Contacts of the helix formed by residues 206 - 229 (chain A) in PDB entry 3AP2
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 206 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ILE* 3.9 4.5 - - - -
203A ASP* 3.1 21.4 + - - +
204A LEU 3.2 1.0 - - - -
205A SER* 1.3 80.9 - - - +
207A TYR* 1.3 57.1 + - - +
208A ARG* 3.3 9.7 + - - +
209A ASP* 2.9 30.2 + - - +
210A CYS* 3.0 26.9 + - - -
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Residues in contact with TYR 207 (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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189A VAL* 3.7 14.4 - - + -
190A HIS* 3.1 47.2 + - + -
193A ILE* 3.3 34.8 - - + +
194A THR* 4.0 9.7 - - - +
205A SER 5.8 1.8 - - - -
206A SER* 1.3 69.0 - - - +
208A ARG* 1.3 60.7 + - - +
211A LEU* 2.8 38.3 + - + +
304A HIS* 3.4 22.4 + - - +
305A ILE* 3.8 28.0 - - + -
306A PRO* 3.8 29.3 - - + +
309A VAL* 4.6 8.1 - - + -
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Residues in contact with ARG 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER* 3.3 7.1 + - - +
207A TYR* 1.3 78.1 - - - +
209A ASP* 1.3 63.4 + - - +
211A LEU* 4.0 1.1 - - - -
212A THR* 3.0 32.1 + - - +
308A ASP* 2.6 41.0 + - - +
309A VAL* 3.8 19.6 - - + +
311A ARG* 4.2 2.6 - - - +
312A ASP* 2.7 31.1 + - - +
316A ILE* 3.5 33.8 - - + +
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Residues in contact with ASP 209 (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 ASP* 3.2 29.1 + - + +
206A SER* 2.9 26.1 + - - +
208A ARG* 1.3 78.0 - - - +
210A CYS* 1.3 56.8 + - - +
212A THR* 3.2 10.2 + - - +
213A LYS* 2.6 70.1 + - - +
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Residues in contact with CYS 210 (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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189A VAL* 3.5 25.9 - - + +
192A MET* 4.3 4.0 - - - -
193A ILE* 4.0 9.6 - - - -
202A PHE* 3.7 25.7 - - + -
203A ASP 3.1 35.7 - - - -
204A LEU* 4.0 19.1 - - - -
206A SER 3.0 13.2 + - - +
209A ASP* 1.3 77.4 - - - +
211A LEU* 1.3 57.0 + - - +
213A LYS 3.4 0.5 + - - -
214A TRP* 2.8 29.6 + - - +
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Residues in contact with LEU 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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185A GLY* 3.7 35.0 - - - +
186A ARG* 3.9 8.5 - - + +
189A VAL* 3.7 15.0 - - + -
207A TYR* 2.8 25.9 + - + +
210A CYS* 1.3 69.6 - - - +
212A THR* 1.3 60.8 + - - +
214A TRP* 3.7 12.7 - - + +
215A ASN* 2.9 30.3 + - - +
305A ILE* 4.5 13.5 - - + -
309A VAL* 3.9 23.6 - - + -
313A MET* 3.9 22.2 - - + -
316A ILE* 3.8 15.8 - - + +
317A ALA* 4.5 6.5 - - + +
320A LEU* 5.2 0.9 - - + -
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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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208A ARG* 3.0 25.8 + - - +
209A ASP* 3.2 10.7 + - - +
211A LEU* 1.3 75.3 - - - +
213A LYS* 1.3 64.8 + - + +
215A ASN* 3.2 6.1 - - - +
216A LYS* 3.2 23.3 + - + +
316A ILE* 3.6 27.0 + - - +
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Residues in contact with LYS 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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201A GLY 2.6 30.0 + - - +
202A PHE* 3.6 30.1 - - + -
203A ASP* 4.4 1.6 - - - +
209A ASP* 2.6 52.6 + - - +
212A THR* 1.3 80.3 - - + +
214A TRP* 1.3 65.2 + - - +
215A ASN 3.0 1.3 - - - -
216A LYS* 3.3 8.6 + - + +
217A ALA* 2.8 25.1 + - - +
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Residues in contact with TRP 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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76A VAL* 3.6 35.2 - - + +
79A SER* 4.7 1.6 + - - -
182A VAL* 5.6 0.4 - - + -
183A ARG 3.5 14.1 + - - -
185A GLY* 3.2 40.8 - - - -
188A SER* 4.1 14.5 + - - -
189A VAL* 4.0 11.0 - - + -
192A MET* 5.2 0.9 - - + -
202A PHE* 3.7 9.9 - - + -
210A CYS 2.8 22.0 + - - +
211A LEU* 3.7 13.0 - - + +
213A LYS* 1.3 69.9 - - - +
215A ASN* 1.3 85.1 - - + +
217A ALA* 3.2 5.2 + - - +
218A ILE* 2.9 49.4 + - + +
317A ALA* 4.2 6.3 - - + -
319A MET* 4.1 20.9 - - + -
320A LEU* 3.9 27.8 - - + -
323A LEU* 4.4 7.9 - - + -
325A TYR* 5.5 1.1 - + - -
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Residues in contact with ASN 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 LEU 2.9 14.1 + - - +
212A THR 3.2 11.6 - - - +
213A LYS 3.0 0.2 - - - -
214A TRP* 1.3 86.6 - - + +
216A LYS* 1.3 59.9 + - - +
218A ILE* 3.5 2.6 - - - +
219A GLU* 2.9 39.9 + - - +
316A ILE 3.9 9.5 - - - +
317A ALA* 3.1 21.3 - - - +
318A PRO* 3.3 11.0 - - - +
319A MET* 2.9 47.2 - - - +
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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
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212A THR* 3.2 9.8 + - + +
213A LYS* 3.3 11.4 + - + +
215A ASN* 1.3 81.6 + - - +
217A ALA* 1.3 62.6 + - - +
219A GLU* 3.4 25.3 + - - +
220A VAL* 3.2 52.1 + - + +
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Residues in contact with ALA 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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76A VAL* 3.8 19.1 - - + -
161A PHE* 4.2 22.4 - - + -
164A LYS* 4.4 9.6 - - + +
202A PHE* 5.0 4.9 - - + -
213A LYS 2.8 20.2 + - - +
214A TRP* 3.2 5.4 + - - +
216A LYS* 1.3 73.6 - - - +
218A ILE* 1.3 60.0 + - - +
220A VAL* 3.3 4.5 + - - +
221A MET* 2.9 30.8 + - + +
1009S ASP* 5.7 1.1 - - - +
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Residues in contact with ILE 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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76A VAL* 3.9 13.8 - - + +
180A LEU* 5.1 7.2 - - + -
181A MET 4.9 3.6 - - - +
182A VAL* 4.0 29.8 - - + -
183A ARG 5.3 0.4 - - - +
214A TRP* 2.9 44.0 + - + +
215A ASN 3.5 8.7 - - - +
217A ALA* 1.3 71.3 - - - +
219A GLU* 1.3 64.3 + - - +
221A MET* 4.1 9.9 - - + -
222A TYR* 2.7 41.1 + - + +
319A MET* 3.9 23.8 - - + -
323A LEU* 3.7 21.5 - - + -
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Residues in contact with GLU 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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215A ASN* 2.9 27.2 + - - +
216A LYS* 3.7 33.1 + - - +
217A ALA 3.3 0.2 - - - -
218A ILE* 1.3 77.1 - - - +
220A VAL* 1.3 60.7 + - - +
222A TYR* 3.9 1.0 - - - +
223A ALA* 3.0 29.3 + - + +
318A PRO* 6.1 0.7 - - - +
319A MET* 3.8 28.7 - - + +
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Residues in contact with VAL 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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164A LYS* 3.7 45.8 - - + +
216A LYS* 3.2 36.4 + - + +
217A ALA 3.7 6.7 - - - +
219A GLU* 1.3 77.7 - - - +
221A MET* 1.3 65.1 + - - +
223A ALA* 3.2 8.0 + - - +
224A GLN* 3.0 28.7 + - + +
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Residues in contact with MET 221 (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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75A GLY* 3.4 44.6 - - - +
76A VAL* 4.0 11.2 - - + +
160A PRO 3.6 10.1 - - - +
161A PHE* 3.6 35.0 - - + -
163A LEU* 3.8 15.0 - - + +
164A LYS* 3.8 26.0 - - + +
166A SER* 5.0 0.2 + - - -
180A LEU* 3.8 17.4 - - + +
217A ALA 2.9 18.3 + - - +
218A ILE* 3.9 6.1 - - - +
220A VAL* 1.3 76.4 - - - +
222A TYR* 1.3 58.1 + - - +
224A GLN* 3.3 4.0 + - - +
225A CYS* 3.0 27.2 + - - +
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Residues in contact with TYR 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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180A LEU* 3.8 21.0 - - + +
182A VAL* 5.3 1.1 - - + -
218A ILE* 2.7 24.6 + - + +
219A GLU 4.0 0.9 - - - +
221A MET* 1.3 71.9 - - - +
223A ALA* 1.3 66.0 + - - +
224A GLN 3.3 0.2 + - - -
225A CYS* 3.4 1.0 + - - +
226A MET* 3.0 63.6 + - + +
235A PRO* 4.2 16.2 - - + +
237A TYR* 5.1 4.9 + - - -
319A MET* 4.0 18.6 - - + -
322A GLN* 5.1 9.5 + - + -
323A LEU* 3.5 31.0 - - + +
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Residues in contact with ALA 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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219A GLU* 3.0 20.8 + - + +
220A VAL* 3.2 6.7 + - - +
222A TYR* 1.3 79.2 - - - +
224A GLN* 1.3 64.1 + - + +
226A MET* 3.5 6.6 + - - +
227A GLU* 3.0 26.3 + - - +
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Residues in contact with GLN 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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163A LEU 3.9 5.2 - - - +
164A LYS 3.3 26.6 + - - +
165A SER* 3.9 1.9 - - - -
166A SER* 3.3 19.2 + - - +
167A VAL* 3.2 38.8 + - + +
168A TYR 4.6 0.2 + - - -
220A VAL* 3.0 21.9 + - + +
221A MET 3.5 6.3 - - - +
222A TYR 3.2 0.2 - - - -
223A ALA* 1.3 74.2 - - - +
225A CYS* 1.3 66.1 + - - +
227A GLU* 3.0 13.6 + - - +
228A VAL* 2.9 26.0 + - - +
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Residues in contact with CYS 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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163A LEU* 5.8 0.9 - - + -
166A SER* 4.0 3.0 + - - -
180A LEU* 3.9 13.5 - - + -
221A MET 3.0 14.5 + - - +
222A TYR 3.6 7.4 - - - +
224A GLN* 1.3 74.9 - - - +
226A MET* 1.3 79.6 + - + +
228A VAL* 3.4 5.6 + - - +
229A GLY* 3.0 19.9 + - - +
233A CYS* 2.1 61.9 - - - +
235A PRO* 4.1 14.6 - - - -
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Residues in contact with MET 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 TYR* 3.0 63.6 + - + +
223A ALA* 3.7 7.2 - - - +
225A CYS* 1.3 95.5 - - + +
227A GLU* 1.3 58.7 + - - +
229A GLY* 3.1 21.2 + - - -
233A CYS 5.6 0.9 - - - +
235A PRO* 4.2 9.4 - - + -
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Residues in contact with GLU 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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167A VAL* 3.8 30.5 - - + +
223A ALA* 3.0 14.8 + - - +
224A GLN* 3.0 18.3 + - - +
226A MET* 1.3 77.2 - - - +
228A VAL* 1.3 60.5 + - - +
229A GLY* 4.6 0.3 - - - -
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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
----------------------------------------------------------
166A SER* 3.8 12.8 - - - +
167A VAL* 3.8 31.6 - - + +
170A SER* 4.0 15.7 - - - +
178A PHE* 4.4 7.2 - - + -
224A GLN 2.9 18.8 + - - +
225A CYS* 3.6 2.2 - - - +
227A GLU* 1.3 76.0 - - - +
229A GLY* 1.3 58.7 + - - +
231A GLU* 5.9 0.5 - - - +
232A LYS* 3.9 22.1 + - + +
233A CYS* 3.3 39.7 - - + +
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Residues in contact with GLY 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 CYS 3.0 11.5 + - - -
226A MET* 3.1 15.4 + - - -
228A VAL* 1.3 77.9 - - - +
230A LYS* 1.3 59.3 + - - -
231A GLU 3.3 2.9 - - - -
232A LYS 3.1 2.9 + - - -
233A CYS* 2.8 35.1 + - - +
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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
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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