Contacts of the helix formed by residues 220 - 242 (chain A) in PDB entry 4J00
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 220 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ALA* 4.4 2.9 - - - +
219A ASP* 1.3 78.4 - - + +
221A GLN* 1.3 66.1 + - - +
222A GLU* 3.3 10.6 + - - +
223A ARG* 2.7 52.9 + - + +
224A THR* 3.0 23.4 + - - -
242B ALA 5.8 1.8 - - - +
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Residues in contact with GLN 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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99A GLU* 4.7 6.9 - - - +
214A PHE* 4.2 21.4 - - + -
215A TYR 4.5 6.6 - - - +
216A ALA* 3.5 30.1 - - + +
218A ALA* 4.6 5.2 + - - -
219A ASP 4.0 2.6 + - - -
220A ASP* 1.3 72.5 + - - +
222A GLU* 1.3 77.7 + - + +
224A THR* 3.1 14.4 + - - -
225A TYR* 3.1 49.5 + - - +
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Residues in contact with GLU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ASP* 3.3 8.1 + - - +
221A GLN* 1.3 90.4 + - + +
223A ARG* 1.3 63.3 + - + +
224A THR 3.1 1.2 + - - -
225A TYR* 3.1 33.7 + - + -
226A ILE* 3.1 46.1 + - + +
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Residues in contact with ARG 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ASP* 2.7 38.5 + - + +
222A GLU* 1.3 73.8 - - + +
224A THR* 1.3 57.4 + - - +
226A ILE* 5.0 1.1 - - - -
227A MET* 3.1 28.2 + - - +
241B TRP* 2.5 88.8 + - + +
242B ALA* 3.8 16.9 - - - +
244B LYS* 3.6 27.0 - - - +
245B ARG 4.6 2.8 + - - +
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Residues in contact with THR 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A THR* 4.4 26.9 - - + +
98A GLN* 4.9 4.4 + - - +
218A ALA* 3.4 21.7 - - + +
220A ASP 3.0 13.7 + - - -
221A GLN* 3.1 8.6 + - - -
222A GLU 3.1 0.8 - - - -
223A ARG* 1.3 78.1 - - - +
225A TYR* 1.3 59.9 + - + +
226A ILE 3.2 4.3 - - - -
227A MET* 3.4 21.5 - - + +
228A VAL* 3.4 23.2 - - + +
242B ALA* 4.8 7.5 + - + +
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Residues in contact with TYR 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLN* 3.2 33.9 - - - +
99A GLU* 5.1 3.8 - - - +
221A GLN* 3.1 56.2 + - - +
222A GLU* 3.1 35.9 + - - -
224A THR* 1.3 75.0 - - + +
226A ILE* 1.3 71.6 + - + +
228A VAL* 4.3 2.6 - - - +
229A GLU* 3.6 23.1 + - - +
15B ALA* 5.6 1.9 - - - +
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Residues in contact with ILE 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 GLU* 3.1 36.9 + - - +
223A ARG* 4.9 1.6 - - - +
225A TYR* 1.3 104.8 - - + +
227A MET* 1.3 53.8 + - - +
228A VAL 3.1 1.8 - - - -
229A GLU* 2.8 25.4 + - - +
230A ASP* 2.3 59.4 + - - +
233A ARG* 4.0 8.5 - - - +
241B TRP* 5.8 3.8 - - + -
250B ARG* 4.2 14.8 - - - +
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Residues in contact with MET 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER* 4.0 16.8 - - - +
30A THR* 5.9 2.7 - - + +
223A ARG 3.1 23.0 + - - +
224A THR* 3.4 24.7 - - + +
226A ILE* 1.3 77.9 - - - +
228A VAL* 1.3 71.4 + - + +
230A ASP* 3.5 12.5 + - - +
231A THR* 2.8 31.7 + - - -
235B PHE* 4.6 11.4 - - + -
238B MET* 3.6 44.7 - - + +
239B ARG* 4.4 9.2 - - + -
241B TRP* 4.7 2.8 - - + -
242B ALA* 3.9 15.5 - - + -
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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
----------------------------------------------------------
26A SER* 4.5 16.2 - - - +
98A GLN* 4.5 14.4 - - - +
224A THR* 3.4 21.1 + - + +
225A TYR* 4.6 6.1 - - - +
226A ILE 3.1 0.2 - - - -
227A MET* 1.3 93.8 - - + +
229A GLU* 1.3 64.7 + - - +
230A ASP 3.2 0.2 - - - -
231A THR* 3.5 5.2 + - - -
232A ALA* 3.1 22.3 + - - +
15B ALA* 4.5 3.8 - - + -
16B MET* 4.2 40.4 - - + +
19B ILE* 4.2 11.7 - - + +
235B PHE* 5.5 4.5 - - + -
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Residues in contact with GLU 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 TYR* 3.6 19.6 + - - +
226A ILE* 2.8 31.8 + - - +
228A VAL* 1.3 80.5 - - - +
230A ASP* 1.3 61.5 + - - +
232A ALA* 3.6 1.6 + - - +
233A ARG* 3.0 52.4 + - + +
15B ALA* 4.1 25.1 - - + +
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Residues in contact with ASP 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ILE* 2.3 41.1 + - - +
227A MET* 3.5 11.7 - - - +
228A VAL 3.2 0.2 - - - -
229A GLU* 1.3 68.2 - - - +
231A THR* 1.3 55.5 + - - +
233A ARG* 2.3 40.1 + - - +
234A PHE* 2.8 36.1 + - - +
291A GLN* 3.1 25.0 + - - +
234B PHE* 4.1 3.8 - - + -
238B MET* 3.8 8.9 - - + +
241B TRP* 5.2 0.2 - - - -
250B ARG* 3.0 32.0 + - - -
252B LEU* 4.3 0.3 - - - +
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Residues in contact with THR 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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19A ILE* 6.2 0.4 - - + -
227A MET 2.8 17.8 + - - -
228A VAL* 3.9 4.9 - - - -
229A GLU 3.5 0.2 - - - -
230A ASP* 1.3 77.0 - - - +
232A ALA* 1.3 52.4 + - - +
234A PHE* 3.2 6.4 - - + +
235A PHE* 2.6 39.0 + - + +
19B ILE* 4.6 13.2 - - + -
231B THR* 4.6 11.4 - - + -
234B PHE* 3.5 31.7 - - + -
235B PHE* 4.1 36.6 - - + -
238B MET* 4.1 4.2 - - - +
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Residues in contact with ALA 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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228A VAL 3.1 13.9 + - - +
229A GLU* 3.9 5.8 - - + +
230A ASP 3.2 0.2 - - - -
231A THR* 1.3 76.3 - - - +
233A ARG* 1.3 51.2 + - - +
235A PHE* 3.1 6.4 + - - +
236A ARG* 2.6 34.1 + - - +
15B ALA* 3.2 31.4 - - + +
18B GLN* 4.2 12.8 - - + -
19B ILE* 4.1 13.6 - - + +
22B TYR* 4.3 5.0 - - - -
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Residues in contact with ARG 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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226A ILE* 4.0 9.5 - - - +
229A GLU* 3.0 52.0 + - - +
230A ASP* 2.3 35.7 + - - +
232A ALA* 1.3 74.5 - - - +
234A PHE* 1.3 64.3 + - - +
236A ARG* 3.3 15.6 - - + +
237A MET* 3.1 35.4 + - + +
289A VAL* 5.3 6.3 - - - -
291A GLN* 3.0 20.9 + - - +
250B ARG* 4.2 1.0 - - - +
252B LEU* 3.3 31.3 - - - +
254B GLU* 5.7 1.2 + - - -
298B GLU* 5.4 5.8 - - - +
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Residues in contact with PHE 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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230A ASP 2.8 19.5 + - - +
231A THR* 3.2 7.6 - - + +
233A ARG* 1.3 76.8 - - - +
235A PHE* 1.3 60.9 + - - +
237A MET* 3.2 12.3 + - - +
238A MET* 2.8 52.0 + - + +
291A GLN* 4.1 5.2 - - + -
230B ASP* 4.0 6.5 - - + -
231B THR* 3.5 33.2 - - + -
234B PHE* 3.4 66.0 - + + -
291B GLN* 5.5 6.3 - - + -
292B MET 5.3 5.2 - - - -
293B VAL* 3.6 28.3 - - + +
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Residues in contact with PHE 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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19A ILE* 4.8 10.1 - - + -
231A THR* 2.6 21.4 + - + +
232A ALA* 3.3 7.9 - - - +
234A PHE* 1.3 76.9 - - + +
236A ARG* 1.3 63.4 + - - +
237A MET 3.2 0.9 + - - -
238A MET* 4.2 5.8 - - + -
239A ARG* 3.2 22.5 + - + +
19B ILE* 4.3 18.2 - - + -
22B TYR* 3.7 46.1 - - + -
23B LEU* 4.0 15.9 - - + -
26B SER* 4.8 0.2 - - - -
227B MET* 4.3 20.4 - - + -
228B VAL* 4.4 15.5 - - + -
231B THR* 3.7 38.1 - - + -
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Residues in contact with ARG 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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232A ALA 2.6 18.6 + - - +
233A ARG* 3.1 17.7 + - - +
235A PHE* 1.3 73.4 - - - +
237A MET* 1.3 69.2 + - - +
239A ARG* 3.2 11.5 - - - +
240A ASP* 2.7 32.1 + - - +
9B LYS* 4.7 9.8 - - - +
18B GLN* 6.4 0.2 - - - -
22B TYR* 4.1 26.2 - - + +
296B LYS* 3.0 29.2 + - - +
297B LYS 3.6 7.5 + - - -
298B GLU* 3.7 42.3 + - - +
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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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233A ARG* 3.1 23.1 + - + +
234A PHE 4.0 0.7 - - - +
235A PHE 3.1 0.2 - - - -
236A ARG* 1.3 98.6 - - - +
238A MET* 1.3 65.7 + - - +
239A ARG 3.2 1.8 - - - -
240A ASP* 3.1 24.9 + - + +
241A TRP* 3.3 5.2 + - - +
248A THR* 3.8 8.5 - - + +
289A VAL* 4.1 26.9 - - + +
291A GLN* 4.2 14.4 - - + +
293B VAL* 3.8 40.2 - - + +
295B GLY* 4.2 15.7 - - - +
296B LYS 3.8 17.0 - - - +
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Residues in contact with MET 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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234A PHE* 2.8 37.6 + - + +
235A PHE* 3.4 10.3 + - + +
237A MET* 1.3 77.5 - - - +
239A ARG* 1.3 61.1 + - - +
241A TRP* 3.4 30.8 + - + +
242A ALA* 3.6 7.1 + - - +
250A ARG* 4.3 28.5 - - + +
227B MET* 3.6 39.7 - - + +
230B ASP* 3.9 30.5 - - + +
231B THR* 4.1 9.0 - - - +
291B GLN* 5.3 1.8 - - - +
293B VAL* 4.7 8.5 - - + -
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Residues in contact with ARG 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 PHE* 3.2 23.2 + - + +
236A ARG* 3.2 13.4 - - - +
238A MET* 1.3 76.6 - - - +
240A ASP* 1.3 90.0 + - - +
242A ALA* 3.4 9.1 + - - +
243A GLU* 2.6 48.9 + - - +
4B ASP* 5.2 15.8 + - - +
8B ILE* 5.7 3.8 - - - +
22B TYR* 4.1 31.2 + - + -
25B PHE* 5.4 11.2 - - - -
227B MET* 4.1 17.6 - - - -
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Residues in contact with ASP 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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236A ARG* 2.7 37.5 + - - +
237A MET* 3.1 14.3 + - - +
239A ARG* 1.3 84.7 - - - +
241A TRP* 1.3 59.6 + - - +
243A GLU* 2.8 23.0 + - - +
245A ARG* 3.1 49.1 + - + +
248A THR* 4.2 11.2 - - + +
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Residues in contact with TRP 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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237A MET 3.3 5.8 + - - +
238A MET* 3.7 26.9 - - + +
239A ARG 3.3 0.4 - - - -
240A ASP* 1.3 77.9 - - - +
242A ALA* 1.3 62.5 + - + +
243A GLU 3.1 0.7 + - - -
244A LYS 3.6 0.5 + - - -
245A ARG 5.2 1.6 - - - +
248A THR* 3.2 39.1 + - + +
249A MET* 3.8 12.2 - - - +
250A ARG* 3.3 48.6 - - + +
223B ARG* 2.4 95.8 + - + +
226B ILE* 3.8 25.8 - - + -
227B MET* 5.4 0.2 - - + -
293B VAL* 5.5 1.3 - - + -
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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
----------------------------------------------------------
238A MET 3.6 8.9 + - - +
239A ARG* 3.4 9.8 + - - +
240A ASP 3.1 1.2 - - - -
241A TRP* 1.3 79.6 - - + +
243A GLU* 1.3 59.4 + - + +
244A LYS* 3.4 4.3 + - - +
223B ARG* 4.0 39.7 + - + +
224B THR* 4.5 8.9 + - - +
227B MET* 4.4 12.8 - - + -
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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