Contacts of the helix formed by residues 175 - 200 (chain X) in PDB entry 2DE0
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 175 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172X GLN 4.2 3.1 - - - -
173X THR 2.7 12.5 + - - -
174X ASP* 1.3 70.9 - - - +
176X ALA* 1.3 63.7 + - - +
177X GLY 3.1 4.5 + - - -
178X ASP* 3.1 17.2 + - - +
179X TRP* 2.8 24.3 + - - +
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Residues in contact with ALA 176 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170X LEU 4.8 1.8 - - - +
171X SER* 3.2 22.7 - - - +
172X GLN 3.7 10.0 + - - -
173X THR 4.0 2.7 - - - +
174X ASP* 3.1 9.0 + - + +
175X GLY* 1.3 75.2 - - - +
177X GLY* 1.3 55.9 + - - +
179X TRP* 3.7 8.0 - - - +
180X ARG* 2.8 39.4 + - - +
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Residues in contact with GLY 177 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171X SER 4.4 0.9 - - - -
172X GLN* 3.3 40.2 + - - +
175X GLY 3.1 1.2 - - - -
176X ALA* 1.3 78.2 - - - +
178X ASP* 1.3 58.8 + - - +
180X ARG* 3.5 7.5 + - - +
181X GLU* 3.0 27.3 + - - +
484X PRO* 4.9 3.1 - - - +
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Residues in contact with ASP 178 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175X GLY* 3.1 17.0 + - - +
177X GLY* 1.3 71.1 - - - +
179X TRP* 1.3 67.5 + - - +
181X GLU* 3.1 15.6 + - - +
182X LYS* 2.9 25.5 + - - +
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Residues in contact with TRP 179 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175X GLY 2.8 19.8 + - - +
176X ALA* 3.7 9.0 - - - +
178X ASP* 1.3 74.8 - - - +
180X ARG* 1.3 92.2 + - + +
181X GLU 2.8 1.4 + - - -
182X LYS* 3.0 28.0 + - - +
183X GLU* 2.9 58.2 + - + +
318X ARG* 3.7 40.2 - - + -
319X VAL* 4.2 10.3 - - + -
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Residues in contact with ARG 180 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171X SER* 2.5 50.7 + - - +
172X GLN* 3.9 9.5 - - - +
176X ALA* 2.8 30.1 + - - +
177X GLY* 3.7 5.7 - - - +
179X TRP* 1.3 89.0 - - + +
181X GLU* 1.3 56.6 + - - +
183X GLU* 3.9 1.4 - - - +
184X ALA* 3.1 29.3 + - - +
318X ARG 4.8 6.0 + - - -
319X VAL* 3.6 36.5 - - + +
484X PRO* 3.7 21.2 - - + +
485X ASP* 4.9 7.1 - - - +
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Residues in contact with GLU 181 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177X GLY 3.0 17.3 + - - +
178X ASP* 3.6 16.1 - - - +
179X TRP 2.8 2.8 + - - -
180X ARG* 1.3 74.8 - - - +
182X LYS* 1.3 64.4 + - - +
184X ALA* 4.0 1.6 - - - +
185X LYS* 3.0 28.1 + - + +
484X PRO* 3.9 21.6 - - + +
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Residues in contact with LYS 182 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178X ASP 2.9 14.9 + - - +
179X TRP* 3.4 41.6 + - - +
181X GLU* 1.3 78.3 + - - +
183X GLU* 1.3 68.6 + - - +
185X LYS* 3.6 13.5 + - + +
186X ASP* 3.0 37.3 + - - +
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Residues in contact with GLU 183 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179X TRP* 2.9 48.8 + - + +
180X ARG 4.0 2.0 - - - +
182X LYS* 1.3 82.5 + - - +
184X ALA* 1.3 60.5 + - - +
186X ASP* 3.1 8.7 - - - +
187X LEU* 3.1 29.8 + - + +
315X ARG* 3.1 43.8 + - - +
318X ARG* 5.6 1.4 - - - -
319X VAL* 3.2 27.3 - - + +
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Residues in contact with ALA 184 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180X ARG 3.1 17.6 + - - +
181X GLU 4.0 2.7 - - - +
183X GLU* 1.3 71.9 - - - +
185X LYS* 1.3 66.6 + - - +
186X ASP 2.9 1.7 + - - -
187X LEU* 3.2 7.2 + - - +
188X THR* 3.0 28.2 + - - +
319X VAL* 3.9 16.2 - - + +
326X TRP* 4.6 9.0 - - - +
483X HIS 4.9 1.8 - - - +
484X PRO* 3.8 26.9 - - + +
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Residues in contact with LYS 185 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181X GLU* 3.0 23.1 + - + +
182X LYS* 3.7 14.8 - - + +
184X ALA* 1.3 76.6 - - - +
186X ASP* 1.3 61.3 + - - +
188X THR* 3.5 5.8 + - - -
189X GLU* 3.1 61.3 + - - +
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Residues in contact with ASP 186 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182X LYS* 3.0 24.3 + - - +
183X GLU* 3.1 20.9 - - - +
185X LYS* 1.3 82.5 - - - +
187X LEU* 1.3 62.2 + - - +
189X GLU* 3.5 10.0 + - - +
190X LEU* 2.9 29.4 + - - +
193X ARG* 5.2 1.4 + - - -
315X ARG* 3.1 19.5 + - - +
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Residues in contact with LEU 187 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183X GLU* 3.1 18.2 + - + +
184X ALA* 3.9 4.3 - - - +
186X ASP* 1.3 79.2 - - - +
188X THR* 1.3 57.7 + - - +
190X LEU* 3.3 6.6 + - + +
191X VAL* 2.9 35.0 + - + +
312X LEU* 4.2 21.3 - - + +
315X ARG* 3.5 52.3 - - + +
316X LEU* 3.8 24.5 - - + -
319X VAL* 4.1 22.4 - - + -
326X TRP* 3.8 19.1 - - + -
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Residues in contact with THR 188 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184X ALA* 3.0 17.5 + - - +
185X LYS* 3.7 6.3 - - - -
187X LEU* 1.3 72.0 - - - +
189X GLU* 1.3 68.2 + - - +
190X LEU 2.9 1.8 + - - -
191X VAL* 2.9 2.4 + - - +
192X GLN* 2.8 29.1 + - + +
326X TRP* 3.6 16.1 + - - -
330X GLN* 3.4 21.4 + - - +
333X LYS* 3.4 33.0 - - - -
481X THR* 5.9 4.0 - - - -
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Residues in contact with GLU 189 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185X LYS* 3.1 57.8 + - - +
186X ASP* 3.8 8.5 - - - +
188X THR* 1.3 77.6 - - + +
190X LEU* 1.3 61.7 + - - +
192X GLN* 4.2 4.9 - - - +
193X ARG* 3.1 36.7 + - + +
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Residues in contact with LEU 190 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186X ASP* 2.9 18.0 + - - +
187X LEU* 3.4 7.6 - - + +
188X THR 2.9 1.8 + - - -
189X GLU* 1.3 78.2 - - - +
191X VAL* 1.3 66.2 + - + +
193X ARG* 3.2 37.4 + - - +
194X ARG* 3.1 49.9 + - + +
312X LEU* 3.9 28.3 - - + -
315X ARG* 4.0 21.5 - - - +
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Residues in contact with VAL 191 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187X LEU* 2.9 23.5 + - - +
188X THR 3.9 1.8 - - - +
190X LEU* 1.3 73.0 - - + +
192X GLN* 1.3 57.4 + - - +
194X ARG* 3.4 13.4 + - - +
195X ILE* 2.9 36.0 + - + +
235X TYR* 4.9 4.5 - - - +
312X LEU* 3.6 35.4 - - + -
326X TRP* 3.9 11.7 - - + -
327X TRP* 3.6 18.4 - - + -
330X GLN* 3.6 31.6 - - + -
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Residues in contact with GLN 192 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188X THR* 2.8 25.8 + - + +
189X GLU* 4.2 4.5 - - - +
191X VAL* 1.3 74.3 - - - +
193X ARG* 1.3 54.9 + - - +
195X ILE* 3.0 15.3 + - - +
196X THR* 2.6 42.2 + - - +
330X GLN* 3.0 39.8 + - - +
333X LYS* 3.4 32.9 - - + +
334X TYR* 3.5 27.7 - - - +
337X ARG* 5.7 0.9 - - - -
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Residues in contact with ARG 193 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186X ASP* 5.2 2.0 + - - -
189X GLU* 3.1 25.9 + - + +
190X LEU* 3.4 46.3 - - - +
192X GLN* 1.3 74.3 - - - +
194X ARG* 1.3 55.5 + - + +
196X THR* 3.6 8.4 - - - +
197X TYR* 2.8 36.9 + - - +
572X GLU* 3.9 37.0 + - - +
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Residues in contact with ARG 194 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190X LEU* 3.1 39.6 + - + +
191X VAL* 3.5 13.7 - - - +
192X GLN 3.2 0.2 - - - -
193X ARG* 1.3 80.9 - - + +
195X ILE* 1.3 61.4 + - - +
197X TYR* 3.4 7.8 - - - +
198X LEU* 3.1 24.4 + - - +
235X TYR* 3.4 31.8 + - + +
309X PRO* 5.6 0.6 - - - +
311X ASP* 2.8 31.9 + - - +
312X LEU* 3.9 17.8 - - - +
568X PRO 5.2 0.6 + - - -
569X THR* 3.0 33.1 + - - +
570X TYR* 4.0 27.6 + - + +
572X GLU* 6.2 1.6 - - + -
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Residues in contact with ILE 195 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191X VAL* 2.9 26.8 + - + +
192X GLN* 3.0 32.1 + - - +
194X ARG* 1.3 72.3 - - - +
196X THR* 1.3 66.9 + - - +
197X TYR 3.2 0.2 + - - -
198X LEU* 3.3 4.3 + - - +
199X GLN* 2.9 23.6 + - - +
231X PHE* 3.6 21.5 - - + -
235X TYR* 4.3 20.6 - - + -
330X GLN* 4.1 12.3 - - + +
331X PHE* 4.1 21.1 - - + -
334X TYR* 3.3 35.7 - - + -
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Residues in contact with THR 196 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192X GLN* 2.6 23.5 + - - +
193X ARG* 3.6 7.2 - - - +
195X ILE* 1.3 72.4 - - - +
197X TYR* 1.3 67.0 + - - +
199X GLN 3.4 1.2 + - - -
200X ASN* 3.2 29.7 + - + +
334X TYR* 3.1 28.1 + - - +
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Residues in contact with TYR 197 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193X ARG 2.8 16.4 + - - +
194X ARG* 3.4 10.1 - - - +
196X THR* 1.3 80.7 - - - +
198X LEU* 1.3 81.2 + - - +
200X ASN* 2.9 17.5 + - - +
201X PRO* 4.4 1.0 - - - +
570X TYR* 4.4 26.2 - + + -
572X GLU* 3.7 50.6 + - + +
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Residues in contact with LEU 198 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194X ARG 3.1 13.4 + - - +
195X ILE* 3.8 3.8 - - - +
197X TYR* 1.3 86.1 - - - +
199X GLN* 1.3 70.0 + - - +
200X ASN 3.2 1.2 + - - -
201X PRO* 3.9 5.9 - - - +
231X PHE* 5.0 6.1 - - + -
234X ALA* 4.9 0.9 - - + -
235X TYR* 3.7 27.1 - - + +
238X GLN* 3.7 9.2 - - - +
239X ARG 3.4 46.0 - - - +
240X THR* 3.0 23.9 + - - +
570X TYR* 3.7 30.5 - - + +
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Residues in contact with GLN 199 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195X ILE 2.9 22.8 + - - +
197X TYR 2.9 1.6 + - - -
198X LEU* 1.3 76.3 - - + +
200X ASN* 1.3 57.1 + - - +
201X PRO* 3.5 3.4 - - - +
231X PHE* 3.7 30.1 - - + -
240X THR* 3.4 18.1 - - - +
241X LEU* 2.9 38.3 + - - +
262X VAL* 2.8 47.9 + - - +
263X SER* 2.5 29.5 + - - -
334X TYR* 3.5 20.6 - - + +
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Residues in contact with ASN 200 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196X THR* 3.2 27.1 + - - +
197X TYR 2.9 12.2 + - - +
198X LEU 3.2 0.2 + - - -
199X GLN* 1.3 81.3 - - - +
201X PRO* 1.3 66.0 - - - +
263X SER* 2.7 7.3 + - - -
264X GLU* 2.5 45.6 + - - +
265X THR* 3.0 19.3 + - + +
334X TYR* 3.6 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
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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) + - + + + + + -
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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