Contacts of the helix formed by residues 262 - 289 (chain E) in PDB entry 5I4V
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 SER 262 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E GLY* 1.3 68.2 - - - -
263E ALA* 1.3 62.0 + - - +
264E SER 3.2 0.7 - - - -
265E GLN* 3.5 26.7 - - - +
266E GLN* 3.0 38.7 + - - +
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Residues in contact with ALA 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253E PRO* 3.5 22.3 - - + +
261E GLY 3.9 8.7 - - - +
262E SER* 1.3 78.7 + - - +
264E SER* 1.3 57.1 + - - +
266E GLN* 3.2 3.5 + - - -
267E ARG* 2.9 54.3 + - - +
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Residues in contact with SER 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E GLY* 3.4 22.3 + - - -
262E SER 3.2 0.2 - - - -
263E ALA* 1.3 79.8 - - - +
265E GLN* 1.3 64.5 + - - +
267E ARG* 3.3 12.9 + - - +
268E PHE* 3.0 24.9 + - - +
342E ARG 4.5 12.1 + - - +
343E ALA 5.2 0.2 - - - -
447E LYS* 5.0 10.9 + - - -
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Residues in contact with GLN 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E GLY 3.8 9.6 - - - +
262E SER* 3.4 29.3 + - - +
263E ALA 3.3 0.4 - - - -
264E SER* 1.3 78.0 - - - +
266E GLN* 1.3 57.1 + - - +
268E PHE* 3.5 8.3 + - - +
269E ALA* 2.9 28.9 + - - +
447E LYS* 5.0 11.2 - - - +
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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
----------------------------------------------------------
250E THR* 4.1 21.5 - - + +
251E PRO* 4.0 16.7 + - - +
253E PRO* 3.9 29.7 - - + +
262E SER* 3.0 26.5 + - - +
263E ALA* 3.5 5.3 - - - +
265E GLN* 1.3 75.5 - - - +
267E ARG* 1.3 54.5 + - - +
269E ALA* 3.2 6.0 + - - +
270E HIS* 2.7 35.6 + - - +
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Residues in contact with ARG 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252E TRP* 3.5 43.4 - - + +
253E PRO* 3.5 33.9 + - + +
254E LEU 4.4 8.1 + - - -
263E ALA* 2.9 44.0 + - - +
264E SER* 3.7 11.0 + - - +
266E GLN* 1.3 76.2 - - - +
268E PHE* 1.3 62.5 + - - +
270E HIS* 3.3 2.8 + - - +
271E PHE* 3.0 28.2 + - - +
342E ARG* 3.6 38.3 + - - +
343E ALA* 3.8 10.8 - - - -
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Residues in contact with PHE 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264E SER 3.0 16.2 + - - +
265E GLN* 3.7 8.7 - - - +
267E ARG* 1.3 76.6 - - - +
269E ALA* 1.3 60.9 + - + +
271E PHE* 3.5 2.8 + - - +
272E THR* 2.8 47.2 + - + -
343E ALA 3.3 23.5 + - - +
344E GLY* 4.7 7.0 - - - -
442E LEU* 4.2 17.7 - - + -
447E LYS* 3.9 39.0 - - + +
448E LYS 3.7 21.8 - - - -
449E LEU* 4.2 13.9 - - + -
501E 67S 3.6 23.6 - - - -
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Residues in contact with ALA 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250E THR* 4.5 8.1 - - + +
265E GLN 2.9 19.0 + - - +
266E GLN* 3.6 7.6 - - - +
268E PHE* 1.3 76.5 - - + +
270E HIS* 1.3 66.6 + - - +
272E THR* 3.7 6.5 - - - -
273E GLU* 2.9 41.8 + - - +
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Residues in contact with HIS 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249E VAL* 3.4 17.9 - - + +
250E THR* 2.5 33.8 + - - +
251E PRO* 4.8 2.5 - - + +
252E TRP* 3.6 32.1 + + + -
266E GLN 2.7 17.9 + - - +
267E ARG 3.4 6.3 - - - +
269E ALA* 1.3 75.4 - - - +
271E PHE* 1.3 65.8 + + - +
273E GLU* 3.1 5.9 + - - +
274E LEU* 3.1 36.9 + - + +
333E PHE* 3.8 26.4 - + - -
335E TYR* 2.5 32.4 + + - -
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Residues in contact with PHE 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252E TRP* 3.5 28.0 - + - -
267E ARG 3.0 8.6 + - - +
268E PHE* 3.9 2.5 - - - +
270E HIS* 1.3 82.4 - + - +
272E THR* 1.3 64.1 + - - +
274E LEU* 3.1 11.1 + - + +
275E ALA* 2.9 22.7 + - - +
329E PHE* 4.3 7.2 - + - -
335E TYR* 3.9 35.0 - + - -
339E ASP 4.6 0.4 - - - -
340E PHE* 4.0 44.2 - + - -
343E ALA* 3.6 28.3 - - + +
345E LEU* 4.5 11.0 - - + -
501E 67S 3.5 34.8 - - - -
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Residues in contact with THR 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E PHE* 2.8 36.6 + - + -
269E ALA* 3.7 8.1 - - - -
271E PHE* 1.3 76.6 - - - +
273E GLU* 1.3 63.5 + - + +
275E ALA* 3.3 5.2 + - - +
276E ILE* 3.1 23.4 + - + +
448E LYS 5.9 0.2 - - - +
450E PRO* 3.1 42.4 - - + -
453E LEU* 3.8 5.6 - - + +
501E 67S 3.3 22.1 - - - -
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Residues in contact with GLU 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248E LYS 3.8 5.4 - - - +
249E VAL* 3.4 16.4 - - + -
250E THR* 2.7 46.8 + - - -
269E ALA* 2.9 25.9 + - - +
270E HIS 3.6 4.5 - - - +
272E THR* 1.3 74.5 - - + +
274E LEU* 1.3 66.9 + - - +
276E ILE* 3.1 17.4 + - + +
277E ILE* 3.0 28.6 + - + +
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Residues in contact with LEU 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249E VAL* 4.1 19.1 - - + -
270E HIS* 3.1 37.0 + - + +
271E PHE* 3.3 12.8 - - + +
273E GLU* 1.3 77.4 - - - +
275E ALA* 1.3 56.8 + - - +
277E ILE* 3.2 4.8 + - + +
278E SER* 2.9 27.5 + - - -
329E PHE* 3.7 33.4 - - + -
330E LEU* 3.8 22.4 - - + -
333E PHE* 4.2 7.0 - - + -
335E TYR* 4.3 4.0 - - + -
501E 67S 3.3 37.8 + - + -
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Residues in contact with ALA 275 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271E PHE 2.9 12.9 + - - +
272E THR* 3.4 9.6 - - - +
274E LEU* 1.3 74.7 - - - +
276E ILE* 1.3 63.1 + - - +
278E SER* 3.0 9.6 + - - -
279E VAL* 3.0 25.8 + - - +
312E MET* 4.7 7.5 - - + +
453E LEU* 4.1 17.7 - - + -
457E TRP* 5.0 1.8 - - + -
501E 67S 3.8 35.1 - - + +
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Residues in contact with ILE 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E THR* 3.1 16.0 + - + +
273E GLU* 3.1 20.4 + - + +
275E ALA* 1.3 77.2 - - - +
277E ILE* 1.3 66.6 + - + +
279E VAL* 3.0 16.1 + - - +
280E GLN* 3.1 32.5 + - - +
450E PRO* 3.7 30.5 - - + -
452E LEU* 4.4 16.1 - - + +
453E LEU* 3.6 23.8 - - + -
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Residues in contact with ILE 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242E SER* 3.8 34.3 - - - +
245E ASP* 3.8 29.6 - - + +
248E LYS* 5.9 0.9 - - + -
249E VAL* 3.9 26.9 - - + -
273E GLU* 3.0 17.5 + - + +
274E LEU* 3.2 8.7 + - - +
276E ILE* 1.3 77.8 - - + +
278E SER* 1.3 58.3 + - - +
280E GLN* 3.2 20.7 + - + +
281E GLU* 2.8 27.0 + - - +
330E LEU* 4.6 9.6 - - + -
501E 67S 3.9 8.7 - - - +
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Residues in contact with SER 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E LEU 2.9 13.8 + - - -
275E ALA* 3.1 15.5 - - - -
277E ILE* 1.3 78.4 - - - +
279E VAL* 1.3 54.1 + - - +
281E GLU* 3.2 4.4 + - - +
282E ILE* 2.9 34.0 + - - +
312E MET* 3.1 31.0 - - - +
315E GLU* 6.0 0.3 - - - +
501E 67S 3.5 36.5 + - - -
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Residues in contact with VAL 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E ALA* 3.0 13.4 + - + +
276E ILE 3.0 7.9 + - - +
278E SER* 1.3 72.7 - - - +
280E GLN* 1.3 67.6 + - - +
282E ILE* 3.1 9.5 + - - +
283E VAL* 2.9 33.3 + - + +
308E THR* 4.1 23.1 - - + +
312E MET* 4.7 4.3 - - - -
452E LEU* 3.8 28.0 - - + -
453E LEU* 4.3 17.9 - - + -
456E ILE* 4.3 19.3 - - + -
457E TRP* 5.7 1.8 - - + -
471E LEU* 5.0 3.4 - - + -
474E LEU* 4.9 2.0 - - + -
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Residues in contact with GLN 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245E ASP* 4.4 10.2 - - - +
276E ILE* 3.1 28.5 + - + +
277E ILE* 3.4 25.1 - - + +
279E VAL* 1.3 76.8 - - - +
281E GLU* 1.3 56.8 + - - +
283E VAL* 3.3 6.8 + - - +
284E ASP* 2.9 38.4 + - - +
452E LEU* 5.0 3.4 - - + +
474E LEU* 4.0 31.2 - - + +
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Residues in contact with GLU 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235E GLN* 5.7 1.0 + - - -
238E CYS* 3.9 20.4 - - + +
239E ASN* 3.0 28.3 + - - -
242E SER* 2.6 35.2 + - - +
277E ILE 2.8 14.5 + - - +
278E SER 3.4 9.0 - - - +
280E GLN* 1.3 74.0 - - - +
282E ILE* 1.3 58.7 + - + +
284E ASP* 3.4 7.4 + - - +
285E PHE* 3.0 28.9 + - + +
315E GLU* 3.9 11.4 - - - +
319E ARG* 4.2 1.4 + - - -
501E 67S 3.2 29.9 + - - +
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Residues in contact with ILE 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E SER* 2.9 31.1 + - - +
279E VAL* 3.1 7.6 + - - +
281E GLU* 1.3 78.0 - - + +
283E VAL* 1.3 57.1 + - + +
285E PHE* 3.3 7.8 + - + +
286E ALA* 2.9 27.3 + - + +
304E LEU* 3.8 21.5 - - + -
308E THR* 3.6 45.3 - - + +
311E ILE* 3.8 40.4 - - + -
312E MET* 4.2 3.4 - - + +
315E GLU* 5.9 2.9 - - + -
378E ILE* 5.7 1.3 - - + -
501E 67S 6.0 0.4 - - - +
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Residues in contact with VAL 283 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E VAL* 2.9 25.7 + - + +
280E GLN* 3.7 6.1 - - - +
282E ILE* 1.3 74.0 - - + +
284E ASP* 1.3 68.9 + - - +
286E ALA* 3.2 6.7 + - - +
287E LYS* 3.2 28.8 + - - +
304E LEU* 4.4 12.3 - - + -
471E LEU* 3.6 28.7 - - + -
474E LEU* 4.0 37.0 - - + +
475E LEU* 4.3 16.8 - - + +
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Residues in contact with ASP 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238E CYS* 3.6 11.4 - - - -
241E ARG* 2.9 43.3 + - - +
280E GLN* 2.9 24.1 + - - +
281E GLU* 3.6 7.7 - - - +
283E VAL* 1.3 80.9 - - - +
285E PHE* 1.3 63.9 + - - +
287E LYS* 3.5 23.0 + - - +
288E GLN* 3.6 18.0 + - - +
474E LEU* 5.6 1.6 - - - +
477E ASP* 5.7 1.0 - - - +
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Residues in contact with PHE 285 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E LEU* 3.6 29.4 - - + -
234E ALA* 3.9 17.3 - - + -
235E GLN* 3.5 36.8 - - + -
238E CYS* 3.5 10.0 - - + -
281E GLU* 3.0 17.6 + - + +
282E ILE* 3.6 7.9 - - + +
283E VAL 3.2 0.2 - - - -
284E ASP* 1.3 74.7 - - - +
286E ALA* 1.3 69.7 + - - +
288E GLN* 2.9 17.4 + - - +
289E VAL* 3.3 32.0 + - + +
311E ILE* 6.3 0.4 - - + -
371E ALA* 4.4 11.9 - - + -
374E ILE* 3.6 31.6 - - + -
375E ALA 4.8 2.0 - - - -
378E ILE* 4.5 6.3 - - + -
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Residues in contact with ALA 286 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E ILE 2.9 16.5 + - - +
283E VAL* 3.2 6.3 + - - +
285E PHE* 1.3 78.5 - - - +
287E LYS* 1.3 58.8 + - - +
289E VAL* 2.9 27.4 + - - +
292E PHE* 3.3 49.4 - - + +
304E LEU* 4.0 14.8 - - + -
378E ILE* 4.6 9.4 - - + -
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Residues in contact with LYS 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B GLY* 5.2 2.4 - - - -
283E VAL* 3.2 18.3 + - - +
284E ASP* 3.7 19.9 + - - +
285E PHE 3.2 0.8 - - - -
286E ALA* 1.3 77.0 - - - +
288E GLN* 1.3 61.3 + - + +
289E VAL 3.7 3.3 + - - +
292E PHE* 4.2 6.5 - - + -
293E LEU* 3.4 40.7 - - + +
474E LEU 3.1 25.2 + - - -
475E LEU* 3.2 39.7 + - + +
477E ASP* 3.3 26.1 + - - +
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Residues in contact with GLN 288 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E GLN* 3.5 26.9 + - - +
231E LEU* 5.0 0.9 - - - +
234E ALA* 3.9 27.7 - - + +
237E GLN* 3.3 35.1 + - - +
238E CYS* 4.1 15.1 - - - -
241E ARG* 4.5 6.1 + - - -
284E ASP 3.7 14.7 - - - +
285E PHE 2.9 10.0 + - - +
287E LYS* 1.3 78.4 - - + +
289E VAL* 1.3 62.5 + - - +
290E PRO* 3.3 10.4 - - - +
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Residues in contact with VAL 289 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E LEU* 4.1 9.6 - - + -
285E PHE* 3.4 45.8 - - + +
286E ALA* 2.9 15.3 + - - +
287E LYS 4.4 2.9 - - - +
288E GLN* 1.3 76.5 - - - +
290E PRO* 1.3 75.0 - - + +
291E GLY 3.0 3.5 + - - -
292E PHE* 3.1 17.6 + - + +
293E LEU 4.6 0.9 + - - -
375E ALA* 4.4 9.2 - - + -
378E ILE* 4.8 7.2 - - + -
379E PHE* 3.8 23.8 - - + -
399E TYR* 3.6 18.8 - - + +
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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