Contacts of the helix formed by residues 243 - 266 (chain E) in PDB entry 5ID3
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 GLU 243 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A GLU* 4.2 15.0 - - - +
247A TYR* 3.2 47.9 + - + +
243D GLU* 2.6 45.2 - - + +
231E ARG* 4.6 0.8 - - - +
242E VAL* 1.4 83.7 - - + +
244E PRO* 1.4 66.2 - - + +
245E VAL* 3.5 4.7 - - - -
246E THR* 3.5 15.0 + - - -
247E TYR* 3.7 13.5 + - + +
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Residues in contact with PRO 244 (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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224E VAL* 5.4 2.2 - - + -
228E LEU* 4.0 16.4 - - + -
231E ARG* 3.4 24.5 - - - +
241E ILE* 3.5 9.4 - - + +
242E VAL 3.2 10.8 - - - +
243E GLU* 1.4 89.1 - - + +
245E VAL* 1.3 63.3 + - + +
247E TYR* 2.7 56.2 - - + +
248E PHE* 3.9 4.6 + - - -
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Residues in contact with VAL 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PHE* 5.7 2.7 - - + -
221E ALA* 4.5 14.3 - - + +
224E VAL* 4.5 12.2 - - + +
225E GLN* 4.4 22.7 - - + -
228E LEU* 4.1 28.4 - - + +
243E GLU 5.2 2.5 - - - +
244E PRO* 1.3 82.0 - - + +
246E THR* 1.4 73.2 + - - +
248E PHE* 3.7 5.2 + - - +
249E ALA* 3.4 17.8 + - + +
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Residues in contact with THR 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A TYR* 3.4 44.7 + - + +
248A PHE* 3.0 41.8 - - + +
251A TYR* 6.5 0.9 - - + -
243E GLU* 3.5 9.3 + - - -
244E PRO 3.3 0.8 - - - -
245E VAL* 1.4 82.4 - - - +
247E TYR* 1.4 59.7 + - - +
249E ALA* 3.0 12.5 + - + +
250E THR* 2.9 33.4 + - + +
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Residues in contact with TYR 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D GLU* 3.5 47.1 - - + +
246D THR* 3.5 40.3 + - + -
247D TYR* 4.7 4.7 - - + -
250D THR* 4.2 14.7 - - + +
243E GLU* 3.7 9.0 + - + +
244E PRO* 2.7 55.7 + - + +
246E THR* 1.4 74.4 - - - +
248E PHE* 1.4 89.5 + + - +
250E THR* 2.5 30.5 + - + +
251E TYR* 3.4 3.6 + - - +
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Residues in contact with PHE 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D THR* 3.2 32.5 - - + -
249D ALA* 5.6 4.5 - - + -
220E ALA* 4.3 28.9 - - + +
221E ALA* 4.7 4.6 - - - +
224E VAL* 3.8 34.1 - - + -
244E PRO 4.1 3.6 - - - -
245E VAL 3.7 6.8 + - - +
246E THR 3.4 0.4 - - - -
247E TYR* 1.4 111.6 - + - +
249E ALA* 1.4 56.6 - - - +
251E TYR* 3.0 40.5 + + + +
252E SER* 3.2 6.4 + - - -
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Residues in contact with ALA 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PHE* 5.3 7.4 - - + -
251A TYR* 3.6 15.4 - - + -
221E ALA* 5.0 11.9 - - + +
245E VAL* 3.4 14.6 + - + +
246E THR* 3.0 20.9 + - + +
248E PHE* 1.4 73.6 - - - +
250E THR* 1.4 56.7 + - - +
252E SER* 2.5 38.5 + - - +
253E THR 3.0 3.5 + - - -
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Residues in contact with THR 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A TYR* 5.4 9.2 - - + +
250A THR* 5.4 8.3 - - - +
251A TYR* 4.8 6.0 - - + -
250D THR* 3.8 16.6 - - - +
253D THR* 5.0 5.1 - - - +
246E THR* 2.9 27.8 + - + +
247E TYR* 2.5 24.5 + - - +
249E ALA* 1.4 73.9 - - - +
251E TYR* 1.4 61.1 + - - +
253E THR* 3.0 36.1 + - + +
254E VAL* 3.4 6.6 + - - +
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Residues in contact with TYR 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D THR* 5.9 1.1 - - + -
249D ALA* 3.4 40.4 + - + +
250D THR* 4.6 7.9 - - + -
252D SER* 4.1 10.2 + - - -
253D THR* 2.9 43.5 + - - -
256D ALA* 6.1 2.0 - - + -
216E TRP* 3.7 35.3 - + + -
220E ALA* 6.1 3.8 - - + -
247E TYR 3.4 2.7 + - - +
248E PHE* 3.0 31.1 + + + +
250E THR* 1.4 81.3 + - - +
252E SER* 1.4 58.4 + - - +
254E VAL* 3.1 25.0 - - + +
255E ALA* 3.4 4.5 + - - +
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Residues in contact with SER 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A TYR* 3.5 18.8 + - - -
216E TRP* 5.8 0.4 - - - -
217E ALA* 4.3 27.8 - - - +
220E ALA* 6.4 0.4 - - - -
221E ALA* 5.5 4.0 - - - -
248E PHE 3.2 6.1 + - - -
249E ALA* 2.5 31.4 + - - +
251E TYR* 1.4 76.2 - - - +
253E THR* 1.4 56.4 + - - +
255E ALA* 2.9 29.8 + - - +
256E ALA* 3.4 5.4 + - - +
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Residues in contact with THR 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A THR 5.7 0.7 - - - +
251A TYR* 2.9 45.3 - - + -
254A VAL* 3.0 37.2 - - + +
249E ALA 3.0 0.4 + - - -
250E THR* 3.0 25.3 + - - +
252E SER* 1.4 80.5 + - - +
254E VAL* 1.4 67.1 + - + +
256E ALA* 3.2 22.4 + - - +
257E THR* 3.5 7.1 + - - -
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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
----------------------------------------------------------
254A VAL* 6.0 0.7 - - + -
253D THR* 3.0 57.0 - - + +
254D VAL* 4.8 3.6 - - - +
256D ALA* 5.2 7.0 - - + -
257D THR* 5.2 8.1 - - - +
216E TRP* 5.5 3.1 - - + -
250E THR 3.4 5.3 + - - +
251E TYR* 3.1 22.2 - - + +
252E SER 3.4 0.4 - - - -
253E THR* 1.4 80.0 - - + +
255E ALA* 1.4 59.5 + - - +
257E THR* 2.7 34.2 + - + +
258E PHE* 2.9 13.7 + - - +
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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
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214E VAL* 4.9 12.9 - - + +
216E TRP* 3.5 31.0 - - + +
217E ALA* 3.9 19.3 - - + -
251E TYR 3.4 6.9 + - - +
252E SER* 2.9 18.7 + - - +
254E VAL* 1.4 76.8 - - - +
256E ALA* 1.4 60.8 + - - +
258E PHE* 3.3 16.3 + - - +
259E GLY* 3.5 8.5 + - - -
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Residues in contact with ALA 256 (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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216A TRP* 5.2 14.8 - - + -
254A VAL* 5.1 8.3 - - + -
258A PHE* 3.7 28.9 - - + -
214E VAL* 6.3 1.6 - - - -
252E SER 3.4 4.4 + - - +
253E THR* 3.2 14.0 + - - +
254E VAL 3.1 0.4 - - - -
255E ALA* 1.4 79.0 - - - +
257E THR* 1.4 60.6 + - - +
259E GLY* 3.4 14.1 + - - -
260E TYR 4.4 0.3 + - - -
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Residues in contact with THR 257 (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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254A VAL* 3.1 29.1 - - + +
257A THR* 4.3 14.3 - - + +
258A PHE* 5.7 0.9 - - - -
260A TYR* 4.9 0.4 - - - +
257D THR* 3.5 24.5 - - - +
260D TYR* 5.9 0.4 - - + -
253E THR 3.5 3.8 + - - -
254E VAL* 2.7 25.0 + - + +
256E ALA* 1.4 70.5 - - - +
258E PHE* 1.4 60.6 + - - -
260E TYR* 2.5 52.5 - - + +
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Residues in contact with PHE 258 (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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210D HIS* 6.5 0.4 - + - -
256D ALA* 4.1 31.2 - - + -
257D THR* 5.9 1.3 - - - -
259D GLY* 5.8 2.7 - - - -
263D TYR* 2.9 31.4 - + - -
216E TRP* 6.4 0.2 - - - +
254E VAL 2.9 13.1 + - - +
255E ALA* 3.3 12.0 + - - +
257E THR* 1.4 72.2 - - - +
259E GLY* 1.3 63.1 + - - +
260E TYR* 3.3 5.7 + - - -
261E TYR* 3.3 13.8 + - + +
262E LEU* 3.3 44.4 - - + +
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Residues in contact with GLY 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PHE* 5.0 5.4 - - - -
214E VAL* 5.9 4.3 - - - -
255E ALA 3.5 6.3 + - - -
256E ALA 3.4 10.4 + - - -
257E THR 3.2 2.0 - - - -
258E PHE* 1.3 78.4 - - - +
260E TYR* 1.4 61.6 + - - +
261E TYR 3.1 1.2 + - - -
262E LEU* 3.4 17.7 + - - +
263E TYR* 3.1 24.9 + - - +
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Residues in contact with TYR 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PHE* 4.5 13.5 - + + -
260A TYR* 2.9 43.7 - + + -
261A TYR* 5.5 10.5 - - + -
257D THR* 4.7 2.3 + - - -
260D TYR* 3.5 37.3 - + + +
256E ALA 4.4 3.7 + - - -
257E THR* 2.5 48.2 + - + +
258E PHE* 4.3 3.0 - - - -
259E GLY* 1.4 71.8 - - - +
261E TYR* 1.4 93.8 + + + +
263E TYR* 3.5 18.4 - - - +
264E THR* 4.9 2.6 + - - -
291E PHE* 5.3 4.7 - - - -
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Residues in contact with TYR 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D TYR* 5.2 9.9 - - + -
263D TYR* 2.9 71.6 - + + +
291D PHE* 2.9 44.3 - + - -
258E PHE* 3.5 11.9 - - + +
259E GLY 3.1 0.6 + - - -
260E TYR* 1.4 93.0 - + + +
262E LEU* 1.4 74.6 + - + +
263E TYR 3.1 5.1 + - - -
264E THR* 4.3 4.0 + - - -
265E GLN* 3.8 20.6 - - + +
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Residues in contact with LEU 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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263D TYR* 5.0 0.2 - - - +
210E HIS* 3.7 34.8 - - + +
213E ARG* 6.0 1.3 - - + -
214E VAL* 4.0 22.2 - - + -
258E PHE* 3.3 49.4 - - + +
259E GLY* 3.7 21.1 - - - +
261E TYR* 1.4 87.2 - - + +
263E TYR* 1.4 64.4 + - - +
264E THR 3.7 0.4 - - - -
265E GLN* 4.1 6.7 - - - -
266E GLN* 3.0 27.1 + - + +
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Residues in contact with TYR 263 (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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258A PHE* 4.9 15.5 - + - -
261A TYR* 2.7 54.0 + + + -
204E GLU* 3.7 24.2 + - - +
259E GLY 3.1 14.8 + - - +
260E TYR* 3.5 18.2 - - - +
261E TYR 3.1 3.4 - - - -
262E LEU* 1.4 73.5 - - - +
264E THR* 1.4 60.2 + - - +
266E GLN* 2.6 32.6 + - - +
291E PHE* 3.9 19.1 - + + -
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Residues in contact with THR 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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204E GLU* 5.6 2.1 - - - +
260E TYR 5.2 1.6 + - - -
261E TYR 4.3 3.1 + - - -
263E TYR* 1.4 79.1 - - - +
265E GLN* 1.4 59.1 + - - +
266E GLN* 2.7 17.8 + - - -
267E SER* 3.5 1.9 + - - -
289E GLN* 3.0 34.8 - - - +
290E ASN 3.5 18.8 + - - +
291E PHE* 3.3 37.4 - - + +
292E ASP* 3.0 29.2 + - - +
293E ILE* 3.6 16.0 - - - +
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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
----------------------------------------------------------
291D PHE* 3.4 46.9 - - + +
261E TYR* 3.8 24.7 - - + +
262E LEU* 3.7 6.0 + - - +
263E TYR 3.6 0.4 - - - -
264E THR* 1.4 72.3 - - - +
266E GLN* 1.4 51.9 + - - +
267E SER* 3.0 6.7 - - - -
268E PHE* 2.8 50.6 + - + +
289E GLN* 4.3 15.3 - - - +
293E ILE* 3.9 27.9 - - + +
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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
----------------------------------------------------------
203E ILE* 5.7 6.3 - - + +
204E GLU* 4.2 17.6 + - - +
207E ALA* 4.2 29.0 - - + +
210E HIS* 3.9 41.4 + - + +
262E LEU* 3.0 18.6 + - - +
263E TYR* 2.6 19.8 + - - +
264E THR 2.7 29.9 + - - -
265E GLN* 1.4 66.8 - - - +
267E SER* 1.3 69.6 + - - +
268E PHE 3.2 1.1 + - - -
269E GLU* 3.5 18.2 + - - +
270E TYR* 5.6 1.7 - - - -
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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