Contacts of the helix formed by residues 251 - 279 (chain E) in PDB entry 1RFU
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 ASN 251 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217E GLN* 3.6 3.9 + - - +
248E HIS* 3.2 36.5 + - + +
249E PRO 3.6 0.4 - - - -
250E ASN* 1.3 81.6 + - - +
252E LEU* 1.3 68.9 + - - +
253E LYS* 2.9 9.5 - - - +
254E VAL* 2.7 43.8 + - + +
255E ALA 2.8 10.3 + - - -
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Residues in contact with LEU 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E THR* 3.7 25.8 - - + -
184E VAL* 4.5 5.6 - - + -
203E GLY* 3.1 40.2 - - - +
204E SER 3.5 18.2 - - - +
205E GLN* 3.4 20.6 + - + +
217E GLN* 3.1 16.8 - - + +
219E ILE* 3.8 5.4 - - + -
241E LEU* 5.3 0.7 - - + -
245E THR* 5.1 11.7 - - + -
248E HIS 4.5 1.0 + - - -
251E ASN* 1.3 74.4 - - - +
253E LYS* 1.3 63.6 + - - +
255E ALA* 4.4 4.5 - - + -
256E CYS* 2.8 49.5 + - - +
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Residues in contact with LYS 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217E GLN* 4.3 4.6 - - - +
219E ILE* 3.6 23.5 - - + +
251E ASN* 2.8 11.5 + - - +
252E LEU* 1.3 76.0 - - - +
254E VAL* 1.3 58.5 + - + +
256E CYS* 3.5 1.4 - - - +
257E GLU* 2.7 73.8 + - - +
308E GLN* 2.8 18.9 - - - +
309E ALA* 3.3 30.1 - - + -
311E VAL* 4.0 21.8 - - + -
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Residues in contact with VAL 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248E HIS* 3.5 29.6 - - + +
251E ASN* 2.7 40.3 + - + +
253E LYS* 1.3 78.8 - - + +
255E ALA* 1.3 68.5 + - - +
257E GLU* 2.9 24.9 + - + +
258E LYS* 3.0 27.5 + - + +
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Residues in contact with ALA 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241E LEU* 4.9 3.1 - - + -
244E TRP* 3.7 17.5 - - + +
245E THR* 3.7 43.5 - - + +
248E HIS* 4.3 8.0 - - + +
251E ASN 2.8 17.8 + - - +
252E LEU* 4.0 5.4 - - - +
254E VAL* 1.3 75.6 - - - +
256E CYS* 1.3 63.1 + - - +
258E LYS 3.6 0.2 + - - -
259E THR* 3.2 25.6 + - - -
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Residues in contact with CYS 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E VAL* 4.4 18.2 - - - -
203E GLY* 5.1 0.4 - - - -
219E ILE* 3.4 22.7 - - + -
221E MET* 4.0 18.6 - - + -
237E PHE* 5.6 2.5 - - - -
241E LEU* 4.6 9.2 - - - -
252E LEU* 2.8 49.0 + - - +
253E LYS 3.5 2.5 - - - +
255E ALA* 1.3 70.7 - - - +
257E GLU* 1.3 65.6 + - - +
259E THR* 3.5 4.4 + - - -
260E VAL* 2.8 34.7 + - + +
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Residues in contact with GLU 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221E MET* 5.1 0.7 - - - -
253E LYS* 2.7 64.7 + - - +
254E VAL* 3.5 12.6 - - + +
256E CYS* 1.3 70.4 - - - +
258E LYS* 1.3 65.5 + - + +
260E VAL* 3.8 0.3 - - - -
261E SER* 2.6 33.1 + - - -
305E ILE* 4.5 15.4 - - + +
307E VAL* 4.0 21.6 - - + +
308E GLN* 3.3 9.5 + - - -
309E ALA* 2.5 38.8 + - + +
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Residues in contact with LYS 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244E TRP* 3.6 51.0 - - + +
247E LYS* 4.2 7.9 - - - +
248E HIS* 3.0 31.6 + - + +
254E VAL* 3.0 27.5 + - + +
257E GLU* 1.3 73.5 - - + +
259E THR* 1.3 68.3 + - - +
261E SER* 2.8 17.5 + - - -
262E ALA 2.9 11.6 + - - -
303E PRO* 3.5 20.7 - - + +
305E ILE* 5.1 17.2 - - + +
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Residues in contact with THR 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237E PHE* 3.2 53.4 - - + +
240E MET* 4.0 9.3 - - + +
241E LEU* 3.6 17.1 + - - +
244E TRP* 3.0 24.2 - - - +
255E ALA 3.2 12.8 + - - -
256E CYS* 3.6 5.2 - - - -
258E LYS* 1.3 79.8 - - - +
260E VAL* 1.3 63.8 + - - +
262E ALA* 3.0 7.0 + - - +
263E MET* 2.8 20.4 + - - +
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Residues in contact with VAL 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201E ALA* 5.9 1.3 - - + -
221E MET* 4.0 19.1 - - + -
223E MET* 3.5 39.7 - - + -
237E PHE* 3.9 21.3 - - + -
256E CYS* 2.8 24.5 + - + +
257E GLU 4.0 1.8 - - - +
259E THR* 1.3 73.9 - - - +
261E SER* 1.3 62.9 + - - +
263E MET* 3.0 10.3 - - + +
264E HIS* 2.9 22.2 + - + +
307E VAL* 4.1 19.0 - - + +
4402E ADP 3.9 4.9 - - - +
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Residues in contact with SER 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257E GLU 2.6 21.8 + - - -
258E LYS* 2.8 12.0 + - - -
260E VAL* 1.3 73.0 - - - +
262E ALA* 1.3 68.4 + - - -
264E HIS* 2.7 15.9 + - - +
265E HIS* 3.0 15.2 + - - -
303E PRO* 4.1 3.8 - - - -
304E GLU 3.1 24.2 - - - -
305E ILE* 3.4 7.6 - - - +
306E VAL* 3.3 28.1 + - - -
307E VAL* 3.9 7.6 - - - +
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Residues in contact with ALA 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E MET* 3.5 27.4 - - + -
244E TRP* 5.6 0.4 - - - +
258E LYS 2.9 8.0 + - - +
259E THR* 3.3 9.6 - - - +
261E SER* 1.3 76.2 - - - +
263E MET* 1.3 64.8 + - - +
265E HIS* 3.1 5.6 + - - +
266E VAL* 2.8 29.6 + - - +
299E ASP 4.3 7.9 - - - +
300E ILE* 4.7 6.1 - - + -
303E PRO* 3.4 25.0 - - + +
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Residues in contact with MET 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E THR* 3.1 40.4 - - + +
236E LEU* 3.5 21.3 - - + -
237E PHE* 3.8 13.0 - - + +
240E MET* 3.4 25.6 - - - -
259E THR 2.8 10.1 + - - +
260E VAL* 3.0 17.7 - - + +
262E ALA* 1.3 77.6 - - - +
264E HIS* 1.3 58.1 + - - +
266E VAL* 3.4 3.8 + - + +
267E LEU* 2.7 39.3 + - + +
291E LEU* 5.5 0.2 - - + -
4402E ADP 3.4 43.3 - - - +
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Residues in contact with HIS 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E HIS* 4.7 26.5 + - + +
226E VAL* 6.3 0.4 - - + -
260E VAL* 2.9 11.6 + - + +
261E SER 2.7 14.3 + - - +
263E MET* 1.3 72.6 - - - +
265E HIS* 1.3 63.4 + + - +
267E LEU* 3.5 6.6 - - - +
268E GLN* 2.5 76.3 + - + +
306E VAL* 3.6 31.5 - - + +
307E VAL* 5.3 7.0 - - + -
4402E ADP 6.2 0.4 - - - -
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Residues in contact with HIS 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E SER 3.0 9.8 + - - -
262E ALA 3.4 5.4 - - - +
264E HIS* 1.3 88.8 - + - +
266E VAL* 1.3 70.7 + - - +
268E GLN* 2.7 17.8 + - - +
269E ARG* 2.8 17.2 + - - +
299E ASP* 3.6 35.8 - - + +
303E PRO* 4.2 5.7 - - - +
304E GLU* 3.2 47.1 + - + +
306E VAL* 3.5 20.9 - - + +
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Residues in contact with VAL 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236E LEU* 4.2 29.4 - - + -
240E MET* 5.4 0.2 - - + -
262E ALA* 2.8 22.1 + - + +
263E MET* 3.5 4.0 - - + +
265E HIS* 1.3 78.5 - - + +
267E LEU* 1.3 65.4 + - + +
269E ARG* 3.2 5.8 + - - +
270E THR* 2.8 33.5 + - - +
291E LEU* 4.5 18.8 - - + -
292E ARG 4.7 3.8 - - - +
293E MET* 5.5 2.0 - - + +
296E SER* 3.7 34.7 + - - +
299E ASP* 5.5 1.3 - - + -
300E ILE* 4.3 15.0 - - + -
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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
----------------------------------------------------------
226E VAL* 4.7 11.0 - - + -
230E PHE* 3.4 45.9 - - + -
233E THR* 3.8 14.1 - - + -
263E MET* 2.7 30.6 + - + +
264E HIS* 3.6 5.4 - - - +
266E VAL* 1.3 73.1 - - + +
268E GLN* 1.3 67.8 + - + +
270E THR* 2.9 4.7 + - - -
271E ILE* 2.9 25.3 + - - +
291E LEU* 4.1 7.6 - - + -
4402E ADP 3.3 51.1 - - + +
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Residues in contact with GLN 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E HIS* 5.0 9.2 + - - +
226E VAL* 3.9 21.0 - - + +
264E HIS* 2.5 61.7 + - + +
265E HIS* 2.7 7.4 + - + +
267E LEU* 1.3 70.7 - - + +
269E ARG* 1.3 61.5 + - - +
271E ILE* 3.0 28.0 - - - +
272E LYS* 3.1 10.0 + - - +
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Residues in contact with ARG 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E HIS 2.8 6.3 + - - +
266E VAL* 3.3 15.6 - - - +
268E GLN* 1.3 77.9 - - - +
270E THR* 1.3 63.3 + - - +
272E LYS* 3.3 13.3 + - - +
273E CYS* 3.2 21.7 + - - +
292E ARG* 4.1 14.1 - - + +
295E GLN* 3.5 43.7 + - - +
296E SER* 2.6 37.0 + - - -
299E ASP* 2.5 31.5 + - - -
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Residues in contact with THR 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E PHE* 3.9 13.5 - - + -
266E VAL* 2.8 19.1 + - - +
267E LEU* 2.9 10.6 + - - -
269E ARG* 1.3 75.3 - - - +
271E ILE* 1.3 67.4 + - - +
272E LYS 3.0 0.3 + - - -
273E CYS* 3.3 1.6 + - - +
274E ALA* 2.8 24.5 + - + +
288E GLN 5.1 0.7 - - - +
289E LEU* 3.4 20.6 - - - +
290E GLU 3.2 26.2 - - - +
291E LEU* 3.7 5.3 - - - +
292E ARG* 3.2 27.7 + - + +
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Residues in contact with ILE 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E VAL* 3.7 33.9 - - + -
227E ASP 4.8 0.4 - - - +
228E ALA* 4.1 18.6 - - + -
230E PHE* 4.4 4.2 - - + -
267E LEU 2.9 15.0 + - - +
268E GLN* 3.0 26.7 - - - +
270E THR* 1.3 75.1 - - - +
272E LYS* 1.3 61.4 + - + +
274E ALA* 3.9 3.6 - - + -
275E LYS* 2.8 63.8 + - + +
284E PRO* 4.6 4.5 - - + -
289E LEU* 4.2 12.6 - - + -
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Residues in contact with LYS 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E GLN 3.1 9.2 + - - +
269E ARG* 3.4 18.4 - - - +
270E THR 3.0 0.4 + - - -
271E ILE* 1.3 84.4 - - + +
273E CYS* 1.3 72.0 + - - +
275E LYS* 3.2 4.5 + - - +
276E ALA* 3.1 16.2 + - + +
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Residues in contact with CYS 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLU* 4.7 2.5 - - - -
269E ARG 3.2 5.0 + - - +
270E THR 3.9 2.0 - - - +
272E LYS* 1.3 79.7 - - - +
274E ALA* 1.3 56.7 + - - +
276E ALA* 2.6 37.5 + - - +
277E LYS* 3.0 38.5 + - - +
292E ARG* 3.6 48.5 - - - +
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Residues in contact with ALA 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E THR 2.8 22.4 + - - +
271E ILE* 3.5 5.2 - - - +
273E CYS* 1.3 73.6 - - - +
275E LYS* 1.3 63.6 + - - +
276E ALA 3.0 0.9 + - - -
277E LYS* 3.1 6.1 + - - +
278E SER* 3.0 21.1 + - - -
284E PRO* 3.8 8.3 - - + +
288E GLN* 3.0 31.3 + - - +
289E LEU* 3.5 25.1 - - + -
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Residues in contact with LYS 275 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E ASP* 4.3 21.4 + - - +
271E ILE* 2.8 46.1 + - + +
272E LYS* 3.8 4.9 - - - +
274E ALA* 1.3 73.9 - - - +
276E ALA* 1.3 57.2 + - - +
278E SER* 3.1 7.6 + - - +
279E GLY* 2.9 32.1 + - - +
282E VAL 5.4 1.8 - - - +
283E LYS* 4.5 16.6 - - - +
284E PRO* 3.9 14.8 - - + -
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Residues in contact with ALA 276 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E LYS* 3.1 11.2 + - + +
273E CYS* 2.6 25.9 + - - +
275E LYS* 1.3 74.4 - - - +
277E LYS* 1.3 59.6 + - + +
278E SER 3.4 0.5 + - - -
279E GLY* 3.7 7.3 + - - -
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Residues in contact with LYS 277 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLU* 4.4 12.3 + - - -
6A ARG* 5.2 10.3 - - - +
16E ARG* 5.6 4.2 - - - +
273E CYS* 3.0 39.2 + - - +
274E ALA 3.1 4.9 + - - +
276E ALA* 1.3 77.0 - - + +
278E SER* 1.3 60.5 + - - +
287E ALA 5.8 0.8 + - - -
288E GLN* 3.2 42.9 + - + +
292E ARG* 5.5 2.2 - - - +
----------------------------------------------------------
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Residues in contact with SER 278 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E ALA 3.0 6.0 + - - -
275E LYS* 3.1 24.1 + - - -
277E LYS* 1.3 81.1 - - - +
279E GLY* 1.3 58.1 + - - +
282E VAL* 3.2 45.8 + - - +
283E LYS 4.0 3.1 - - - -
284E PRO* 3.4 12.8 - - - +
288E GLN* 3.6 20.6 - - - +
----------------------------------------------------------
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Residues in contact with GLY 279 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E LYS* 2.9 18.4 + - - +
276E ALA 3.7 6.0 + - - -
277E LYS 3.6 1.4 - - - -
278E SER* 1.3 84.1 + - - +
280E GLU* 1.3 69.7 + - - +
281E GLY 3.6 0.2 + - - -
282E VAL* 3.3 18.0 + - - +
----------------------------------------------------------
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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