.8 39.1 + - + +
249A ILE* 3.9 14.1 - - + +
251A ASN* 1.3 80.1 - - + +
253A THR* 1.3 56.5 + - - +
255A GLY* 3.3 2.7 + - - +
256A ALA* 2.9 28.4 + - - +
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Residues in contact with THR 253 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ILE* 2.8 32.9 + - - +
250A THR* 3.7 6.7 - - - -
252A LEU* 1.3 73.6 - - - +
254A GLU* 1.3 65.1 + - + +
256A ALA* 3.3 9.3 + - + +
257A SER* 3.0 30.2 + - - +
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Residues in contact with GLU 254 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A THR* 3.0 40.6 + - + +
251A ASN* 3.7 14.8 - - - +
253A THR* 1.3 76.9 - - + +
255A GLY* 1.3 56.9 + - - +
257A SER* 3.1 10.2 + - - -
258A ARG* 2.9 52.1 + - + +
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Residues in contact with GLY 255 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ASN 2.9 14.3 + - - -
252A LEU* 3.6 5.2 - - - -
254A GLU* 1.3 75.2 - - - +
256A ALA* 1.3 60.0 + - - +
258A ARG* 3.3 22.4 + - - +
259A LYS* 3.1 23.0 + - - +
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Residues in contact with ALA 256 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A LEU 2.9 12.9 + - - +
253A THR* 3.4 12.6 - - + +
255A GLY* 1.3 71.6 - - - +
257A SER* 1.3 67.0 + - - +
259A LYS* 3.2 8.9 + - - +
260A GLN* 3.0 26.4 + - - +
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Residues in contact with SER 257 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A THR* 3.0 19.9 + - - +
254A GLU* 3.1 9.9 + - - -
256A ALA* 1.3 76.0 - - - +
258A ARG* 1.3 59.7 + - - +
260A GLN* 3.0 10.3 + - - +
261A LEU* 2.9 36.4 + - - +
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Residues in contact with ARG 258 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ASN 4.9 2.4 + - - -
254A GLU* 2.9 47.5 + - + +
255A GLY* 3.8 22.2 - - - +
256A ALA 3.2 0.2 - - - -
257A SER* 1.3 76.3 - - - +
259A LYS* 1.3 57.3 + - - +
261A LEU* 3.3 15.1 + - + +
262A ARG* 2.9 38.5 + - + +
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Residues in contact with LYS 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A GLY 3.1 13.7 + - - +
256A ALA* 3.5 10.5 - - - +
258A ARG* 1.3 74.1 - - - +
260A GLN* 1.3 67.3 + - + +
262A ARG* 3.3 9.2 + - + +
263A ASP* 2.8 54.5 + - - +
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Residues in contact with GLN 260 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ALA* 3.0 17.0 + - + +
257A SER* 3.0 12.1 + - - +
259A LYS* 1.3 79.4 - - + +
261A LEU* 1.3 58.8 + - + +
263A ASP* 3.2 5.6 + - - +
264A ALA* 2.9 31.3 + - - +
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Residues in contact with LEU 261 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A SER* 2.9 23.7 + - - +
258A ARG* 3.7 16.6 - - + +
259A LYS 3.2 0.2 - - - -
260A GLN* 1.3 78.6 - - + +
262A ARG* 1.3 55.2 + - + +
264A ALA* 3.4 8.1 + - + +
265A GLU* 2.9 31.1 + - - +
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Residues in contact with ARG 262 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ARG* 2.9 23.6 + - + +
259A LYS* 3.7 8.5 - - + +
261A LEU* 1.3 77.6 - - + +
263A ASP* 1.3 59.7 + - - +
265A GLU* 3.3 7.3 + - - +
266A ALA* 3.0 27.9 + - - +
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Residues in contact with ASP 263 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LYS* 2.8 43.7 + - - +
260A GLN* 3.7 6.0 - - - +
262A ARG* 1.3 73.0 - - - +
264A ALA* 1.3 62.3 + - - +
266A ALA* 3.2 8.5 + - - +
267A LEU* 2.8 40.8 + - + +
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Residues in contact with ALA 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLN 2.9 16.7 + - - +
261A LEU* 3.8 9.6 - - + +
263A ASP* 1.3 76.9 - - - +
265A GLU* 1.3 58.1 + - - +
267A LEU* 3.4 9.1 + - - +
268A TYR* 2.9 29.8 + - - +
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Residues in contact with GLU 265 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A LEU 2.9 18.3 + - - +
262A ARG* 3.7 7.0 - - - +
263A ASP 3.3 0.4 - - - -
264A ALA* 1.3 75.8 - - - +
266A ALA* 1.3 55.9 + - - +
268A TYR* 3.3 19.6 + - - +
269A GLY* 3.0 26.3 + - - -
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Residues in contact with ALA 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ARG 3.0 14.0 + - - +
263A ASP* 3.2 11.0 + - - +
265A GLU* 1.3 72.6 - - - +
267A LEU* 1.3 65.3 + - + +
269A GLY* 3.4 2.5 + - - -
270A LEU* 3.1 34.5 + - + +
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Residues in contact with LEU 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASP* 2.8 27.4 + - + +
264A ALA* 3.9 8.1 - - - +
266A ALA* 1.3 76.4 - - + +
268A TYR* 1.3 56.5 + - - +
270A LEU* 3.2 18.2 + - + +
271A LEU* 2.8 31.3 + - - +
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Residues in contact with TYR 268 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ALA 2.9 18.4 + - - +
265A GLU* 3.5 21.3 - - - +
267A LEU* 1.3 75.6 - - - +
269A GLY* 1.3 67.3 + - - +
271A LEU* 3.4 12.7 + - + +
272A LYS* 2.9 60.7 + - + +
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Residues in contact with GLY 269 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A GLU 3.0 14.4 + - - -
266A ALA* 3.8 3.6 - - - -
268A TYR* 1.3 80.7 - - - +
270A LEU* 1.3 57.3 + - - +
272A LYS* 3.4 5.6 + - - +
273A GLU* 3.0 43.0 + - - +
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Residues in contact with LEU 270 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ALA* 3.1 24.9 + - + +
267A LEU* 3.5 21.1 - - + +
269A GLY* 1.3 72.9 - - - +
271A LEU* 1.3 61.5 + - - +
273A GLU* 3.5 18.4 + - - +
274A GLU* 2.9 30.2 + - - +
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Residues in contact with LEU 271 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU 2.8 20.3 + - - +
268A TYR* 3.7 12.8 - - + +
270A LEU* 1.3 74.8 - - - +
272A LYS* 1.3 51.8 + - - +
274A GLU* 3.2 10.5 + - + +
275A MET* 2.7 68.4 + - + +
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Residues in contact with LYS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A TYR* 2.9 56.7 + - + +
269A GLY* 3.7 6.1 - - - +
271A LEU* 1.3 73.9 - - - +
273A GLU* 1.3 56.2 + - - +
275A MET* 3.2 8.3 + - - +
276A GLY* 2.9 26.0 + - - -
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Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLY* 3.0 26.5 + - - +
270A LEU* 3.6 23.0 - - - +
272A LYS* 1.3 74.9 - - - +
274A GLU* 1.3 65.2 + - - +
276A GLY* 2.9 14.4 + - - -
277A GLU* 3.5 8.1 + - - +
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Residues in contact with GLU 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU 2.9 19.7 + - - +
271A LEU* 3.2 12.3 + - + +
273A GLU* 1.3 73.9 - - - +
275A MET* 1.3 59.9 + - + +
277A GLU* 3.0 34.3 + - - +
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Residues in contact with MET 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 2.7 54.4 + - + +
272A LYS* 3.6 7.2 - - - +
274A GLU* 1.3 73.5 - - + +
276A GLY* 1.3 68.4 + - - +
277A GLU* 2.8 16.5 + - - +
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Residues in contact with GLY 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS 2.9 14.2 + - - -
273A GLU* 2.9 7.2 + - - -
275A MET* 1.3 77.2 - - - +
277A GLU* 1.3 61.2 - - - +
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Residues in contact with GLU 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A GLU 3.5 6.2 + - - +
274A GLU* 3.0 26.3 + - - +
275A MET* 2.8 22.4 - - - +
276A GLY* 1.3 77.6 - - - +
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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