Contacts of the helix formed by residues 236 - 258 (chain A) in PDB entry 1RRM
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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190A LYS* 5.6 0.9 + - - -
231A GLY* 2.9 20.8 + - - +
232A SER* 4.1 3.3 + - - -
234A ALA* 3.6 2.1 - - + +
235A GLY* 1.3 77.5 - - - +
237A LYS* 1.3 65.3 + - - +
238A ASP* 3.2 13.5 + - - +
239A ALA* 2.9 33.6 + - + +
240A GLY* 3.2 17.2 + - - -
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Residues in contact with LYS 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 ARG* 2.9 42.2 + - - +
183A ASP* 5.3 4.5 - - - +
235A GLY 3.3 6.5 + - - +
236A ASP* 1.3 71.8 + - - +
238A ASP* 1.3 70.3 + - - +
240A GLY 3.1 7.8 + - - -
241A GLU 3.1 4.2 + - - -
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Residues in contact with ASP 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 5.6 1.4 + - - -
236A ASP* 3.2 10.7 + - - +
237A LYS* 1.3 80.7 - - - +
239A ALA* 1.3 57.0 + - - +
241A GLU* 3.1 17.9 + - - +
242A GLU* 2.9 41.4 + - - +
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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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228A ALA* 3.5 19.5 - - + +
231A GLY* 3.6 8.3 - - - -
232A SER* 3.3 29.4 - - - +
236A ASP* 2.9 18.8 + - + +
237A LYS 3.2 0.2 - - - -
238A ASP* 1.3 76.7 - - - +
240A GLY* 1.3 58.8 + - - +
242A GLU* 3.2 7.7 + - - +
243A MSE 2.9 32.2 + - - +
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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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16A ARG* 4.5 4.3 - - - -
179A ALA* 4.0 8.8 - - - +
182A MSE 4.9 2.9 - - - +
183A ASP* 5.3 2.7 - - - -
190A LYS* 6.3 0.2 - - - -
232A SER* 3.6 16.6 + - - -
236A ASP 3.2 10.0 + - - -
237A LYS 3.1 8.6 + - - -
239A ALA* 1.3 78.3 - - - +
241A GLU* 1.3 55.5 + - - +
243A MSE 3.3 4.7 + - - +
244A ALA* 3.0 26.9 + - - +
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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* 3.7 10.8 - - - -
16A ARG* 3.2 47.3 + - + +
179A ALA* 3.8 12.5 - - + +
237A LYS 3.1 11.0 + - - +
238A ASP* 3.1 19.8 + - - +
240A GLY* 1.3 72.3 - - - +
242A GLU* 1.3 65.1 + - + +
244A ALA* 3.3 4.3 + - + +
245A LEU* 3.3 20.1 + - - +
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Residues in contact with GLU 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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224A ILE* 3.3 20.6 - - + +
227A GLY 4.8 3.3 - - - +
228A ALA* 3.3 24.6 + - + +
238A ASP* 2.9 27.0 + - - +
239A ALA* 3.5 11.1 - - - +
241A GLU* 1.3 79.1 - - + +
243A MSE 1.3 57.3 + - - +
245A LEU* 3.1 7.3 + - - +
246A GLY 2.9 24.3 + - - -
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Residues in contact with MSE 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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142A ALA* 3.8 22.6 - - + +
190A LYS 5.4 0.2 - - - +
194A GLY* 3.6 31.4 - - - +
197A ALA* 4.8 3.4 - - + -
225A ILE* 3.8 36.6 - - + +
228A ALA* 4.2 5.2 - - + -
229A LEU* 3.7 29.6 - - + -
232A SER* 3.8 22.0 - - - +
239A ALA 2.9 20.0 + - - +
240A GLY* 3.6 7.6 - - - +
242A GLU* 1.3 77.4 - - - +
244A ALA* 1.3 61.3 + - - +
246A GLY* 4.4 1.3 - - - +
247A GLN* 3.0 29.8 + - - +
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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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142A ALA* 4.4 0.2 - - - +
177A ILE* 3.4 22.9 - - + +
179A ALA* 4.4 9.0 - - + +
182A MSE 3.6 28.9 - - + -
240A GLY 3.0 11.4 + - - +
241A GLU* 3.5 13.5 - - + +
242A GLU 3.2 0.2 - - - -
243A MSE 1.3 76.6 - - - +
245A LEU* 1.3 61.9 + - - +
247A GLN* 3.1 29.0 + - - +
248A TYR* 3.7 1.2 + - - +
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Residues in contact with LEU 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 PHE* 4.0 27.1 - - + -
177A ILE* 5.0 2.7 - - - -
224A ILE* 4.4 15.9 - - + -
241A GLU 3.3 8.1 + - - +
242A GLU* 3.1 10.3 + - - +
244A ALA* 1.3 78.5 - - - +
246A GLY* 1.3 65.1 + - - +
248A TYR* 3.1 6.1 + - - +
249A VAL* 2.9 43.3 + - + +
211B TRP* 4.2 18.4 - - + -
212B ALA* 3.8 27.8 - - + -
213B LEU* 4.4 13.5 - - + +
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Residues in contact with GLY 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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221A ALA* 3.6 11.2 - - - +
224A ILE* 3.7 31.4 - - - +
225A ILE* 3.8 12.4 - - - +
242A GLU 2.9 12.0 + - - -
243A MSE 3.3 1.5 + - - -
245A LEU* 1.3 77.1 - - - +
247A GLN* 1.3 61.1 + - - +
249A VAL* 3.4 2.0 + - - -
250A ALA* 3.1 20.3 + - - +
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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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139A PRO* 4.8 0.4 - - - +
141A THR 4.2 4.5 - - - +
142A ALA* 3.8 17.7 - - - +
143A GLY* 3.4 18.3 + - - +
144A THR 3.8 0.2 + - - -
145A ALA* 3.1 44.5 + - - +
147A GLU* 2.9 24.6 + - - +
177A ILE* 4.2 6.7 - - - +
182A MSE 4.4 7.1 - - - +
197A ALA* 3.7 29.8 - - + -
200A HIS* 5.4 0.7 + - - -
225A ILE* 4.3 2.2 - - - +
243A MSE 3.0 22.1 + - + +
244A ALA* 3.1 18.5 + - - +
246A GLY* 1.3 76.2 - - - +
248A TYR* 1.3 67.2 + - - +
250A ALA* 3.5 4.6 - - - +
251A GLY 3.4 7.4 + - - -
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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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8A LEU* 5.9 0.5 - - - +
9A ASN* 2.5 38.1 + - - +
12A ALA* 3.7 10.6 - - + +
14A PHE* 3.4 32.5 - + + -
145A ALA* 4.4 4.0 - - - -
147A GLU* 3.4 26.5 - - + -
148A VAL* 3.4 19.3 - - + +
177A ILE* 3.7 19.1 - - + -
244A ALA 3.7 10.5 - - - +
245A LEU 3.1 9.5 + - - +
247A GLN* 1.3 86.1 - - - +
249A VAL* 1.3 70.0 + - + +
250A ALA 3.1 1.6 - - - -
251A GLY* 2.9 12.6 + - - -
252A MSE 3.0 38.9 + - + +
8B LEU* 6.1 1.3 - - + +
213B LEU* 5.7 0.2 - - + -
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Residues in contact with VAL 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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217A LEU* 3.3 47.6 - - + +
220A LYS* 4.8 7.6 - - + -
221A ALA* 4.1 9.2 - - + +
224A ILE* 4.8 6.1 - - + -
245A LEU* 2.9 42.3 + - + +
246A GLY* 3.8 6.1 - - - +
248A TYR* 1.3 76.4 - - + +
250A ALA* 1.3 63.9 + - - +
252A MSE 3.2 25.4 + - - +
253A GLY 3.5 3.3 + - - -
213B LEU* 4.1 17.9 - - + -
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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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197A ALA* 4.0 20.9 - - - +
200A HIS* 4.2 6.3 - - + -
201A ALA* 4.1 11.4 - - + +
218A HIS* 3.3 10.6 - - - -
221A ALA* 3.7 16.5 - - + +
225A ILE* 4.7 0.7 - - + -
246A GLY 3.1 13.0 + - - +
247A GLN* 3.5 13.0 - - - +
248A TYR 3.1 0.4 - - - -
249A VAL* 1.3 77.3 - - - +
251A GLY* 1.3 61.8 + - - +
253A GLY 3.1 3.5 + - - -
254A PHE* 3.1 25.4 + - + -
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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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145A ALA* 3.7 13.2 - - - -
148A VAL* 3.9 8.6 - - - +
149A THR* 4.1 1.3 - - - -
247A GLN 3.4 4.2 + - - -
248A TYR 2.9 8.6 + - - -
250A ALA* 1.3 76.1 - - - +
252A MSE 1.3 61.7 + - - +
253A GLY 2.9 5.9 + - - -
254A PHE* 3.5 20.4 - - - -
255A SER* 3.2 28.8 + - - -
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Residues in contact with MSE 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 MSE 3.5 12.6 - - - +
8A LEU* 3.9 28.4 - - + +
148A VAL* 4.0 5.6 - - + +
217A LEU* 4.0 26.5 - - + -
248A TYR* 3.0 47.6 + - + +
249A VAL* 3.2 22.4 + - - +
251A GLY* 1.3 75.6 - - - +
253A GLY* 1.3 57.8 + - - +
256A ASN* 2.9 22.9 - - - +
6B MSE 5.9 0.9 - - + -
8B LEU* 4.0 26.0 - - + -
213B LEU* 4.8 15.9 - - + -
217B LEU* 5.8 2.7 - - + -
252B MSE 4.2 11.4 - - + -
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Residues in contact with GLY 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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214A THR* 3.8 15.0 - - - +
217A LEU* 4.2 7.6 - - - +
218A HIS* 3.3 18.2 - - - -
249A VAL 3.5 3.5 + - - -
250A ALA 3.1 6.1 + - - -
251A GLY 2.9 1.8 - - - -
252A MSE 1.3 78.8 - - - +
254A PHE* 1.3 63.8 + - - +
255A SER 3.2 2.0 - - - -
256A ASN* 3.0 16.1 + - - +
257A VAL* 3.3 12.4 + - - +
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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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144A THR 3.9 4.3 - - - -
145A ALA* 4.3 2.7 - - + -
149A THR* 3.6 18.6 - - + -
151A ASN* 4.3 5.6 - - - +
200A HIS* 3.4 47.6 - + + +
218A HIS* 2.9 22.3 - - + -
250A ALA 3.1 23.6 + - - -
251A GLY* 3.5 19.7 - - - -
253A GLY* 1.3 68.2 - - - -
255A SER* 1.3 63.4 + - - +
257A VAL* 3.8 5.8 - - - -
258A GLY* 2.8 31.3 + - - +
259A LEU* 3.6 37.0 - - + -
390A PGO 3.6 31.0 - - + -
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Residues in contact with SER 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 ILE 4.9 1.1 + - - -
148A VAL 4.1 3.3 + - - -
149A THR* 3.2 24.0 - - - -
150A ILE* 2.9 49.2 + - - +
151A ASN* 4.5 8.7 + - - +
166A VAL* 5.6 0.7 - - - +
251A GLY 3.2 19.3 + - - -
252A MSE 5.4 0.2 - - - -
253A GLY 3.2 0.2 + - - -
254A PHE* 1.3 86.3 - - - +
256A ASN* 1.3 66.5 + - - +
257A VAL 3.9 0.3 + - - -
258A GLY 4.9 0.5 + - - -
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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 ARG* 3.7 15.7 + - - +
6A MSE 3.4 27.4 - - - +
7A ILE* 2.7 56.4 + - - +
150A ILE* 5.3 2.8 - - - +
211A TRP* 5.4 0.6 + - - +
214A THR* 4.7 1.6 - - + -
252A MSE 2.9 22.3 - - - +
253A GLY 3.0 8.3 + - - +
255A SER* 1.3 86.9 + - - +
257A VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 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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4A ASN* 5.9 0.2 - - - +
204A GLY 4.0 2.5 - - - +
207A THR* 3.7 28.8 + - + +
209A GLY* 3.4 32.2 + - - +
210A ALA* 4.8 0.2 - - - -
211A TRP* 3.8 9.4 - - + +
214A THR* 3.5 29.2 - - + +
218A HIS* 3.9 12.6 - - - +
253A GLY 3.3 15.0 - - - +
254A PHE* 3.9 7.2 - - - -
256A ASN* 1.3 82.6 - - - +
258A GLY* 1.3 63.6 + - - +
365A GLY* 5.8 1.4 - - - -
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Residues in contact with GLY 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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204A GLY* 3.5 22.5 - - - -
207A THR* 3.6 8.9 - - - +
254A PHE* 2.8 21.7 + - - +
255A SER 4.8 0.8 + - - -
257A VAL* 1.3 75.0 - - - +
259A LEU* 1.3 69.7 + - - +
365A GLY* 5.8 1.8 - - - -
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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
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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