Contacts of the helix formed by residues 203 - 235 (chain A) in PDB entry 4DYL
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 LEU 203 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A HIS* 2.9 47.4 + - + +
201A HIS 3.7 0.4 - - - -
202A GLN* 1.3 95.1 - - + +
204A LEU* 1.3 56.8 + - + +
205A LEU 3.6 0.9 - - - -
206A PRO* 3.7 1.1 - - - -
207A GLY* 2.7 33.8 + - - -
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Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 3.9 38.1 - - + +
196A HIS* 4.8 15.3 - - + +
199A HIS* 2.8 24.6 + - + +
200A HIS* 3.8 28.5 - - + +
203A LEU* 1.3 74.5 - - + +
205A LEU* 1.3 63.2 + - - +
207A GLY* 3.7 0.5 - - - -
208A LEU* 3.0 23.0 + - - +
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Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A CYS* 3.6 24.2 - - - -
9A SER 5.5 0.4 - - - +
120A TRP* 3.3 39.7 - - + +
123A LEU* 4.3 7.4 - - + +
124A GLN* 5.1 5.6 - - - +
200A HIS* 3.0 33.4 + - + +
201A HIS* 5.2 0.9 - - + -
204A LEU* 1.3 72.7 - - - +
206A PRO* 1.3 63.5 - - + +
208A LEU* 3.2 12.3 + - + +
209A LEU* 2.9 44.8 + - + +
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Residues in contact with PRO 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 3.2 33.9 - - - +
8A CYS* 4.1 9.2 - - - -
200A HIS 3.6 3.6 - - - +
201A HIS 3.2 26.5 - - - +
202A GLN* 3.5 18.6 - - - +
203A LEU 3.7 5.4 - - - +
204A LEU 3.7 1.8 - - - -
205A LEU* 1.3 95.2 - - + +
207A GLY* 1.3 55.7 + - - +
209A LEU* 3.4 1.1 + - + -
210A ARG* 2.9 28.2 + - - +
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Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU 2.7 24.4 + - - -
204A LEU 3.7 0.9 - - - -
206A PRO* 1.3 71.1 - - - +
208A LEU* 1.3 61.6 + - - +
210A ARG* 3.5 6.6 + - - +
211A SER* 3.1 24.6 + - - -
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Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TYR* 4.0 27.4 - - + -
119A GLN* 3.0 37.2 - - + +
120A TRP* 3.8 40.8 - - + +
123A LEU* 4.1 13.2 - - + -
204A LEU 3.0 13.8 + - - +
205A LEU* 3.5 10.5 - - + +
207A GLY* 1.3 74.6 - - - +
209A LEU* 1.3 61.3 + - - +
211A SER* 2.8 25.9 + - - +
212A LEU* 3.1 9.9 + - + +
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Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 3.6 22.8 - - - +
4A SER* 3.6 18.4 - - - +
7A LEU 3.8 5.8 - - - +
8A CYS* 3.5 42.2 - - + -
13A HIS* 5.9 0.4 - - - -
16A LEU* 3.4 33.4 - - + -
116A TYR* 3.5 17.7 - - + +
120A TRP* 5.2 1.6 - - + +
205A LEU* 2.9 32.1 + - + +
206A PRO 3.8 0.2 - - - +
208A LEU* 1.3 71.9 - - - +
210A ARG* 1.3 60.8 + - - +
212A LEU* 3.2 7.5 + - - +
213A GLN 3.0 23.7 + - - -
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Residues in contact with ARG 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 4.0 14.5 - - - +
206A PRO 2.9 18.0 + - - +
207A GLY* 3.6 8.1 - - - +
209A LEU* 1.3 74.0 - - - +
211A SER* 1.3 61.9 + - - +
213A GLN* 3.2 14.7 + - - +
214A ASP* 2.9 48.0 + - - +
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Residues in contact with SER 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLY 3.1 12.6 + - - -
208A LEU* 2.8 25.1 + - - +
210A ARG* 1.3 76.8 - - - +
212A LEU* 1.3 62.4 + - - +
214A ASP* 3.6 11.8 - - - +
215A LEU* 3.0 27.4 + - - +
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Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 4.1 10.1 - - + -
16A LEU* 3.9 26.0 - - + -
19A MET* 4.7 2.2 - - + -
20A GLN* 3.8 16.2 - - - +
112A LEU* 4.7 9.9 - - + -
116A TYR* 3.7 46.2 - - + -
208A LEU* 3.1 9.3 + - + +
209A LEU* 3.2 8.9 + - + +
211A SER* 1.3 81.5 + - - +
213A GLN* 1.3 55.2 - - - +
215A LEU* 3.3 6.1 + - + +
216A HIS* 2.9 62.4 + - + +
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Residues in contact with GLN 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 4.4 4.6 + - - -
2A GLY* 3.2 13.5 - - - -
3A PHE* 2.8 64.6 + - + +
4A SER 4.6 1.2 + - - -
209A LEU 3.0 9.2 + - - +
210A ARG* 3.2 17.7 + - - +
212A LEU* 1.3 75.7 - - - +
214A ASP* 1.3 62.1 + - - +
216A HIS* 3.1 2.1 + - - +
217A GLU* 2.8 63.4 + - + +
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Residues in contact with ASP 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ARG* 2.9 47.3 + - - +
211A SER* 3.6 11.3 - - - +
213A GLN* 1.3 73.4 - - - +
215A LEU* 1.3 59.3 + - + +
217A GLU* 3.3 9.6 + - - +
218A GLU* 2.9 29.9 + - - +
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Residues in contact with LEU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.3 20.2 - - + -
211A SER 3.0 17.0 + - - +
212A LEU* 3.4 9.4 - - + +
214A ASP* 1.3 78.4 - - + +
216A HIS* 1.3 59.2 + - - +
218A GLU* 3.2 12.1 + - + +
219A MET* 2.8 54.7 + - + +
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Residues in contact with HIS 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 4.7 8.1 - + + -
19A MET* 3.5 32.4 - - + +
20A GLN* 4.0 14.4 - - + +
23A GLU* 3.1 28.2 + - - -
109A ARG* 3.7 15.1 + - + -
112A LEU* 5.3 4.3 - - + -
212A LEU* 2.9 49.8 + - + +
213A GLN* 3.7 6.3 - - - +
215A LEU* 1.3 74.6 - - - +
217A GLU* 1.3 63.2 + - + +
219A MET* 3.2 20.3 + - + +
220A ALA* 2.8 26.9 + - - +
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Residues in contact with GLU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLN* 2.8 51.5 + - + +
214A ASP* 3.9 8.3 - - - +
216A HIS* 1.3 77.9 - - + +
218A GLU* 1.3 62.6 + - - +
220A ALA* 3.1 11.5 + - + +
221A CYS* 3.1 20.4 + - - +
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Residues in contact with GLU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ASP 2.9 17.7 + - - +
215A LEU* 3.5 13.9 - - + +
217A GLU* 1.3 75.1 - - - +
219A MET* 1.3 59.2 + - + +
221A CYS* 3.0 18.4 + - - +
222A ILE* 2.9 47.1 + - + +
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Residues in contact with MET 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 3.8 22.5 - - + +
108A GLU* 5.5 4.9 - - - -
109A ARG* 3.6 57.3 + - + +
112A LEU* 5.5 4.7 - - + -
215A LEU* 2.8 39.5 + - + +
216A HIS* 3.2 36.1 + - + +
218A GLU* 1.3 79.3 - - + +
220A ALA* 1.3 61.3 + - - +
222A ILE* 3.3 13.4 + - + +
223A LEU* 2.9 24.1 + - - +
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Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 5.1 1.1 - - - +
216A HIS 2.8 13.2 + - - +
217A GLU* 3.1 14.1 + - + +
219A MET* 1.3 76.7 - - - +
221A CYS* 1.3 56.7 - - - +
223A LEU* 3.4 8.5 + - - +
224A LYS* 3.0 27.5 + - - +
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Residues in contact with CYS 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLU 3.1 9.8 + - - +
218A GLU* 3.0 23.7 + - - +
220A ALA* 1.3 74.9 - - - +
222A ILE* 1.3 65.6 + - - +
224A LYS* 3.2 10.5 + - - +
225A GLU* 3.0 40.1 + - - +
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Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LYS* 5.9 2.0 - - + +
105A LEU* 4.3 17.3 - - + -
218A GLU* 2.9 38.3 + - + +
219A MET* 3.6 21.1 - - + +
221A CYS* 1.3 78.3 - - - +
223A LEU* 1.3 57.8 + - - +
225A GLU* 3.2 9.8 + - - +
226A ILE* 2.9 44.5 + - + +
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Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 5.0 5.4 - - + -
27A LEU* 3.5 33.9 - - + -
30A MET* 3.6 32.8 - - + -
102A LEU* 4.2 6.1 - - + -
105A LEU* 4.2 11.2 - - + +
109A ARG* 6.2 1.8 - - - +
219A MET 2.9 17.0 + - - +
220A ALA* 3.6 7.4 - - - +
222A ILE* 1.3 74.5 - - - +
224A LYS* 1.3 60.6 + - - +
226A ILE* 3.1 11.5 + - + +
227A LEU* 2.9 36.1 + - + +
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Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ALA 3.0 13.8 + - - +
221A CYS* 3.2 14.3 + - - +
223A LEU* 1.3 76.5 - - - +
225A GLU* 1.3 60.4 + - + +
227A LEU* 3.2 10.1 + - - +
228A GLN* 2.9 62.8 + - + +
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Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A CYS* 3.0 26.5 + - - +
222A ILE* 3.2 10.3 + - - +
224A LYS* 1.3 80.6 - - + +
226A ILE* 1.3 54.8 + - - +
228A GLN* 3.9 17.6 - - - +
229A GLU* 2.9 31.4 + - - +
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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
----------------------------------------------------------
30A MET* 5.1 0.2 - - - -
34A MET* 4.0 16.2 - - + -
98A PRO* 3.8 26.4 - - + +
101A LYS* 4.2 24.0 - - + +
102A LEU* 3.9 24.0 - - + +
105A LEU* 3.8 28.0 - - + -
222A ILE* 2.9 27.9 + - + +
223A LEU* 3.1 17.9 + - + +
225A GLU* 1.3 74.1 - - - +
227A LEU* 1.3 58.8 + - - +
229A GLU* 3.4 7.0 + - - +
230A TYR* 2.9 26.2 + - - +
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A MET* 3.5 41.7 - - + -
33A TRP* 5.4 7.0 - - + -
34A MET* 4.1 11.2 - - + -
223A LEU* 2.9 25.3 + - + +
224A LYS* 3.7 7.4 - - - +
226A ILE* 1.3 77.2 - - - +
228A GLN* 1.3 58.4 + - + +
230A TYR* 3.2 8.7 + - + +
231A LEU* 3.0 37.6 + - + +
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Residues in contact with GLN 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LYS* 2.9 49.3 + - + +
225A GLU* 3.9 20.2 - - - +
227A LEU* 1.3 76.2 - - + +
229A GLU* 1.3 63.4 + - - +
231A LEU* 3.3 14.2 + - + +
232A GLU* 3.0 37.3 + - + +
----------------------------------------------------------
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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
----------------------------------------------------------
97A GLY* 4.5 4.0 - - - -
98A PRO* 3.8 22.4 - - + +
101A LYS* 2.7 40.4 + - - +
225A GLU 2.9 19.8 + - - +
226A ILE* 3.7 5.3 - - - +
228A GLN* 1.3 76.8 - - - +
230A TYR* 1.3 61.8 + - - +
232A GLU* 3.4 12.5 + - - +
233A ILE* 3.0 45.5 + - + +
----------------------------------------------------------
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Residues in contact with TYR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 3.4 42.1 - + - -
34A MET* 3.6 27.6 - - + -
37A ARG* 3.1 39.0 + - + +
94A LEU* 3.5 38.8 - - + -
98A PRO* 4.0 9.5 - - + +
226A ILE 2.9 14.2 + - - +
227A LEU* 3.3 11.7 - - + +
229A GLU* 1.3 76.4 - - - +
231A LEU* 1.3 79.8 - - + +
233A ILE* 3.8 1.8 - - - +
234A SER* 2.8 46.1 + - - -
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Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 5.8 0.7 - - + -
227A LEU* 3.0 23.7 + - + +
228A GLN* 3.3 14.3 + - + +
230A TYR* 1.3 98.0 - - + +
232A GLU* 1.3 59.0 + - + +
234A SER* 3.7 4.8 + - - +
235A SER* 3.1 31.7 + - - -
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Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLN* 3.0 29.5 + - - +
229A GLU* 3.7 11.7 - - - +
231A LEU* 1.3 75.4 - - + +
233A ILE* 1.3 62.0 + - + +
235A SER* 3.9 3.2 - - - -
238A GLN* 2.8 30.3 + - - +
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Residues in contact with ILE 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A HIS* 3.2 50.1 + - + +
93A ASP* 3.5 42.0 - - + +
94A LEU* 3.7 7.6 - - + +
97A GLY* 5.2 0.2 - - - -
98A PRO* 3.6 22.7 - - + -
229A GLU* 3.0 28.7 + - + +
230A TYR* 3.9 3.6 - - - +
232A GLU* 1.3 78.4 - - + +
234A SER* 1.3 57.1 + - - +
238A GLN* 3.3 9.0 + - - +
----------------------------------------------------------
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Residues in contact with SER 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 3.3 37.9 + - - -
41A ASP* 4.5 3.8 - - - -
90A HIS* 3.9 9.4 + - - -
94A LEU* 4.4 10.5 - - - -
230A TYR* 2.8 45.8 + - - -
231A LEU* 3.7 5.5 + - - +
233A ILE* 1.3 77.2 - - - +
235A SER* 1.3 66.6 + - - +
236A LEU* 3.2 7.3 + - - +
----------------------------------------------------------
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Residues in contact with SER 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A HIS* 3.2 9.8 - - - -
231A LEU 3.1 19.8 + - - -
232A GLU* 3.9 3.6 - - - -
233A ILE 3.4 1.6 - - - -
234A SER* 1.3 75.1 - - - +
236A LEU* 1.3 57.5 + - - +
237A VAL* 3.1 27.0 + - - +
238A GLN* 2.6 47.5 + - - +
241A VAL* 4.0 0.3 - - - +
----------------------------------------------------------
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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