Contacts of the helix formed by residues 232 - 256 (chain A) in PDB entry 2R8J
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 232 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 2.7 31.4 + - - -
3A LYS* 3.4 25.3 + - - +
4A PHE* 3.8 17.0 - - + -
208A ILE* 3.6 13.8 - - - +
230A ILE* 4.5 0.7 - - - +
231A THR* 1.3 85.0 + - - +
233A TRP* 1.3 86.2 + - - +
234A ASP* 3.3 12.8 - - - +
235A ASP* 3.0 20.2 + - - +
236A VAL* 3.4 7.1 + - - +
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Residues in contact with TRP 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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2A SER* 3.4 9.4 + - - -
4A PHE* 4.9 0.4 - + + -
9A LEU* 5.5 5.2 - - + -
23A LEU* 4.0 17.3 - - + -
169A LEU* 4.3 19.7 - - + -
187A LEU* 3.7 24.2 - - + -
190A ILE* 3.9 33.2 - - + -
205A LEU* 3.5 27.1 - - + +
206A PRO* 3.0 25.4 + - + -
207A LEU 4.5 1.1 - - - -
208A ILE* 3.4 23.9 - - + +
209A PRO* 3.6 21.8 - - + -
232A ASP* 1.3 97.8 + - - +
234A ASP* 1.3 56.3 + - - +
236A VAL* 2.9 23.1 + - + +
237A ILE* 2.7 38.6 + - + +
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Residues in contact with ASP 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 5.4 1.6 + - - -
4A PHE* 3.0 28.2 - - + -
22A SER 4.7 4.0 - - - +
23A LEU* 3.4 24.7 - - + +
232A ASP* 3.6 11.2 - - - +
233A TRP* 1.3 74.3 - - - +
235A ASP* 1.3 79.3 + - - +
237A ILE* 3.9 5.3 - - - +
238A LEU* 2.9 30.5 + - - +
288A ASN* 3.5 30.5 - - - +
289A ASP* 5.1 5.0 - - - +
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Residues in contact with ASP 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A PHE* 3.6 5.6 - - - -
229A LEU 3.4 21.3 - - - +
230A ILE* 3.8 11.6 - - + +
231A THR* 3.2 28.1 + - - -
232A ASP 3.3 10.8 + - - +
233A TRP 3.0 0.4 - - - -
234A ASP* 1.3 89.2 + - - +
236A VAL* 1.3 60.3 + - - +
238A LEU* 4.2 4.6 - - - +
239A ALA* 2.8 30.5 + - - +
287A LYS* 3.2 38.0 + - - +
288A ASN 5.1 1.2 + - - -
289A ASP* 4.3 5.9 - - - +
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 3.9 27.6 - - + -
208A ILE* 4.4 0.9 - - + -
212A ILE* 3.8 31.6 - - + -
215A LEU* 3.9 17.0 - - + -
230A ILE* 4.2 12.6 - - + -
232A ASP 3.7 13.7 - - - +
233A TRP* 2.9 26.3 + - + +
235A ASP* 1.3 75.2 - - - +
237A ILE* 1.3 66.0 + - + +
239A ALA* 3.0 6.6 + - - +
240A LEU* 2.9 27.9 + - + +
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Residues in contact with ILE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 4.2 7.6 - - + -
12A LEU* 3.9 24.2 - - + -
23A LEU* 3.6 25.1 - - + +
24A ALA 5.4 0.2 - - - +
25A CYS* 3.9 14.3 - - + -
165A CYS* 3.5 34.9 - - + +
166A PHE 4.8 0.2 - - - +
169A LEU* 3.5 33.4 - - + -
233A TRP* 2.7 25.9 + - + +
234A ASP* 3.9 5.2 - - - +
236A VAL* 1.3 73.5 - - - +
238A LEU* 1.3 58.2 + - - +
240A LEU* 3.4 3.1 + - + +
241A GLY* 2.9 24.1 + - - -
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Residues in contact with LEU 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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25A CYS* 4.0 18.4 - - + -
217A PHE* 4.0 8.5 - - + -
234A ASP 2.9 21.0 + - - +
235A ASP* 3.7 6.3 - - - +
236A VAL 3.2 0.2 - - - -
237A ILE* 1.3 78.3 - - - +
239A ALA* 1.3 56.9 + - - +
241A GLY* 3.2 0.7 + - - -
242A SER* 2.8 29.5 + - - -
264A LEU* 3.9 25.1 - - + -
265A SER* 4.1 14.8 - - - +
285A ILE* 3.5 26.9 - - + -
286A VAL 4.0 5.6 - - - +
287A LYS* 3.9 28.7 - - + -
288A ASN* 6.1 0.9 - - - +
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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
----------------------------------------------------------
215A LEU* 3.5 26.9 - - + -
216A LYS 4.3 5.0 - - - +
217A PHE* 3.5 27.1 - - + -
230A ILE* 4.3 4.3 - - + -
235A ASP 2.8 21.9 + - - +
236A VAL* 3.0 5.4 + - - +
238A LEU* 1.3 72.9 - - - +
240A LEU* 1.3 62.2 + - - +
242A SER* 2.5 20.6 + - - -
243A GLN* 3.1 12.1 + - - +
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Residues in contact with LEU 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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165A CYS* 4.0 26.0 - - + +
168A MET* 3.8 26.0 - - + -
169A LEU* 4.0 31.2 - - + +
175A TYR* 4.4 7.0 - - + -
183A LEU* 4.1 18.2 - - + -
215A LEU* 3.9 28.3 - - + -
236A VAL* 2.9 21.4 + - + +
237A ILE* 3.8 5.6 - - - +
239A ALA* 1.3 75.2 - - - +
241A GLY* 1.3 63.8 + - - +
243A GLN* 2.9 8.3 + - + +
244A VAL* 2.8 27.8 + - - +
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Residues in contact with GLY 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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25A CYS* 4.0 4.0 - - - -
161A LEU* 3.5 13.3 - - - +
165A CYS* 3.5 22.2 - - - -
237A ILE 2.9 11.6 + - - -
238A LEU 3.5 4.0 - - - -
240A LEU* 1.3 77.1 - - - +
242A SER* 1.3 51.4 + - - +
244A VAL* 3.2 2.1 + - - +
245A CYS* 2.7 36.6 + - - +
264A LEU* 3.5 6.5 - - - -
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Residues in contact with SER 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A PHE* 3.7 5.0 - - - -
218A GLU* 3.1 44.7 + - - +
238A LEU 2.8 14.9 + - - -
239A ALA* 2.5 23.0 + - - -
241A GLY* 1.3 71.6 - - - +
243A GLN* 1.3 60.3 + - - +
245A CYS* 3.6 3.4 - - - +
246A LYS* 3.1 17.2 + - - +
264A LEU* 3.3 15.5 - - - +
283A GLN* 3.7 4.5 - - - +
285A ILE* 3.8 15.5 - - - -
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Residues in contact with GLN 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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168A MET* 5.5 3.6 - - + -
175A TYR* 3.3 36.7 + - + +
215A LEU* 5.2 1.8 - - + -
216A LYS* 3.2 24.0 + - - +
217A PHE 4.1 0.8 - - - -
218A GLU* 3.3 38.5 + - - +
239A ALA 3.1 11.9 + - - +
240A LEU* 2.9 14.2 + - + +
242A SER* 1.3 78.5 + - - +
244A VAL* 1.3 69.0 + - + +
246A LYS* 3.0 18.8 + - - +
247A GLY* 3.3 4.5 + - - -
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Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 4.9 7.2 - - + -
164A ILE* 3.7 42.6 - - + -
165A CYS* 5.4 2.2 - - - -
168A MET* 3.5 34.1 - - + -
240A LEU* 2.8 20.9 + - + +
241A GLY* 3.6 9.0 - - - +
243A GLN* 1.3 72.1 - - - +
245A CYS* 1.3 64.2 + - - +
247A GLY* 3.1 12.4 + - - +
248A ILE* 3.3 21.7 + - + +
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Residues in contact with CYS 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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27A ALA* 4.1 13.9 - - - -
29A ILE* 4.5 10.3 - - - -
159A LEU* 5.2 4.3 - - - -
161A LEU* 4.4 6.9 - - + +
241A GLY 2.7 22.7 + - - +
242A SER* 3.6 4.0 - - - +
244A VAL* 1.3 76.2 - - - +
246A LYS* 1.3 62.3 + - - +
247A GLY 3.3 0.2 + - - -
248A ILE* 3.3 10.4 + - - +
249A ARG* 3.1 27.1 + - - +
262A CYS* 3.3 34.1 - - - -
264A LEU* 3.8 8.7 - - + -
283A GLN* 3.4 12.3 - - - +
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Residues in contact with LYS 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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218A GLU* 3.5 41.7 + - + +
242A SER 3.1 6.7 + - - +
243A GLN 3.0 11.5 + - - +
245A CYS* 1.3 75.9 - - - +
247A GLY* 1.3 60.9 + - - +
249A ARG* 3.4 15.3 + - + +
250A ASP* 2.6 61.0 + - - +
281A ASP* 5.7 3.0 + - - -
283A GLN* 3.9 13.6 + - - +
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Residues in contact with GLY 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 GLN 3.3 5.1 + - - -
244A VAL* 3.1 9.0 + - - -
246A LYS* 1.3 77.8 - - - +
248A ILE* 1.3 62.9 + - - +
250A ASP* 2.9 11.8 + - - +
251A SER* 2.8 24.9 + - - -
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Residues in contact with ILE 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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29A ILE* 5.1 2.0 - - + -
141A ILE* 5.3 2.5 - - + +
142A PHE* 3.8 34.8 - - + +
145A ALA* 3.7 39.7 - - + +
146A CYS* 5.0 3.4 - - + -
159A LEU* 4.1 22.4 - - + -
161A LEU* 5.8 3.6 - - + -
164A ILE* 5.2 2.0 - - + -
244A VAL* 3.3 25.0 + - + +
245A CYS* 3.3 11.3 + - - +
247A GLY* 1.3 72.4 - - - +
249A ARG* 1.3 66.2 + - + +
251A SER* 2.9 27.4 + - - -
252A ILE* 3.2 8.4 + - + +
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Residues in contact with ARG 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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29A ILE* 4.0 20.0 - - + -
245A CYS 3.1 13.7 + - - +
246A LYS* 3.7 20.4 - - + +
248A ILE* 1.3 78.4 - - - +
250A ASP* 1.3 63.7 + - - +
252A ILE* 3.1 21.9 + - + +
253A LYS* 3.1 12.6 + - - +
258A TYR 5.0 0.9 - - - +
260A THR* 2.8 46.1 + - - +
262A CYS* 3.5 24.7 - - - +
281A ASP* 3.5 18.4 + - - -
282A ALA 3.0 17.6 + - - +
283A GLN* 3.2 40.3 - - - +
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Residues in contact with ASP 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 LYS* 2.6 58.4 + - - +
247A GLY* 2.9 11.6 + - - +
249A ARG* 1.3 73.3 - - - +
251A SER* 1.3 60.2 + - - +
253A LYS* 3.1 9.5 + - - +
254A ASP* 2.8 42.9 + - - +
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Residues in contact with SER 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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141A ILE* 4.2 16.8 - - - -
247A GLY 2.8 17.9 + - - -
248A ILE* 2.9 18.5 + - - -
250A ASP* 1.3 75.1 - - - +
252A ILE* 1.3 56.2 + - - +
254A ASP* 3.9 4.2 - - - -
255A ILE* 2.9 43.6 + - - +
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Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 5.4 3.1 - - + -
31A MET* 4.6 10.1 - - + -
138A ALA* 4.9 5.2 - - + +
141A ILE* 4.4 22.0 - - + -
142A PHE* 3.1 46.9 - - + -
248A ILE 3.6 11.7 - - - +
249A ARG* 3.1 13.4 + - - +
250A ASP 3.0 0.6 - - - -
251A SER* 1.3 75.1 - - - +
253A LYS* 1.3 60.5 + - - +
254A ASP 3.0 1.6 - - - -
256A LEU* 2.8 41.9 + - + +
257A GLY 2.9 5.4 + - - -
258A TYR* 3.8 27.6 - - + +
260A THR* 5.2 6.5 - - + +
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Residues in contact with LYS 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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47A LYS* 5.5 7.9 - - - -
249A ARG 3.1 11.2 + - - +
250A ASP* 3.1 13.9 + - - +
252A ILE* 1.3 77.5 - - - +
254A ASP* 1.3 63.8 + - - +
257A GLY* 3.0 42.8 + - - -
258A TYR 3.9 14.1 + - - +
259A THR* 4.6 15.0 - - + -
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Residues in contact with ASP 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ASP* 2.8 26.2 + - - +
251A SER* 3.9 4.9 - - - +
253A LYS* 1.3 88.2 - - - +
255A ILE* 1.3 67.0 + - + +
257A GLY 4.8 0.2 + - - -
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Residues in contact with ILE 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE* 3.4 35.9 - - + -
251A SER* 2.9 26.4 + - - +
254A ASP* 1.3 81.9 - - + +
256A LEU* 1.3 76.0 + - + +
171B PHE* 5.1 10.3 - - + -
173B ASN* 6.3 0.7 - - - +
195B ILE* 5.3 13.5 - - + -
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A MET* 3.7 17.8 - - - +
134A GLU* 4.5 5.3 - - - +
137A LYS* 4.1 28.5 - - + +
138A ALA* 3.6 40.4 - - + +
141A ILE* 4.0 11.9 - - + -
252A ILE* 2.8 14.8 + - + +
255A ILE* 1.3 95.4 - - + +
257A GLY* 1.3 64.2 + - - +
258A TYR* 3.7 32.5 - - + +
195B ILE* 5.2 4.3 - - + -
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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