Contacts of the helix formed by residues 228 - 251 (chain A) in PDB entry 4IVR
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 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A TYR* 4.7 12.7 - - + -
104A GLN* 3.7 25.6 - - - +
105A HIS* 5.5 0.9 + - - -
108A ASP* 4.5 4.8 - - - +
176A ARG* 4.9 0.3 + - - -
179A MET* 3.7 4.6 - - - +
217A LEU* 5.6 2.5 - - - +
226A ARG* 2.9 13.4 + - + +
227A LEU* 1.3 74.7 - - - +
229A LEU* 1.3 56.8 + - - +
230A ALA* 3.4 12.1 + - - +
231A MET* 2.9 51.0 + - + +
232A LEU* 3.0 13.6 + - - +
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Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLU* 5.6 0.3 - - - +
214A ILE* 3.9 41.1 - - + -
227A LEU* 3.7 32.2 + - + +
228A ASP* 1.3 71.8 - - - +
230A ALA* 1.3 57.5 + - - +
232A LEU* 3.4 10.8 + - + +
233A ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A MET* 3.6 21.4 - - + +
228A ASP* 3.1 9.8 + - - +
229A LEU* 1.3 76.9 - - - +
231A MET* 1.3 64.2 + - - +
233A ALA* 3.5 6.6 + - - +
234A ALA* 3.0 22.5 + - - +
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Residues in contact with MET 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A HIS* 5.3 8.1 - - + -
101A TYR* 4.7 8.3 - - + +
172A TYR* 4.1 22.7 - - + -
175A ALA* 3.6 27.6 - - + +
176A ARG* 3.3 48.0 - - + +
179A MET* 3.7 26.6 - - + +
228A ASP* 2.9 33.9 + - + +
230A ALA* 1.3 74.2 - - - +
232A LEU* 1.3 57.1 + - - +
234A ALA* 2.9 3.4 + - - +
235A ILE* 2.8 34.9 + - + +
501A N50 5.7 0.2 - - - -
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Residues in contact with LEU 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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58A HIS* 4.9 7.0 - - - +
210A GLU* 5.4 2.0 - - + +
213A HIS* 3.5 40.2 - - + +
214A ILE* 3.6 44.9 - - + +
217A LEU* 4.1 25.6 - - + -
227A LEU* 5.9 0.2 - - + -
228A ASP 3.0 11.4 + - - +
229A LEU* 3.6 15.5 - - + +
231A MET* 1.3 76.1 - - - +
233A ALA* 1.3 57.3 + - - +
235A ILE* 3.4 12.2 - - + +
236A ARG* 2.9 44.5 + - + +
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLU* 4.5 15.3 - - - +
229A LEU 2.9 17.6 + - - +
230A ALA* 3.7 7.9 - - - +
232A LEU* 1.3 77.7 - - - +
234A ALA* 1.3 58.5 + - - +
236A ARG* 3.6 9.1 - - - +
237A ARG* 2.9 28.4 + - - +
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ALA* 3.9 26.9 - - + +
178A LEU* 4.1 19.2 - - + +
179A MET* 4.3 8.7 - - + -
230A ALA 3.0 14.1 + - - +
231A MET 2.9 9.0 + - - +
233A ALA* 1.3 74.0 - - - +
235A ILE* 1.3 61.0 + - - +
237A ARG* 3.2 6.0 + - - +
238A VAL* 2.9 32.1 + - - +
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Residues in contact with ILE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO* 4.0 17.9 - - + -
58A HIS* 4.4 15.7 - - + -
171A CYS* 3.7 24.0 - - + +
172A TYR* 3.8 34.1 - - + +
175A ALA* 3.7 13.1 - - + +
231A MET* 2.8 20.3 + - + +
232A LEU* 3.4 18.6 - - + +
234A ALA* 1.3 72.0 - - - +
236A ARG* 1.3 65.4 + - - +
238A VAL* 3.3 2.6 + - + +
239A TYR* 3.1 53.7 + - + -
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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
----------------------------------------------------------
57A PRO* 4.2 11.2 - - + -
60A MET* 5.9 0.4 - - - -
208A LEU* 2.8 31.1 + - - +
209A PRO* 4.4 0.8 - - - +
210A GLU* 3.4 36.8 - - - +
213A HIS* 2.9 46.3 + - + +
232A LEU* 2.9 38.2 + - + +
233A ALA* 3.6 8.1 - - - +
234A ALA 3.2 0.2 - - - -
235A ILE* 1.3 79.1 - - - +
237A ARG* 1.3 62.2 + - - +
239A TYR* 3.6 1.7 + - - +
240A GLY* 3.2 18.4 + - - -
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Residues in contact with ARG 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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178A LEU* 3.8 33.7 - - + +
233A ALA 2.9 17.3 + - - +
234A ALA* 3.2 7.4 + - - +
236A ARG* 1.3 75.6 - - - +
238A VAL* 1.3 57.9 + - - +
240A GLY* 3.2 3.3 + - - -
241A LEU* 2.9 45.3 + - + +
290A THR* 4.0 24.5 + - - +
291A LEU* 4.1 10.2 - - - +
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Residues in contact with VAL 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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170A LEU* 5.9 0.2 - - + -
171A CYS* 3.5 41.1 - - + +
174A ALA* 4.1 11.7 - - + -
175A ALA* 3.8 23.6 - - - +
178A LEU* 3.9 15.5 - - + -
234A ALA 2.9 19.7 + - - +
235A ILE* 3.7 7.2 - - + +
236A ARG 3.2 0.6 - - - -
237A ARG* 1.3 75.9 - - - +
239A TYR* 1.3 60.0 + - - +
241A LEU* 3.1 11.1 + - + +
242A LEU* 2.9 25.8 + - - +
288A LEU* 3.7 10.2 - - + +
291A LEU* 4.8 6.1 - - + -
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Residues in contact with TYR 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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55A ASP* 2.6 34.1 + - - -
56A GLY* 3.3 23.8 - - - -
57A PRO* 3.5 25.6 - - + -
163A ARG* 3.4 7.8 + - - -
166A ILE* 5.8 0.9 - - + -
167A ALA* 3.6 9.0 - - - +
171A CYS* 3.5 30.0 - - + +
172A TYR* 3.8 4.4 - + - -
205A LEU* 3.9 24.1 - - + +
206A GLY 6.2 0.2 - - - +
235A ILE* 3.1 50.7 + - + +
236A ARG 4.3 1.8 - - - +
238A VAL* 1.3 75.7 - - - +
240A GLY* 1.3 62.0 + - - +
242A LEU* 3.4 13.8 + - + +
243A ALA* 3.1 23.6 + - - +
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Residues in contact with GLY 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 3.2 13.9 + - - -
237A ARG* 3.5 5.4 - - - -
238A VAL 3.1 1.0 - - - -
239A TYR* 1.3 75.7 - - - +
241A LEU* 1.3 64.2 + - - +
243A ALA* 3.5 5.2 + - - +
244A ASN* 3.2 28.9 + - - +
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Residues in contact with LEU 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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178A LEU* 5.8 0.2 - - + -
237A ARG* 2.9 44.9 + - + +
238A VAL* 3.1 8.5 + - + +
240A GLY* 1.3 76.2 - - - +
242A LEU* 1.3 52.6 - - - +
244A ASN* 3.2 6.0 + - - +
245A THR* 2.5 36.9 + - - -
285A GLY 4.8 1.3 - - - +
286A ASP* 3.4 29.8 - - - +
287A THR* 3.8 18.0 - - - +
288A LEU* 3.6 11.0 - - + -
290A THR* 4.5 5.4 - - + -
291A LEU* 4.1 34.3 - - + -
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Residues in contact with LEU 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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166A ILE* 3.7 26.5 - - + -
170A LEU* 4.3 2.9 - - + -
171A CYS* 3.7 18.6 - - - -
203A ILE* 5.8 1.6 - - + -
205A LEU* 4.2 13.2 - - + -
238A VAL 2.9 13.3 + - - +
239A TYR* 3.5 23.6 - - + +
240A GLY 3.1 0.2 - - - -
241A LEU* 1.3 74.2 - - - +
243A ALA* 1.3 66.9 + - - +
245A THR* 3.0 11.1 + - - -
246A VAL* 3.2 19.4 + - + +
288A LEU* 3.7 17.5 - - + +
319A LEU* 3.7 37.0 - - + -
322A MET* 5.8 0.4 - - - -
324A VAL* 6.0 1.1 - - + -
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 3.9 17.7 - - + -
239A TYR 3.1 13.7 + - - +
240A GLY* 3.9 5.6 - - - +
241A LEU 3.4 0.2 - - - -
242A LEU* 1.3 78.7 - - - +
244A ASN* 1.3 63.0 + - - +
246A VAL* 3.6 5.3 + - - +
247A ARG* 3.3 21.1 + - - +
324A VAL* 4.6 11.3 - - + +
326A ILE* 4.4 15.9 - - + -
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Residues in contact with ASN 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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240A GLY 3.2 14.9 + - - +
241A LEU* 3.2 7.8 + - - +
242A LEU 3.2 0.4 - - - -
243A ALA* 1.3 78.9 - - - +
245A THR* 1.3 53.2 + - - +
247A ARG* 3.3 2.1 + - - +
248A TYR* 2.6 35.7 + - - +
282A PRO* 3.4 25.9 - - + +
286A ASP* 2.7 41.8 + - - +
287A THR* 4.2 1.1 - - - -
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Residues in contact with THR 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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241A LEU 2.5 23.4 + - - -
242A LEU 3.0 8.2 + - - -
244A ASN* 1.3 73.8 - - - +
246A VAL* 1.3 62.5 + - - +
248A TYR* 3.3 0.7 + - - +
249A LEU* 2.9 45.9 + - + +
287A THR* 3.3 10.8 - - + -
288A LEU* 3.0 27.8 + - + +
289A PHE* 4.0 22.9 - - + -
315A LEU* 5.2 0.9 - - + -
319A LEU* 3.7 26.7 - - + -
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Residues in contact with VAL 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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242A LEU* 3.2 23.1 + - + +
243A ALA 3.9 3.8 - - - +
245A THR* 1.3 75.2 - - - +
247A ARG* 1.3 57.6 + - - +
249A LEU* 3.2 6.7 + - - +
250A GLN* 2.8 43.7 + - - +
277A ASN 5.7 1.3 - - - +
319A LEU* 3.8 30.5 - - + +
320A ARG* 5.1 0.2 - - - -
322A MET* 3.4 31.0 - - + +
324A VAL* 3.6 30.7 - - + +
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Residues in contact with ARG 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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243A ALA 3.3 11.1 + - - +
244A ASN* 3.3 9.4 + - - +
245A THR 3.2 0.6 - - - -
246A VAL* 1.3 80.0 - - - +
248A TYR* 1.3 62.9 + - - +
250A GLN* 3.2 18.4 + - - +
251A CYS* 3.0 43.4 + - - -
277A ASN* 2.9 45.0 + - - +
278A ALA* 3.3 18.9 + - - +
279A GLY 3.1 25.5 + - - +
280A PRO 3.8 16.4 - - - +
282A PRO* 4.0 8.7 - - + -
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Residues in contact with TYR 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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244A ASN 2.6 21.2 + - - +
245A THR 3.5 3.8 - - - +
247A ARG* 1.3 74.9 - - - +
249A LEU* 1.3 70.5 + - + +
251A CYS 3.5 2.9 + - - -
253A GLY* 2.9 41.5 + - - -
254A SER 3.1 23.9 + - - -
255A TRP* 3.5 10.1 + - - -
258A ASP* 2.6 27.1 + - - +
281A ARG* 3.2 26.5 - - + -
282A PRO* 3.3 34.0 - - + +
284A ILE* 4.0 18.1 - - + +
287A THR* 3.7 18.4 - - + -
289A PHE* 4.2 19.3 - + - -
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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
----------------------------------------------------------
245A THR* 2.9 31.5 + - + +
246A VAL 3.7 3.1 - - - +
248A TYR* 1.3 84.8 - - + +
250A GLN* 1.3 61.7 + - - +
252A GLY* 3.1 18.5 + - - -
253A GLY 3.8 19.4 + - - +
254A SER* 5.5 1.3 - - - -
255A TRP 5.6 0.9 - - - +
289A PHE* 4.4 6.7 - - + -
316A ALA* 3.6 49.4 - - + +
319A LEU* 3.7 12.1 - - + -
320A ARG* 3.7 30.0 - - + +
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Residues in contact with GLN 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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246A VAL* 2.8 31.5 + - - +
247A ARG* 4.0 23.8 + - - +
249A LEU* 1.3 69.5 - - - +
251A CYS* 1.3 58.2 + - - +
252A GLY 3.1 8.3 + - - -
277A ASN* 4.1 8.1 + - - -
320A ARG* 3.0 26.9 + - + +
321A SER* 4.3 1.4 - - - +
322A MET 2.7 29.9 + - - +
323A HIS* 4.9 6.9 + - - +
324A VAL 5.7 0.7 + - - -
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Residues in contact with CYS 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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247A ARG* 3.0 49.2 + - - +
249A LEU 3.2 0.6 - - - -
250A GLN* 1.3 76.6 - - - +
252A GLY* 1.3 59.2 + - - +
253A GLY 3.1 5.9 + - - -
279A GLY 4.5 0.9 - - - -
280A PRO* 4.3 1.6 - - - -
281A ARG* 3.2 51.1 + - + -
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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
------------------------------------------------------------
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