Contacts of the helix formed by residues 210 - 233 (chain A) in PDB entry 3JRQ
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 GLY 210 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A MET 4.2 0.2 + - - -
207A LEU 3.2 14.6 + - - -
208A CYS 3.4 1.8 - - - -
209A ASP* 1.3 72.7 - - - +
211A ASP* 1.3 53.9 + - - -
212A THR 3.0 4.3 - - - -
213A TRP* 2.6 37.8 + - - +
214A LEU* 3.7 1.6 + - - +
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Residues in contact with ASP 211 (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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209A ASP 3.5 1.8 + - - -
210A GLY* 1.3 69.9 - - - -
212A THR* 1.3 60.6 + - + +
213A TRP 3.1 0.4 - - - -
214A LEU* 3.1 42.5 + - + +
215A GLU* 3.2 20.7 + - - +
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Residues in contact with THR 212 (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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209A ASP* 3.4 29.9 + - - +
210A GLY 2.9 0.8 + - - -
211A ASP* 1.3 79.1 - - + +
213A TRP* 1.3 56.7 + - - +
215A GLU* 3.6 11.3 - - - +
216A LYS* 2.7 49.6 + - - +
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Residues in contact with TRP 213 (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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167A GLN* 3.0 24.7 + - + -
205A PRO* 3.5 19.7 - - + -
206A MET 3.6 32.8 - - - +
207A LEU* 3.3 30.9 - - + +
209A ASP* 4.3 1.2 + - - -
210A GLY 2.6 23.0 + - - +
212A THR* 1.3 75.1 + - - +
214A LEU* 1.3 81.0 + - + +
216A LYS* 3.9 4.7 - - - +
217A TRP* 3.1 30.5 + + - +
250A PHE* 3.8 40.4 - + + -
252A SER* 5.0 1.8 - - - -
253A HIS* 3.8 27.1 - + - -
255A PHE* 3.8 27.8 - + - -
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Residues in contact with LEU 214 (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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210A GLY 5.0 0.9 - - - +
211A ASP* 3.1 36.7 + - + +
213A TRP* 1.3 94.9 - - + +
215A GLU* 1.3 68.7 + - - +
217A TRP 3.4 0.3 + - - -
218A LYS* 3.1 34.0 + - + +
253A HIS* 3.5 37.5 - - + +
255A PHE* 3.7 16.5 - - + -
332A ALA* 4.2 11.9 - - + -
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Residues in contact with GLU 215 (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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211A ASP* 3.2 21.9 + - - +
212A THR* 3.2 11.4 + - - +
214A LEU* 1.3 83.9 - - - +
216A LYS* 1.3 63.2 + - - +
218A LYS* 3.4 27.5 + - + +
219A LYS* 3.0 26.4 + - - +
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Residues in contact with LYS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A GLU* 3.2 47.2 + - + +
204A LYS 4.0 5.9 + - - -
205A PRO* 3.8 29.6 - - + -
206A MET* 5.1 1.7 - - - +
209A ASP* 4.7 11.1 + - + +
212A THR* 2.7 34.5 + - - +
213A TRP* 3.9 2.0 - - - +
215A GLU* 1.3 74.2 - - + +
217A TRP* 1.3 56.3 + - - +
219A LYS* 3.5 8.8 + - + +
220A ALA* 2.9 30.1 + - - +
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Residues in contact with TRP 217 (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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151A PHE* 3.7 28.5 - + - -
152A LEU* 3.8 19.5 - - + -
167A GLN* 2.6 26.9 + - - -
196A LEU* 4.2 10.5 - - + -
200A ILE* 3.6 31.2 - - + -
205A PRO* 3.5 22.9 - - + +
213A TRP* 3.1 29.4 + + - +
215A GLU 3.4 0.2 - - - -
216A LYS* 1.3 75.2 - - - +
218A LYS* 1.3 57.1 + - - +
220A ALA* 3.3 4.1 + - - +
221A LEU* 2.9 39.2 + - + +
248A VAL* 3.9 23.6 - - + -
250A PHE* 3.5 28.0 - + - -
255A PHE* 3.5 27.8 - + + -
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Residues in contact with LYS 218 (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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214A LEU* 3.1 27.3 + - + +
215A GLU* 3.7 25.6 + - + +
216A LYS 3.3 0.4 - - - -
217A TRP* 1.3 74.3 - - - +
219A LYS* 1.3 58.3 + - - +
221A LEU* 3.5 3.2 + - - +
222A PHE* 2.9 29.3 + - - +
255A PHE* 4.1 9.6 - - + -
330A VAL* 3.5 48.8 - - + +
331A THR* 4.6 4.0 - - - +
332A ALA* 4.4 18.6 - - + +
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Residues in contact with LYS 219 (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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203A GLU* 3.5 30.3 + - + +
215A GLU 3.0 17.6 + - - +
216A LYS* 3.6 7.9 - - + +
218A LYS* 1.3 75.5 - - - +
220A ALA* 1.3 57.2 + - - +
222A PHE* 3.4 8.2 + - + +
223A ASN* 2.9 57.0 + - - +
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Residues in contact with ALA 220 (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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196A LEU* 3.8 2.0 - - + -
199A GLU* 3.7 28.9 - - + +
200A ILE* 3.5 32.3 - - + -
203A GLU* 4.3 7.6 - - + -
216A LYS 2.9 17.9 + - - +
217A TRP 3.3 1.5 + - - +
219A LYS* 1.3 69.8 - - - +
221A LEU* 1.3 60.0 + - - +
223A ASN* 4.4 1.6 - - - +
224A SER* 2.5 35.8 + - - -
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 3.8 31.4 - - + +
217A TRP* 2.9 24.0 + - + +
218A LYS 3.5 4.5 - - - +
220A ALA* 1.3 72.9 - - - +
222A PHE* 1.3 68.8 + - - +
224A SER* 3.2 11.3 + - - -
225A PHE* 3.2 23.0 + - + -
246A VAL* 4.0 22.0 - - + +
248A VAL* 4.2 6.7 - - + -
255A PHE* 3.8 32.1 - - + -
257A ALA* 4.1 21.1 - - + +
328A PRO* 4.7 0.9 - - - -
330A VAL* 4.0 17.3 - - + -
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Residues in contact with PHE 222 (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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218A LYS 2.9 18.7 + - - +
219A LYS* 3.4 9.2 - - + +
221A LEU* 1.3 78.1 - - - +
223A ASN* 1.3 72.7 + - - +
225A PHE* 3.3 10.7 + - - +
226A LEU* 3.4 40.2 + - + +
327A ASP* 3.7 33.7 - - + -
328A PRO* 3.5 40.8 - - + +
330A VAL* 4.3 6.6 - - + +
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Residues in contact with ASN 223 (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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199A GLU* 3.7 34.7 + - + +
203A GLU* 4.1 2.8 + - - -
219A LYS* 2.9 54.5 + - - +
221A LEU 3.2 0.2 - - - -
222A PHE* 1.3 86.0 - - - +
224A SER* 1.3 52.6 + - - +
226A LEU* 3.5 12.3 + - - +
227A ARG* 2.8 34.3 + - - +
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Residues in contact with SER 224 (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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192A MET* 4.1 11.7 - - - -
195A ALA* 4.4 5.8 - - - -
196A LEU* 3.0 41.0 + - - +
199A GLU* 3.6 8.2 - - - +
220A ALA 2.5 22.6 + - - -
221A LEU* 3.2 8.3 + - - -
223A ASN* 1.3 73.4 - - - +
225A PHE* 1.3 66.3 + - - +
227A ARG* 4.1 2.0 - - - +
228A VAL* 3.0 31.0 + - - +
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Residues in contact with PHE 225 (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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192A MET* 3.9 15.5 - - + -
221A LEU* 3.2 16.7 + - + -
222A PHE 3.3 7.6 + - - +
224A SER* 1.3 77.7 - - - +
226A LEU* 1.3 56.7 + - - +
228A VAL* 3.9 1.7 - - - +
229A ASP* 2.9 31.3 + - - +
244A SER* 3.2 37.2 - - - -
246A VAL* 3.9 19.5 - - + -
257A ALA* 3.7 33.4 - - + -
259A CYS* 3.5 25.1 - - + -
315A ILE* 3.7 18.9 - - + +
326A PRO* 4.0 6.3 - - - +
328A PRO* 3.6 25.6 - - + -
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Residues in contact with LEU 226 (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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222A PHE* 3.4 45.1 + - + +
223A ASN* 3.8 13.7 - - - +
224A SER 3.4 0.2 - - - -
225A PHE* 1.3 71.6 - - - +
227A ARG* 1.3 66.6 + - - +
229A ASP* 3.3 6.7 + - - +
230A SER* 3.0 23.9 + - - -
326A PRO* 4.2 10.8 - - + -
327A ASP* 4.0 32.3 - - - +
328A PRO* 4.2 0.9 - - + -
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Residues in contact with ARG 227 (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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191A ARG* 4.0 7.2 - - - +
195A ALA* 3.6 15.8 + - + +
198A GLU* 3.9 23.5 + - - +
199A GLU* 3.2 32.0 + - - +
202A LYS* 2.5 42.5 - - - +
223A ASN 2.8 17.4 + - - +
224A SER* 4.1 2.9 - - - +
225A PHE 3.3 0.2 - - - -
226A LEU* 1.3 70.7 - - - +
228A VAL* 1.3 65.0 + - - +
230A SER* 3.0 13.7 + - - +
231A GLU* 2.9 46.8 + - + +
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Residues in contact with VAL 228 (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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187A TYR* 4.3 11.2 - - + -
188A CYS* 4.2 16.4 - - - -
191A ARG* 4.1 13.5 - - + -
192A MET* 3.7 21.3 - - + -
195A ALA* 3.7 22.0 - - + -
224A SER 3.0 22.5 + - - +
225A PHE 3.9 2.9 - - - +
227A ARG* 1.3 74.9 - - - +
229A ASP* 1.3 63.4 + - - +
231A GLU* 2.9 20.7 + - - +
232A ILE* 3.0 22.1 + - + +
315A ILE* 4.0 18.2 - - + -
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Residues in contact with ASP 229 (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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225A PHE 2.9 19.4 + - - +
226A LEU 3.7 4.9 - - - +
227A ARG 3.2 0.2 - - - -
228A VAL* 1.3 74.9 - - - +
230A SER* 1.3 64.5 + - - +
232A ILE* 3.3 12.6 + - - +
233A GLU* 3.2 20.3 - - - +
314A SER 4.3 0.3 - - - +
315A ILE* 4.0 13.9 - - + -
316A GLY* 3.0 27.2 + - - +
321A LYS* 3.0 28.1 + - - -
326A PRO* 3.5 33.1 - - + +
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Residues in contact with SER 230 (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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226A LEU 3.0 14.3 + - - -
227A ARG* 3.0 18.4 + - - +
229A ASP* 1.3 81.2 + - - +
231A GLU* 1.3 60.4 + - - +
233A GLU* 3.4 28.5 + - - +
234A SER* 4.7 1.9 + - - -
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Residues in contact with GLU 231 (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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187A TYR* 2.7 29.8 + - + +
191A ARG* 2.7 51.6 + - - +
195A ALA* 5.1 0.5 - - - +
227A ARG* 2.9 32.7 + - + +
228A VAL* 2.9 12.3 + - - +
230A SER* 1.3 71.9 - - - +
232A ILE* 1.3 66.8 + - - +
233A GLU 3.1 3.3 + - - -
234A SER* 3.2 15.1 + - - -
235A VAL* 3.4 13.3 - - + +
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Residues in contact with ILE 232 (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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184A VAL* 4.1 33.2 - - + -
187A TYR* 3.6 32.5 - - + -
228A VAL* 3.0 24.3 + - + +
229A ASP* 3.3 14.5 + - - +
231A GLU* 1.3 72.4 - - - +
233A GLU* 1.3 60.1 + - + +
234A SER 2.8 12.4 + - - -
235A VAL* 3.0 19.8 + - + -
236A ALA* 3.2 13.7 + - + +
237A PRO 5.5 0.2 - - - +
240A VAL 4.7 1.8 - - - +
315A ILE* 4.6 0.4 - - + -
316A GLY* 3.4 35.4 - - - +
317A ASP 4.9 0.2 - - - +
318A ARG* 4.1 13.5 - - + +
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Residues in contact with GLU 233 (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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229A ASP* 3.2 23.6 - - - +
230A SER* 3.4 19.6 - - - +
231A GLU 3.1 1.2 - - - -
232A ILE* 1.3 77.1 - - + +
234A SER* 1.3 62.4 + - - +
235A VAL 3.7 0.2 - - - -
318A ARG* 3.6 46.8 + - - +
321A LYS* 3.1 31.7 + - - +
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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) + - + + + + + -
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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