Contacts of the helix formed by residues 206 - 234 (chain A) in PDB entry 2RIB
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 SER 206 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 1.3 64.5 + - - +
208A ARG* 3.2 4.5 - - - +
209A GLN* 3.1 22.6 + - - +
210A GLN* 3.0 43.2 + - - +
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Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER* 1.3 81.6 + - - +
208A ARG* 1.3 62.8 + - - +
210A GLN* 3.3 19.5 + - - +
211A VAL* 3.1 27.8 + - - +
204B VAL 5.0 3.8 - - - +
207B LEU* 4.1 9.4 - - + -
208B ARG* 3.9 38.6 - - + +
211B VAL* 3.9 27.6 - - + -
207C LEU* 3.6 25.8 - - + -
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Residues in contact with ARG 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER* 3.2 2.1 - - - +
207A LEU* 1.3 78.4 - - - +
209A GLN* 1.3 64.5 + - + +
211A VAL* 3.4 2.9 + - - +
212A GLU* 3.0 29.5 + - + +
206C SER* 2.8 29.5 + - - -
207C LEU* 3.6 30.7 - - + +
210C GLN* 3.0 47.3 + - - +
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Residues in contact with GLN 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER* 3.1 24.2 + - - +
208A ARG* 1.3 81.3 - - + +
210A GLN* 1.3 59.5 + - + +
212A GLU* 3.2 13.6 + - - +
213A ALA* 2.8 29.0 + - - +
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Residues in contact with GLN 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER* 3.0 34.8 + - - +
207A LEU* 3.6 23.0 - - - +
209A GLN* 1.3 72.7 - - + +
211A VAL* 1.3 56.7 + - - +
213A ALA* 3.1 5.8 + - - +
214A LEU* 2.6 39.4 + - - +
211B VAL* 4.2 11.6 - - + +
215B GLN* 3.1 28.7 + - - +
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Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU 3.1 16.7 + - - +
208A ARG 3.6 7.4 - - - +
210A GLN* 1.3 75.4 - - - +
212A GLU* 1.3 58.5 + - - +
214A LEU* 4.1 5.0 - - - +
215A GLN* 3.0 33.9 + - + +
211B VAL* 3.8 27.4 - - + -
214B LEU* 6.4 0.2 - - + -
207C LEU* 3.8 17.9 - - + -
210C GLN* 4.2 36.1 - - + +
211C VAL* 3.8 7.9 - - + -
214C LEU* 4.2 14.3 - - + +
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Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ARG* 3.0 15.5 + - - +
209A GLN* 3.3 18.2 - - - +
211A VAL* 1.3 78.1 - - - +
213A ALA* 1.3 60.4 + - - +
215A GLN* 3.5 12.4 + - - +
216A GLY* 3.2 17.7 + - - -
210C GLN* 5.5 4.9 + - - -
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Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLN 2.8 15.9 + - - +
210A GLN* 3.5 7.4 - - - +
212A GLU* 1.3 75.2 - - - +
214A LEU* 1.3 64.6 + - - +
216A GLY* 3.1 11.6 + - - -
217A GLN* 3.1 19.0 + - + +
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Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLN 2.6 21.9 + - - +
211A VAL* 4.1 0.9 - - - +
213A ALA* 1.3 73.9 - - - +
215A GLN* 1.3 58.1 + - - +
217A GLN* 3.4 21.0 + - - +
218A VAL* 2.9 33.9 + - + +
211B VAL* 4.2 7.2 - - + +
214B LEU* 3.6 32.8 - - + +
215B GLN* 3.7 31.2 - - + +
218B VAL* 3.9 29.2 - - + -
214C LEU* 3.9 16.8 - - + -
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Residues in contact with GLN 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A VAL* 3.0 23.2 + - + +
212A GLU* 3.8 15.0 - - - +
214A LEU* 1.3 74.1 - - - +
216A GLY* 1.3 61.3 + - - +
218A VAL* 3.8 0.4 - - - +
219A GLN* 2.9 50.6 + - - +
210C GLN* 4.8 4.6 + - - +
213C ALA* 4.7 9.1 - - - +
214C LEU* 3.8 29.4 - - + +
217C GLN* 3.4 23.6 + - - +
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Residues in contact with GLY 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLU 3.2 10.5 + - - -
213A ALA* 3.1 8.9 + - - -
215A GLN* 1.3 77.8 - - - +
217A GLN* 1.3 56.0 + - - +
219A GLN* 3.4 6.6 + - - +
220A HIS* 2.9 44.6 + - - -
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Residues in contact with GLN 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ALA* 3.1 14.0 + - - +
214A LEU* 3.6 28.5 - - + +
215A GLN 3.3 0.2 - - - -
216A GLY* 1.3 78.1 - - - +
218A VAL* 1.3 56.7 + - - +
220A HIS* 3.3 11.1 + - - +
221A LEU* 2.8 28.6 + - - +
218B VAL* 4.9 3.2 - - + +
222B GLN* 3.6 33.9 + - - +
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Residues in contact with VAL 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 2.9 23.0 + - + +
215A GLN 3.8 3.8 - - - +
216A GLY 3.3 0.2 - - - -
217A GLN* 1.3 76.0 - - - +
219A GLN* 1.3 60.9 + - - +
221A LEU* 3.1 9.5 + - + +
222A GLN* 2.8 32.6 + - - +
218B VAL* 3.6 31.6 - - + -
214C LEU* 3.8 17.7 - - + -
217C GLN* 4.1 31.0 - - + +
218C VAL* 4.0 7.6 - - + -
221C LEU* 4.2 13.9 - - + -
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Residues in contact with GLN 219 (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 GLN* 2.9 42.7 + - + +
216A GLY* 4.0 5.1 - - - +
218A VAL* 1.3 74.8 - - - +
220A HIS* 1.3 68.7 + - + +
222A GLN* 3.6 13.6 - - - +
223A ALA* 3.0 22.5 + - - +
217C GLN* 3.4 28.8 + - - +
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Residues in contact with HIS 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLY* 2.9 31.5 + - - +
217A GLN* 3.6 9.0 - - - +
219A GLN* 1.3 79.9 - - + +
221A LEU* 1.3 58.4 + - - +
223A ALA* 3.2 8.5 + - + +
224A ALA* 3.0 28.2 + - - +
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Residues in contact with LEU 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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217A GLN 2.8 17.0 + - - +
218A VAL* 3.3 8.5 - - + +
220A HIS* 1.3 78.5 - - - +
222A GLN* 1.3 55.7 + - - +
224A ALA* 3.3 4.1 + - + +
225A PHE* 2.8 33.8 + - + +
218B VAL* 4.7 8.5 - - + +
221B LEU* 3.8 27.4 - - + -
222B GLN* 4.3 25.4 - - + +
225B PHE* 3.8 35.4 - - + -
221C LEU* 3.8 24.0 - - + -
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Residues in contact with GLN 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A VAL* 2.8 20.4 + - - +
219A GLN* 3.6 14.4 + - - +
220A HIS 3.2 0.2 - - - -
221A LEU* 1.3 77.4 - - - +
223A ALA* 1.3 56.9 + - - +
225A PHE* 3.8 5.9 - - - +
226A SER* 2.9 31.5 + - - -
217C GLN* 3.3 51.5 - - - +
221C LEU* 3.9 22.8 - - + +
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Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A GLN 3.0 13.5 + - - +
220A HIS* 3.5 12.3 - - + +
222A GLN* 1.3 74.0 - - - +
224A ALA* 1.3 65.8 + - - +
226A SER* 3.4 6.0 + - - -
227A GLN* 3.1 22.7 + - - +
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Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A HIS 3.0 15.7 + - - +
221A LEU* 3.8 5.6 - - + +
223A ALA* 1.3 77.0 - - - +
225A PHE* 1.3 63.6 + - - +
227A GLN* 3.2 11.6 + - - +
228A TYR* 3.0 32.1 + - + -
225B PHE* 3.7 22.9 - - + -
229B LYS* 5.6 2.2 - - + +
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Residues in contact with PHE 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 2.8 20.6 + - + +
222A GLN 3.8 4.7 - - - +
224A ALA* 1.3 77.6 - - - +
226A SER* 1.3 59.9 + - - +
228A TYR* 3.3 1.8 + - + -
229A LYS* 2.9 52.1 + - + +
225B PHE* 3.8 26.2 - + + -
221C LEU* 4.0 22.4 - - + -
224C ALA* 3.6 42.2 - - + -
225C PHE* 3.9 17.5 - + + -
228C TYR* 3.7 35.7 - + + -
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Residues in contact with SER 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A GLN 2.9 18.8 + - - -
223A ALA* 3.7 6.3 - - - -
224A ALA 3.3 0.2 - - - -
225A PHE* 1.3 80.5 - - - +
227A GLN* 1.3 62.7 + - - +
229A LYS* 3.4 8.7 + - - +
230A LYS* 3.3 29.6 + - - +
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Residues in contact with GLN 227 (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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223A ALA 3.1 12.8 + - - +
224A ALA* 3.5 11.0 - - - +
225A PHE 3.2 0.2 - - - -
226A SER* 1.3 74.5 - - - +
228A TYR* 1.3 73.6 + - - +
230A LYS* 3.2 15.4 + - - +
231A VAL* 3.1 20.8 + - - +
242B GLU* 2.9 27.7 + - - +
244B ILE* 3.5 27.6 - - + +
355B PHE* 3.1 37.6 + - + +
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Residues in contact with TYR 228 (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 ALA* 3.0 28.3 + - + +
225A PHE* 3.9 3.4 - - + +
227A GLN* 1.3 84.9 - - - +
229A LYS* 1.3 57.3 + - - +
231A VAL* 3.7 3.6 - - - -
232A GLU* 2.8 11.4 + - - +
225B PHE* 3.7 20.9 - + + -
229B LYS* 3.5 57.0 - - + +
232B GLU* 2.6 51.1 - - - +
233B LEU* 3.6 27.2 - - + +
239B SER* 4.0 9.7 + - - -
244B ILE* 3.4 25.9 - - + +
228C TYR* 4.8 3.6 - - + +
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Residues in contact with LYS 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 PHE* 2.9 45.2 + - + +
226A SER* 3.6 9.4 - - - +
227A GLN 3.1 0.2 - - - -
228A TYR* 1.3 75.4 - - - +
230A LYS* 1.3 66.1 + - + +
232A GLU* 3.2 7.5 + - + +
233A LEU* 3.1 38.5 + - + +
239A SER* 5.4 4.6 - - - -
244A ILE* 3.9 24.7 - - + +
224C ALA* 5.0 8.4 + - - +
227C GLN* 4.3 13.1 + - - -
228C TYR* 4.8 11.6 - - + -
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Residues in contact with LYS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A SER* 3.3 18.8 + - - +
227A GLN* 3.2 13.1 + - - +
229A LYS* 1.3 77.8 - - + +
231A VAL* 1.3 61.6 + - - +
233A LEU* 3.4 8.4 + - - +
234A PHE* 3.3 21.5 + - - +
264B ALA* 4.1 15.3 - - - +
265B GLY* 2.8 32.6 + - - +
355B PHE* 4.0 30.3 + - + +
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Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLN 3.1 13.3 + - - +
228A TYR* 3.5 3.8 - - + +
230A LYS* 1.3 77.8 - - - +
232A GLU* 1.3 60.4 + - - +
234A PHE* 3.3 9.7 + - - +
232B GLU* 3.2 19.1 - - + +
233B LEU* 4.2 10.5 - - + -
244B ILE* 3.7 35.4 - - + -
246B LYS* 3.0 43.8 + - + +
355B PHE* 3.7 34.8 - - + -
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Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A TYR 2.8 18.6 + - - +
229A LYS* 3.4 8.5 - - + +
231A VAL* 1.3 78.0 - - - +
233A LEU* 1.3 64.6 + - + +
234A PHE 3.4 4.3 + - - +
236A ASN* 5.3 1.2 + - - +
237A GLY 5.1 0.7 + - - -
246A LYS* 3.0 35.0 + - - +
232B GLU* 3.0 18.9 + - - +
246B LYS* 4.2 4.6 + - - +
228C TYR* 3.8 14.3 - - + -
231C VAL* 3.6 20.1 - - + +
232C GLU* 2.3 45.3 - - - +
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LYS* 3.1 29.9 + - + +
230A LYS* 3.4 7.2 + - - +
231A VAL 3.3 0.2 - - - -
232A GLU* 1.3 79.4 - - + +
234A PHE* 1.3 58.1 + - - +
235A PRO* 3.5 1.4 - - - +
236A ASN 3.3 1.6 + - - -
237A GLY* 2.8 51.1 + - - +
238A GLN* 4.6 0.7 - - - -
239A SER* 3.8 36.1 - - - +
244A ILE* 3.7 30.5 - - + -
264B ALA* 6.1 0.4 - - - -
231C VAL* 4.4 12.6 - - + -
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Residues in contact with PHE 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LYS 3.3 7.8 + - - +
231A VAL 3.3 5.1 + - - +
232A GLU 4.1 1.0 - - - +
233A LEU* 1.3 77.9 - - - +
235A PRO* 1.3 71.6 - - + +
236A ASN 3.6 1.1 - - - -
246B LYS* 2.6 64.6 + - + -
248B ALA* 3.7 32.1 - - + -
260B LEU* 4.0 23.8 - - + -
264B ALA* 3.7 21.1 - - + -
351B VAL* 4.0 8.5 - - + -
353B CYS* 3.2 30.3 - - - -
355B PHE* 3.8 24.5 - + + -
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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