Contacts of the helix formed by residues 236 - 258 (chain A) in PDB entry 3OX4
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 ASP 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A THR* 3.7 22.9 - - + +
233A ASN* 2.8 33.1 + - - +
234A GLY 3.3 0.2 - - - -
235A LYS* 1.3 75.5 - - - +
237A MET* 1.3 63.9 + - - +
238A PRO* 3.6 13.8 - - - +
239A ALA* 2.7 35.6 + - + +
240A ARG* 3.1 23.9 + - - +
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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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16A GLU* 4.0 20.6 - - + +
177A PRO* 3.9 33.7 - - + +
178A LEU* 4.1 32.1 - - + -
181A VAL* 4.7 18.6 - - + -
235A LYS 2.9 11.4 + - - +
236A ASP* 1.3 71.4 - - - +
238A PRO* 1.3 66.3 - - + +
240A ARG* 3.2 6.6 + - + +
241A GLU* 2.9 34.7 + - - +
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Residues in contact with PRO 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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226A ASN* 4.4 2.8 - - - +
236A ASP* 3.5 16.8 - - - +
237A MET* 1.3 94.8 - - + +
239A ALA* 1.3 55.6 + - - +
241A GLU* 3.9 6.0 - - + +
242A ALA* 3.0 27.5 + - - +
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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
----------------------------------------------------------
226A ASN* 3.8 23.7 - - - +
229A THR* 3.7 26.7 - - + -
230A ALA* 3.9 9.4 - - + +
236A ASP* 2.7 28.1 + - + +
238A PRO* 1.3 71.3 - - - +
240A ARG* 1.3 61.8 + - - +
242A ALA* 3.3 2.1 + - - +
243A MET* 2.9 34.4 + - - +
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Residues in contact with ARG 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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140A ALA* 5.8 0.2 - - - +
177A PRO* 4.1 19.4 - - + +
180A MET* 3.3 24.9 + - + +
181A VAL* 3.2 23.4 + - + +
183A MET* 2.9 43.6 + - - +
188A THR* 3.0 33.5 + - - +
230A ALA* 4.1 13.9 + - + +
234A GLY* 2.9 36.5 + - - +
236A ASP 3.1 16.8 + - - +
237A MET* 3.6 13.2 - - - +
239A ALA* 1.3 75.7 - - - +
241A GLU* 1.3 60.2 + - - +
243A MET* 3.3 6.4 + - - +
244A ALA* 3.0 28.6 + - - +
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Residues in contact with GLU 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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15A GLY* 4.5 12.0 - - - -
16A GLU* 4.5 11.8 + - - +
177A PRO* 4.0 20.5 - - + +
237A MET* 2.9 21.3 + - + +
238A PRO* 3.9 6.6 - - + +
240A ARG* 1.3 76.0 - - - +
242A ALA* 1.3 63.1 + - - +
244A ALA* 3.3 4.1 + - + +
245A TYR* 3.1 54.8 + - + -
2B ALA 4.5 16.1 + - - +
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Residues in contact with ALA 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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222A MET* 3.4 22.5 - - + +
226A ASN* 3.4 36.6 - - - +
238A PRO 3.0 19.4 + - - +
239A ALA 3.6 1.1 - - - +
241A GLU* 1.3 77.9 - - - +
243A MET* 1.3 52.1 + - - +
245A TYR* 3.3 2.2 + - - -
246A ALA* 2.7 36.4 + - - +
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Residues in contact with MET 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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140A ALA* 3.8 24.6 - - + +
188A THR* 5.5 1.1 - - + +
192A GLY* 3.8 29.2 - - - +
195A ALA* 5.0 1.3 - - + -
223A ILE* 4.0 34.8 - - + -
226A ASN* 4.2 13.0 - - + +
227A LEU* 3.9 30.5 - - + -
230A ALA* 4.4 11.2 - - + -
239A ALA 2.9 21.4 + - - +
240A ARG* 3.8 7.4 - - - +
241A GLU 3.3 0.2 - - - -
242A ALA* 1.3 75.0 - - - +
244A ALA* 1.3 59.1 + - - +
246A ALA* 3.6 2.6 - - + +
247A GLN* 2.8 33.3 + - - +
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Residues in contact with ALA 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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14A MET* 6.1 1.3 - - + -
15A GLY 5.9 0.7 - - - +
140A ALA* 4.5 0.8 - - - +
175A ASN* 4.4 22.5 - - + +
177A PRO* 4.8 3.8 - - + -
180A MET* 3.8 26.5 - - + -
240A ARG 3.0 17.4 + - - +
241A GLU* 3.6 9.2 - - + +
242A ALA 3.3 0.2 - - - -
243A MET* 1.3 74.7 - - - +
245A TYR* 1.3 64.2 + - + +
247A GLN* 3.1 26.3 + - - +
248A PHE* 3.2 10.4 + - - +
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Residues in contact with TYR 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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14A MET* 3.7 40.6 + - + +
15A GLY* 4.8 3.5 - - - -
222A MET* 3.7 12.8 - - + -
241A GLU* 3.1 55.4 + - + -
242A ALA* 3.6 8.1 - - - +
244A ALA* 1.3 76.7 - - + +
246A ALA* 1.3 58.4 + - - +
248A PHE* 3.1 7.5 + - - +
249A LEU* 2.9 33.2 + - + +
2B ALA 4.3 6.6 + - - -
4B SER* 2.9 28.7 + - - -
209B THR* 4.4 9.4 - - - +
210B PRO* 4.0 31.4 - - + +
211B ILE* 4.0 16.8 - - + -
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Residues in contact with ALA 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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219A ALA* 3.5 12.5 - - - +
222A MET* 3.8 24.2 - - + -
223A ILE* 3.8 28.7 - - + +
242A ALA 2.7 21.9 + - - +
243A MET* 3.6 8.3 - - + +
245A TYR* 1.3 73.3 - - - +
247A GLN* 1.3 57.7 + - - +
249A LEU* 3.2 5.2 + - - -
250A ALA* 2.9 25.3 + - - +
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Residues in contact with GLN 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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137A ASN* 3.6 11.0 + - - +
140A ALA* 3.6 7.6 - - - +
141A GLY* 3.5 26.7 + - - +
142A THR 3.5 7.1 + - - -
143A ALA* 2.9 37.8 + - - +
145A GLU* 2.6 26.0 + - - -
175A ASN* 3.0 20.8 + - - +
195A ALA* 4.2 13.2 - - + +
243A MET* 2.8 19.6 + - - +
244A ALA* 3.1 19.4 + - - +
246A ALA* 1.3 73.3 - - - +
248A PHE* 1.3 71.9 + - - +
250A ALA* 3.4 3.7 + - - +
251A GLY 3.1 16.5 + - - -
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Residues in contact with PHE 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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8A ILE* 4.1 12.8 - - + -
12A ASN* 3.3 35.4 - - - -
14A MET* 3.4 28.3 - - + -
143A ALA* 4.9 2.9 - - - -
145A GLU* 4.2 1.3 - - - -
146A MET* 3.6 29.2 - - + +
173A SER* 3.7 9.4 - - - -
175A ASN* 3.7 20.2 - - - +
244A ALA 3.6 8.3 - - - +
245A TYR* 3.1 12.2 + - - +
247A GLN* 1.3 86.3 - - - +
249A LEU* 1.3 60.0 + - - +
251A GLY* 2.9 3.6 + - - -
252A MET* 2.8 60.1 + - + +
6B PHE* 5.0 2.5 - + - -
211B ILE* 3.8 6.1 - - + -
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Residues in contact with LEU 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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215A CYS* 3.5 39.2 - - + +
218A LYS* 3.5 30.5 - - + -
219A ALA* 3.8 4.7 - - + +
222A MET* 3.7 20.6 - - - -
245A TYR 2.9 16.5 + - - +
246A ALA* 3.2 7.2 + - - +
248A PHE* 1.3 76.3 - - - +
250A ALA* 1.3 61.5 + - - +
252A MET* 3.1 35.0 + - - +
253A ALA* 3.1 9.2 + - - +
210B PRO* 4.7 4.0 - - + +
211B ILE* 4.0 31.2 - - + -
214B ALA* 5.0 3.6 - - + -
215B CYS* 6.2 0.2 - - - -
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Residues in contact with ALA 250 (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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195A ALA* 3.5 29.8 - - + +
198A HIS* 3.8 12.9 - - + +
199A ALA* 4.4 4.5 - - - +
215A CYS 5.0 0.2 - - - -
219A ALA* 3.7 12.7 - - + +
246A ALA 2.9 13.6 + - - +
247A GLN* 3.5 11.7 - - - +
248A PHE 3.2 0.2 - - - -
249A LEU* 1.3 76.2 - - - +
251A GLY* 1.3 58.5 + - - +
253A ALA* 3.2 7.7 + - - +
254A PHE* 2.9 32.5 + - - +
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Residues in contact with GLY 251 (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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143A ALA* 3.5 20.8 - - - +
146A MET* 3.7 8.1 - - - -
247A GLN 3.1 6.3 + - - -
248A PHE 2.9 7.5 + - - -
250A ALA* 1.3 74.6 - - - +
252A MET* 1.3 64.6 + - - +
253A ALA 3.0 2.0 - - - -
254A PHE* 3.5 15.0 - - - -
255A ASN* 2.9 30.5 + - - +
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Residues in contact with MET 252 (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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6A PHE* 3.4 19.1 - - + -
8A ILE* 4.0 13.0 - - + -
146A MET* 3.6 13.6 - - + +
215A CYS* 3.9 17.0 - - - -
248A PHE* 2.8 45.8 + - + +
249A LEU* 3.1 29.8 + - - +
251A GLY* 1.3 75.0 - - - +
253A ALA* 1.3 59.2 - - - +
256A ASN* 2.7 28.5 + - - +
6B PHE* 4.1 12.6 - - + -
211B ILE* 4.1 8.7 - - + -
252B MET* 3.6 31.6 - - + -
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Residues in contact with ALA 253 (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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198A HIS 5.1 0.7 - - - +
199A ALA* 5.5 0.2 - - - -
202A ALA* 3.6 17.7 - - + -
212A THR* 3.5 34.0 - - - +
215A CYS* 4.3 0.9 - - + +
216A ALA* 3.9 13.0 - - + +
249A LEU 3.1 10.1 + - - +
250A ALA* 3.4 8.5 - - - +
251A GLY 3.0 1.2 - - - -
252A MET* 1.3 76.9 - - - +
254A PHE* 1.3 60.3 + - - +
256A ASN 3.2 2.1 + - - -
257A ALA* 2.8 30.5 + - - +
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Residues in contact with PHE 254 (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 THR 3.6 24.7 - - - -
143A ALA* 4.0 1.3 - - + -
147A THR* 3.9 15.9 - - + -
149A PHE* 4.0 26.7 - + - -
198A HIS* 3.6 27.6 - + - +
202A ALA* 3.8 5.6 - - - -
250A ALA 2.9 28.5 + - - +
251A GLY* 3.5 16.8 - - - -
253A ALA* 1.3 69.5 - - - +
255A ASN* 1.3 61.6 + - - +
256A ASN 3.0 2.7 - - - -
258A SER* 2.9 31.1 + - - +
259A LEU* 3.4 48.2 - - + -
1385A NAD 4.1 20.4 - + - -
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Residues in contact with ASN 255 (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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7A TYR* 3.1 42.4 + - - +
146A MET* 3.9 14.4 + - + +
147A THR* 3.3 22.1 - - + -
148A ARG* 2.7 73.2 + - - +
149A PHE* 3.7 12.8 - - - -
169A THR* 5.7 0.2 + - - -
251A GLY 2.9 22.2 + - - +
254A PHE* 1.3 80.0 - - - +
256A ASN* 1.3 55.0 + - - +
258A SER 4.9 0.2 + - - -
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Residues in contact with ASN 256 (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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5A THR 3.4 13.6 - - - +
6A PHE* 3.1 26.0 - - + -
7A TYR* 2.6 52.5 + - - +
148A ARG* 4.2 7.0 + - - +
207A ALA* 4.4 7.4 - - - +
209A THR* 5.8 1.7 - - - +
212A THR* 3.8 14.6 - - + -
252A MET* 2.7 28.9 + - - +
253A ALA 3.2 1.4 + - - -
254A PHE 3.0 0.2 - - - -
255A ASN* 1.3 84.4 - - - +
257A ALA* 1.3 61.2 + - - +
258A SER* 3.4 1.6 - - - -
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Residues in contact with ALA 257 (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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202A ALA* 3.6 24.5 - - + +
205A SER* 2.5 25.5 + - - -
207A ALA* 3.4 16.6 - - - +
208A ALA* 3.9 11.4 - - - -
212A THR* 3.7 18.6 - - - +
253A ALA 2.8 18.7 + - - +
256A ASN* 1.3 73.3 - - - +
258A SER* 1.3 67.8 - - - +
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Residues in contact with SER 258 (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 PHE* 5.3 10.1 - - - -
201A GLU 4.1 0.5 - - - +
202A ALA* 3.6 19.2 - - - -
207A ALA* 5.3 0.4 - - - -
254A PHE* 2.9 21.2 + - - +
255A ASN 4.9 0.4 + - - -
256A ASN 3.4 2.2 - - - -
257A ALA* 1.3 87.6 - - - +
259A LEU* 1.3 73.4 + - - +
361A ALA 4.9 3.1 + - - -
362A CYS* 4.8 10.4 - - - -
365A THR* 3.6 19.6 + - - +
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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