Contacts of the helix formed by residues 222 - 249 (chain A) in PDB entry 4DJ9
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 222 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A THR* 4.2 15.4 - - - +
221A GLN* 1.3 77.3 - - - +
223A ILE* 1.3 61.5 - - - +
225A GLU* 3.6 14.3 + - - +
226A ALA* 3.6 12.8 + - - +
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Residues in contact with ILE 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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152A GLU* 6.0 0.9 - - - +
212A PHE* 3.6 33.8 - - + +
215A THR* 3.7 31.2 + - - +
221A GLN 4.1 13.7 - - - +
222A GLY* 1.3 76.3 - - - +
224A GLU* 1.4 66.9 + - - +
225A GLU 3.3 0.2 + - - -
226A ALA* 3.4 2.1 + - - +
227A LEU* 3.0 35.4 + - + +
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Residues in contact with GLU 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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221A GLN* 3.5 17.0 + - - +
222A GLY 3.4 0.6 - - - -
223A ILE* 1.4 85.6 - - + +
225A GLU* 1.3 56.5 + - - +
227A LEU* 4.0 18.3 - - - +
228A LYS* 3.3 26.7 + - - +
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Residues in contact with GLU 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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221A GLN 3.9 6.5 + - - +
222A GLY* 3.6 10.0 + - - +
223A ILE 3.3 0.6 - - - -
224A GLU* 1.3 76.3 - - - +
226A ALA* 1.4 63.2 + - - +
227A LEU 3.3 0.2 - - - -
228A LYS* 3.2 7.2 + - + +
229A ASN* 3.2 42.0 + - - +
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Residues in contact with ALA 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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208A ALA* 4.1 7.5 - - - +
211A ILE* 3.7 29.8 - - + -
212A PHE* 3.9 22.6 - - + +
215A THR* 4.0 8.7 - - + +
222A GLY 3.6 6.2 + - - +
223A ILE 3.4 6.8 + - - +
225A GLU* 1.4 75.0 - - - +
227A LEU* 1.3 62.5 + - - +
229A ASN* 3.7 7.0 + - - +
230A ARG* 3.2 23.7 + - - +
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Residues in contact with LEU 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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212A PHE* 4.0 26.4 - - + -
223A ILE* 3.0 21.5 + - + +
224A GLU* 4.0 22.0 - - - +
226A ALA* 1.3 75.8 - - - +
228A LYS* 1.4 61.4 + - + +
230A ARG* 3.4 22.2 + - - +
231A ASN* 2.9 60.5 + - - +
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Residues in contact with LYS 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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224A GLU 3.3 17.4 + - - +
225A GLU* 3.2 9.7 + - - +
227A LEU* 1.4 83.0 - - + +
229A ASN* 1.3 60.7 + - - +
231A ASN* 3.5 5.8 + - - +
232A PHE* 2.9 29.2 + - - +
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Residues in contact with ASN 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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208A ALA* 4.3 10.1 - - + -
225A GLU* 3.2 33.1 + - - +
226A ALA* 4.1 6.1 - - - +
228A LYS* 1.3 75.9 - - - +
230A ARG* 1.3 59.4 + - - +
232A PHE* 3.6 11.0 - - - +
233A THR* 2.8 33.8 + - - -
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Residues in contact with ARG 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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148A ALA* 4.0 13.8 + - - +
149A GLU* 3.4 38.2 + - - +
205A LEU* 3.8 9.4 - - + +
208A ALA* 3.8 15.4 - - + +
209A MET* 3.6 35.7 - - + +
212A PHE* 3.4 43.8 - - + -
226A ALA 3.2 18.6 + - - +
227A LEU* 3.7 23.4 - - - +
229A ASN* 1.3 75.5 - - - +
231A ASN* 1.4 85.0 + - - +
233A THR* 3.4 4.7 + - - -
234A VAL* 3.1 31.0 + - + +
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Residues in contact with ASN 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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149A GLU* 4.6 6.0 + - - +
227A LEU* 2.9 41.3 + - - +
228A LYS* 3.8 6.4 - - - +
230A ARG* 1.4 103.7 + - - +
232A PHE* 1.3 55.6 + - - +
234A VAL* 3.6 6.9 + - - +
235A GLU* 3.1 28.8 + - - +
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Residues in contact with PHE 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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201A LEU* 5.9 5.6 - - + -
228A LYS 2.9 18.6 + - - +
229A ASN* 3.6 13.7 - - - +
230A ARG 3.3 0.2 - - - -
231A ASN* 1.3 74.7 - - - +
233A THR* 1.4 68.0 + - - +
235A GLU* 3.3 13.8 + - - +
236A LYS* 3.0 72.0 + - + +
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Residues in contact with THR 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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201A LEU* 3.4 36.8 - - + +
204A VAL* 4.1 16.8 + - + +
205A LEU* 3.7 26.6 - - + +
208A ALA* 4.7 1.6 - - - +
229A ASN 2.8 17.0 + - - -
230A ARG* 3.4 5.4 + - - -
232A PHE* 1.4 81.8 - - - +
234A VAL* 1.3 59.6 + - - +
236A LYS* 3.4 4.5 + - - +
237A MET* 2.9 34.8 + - - +
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Residues in contact with VAL 234 (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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145A LEU* 3.8 34.8 - - + +
146A THR* 4.9 4.5 - - + +
148A ALA* 4.0 9.6 - - + -
205A LEU* 3.7 24.5 - - + -
230A ARG* 3.1 20.1 + - + +
231A ASN* 3.9 7.9 - - - +
232A PHE 3.4 0.2 - - - -
233A THR* 1.3 74.1 - - - +
235A GLU* 1.3 50.9 + - - +
237A MET* 3.3 7.6 + - - +
238A SER* 2.7 50.8 + - - +
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Residues in contact with GLU 235 (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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231A ASN 3.1 16.9 + - - +
232A PHE* 3.4 14.0 - - - +
234A VAL* 1.3 76.5 - - - +
236A LYS* 1.4 83.0 + - - +
238A SER* 3.4 5.5 + - - -
239A ALA* 3.0 30.4 + - + +
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Residues in contact with LYS 236 (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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197A THR* 5.9 0.7 - - + -
201A LEU* 3.7 24.5 - - + -
232A PHE* 3.0 57.9 + - + +
233A THR* 3.9 1.3 - - - +
235A GLU* 1.4 99.0 + - + +
237A MET* 1.3 63.9 + - - +
239A ALA* 3.5 6.9 + - + +
240A GLU* 3.3 27.7 + - - +
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Residues in contact with MET 237 (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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145A LEU* 3.9 24.9 - - + -
168A MET* 3.8 25.4 - - + -
198A VAL* 3.7 30.2 - - + +
201A LEU* 3.6 37.7 - - + +
202A LEU* 3.8 16.4 - - + -
205A LEU* 4.1 14.6 - - + -
233A THR* 2.9 27.9 + - - +
234A VAL 3.8 3.1 - - - +
236A LYS* 1.3 75.8 - - - +
238A SER* 1.3 62.9 + - - +
240A GLU* 3.3 7.8 + - - +
241A ILE* 3.1 26.0 + - - +
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Residues in contact with SER 238 (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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142A LEU* 3.7 25.7 + - - +
145A LEU* 4.0 11.2 - - - +
146A THR* 5.9 1.6 - - - +
234A VAL* 2.7 39.4 + - - +
235A GLU* 3.8 6.3 - - - -
237A MET* 1.3 73.2 - - - +
239A ALA* 1.4 54.3 + - - +
241A ILE* 3.3 1.2 + - - -
242A ASN* 2.9 39.8 + - - -
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Residues in contact with ALA 239 (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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235A GLU* 3.0 18.9 + - + +
236A LYS* 3.8 9.2 - - + +
238A SER* 1.4 71.3 - - - +
240A GLU* 1.3 63.6 + - + +
242A ASN* 3.6 8.2 + - - +
243A GLU* 3.1 26.5 + - - +
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Residues in contact with GLU 240 (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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193A ASN 5.0 0.3 - - - -
194A SER* 2.8 35.6 + - - +
197A THR* 3.8 32.7 + - + +
198A VAL* 3.5 22.0 - - + -
236A LYS 3.3 14.2 + - - +
237A MET* 3.3 3.0 + - - +
239A ALA* 1.3 75.8 - - - +
241A ILE* 1.3 60.4 + - - +
243A GLU* 3.1 8.9 + - - +
244A ILE* 3.0 32.9 + - - +
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Residues in contact with ILE 241 (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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138A CYS* 3.6 26.7 - - + +
141A ILE* 3.6 32.3 - - + -
142A LEU* 3.5 27.4 - - + +
145A LEU* 3.6 22.7 - - + -
171A MET* 3.8 16.6 - - + -
198A VAL* 4.0 20.9 - - + -
237A MET 3.1 16.0 + - - +
238A SER 3.8 4.5 - - - +
240A GLU* 1.3 75.7 - - - +
242A ASN* 1.3 56.1 + - - +
244A ILE* 3.0 9.6 + - - +
245A ILE* 3.0 26.2 + - + +
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Residues in contact with ASN 242 (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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142A LEU* 3.4 28.8 - - - +
238A SER* 2.9 28.5 + - - +
239A ALA* 3.9 7.4 - - - +
240A GLU 3.3 0.2 - - - -
241A ILE* 1.3 75.0 - - - +
243A GLU* 1.3 61.4 + - - +
245A ILE* 3.6 13.1 + - - +
246A ARG* 3.1 22.0 + - - +
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Residues in contact with GLU 243 (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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190A MET* 3.2 31.8 - - + +
194A SER* 3.8 16.8 - - - +
239A ALA 3.1 15.4 + - - +
240A GLU* 3.1 12.1 + - - +
242A ASN* 1.3 75.1 - - - +
244A ILE* 1.3 58.3 + - - +
246A ARG* 2.9 33.2 + - - +
247A VAL* 2.9 39.4 + - + +
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Residues in contact with ILE 244 (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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138A CYS* 4.1 8.3 - - - -
171A MET* 3.9 9.0 - - + -
175A ILE* 3.6 29.4 - - + -
190A MET 5.2 0.2 - - - +
191A LEU* 3.9 19.9 - - + +
194A SER* 3.5 20.0 - - - +
195A MET* 3.5 45.3 - - + +
198A VAL* 4.6 2.7 - - + -
240A GLU 3.0 16.3 + - - +
241A ILE* 3.0 11.2 + - - +
243A GLU* 1.3 73.4 - - - +
245A ILE* 1.4 65.8 + - - +
247A VAL* 3.2 1.8 + - - -
248A LEU* 2.9 37.4 + - + +
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Residues in contact with ILE 245 (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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135A ILE* 4.2 22.2 - - + +
138A CYS* 3.7 28.0 - - + -
139A LYS* 3.9 24.5 - - + +
142A LEU* 3.8 29.6 - - + -
241A ILE 3.0 13.8 + - - +
242A ASN* 3.8 15.5 - - - +
244A ILE* 1.4 76.7 - - - +
246A ARG* 1.3 60.0 + - - +
248A LEU* 3.7 11.1 + - - +
249A GLN* 2.9 39.0 + - - +
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Residues in contact with ARG 246 (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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190A MET* 3.3 20.0 - - - +
242A ASN 3.1 15.0 + - - +
243A GLU* 2.9 44.5 + - - +
244A ILE 3.2 0.2 - - - -
245A ILE* 1.3 77.6 - - - +
247A VAL* 1.4 67.8 + - - +
249A GLN* 3.5 19.9 + - - +
250A LEU* 3.7 37.0 - - + +
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Residues in contact with VAL 247 (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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182A LEU* 5.7 2.1 - - - +
187A HIS* 3.6 42.6 - - + +
190A MET* 3.9 24.0 - - + -
191A LEU* 3.9 19.3 - - + +
243A GLU* 2.9 28.2 + - + +
246A ARG* 1.4 94.1 - - - +
248A LEU* 1.3 63.9 + - - +
250A LEU* 3.2 29.1 + - + +
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Residues in contact with LEU 248 (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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131A VAL* 3.4 32.3 - - + +
134A ILE* 3.5 32.8 - - + -
135A ILE* 4.3 11.9 - - + -
138A CYS* 4.2 7.2 - - - -
175A ILE* 4.1 9.9 - - + -
178A ARG* 3.7 40.4 + - + +
182A LEU* 5.9 2.1 - - - +
191A LEU* 3.9 19.7 - - + -
244A ILE* 2.9 40.2 + - + +
245A ILE* 3.9 5.8 - - - +
247A VAL* 1.3 77.6 - - - +
249A GLN* 1.4 56.7 + - - +
250A LEU 3.4 3.7 + - - +
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Residues in contact with GLN 249 (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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131A VAL* 4.3 6.7 - - + -
135A ILE* 3.6 22.4 - - + +
245A ILE* 2.9 38.4 + - - +
246A ARG* 3.5 12.6 + - - +
247A VAL 3.2 1.0 - - - -
248A LEU* 1.4 73.0 - - - +
250A LEU* 1.4 63.7 + - + +
251A THR* 3.7 10.7 + - - +
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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