Contacts of the helix formed by residues 241 - 266 (chain A) in PDB entry 3RHW
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 ALA 241 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A PHE* 4.8 2.6 - - + +
238A ASP* 3.1 32.6 + - - +
239A ARG 4.7 0.2 - - - -
240A THR* 1.3 77.3 + - - +
242A ILE* 1.3 63.5 + - - +
243A PRO* 3.2 8.5 - - + -
244A ALA* 3.5 22.6 + - + +
245A ARG* 3.8 7.7 + - - +
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Residues in contact with ILE 242 (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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239A ARG* 4.4 5.1 + - - +
240A THR 3.1 7.3 + - - +
241A ALA* 1.3 69.9 - - - +
243A PRO* 1.3 81.2 - - + +
244A ALA 3.1 2.2 - - - -
245A ARG* 2.9 39.5 + - + +
246A VAL* 3.0 17.6 + - + +
294A PHE* 3.9 26.9 - - + +
297A VAL* 6.3 0.2 - - + -
298A ASN* 4.0 21.8 - - + +
237B PHE* 3.4 27.8 - - + -
241B ALA* 4.2 16.8 - - + -
244B ALA* 4.0 19.3 - - + -
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Residues in contact with PRO 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A THR 4.4 2.2 - - - +
241A ALA* 3.2 10.3 - - + -
242A ILE* 1.3 100.6 - - + +
244A ALA* 1.3 61.4 + - - +
246A VAL* 3.7 5.2 + - + +
247A THR* 3.0 29.2 + - - -
241B ALA* 5.7 3.8 - - + -
243B PRO* 4.7 22.9 - - + -
244B ALA* 5.0 7.2 - - + +
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Residues in contact with ALA 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A PHE* 4.5 27.6 - - + -
241A ALA* 3.5 17.8 + - + +
242A ILE 3.1 0.4 - - - -
243A PRO* 1.3 79.0 - - - +
245A ARG* 1.3 62.8 + - - +
247A THR* 3.5 6.2 + - - -
248A LEU* 3.1 29.7 + - - +
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Residues in contact with ARG 245 (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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234A SER* 2.7 37.7 + - - +
235A PHE* 3.7 8.8 + - - -
237A PHE* 3.1 30.5 + - + -
238A ASP 4.5 3.3 + - - -
239A ARG* 4.2 8.4 - - - +
241A ALA 4.1 10.5 - - - +
242A ILE* 2.9 24.4 + - + +
244A ALA* 1.3 74.2 - - - +
246A VAL* 1.3 59.8 + - - +
248A LEU* 3.3 2.6 + - - +
249A GLY 2.9 25.6 + - - -
293A GLU* 3.4 17.0 + - - -
294A PHE* 3.1 35.6 + - + +
297A VAL* 4.0 14.6 - - - +
316A ASP* 2.6 43.0 + - - -
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Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 3.0 22.8 + - + +
243A PRO* 4.1 2.9 - - + +
245A ARG* 1.3 75.5 - - - +
247A THR* 1.3 58.8 + - - +
250A VAL* 2.8 49.0 + - + +
291A LEU* 4.4 10.8 - - + -
294A PHE* 5.1 1.1 - - + -
237B PHE* 3.8 30.7 - - + -
244B ALA* 4.0 21.8 - - + +
247B THR* 3.7 24.2 - - + -
248B LEU* 3.9 15.3 - - + -
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Residues in contact with THR 247 (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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243A PRO* 3.0 19.4 + - - +
244A ALA* 3.7 6.7 - - - +
245A ARG 3.3 0.2 - - - -
246A VAL* 1.3 77.7 - - - +
248A LEU* 1.3 64.9 + - + +
250A VAL* 4.4 0.4 - - - +
251A THR* 2.7 38.5 + - - +
247B THR* 4.8 16.3 + - - +
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Residues in contact with LEU 248 (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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230A VAL* 3.6 33.4 - - + +
231A SER* 5.2 1.3 - - - -
233A VAL* 3.6 15.7 - - + -
234A SER* 3.6 21.1 - - - +
237A PHE* 3.6 31.4 - - + -
244A ALA 3.1 12.3 + - - +
245A ARG 3.6 6.7 - - - +
246A VAL 3.2 0.2 - - - -
247A THR* 1.3 81.2 - - + +
249A GLY* 1.3 64.6 + - - +
250A VAL 3.0 0.7 + - - -
251A THR* 3.1 3.6 + - - -
252A THR* 3.0 31.4 + - + +
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Residues in contact with GLY 249 (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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231A SER* 4.9 6.3 - - - -
234A SER* 5.1 0.2 + - - -
245A ARG 2.9 18.5 + - - -
246A VAL 3.9 0.4 - - - -
248A LEU* 1.3 72.9 - - - +
250A VAL* 1.3 56.4 + - - +
252A THR* 3.1 15.5 + - - -
253A LEU* 3.3 17.2 + - - +
287A ILE* 3.4 10.6 - - - +
290A ALA* 5.5 0.4 - - - -
291A LEU* 3.9 21.5 - - - +
294A PHE* 4.1 9.5 - - - -
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Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL* 2.8 32.3 + - + +
247A THR* 4.4 1.1 - - - +
249A GLY* 1.3 70.8 - - - +
251A THR* 1.3 63.4 + - - +
252A THR 3.3 0.2 - - - -
253A LEU* 3.3 7.7 + - + +
254A LEU* 2.9 27.9 + - - +
291A LEU* 4.0 12.3 - - + -
230B VAL* 5.2 1.6 - - + -
247B THR* 4.7 5.6 - - + +
248B LEU* 3.3 34.8 - - + -
251B THR* 3.3 39.9 - - + +
252B THR* 6.1 2.2 - - + -
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Residues in contact with THR 251 (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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247A THR* 2.7 30.9 + - - +
248A LEU* 3.8 2.7 - - - -
250A VAL* 1.3 78.6 - - - +
252A THR* 1.3 59.6 + - + +
254A LEU* 3.8 6.0 - - + +
255A THR* 2.9 42.7 + - - +
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Residues in contact with THR 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 3.7 37.1 - - + +
230A VAL* 3.7 30.5 - - + -
231A SER* 3.8 6.4 - - - +
248A LEU* 3.0 21.1 + - + +
249A GLY* 3.1 10.0 + - - -
251A THR* 1.3 78.3 - - + +
253A LEU* 1.3 60.0 + - - +
255A THR* 4.5 1.3 - - - -
256A MET* 3.0 27.0 + - - +
287A ILE* 3.3 20.2 - - - +
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Residues in contact with LEU 253 (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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249A GLY 3.3 15.9 + - - +
250A VAL* 3.3 7.5 + - + +
251A THR 3.3 0.2 - - - -
252A THR* 1.3 81.0 + - - +
254A LEU* 1.3 65.0 + - - +
256A MET* 3.2 7.2 - - - +
257A THR* 3.1 21.4 + - - +
284A MET* 3.8 21.1 - - + +
287A ILE* 3.7 19.7 - - + -
288A PHE* 4.1 7.9 - - + +
291A LEU* 4.7 9.2 - - + -
226B MET* 3.2 38.1 - - + -
227B LEU* 5.1 7.6 - - + -
230B VAL* 4.2 23.6 - - + -
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Residues in contact with LEU 254 (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 VAL 2.9 17.0 + - - +
251A THR* 3.8 6.1 - - + +
253A LEU* 1.3 77.8 - - - +
255A THR* 1.3 67.4 + - - +
257A THR* 3.0 20.1 + - + -
258A ALA* 3.1 18.1 + - + -
251B THR* 3.3 25.6 - - + +
254B LEU* 5.6 8.7 - - + -
255B THR* 3.3 32.1 - - + +
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Residues in contact with THR 255 (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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227A LEU* 3.4 31.4 - - + -
251A THR* 2.9 32.3 + - - +
252A THR* 3.9 2.2 - - - -
254A LEU* 1.3 80.1 - - - +
256A MET* 1.3 64.4 + - - +
258A ALA* 3.2 7.7 + - + +
259A GLN* 2.9 25.2 + - + +
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Residues in contact with MET 256 (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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224A SER* 3.3 32.3 - - - +
227A LEU* 3.6 17.6 - - - +
252A THR 3.0 16.0 + - - +
253A LEU* 3.2 13.7 - - + +
254A LEU 3.2 0.2 - - - -
255A THR* 1.3 77.1 - - - +
257A THR* 1.3 62.6 + - - +
259A GLN* 3.3 6.3 + - - +
260A SER* 3.1 22.5 + - - -
279A TRP* 4.6 0.2 - - + -
280A ILE* 4.0 28.0 - - + +
283A CYS* 3.3 32.1 - - + -
284A MET* 3.4 28.0 - - - -
287A ILE* 4.4 10.1 - - + -
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Residues in contact with THR 257 (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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253A LEU* 3.1 4.9 + - - +
254A LEU* 3.0 14.9 + - + +
256A MET* 1.3 78.4 - - - +
258A ALA* 1.3 66.3 + - - +
260A SER* 3.0 9.3 + - - -
261A ALA* 2.9 23.8 + - + +
284A MET* 3.0 28.5 - - + +
223B PRO* 6.1 5.8 - - + +
226B MET* 5.5 0.2 - - - -
227B LEU* 5.3 5.9 - - - +
255B THR* 4.7 19.8 - - + +
259B GLN* 6.2 3.6 - - + -
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Residues in contact with ALA 258 (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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254A LEU* 3.1 15.3 + - + +
255A THR* 3.2 12.5 + - + +
257A THR* 1.3 79.5 - - - +
259A GLN* 1.3 63.7 + - - +
261A ALA* 3.0 10.8 + - - +
262A GLY* 3.0 18.9 + - - -
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Residues in contact with GLN 259 (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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219A GLN 3.8 8.8 + - - +
220A LEU* 2.9 52.6 + - + +
223A PRO* 4.0 9.5 - - - +
224A SER* 3.0 21.7 + - - -
227A LEU* 4.2 17.2 - - - +
255A THR* 2.9 15.3 + - + +
256A MET* 3.5 12.1 - - - +
258A ALA* 1.3 75.7 - - - +
260A SER* 1.3 64.4 + - - +
262A GLY* 3.1 12.2 + - - -
263A ILE* 3.3 16.1 + - + +
280A ILE* 4.8 1.5 - - - +
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Residues in contact with SER 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A MET 3.1 5.6 + - - -
257A THR* 3.0 11.2 + - - -
259A GLN* 1.3 75.7 - - - +
261A ALA* 1.3 60.2 + - - +
263A ILE* 3.2 6.4 + - - +
264A ASN* 2.8 49.1 + - - +
280A ILE* 3.6 42.2 - - - +
284A MET* 6.1 0.2 - - - -
219B GLN* 4.6 2.9 + - - -
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Residues in contact with ALA 261 (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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257A THR* 2.9 17.2 + - + +
258A ALA* 3.3 13.5 - - - +
260A SER* 1.3 76.1 - - - +
262A GLY* 1.3 62.2 + - - +
264A ASN* 3.9 5.0 - - - +
265A SER* 3.1 26.0 + - - -
219B GLN* 5.7 2.2 - - - -
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Residues in contact with GLY 262 (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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258A ALA 3.0 12.3 + - - -
259A GLN* 3.1 5.6 + - - -
260A SER 3.1 0.4 - - - -
261A ALA* 1.3 75.8 - - - +
263A ILE* 1.3 62.5 + - - +
265A SER* 2.6 25.8 + - - -
266A GLN* 3.9 11.6 + - - +
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Residues in contact with ILE 263 (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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137A TYR* 4.1 29.2 + - + +
215A PHE* 5.0 18.8 - - + -
216A TYR* 5.4 5.4 - - + -
219A GLN* 4.8 12.6 - - + +
220A LEU* 3.8 29.2 - - + -
259A GLN* 3.3 14.1 + - + +
260A SER* 3.2 7.9 + - - +
262A GLY* 1.3 74.4 - - - +
264A ASN* 1.3 66.0 + - - +
265A SER 3.1 1.6 + - - -
266A GLN* 3.2 22.6 + - - +
267A LEU* 3.8 12.4 - - + +
276A ILE* 4.3 18.4 - - + -
280A ILE* 6.0 0.9 - - + -
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Residues in contact with ASN 264 (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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260A SER* 2.8 40.7 + - - +
261A ALA* 4.1 4.5 - - - +
263A ILE* 1.3 76.2 - - - +
265A SER* 1.3 60.0 + - - +
266A GLN 3.3 0.2 - - - -
267A LEU* 3.5 35.1 + - - +
274A LYS* 4.3 7.1 + - - -
276A ILE* 5.1 4.7 - - - +
277A ASP* 4.1 13.8 + - - +
280A ILE* 5.6 2.6 - - - +
215B PHE* 4.8 11.3 - - + -
219B GLN* 3.0 41.7 + - + +
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Residues in contact with SER 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 5.3 2.3 - - - +
261A ALA 3.1 15.9 + - - -
262A GLY* 2.6 20.7 + - - -
263A ILE 3.1 0.2 - - - -
264A ASN* 1.3 77.5 - - - +
266A GLN* 1.3 64.1 + - - +
267A LEU 3.2 6.8 + - - +
266B GLN* 5.9 6.2 + - - +
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Residues in contact with GLN 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 4.8 5.2 - - - +
45A VAL* 3.5 19.1 - - - +
137A TYR* 5.1 6.4 + - - +
215A PHE* 5.4 13.3 - - - -
216A TYR* 5.7 0.3 + - - -
262A GLY 4.1 10.6 + - - +
263A ILE* 3.2 14.5 + - - +
265A SER* 1.3 83.9 - - - +
267A LEU* 1.3 65.8 + - + +
268A PRO* 4.4 0.5 - - - +
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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