Contacts of the helix formed by residues 260 - 285 (chain E) in PDB entry 5MGX
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 THR 260 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259E MET* 1.3 76.2 - - - +
261E PHE* 1.3 63.7 + - - +
262E GLU* 3.8 15.8 + - - +
263E GLU* 2.8 41.3 + - - +
264E GLU* 3.1 21.8 + - - +
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Residues in contact with PHE 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E THR* 1.3 73.9 - - - +
262E GLU* 1.3 76.5 + - + +
264E GLU* 3.2 13.1 + - + +
265E ALA* 3.0 42.1 + - + +
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Residues in contact with GLU 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E THR* 3.3 14.3 - - - +
261E PHE* 1.3 101.8 + - + +
263E GLU* 1.3 55.7 + - + +
265E ALA* 3.9 5.4 - - - +
266E GLN* 3.1 29.1 + - - +
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Residues in contact with GLU 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E THR* 5.3 1.6 + - - -
214E GLY* 3.8 17.6 + - - -
215E GLN* 3.7 19.0 + - - +
218E VAL* 5.0 2.1 - - + +
259E MET* 3.3 25.8 - - + +
260E THR* 2.8 46.9 + - - +
261E PHE 3.2 0.4 - - - -
262E GLU* 1.3 75.2 - - + +
264E GLU* 1.4 58.1 + - - +
266E GLN* 3.4 14.3 + - - +
267E LEU* 3.0 34.2 + - + +
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Residues in contact with GLU 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E SER* 5.0 8.7 + - - -
257E VAL 5.4 2.1 - - - +
259E MET* 3.7 33.7 + - + +
260E THR 3.1 20.8 + - - +
261E PHE* 3.2 14.6 + - + +
263E GLU* 1.4 72.4 - - - +
265E ALA* 1.4 57.8 + - - +
267E LEU* 3.3 5.2 + - - +
268E LEU* 2.9 36.7 + - + +
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Residues in contact with ALA 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261E PHE* 3.0 32.1 + - + +
262E GLU* 3.9 7.9 - - - +
264E GLU* 1.4 72.8 - - - +
266E GLN* 1.3 64.9 + - - +
268E LEU* 3.1 14.9 + - - +
269E GLN* 3.0 28.8 + - + +
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Residues in contact with GLN 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E VAL* 3.9 35.7 - - + +
222E ASN* 5.9 0.2 - - - +
262E GLU 3.1 19.9 + - - +
263E GLU* 3.6 12.5 - - - +
265E ALA* 1.3 74.1 - - - +
267E LEU* 1.3 61.1 + - - +
269E GLN* 3.4 10.4 + - + +
270E LEU* 3.2 23.0 + - + +
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Residues in contact with LEU 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E GLY 4.2 6.3 - - - +
217E ARG* 3.9 36.6 - - + +
218E VAL* 3.8 17.9 - - + -
251E ILE* 3.6 42.6 - - + +
259E MET* 3.0 40.4 - - + -
263E GLU 3.0 12.8 + - - +
264E GLU* 3.7 5.2 - - - +
266E GLN* 1.3 73.1 - - - +
268E LEU* 1.4 59.6 + - - +
270E LEU* 3.4 9.2 + - + +
271E LYS* 3.0 28.2 + - - +
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Residues in contact with LEU 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264E GLU* 2.9 21.4 + - + +
265E ALA* 3.1 15.7 + - - +
267E LEU* 1.4 72.5 - - - +
269E GLN* 1.4 68.8 + - - +
271E LYS* 3.3 22.0 + - - +
272E VAL* 3.2 29.9 + - + +
301E HIS* 3.6 35.2 - - + +
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Residues in contact with GLN 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E ALA* 3.0 19.0 + - + +
266E GLN* 3.5 12.1 - - - +
267E LEU 3.4 0.2 - - - -
268E LEU* 1.4 80.4 - - - +
270E LEU* 1.3 58.1 + - - +
272E VAL* 3.8 6.4 + - - +
273E LYS* 3.3 34.2 + - - +
302E GLN* 3.7 26.3 + - - +
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Residues in contact with LEU 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E VAL* 3.9 24.2 - - + +
221E ALA* 3.8 21.8 - - + +
222E ASN* 3.6 28.9 - - - +
225E ARG* 4.4 11.0 - - - +
251E ILE* 3.7 10.3 - - + -
266E GLN* 3.2 11.5 + - + +
267E LEU* 3.5 17.0 - - + +
268E LEU 3.2 0.2 - - - -
269E GLN* 1.3 77.6 - - - +
271E LYS* 1.3 58.9 + - - +
273E LYS* 3.3 10.6 + - + +
274E CYS* 2.9 52.8 + - - -
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Residues in contact with LYS 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E ILE* 4.6 9.8 - - + +
251E ILE* 3.7 22.6 - - + +
252E THR* 3.9 27.1 - - + -
267E LEU 3.0 16.9 + - - +
268E LEU* 3.3 27.8 + - - +
270E LEU* 1.3 77.2 - - - +
272E VAL* 1.4 51.7 + - - +
274E CYS* 3.3 4.3 + - - +
275E LEU* 2.8 58.9 + - + +
297E LEU* 5.6 4.9 - - - +
301E HIS* 3.7 21.5 + - - -
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Residues in contact with VAL 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E LEU* 3.2 18.9 + - + +
269E GLN* 4.0 5.8 - - - +
271E LYS* 1.4 71.8 - - + +
273E LYS* 1.4 60.5 + - + +
275E LEU* 3.4 7.6 + - + -
276E ASN* 3.0 32.1 + - - +
298E VAL* 3.5 33.3 - - + +
301E HIS* 3.7 35.7 - - + +
302E GLN* 3.7 32.8 - - - +
305E ASN* 4.5 2.9 - - - +
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Residues in contact with LYS 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709C ASP* 3.7 41.0 + - + +
225E ARG* 4.6 11.4 - - - +
269E GLN* 3.3 22.1 + - - +
270E LEU* 3.3 12.4 + - + +
272E VAL* 1.4 77.5 - - + +
274E CYS* 1.4 55.7 + - - +
276E ASN* 3.6 5.8 + - - +
277E ASN* 3.0 37.2 + - - +
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Residues in contact with CYS 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E ARG* 4.0 17.0 - - - -
244E TYR* 3.9 12.0 - - + +
247E ALA* 3.8 22.2 - - - -
248E ILE* 3.7 20.2 - - + -
251E ILE* 4.4 4.0 - - - -
270E LEU* 2.9 45.4 + - - +
271E LYS* 3.3 4.9 + - - +
273E LYS* 1.4 73.5 - - - +
275E LEU* 1.4 55.5 + - - +
277E ASN* 3.4 8.6 + - - +
278E LEU* 2.8 33.3 + - - +
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Residues in contact with LEU 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E ILE* 3.9 24.7 - - + -
271E LYS* 2.8 50.5 + - + +
272E VAL* 3.8 3.8 - - - +
274E CYS* 1.4 69.8 - - - +
276E ASN* 1.3 59.9 + - - +
278E LEU* 3.4 14.2 + - + +
279E ALA* 2.9 27.0 + - - +
294E SER* 3.6 17.4 - - - +
297E LEU* 4.1 37.5 - - + +
298E VAL* 3.6 18.6 - - + +
301E HIS* 5.6 1.6 - - + -
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Residues in contact with ASN 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709C ASP* 4.3 11.5 + - - +
272E VAL* 3.0 17.5 + - - +
273E LYS* 3.7 6.8 - - - +
275E LEU* 1.3 74.1 - - - +
277E ASN* 1.3 60.3 + - - +
279E ALA* 3.2 7.5 + - - +
280E ALA 2.9 23.7 + - - -
298E VAL* 3.5 13.9 - - + +
305E ASN* 3.0 39.8 + - - +
307E LYS* 4.0 5.5 - - - +
308E ALA* 3.6 18.8 + - - +
311E ARG* 3.0 35.9 + - - +
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Residues in contact with ASN 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708C VAL* 3.5 16.3 - - - +
709C ASP* 2.9 49.0 + - - +
225E ARG* 4.1 6.7 - - - +
229E ASN* 3.1 17.2 + - - -
244E TYR* 3.4 24.2 - - + -
273E LYS 3.0 23.2 + - - +
274E CYS 3.4 6.1 - - - +
276E ASN* 1.3 73.5 - - - +
278E LEU* 1.3 61.6 + - - +
280E ALA* 3.5 4.3 + - - +
281E SER* 3.0 27.9 + - - -
311E ARG* 4.9 1.7 + - - -
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Residues in contact with LEU 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E ALA* 3.4 41.5 - - + +
244E TYR* 3.8 11.2 - - + -
245E ASP* 4.5 12.8 - - + +
248E ILE* 3.8 21.1 - - + -
274E CYS 2.8 17.0 + - - +
275E LEU* 3.5 11.7 - - + +
276E ASN 3.3 0.2 - - - -
277E ASN* 1.3 73.9 - - - +
279E ALA* 1.4 51.9 + - - +
281E SER* 3.2 3.5 + - - -
282E GLN* 2.7 60.3 + - - +
294E SER* 3.8 13.7 - - - +
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Residues in contact with ALA 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E LEU 2.9 13.9 + - - +
276E ASN* 3.2 15.0 - - - +
278E LEU* 1.4 72.1 - - - +
280E ALA* 1.3 65.5 + - - +
281E SER 3.3 0.2 + - - -
282E GLN* 3.3 5.6 + - - +
283E LEU* 2.9 26.3 + - - +
291E ALA* 4.0 6.9 - - - +
294E SER* 3.9 15.7 - - - -
295E CYS* 3.8 30.5 - - - +
311E ARG* 4.6 5.8 - - - -
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Residues in contact with ALA 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708C VAL* 4.1 5.2 - - + -
232E TYR* 3.8 23.5 + - + +
276E ASN 2.9 8.4 + - - +
277E ASN 3.5 9.9 - - - +
279E ALA* 1.3 75.6 - - - +
281E SER* 1.4 61.7 + - - +
283E LEU* 3.5 9.5 - - - +
284E LYS* 3.4 25.1 + - - +
311E ARG* 3.5 39.6 - - - +
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Residues in contact with SER 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E TYR* 3.5 17.8 - - - -
237E PHE* 3.8 23.3 - - - +
240E ALA* 3.7 4.4 - - - +
241E ALA* 4.1 13.2 - - - -
244E TYR* 3.4 16.1 - - - -
277E ASN 3.0 13.0 + - - -
278E LEU 3.2 8.7 + - - -
280E ALA* 1.4 75.1 - - - +
282E GLN* 1.3 62.8 + - - +
284E LYS* 3.3 14.7 + - - +
285E LEU* 3.3 18.7 + - - +
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Residues in contact with GLN 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E ALA* 5.0 4.6 - - + +
278E LEU* 2.7 47.1 + - + +
281E SER* 1.3 69.2 - - - +
283E LEU* 1.4 60.1 + - - +
285E LEU* 3.4 9.1 + - + +
286E ASP 3.4 2.4 + - - -
287E HIS* 2.8 49.2 + - + +
290E ALA* 3.4 29.7 - - - +
291E ALA* 3.4 15.5 + - + -
294E SER* 2.7 32.8 + - - -
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Residues in contact with LEU 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706C GLU* 5.8 0.2 - - - +
279E ALA 2.9 17.2 + - - +
280E ALA* 3.5 7.6 - - - +
281E SER 3.3 0.2 - - - -
282E GLN* 1.4 76.1 - - - +
284E LYS* 1.3 73.7 + - - +
286E ASP* 3.1 24.3 + - - +
287E HIS 5.0 0.2 - - - +
288E TYR* 4.2 5.0 - - + -
291E ALA* 4.0 6.4 - - + +
310E PHE* 5.8 0.7 - - + -
311E ARG* 4.2 26.0 - - + +
314E LYS* 4.0 34.3 - - + +
315E VAL* 3.8 26.7 - - + -
318E GLN* 3.8 22.2 - - - +
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Residues in contact with LYS 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706C GLU* 3.1 36.4 + - - -
232E TYR* 4.5 9.6 + - - +
237E PHE* 3.6 49.5 - - + -
280E ALA 3.4 11.2 + - - +
281E SER 3.3 10.4 + - - +
283E LEU* 1.3 94.6 - - - +
285E LEU* 1.3 59.6 + - - +
286E ASP* 3.3 3.4 + - - +
314E LYS* 4.6 5.9 - - - +
352G LYS* 3.8 14.9 - - - -
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Residues in contact with LEU 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237E PHE* 3.7 38.4 - - + +
238E VAL* 3.7 28.5 - - + +
241E ALA* 4.8 6.1 - - + -
281E SER 3.3 15.9 + - - +
282E GLN* 3.4 9.2 + - + +
283E LEU 3.2 0.6 - - - -
284E LYS* 1.3 76.7 - - - +
286E ASP* 1.3 69.3 + - - +
287E HIS* 3.1 9.5 + - + +
322G TYR* 4.3 1.9 + - - -
351G LYS* 4.5 12.6 - - - +
352G LYS* 3.6 36.9 - - + +
355G ALA* 4.2 18.6 - - + -
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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
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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