Contacts of the helix formed by residues 203 - 233 (chain A) in PDB entry 3L6D
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 PRO 203 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASP* 5.3 3.1 - - - +
201A GLY 3.6 8.4 - - - +
202A LEU* 1.3 83.5 - - + +
204A VAL* 1.3 64.9 + - - +
205A SER* 3.2 15.1 + - - +
206A LYS* 4.5 15.7 - - + -
207A THR* 2.7 31.8 + - - +
171B GLU* 5.8 4.3 - - - +
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A VAL* 3.8 22.7 - - + +
198A ASP* 4.1 27.6 + - + +
202A LEU 3.4 1.8 + - - +
203A PRO* 1.3 71.3 - - - +
205A SER* 1.3 62.5 + - - +
206A LYS 3.1 1.7 + - - -
207A THR* 4.5 4.5 - - - +
208A ALA* 3.3 22.3 + - - +
230B LEU* 3.6 48.4 - - + +
231B GLU* 5.2 0.9 - - - +
233B GLN* 4.6 8.1 - - - +
290B THR* 4.5 8.3 - - + -
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Residues in contact with SER 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PRO* 4.0 13.2 - - - +
204A VAL* 1.3 78.9 - - - +
206A LYS* 1.3 71.3 + - - +
209A ARG 5.8 0.2 - - - -
230B LEU 4.7 2.0 + - - -
231B GLU* 3.6 41.5 - - - +
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Residues in contact with LYS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A PRO* 3.2 15.5 + - + +
204A VAL 3.2 0.2 - - - -
205A SER* 1.3 89.3 + - - +
207A THR* 1.3 67.0 + - - +
208A ALA 3.4 2.5 - - - -
209A ARG* 3.5 7.5 + - - +
210A LEU* 3.2 23.8 + - + +
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Residues in contact with THR 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A VAL* 5.8 6.7 - - - +
197A GLY* 5.1 4.9 - - - -
202A LEU* 3.4 42.2 - - + +
203A PRO* 2.7 28.3 + - - +
204A VAL* 4.6 1.8 - - - -
206A LYS* 1.3 77.5 - - - +
208A ALA* 1.3 60.0 + - - +
210A LEU* 3.7 5.5 - - + +
211A LEU* 2.8 35.4 + - + +
175B PHE* 4.1 16.6 - - + -
178B VAL* 5.1 3.8 - - + -
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Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 3.4 9.4 - - + -
194A VAL* 4.0 21.4 - - + +
204A VAL* 3.3 15.2 + - - +
207A THR* 1.3 76.5 - - - +
209A ARG* 1.3 64.3 + - - +
211A LEU* 3.3 0.9 + - - +
212A LEU* 3.0 21.0 + - - +
227B VAL* 3.9 14.4 - - + -
230B LEU* 3.6 34.8 - - + -
231B GLU* 5.9 1.3 - - + -
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Residues in contact with ARG 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL 4.9 0.2 + - - -
205A SER 5.7 0.2 + - - -
206A LYS* 3.5 9.4 + - - +
207A THR 3.3 0.6 - - - -
208A ALA* 1.3 79.5 - - - +
210A LEU* 1.3 62.6 - - - +
212A LEU* 3.2 5.4 + - + +
213A GLU* 2.9 54.8 + - - +
224B GLU* 2.8 31.7 + - - -
227B VAL* 3.7 25.5 - - + +
228B ARG* 4.7 9.7 - - - +
231B GLU* 3.0 43.2 + - - +
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Residues in contact with LEU 210 (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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206A LYS 3.2 16.3 + - - +
207A THR* 3.9 6.1 - - - +
209A ARG* 1.3 78.0 - - - +
211A LEU* 1.3 57.9 + - - +
213A GLU* 4.7 7.6 - - + +
214A THR* 2.7 46.9 + - - +
165B VAL* 4.8 23.1 - - + -
167B LEU* 4.4 17.9 - - + -
175B PHE* 3.6 33.7 - - + -
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 4.1 11.7 - - + -
193A ALA* 3.7 32.5 - - + +
194A VAL* 3.8 24.0 - - + +
207A THR* 2.8 23.0 + - + +
208A ALA 3.6 4.5 - - - +
210A LEU* 1.3 74.5 - - - +
212A LEU* 1.3 60.6 + - - +
215A SER* 2.8 30.3 + - - -
175B PHE* 3.4 22.8 - - + -
178B VAL* 3.8 9.0 - - + +
179B LEU* 3.3 40.2 - - + +
182B HIS* 4.6 5.6 - - + -
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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
----------------------------------------------------------
190A PHE* 3.8 12.9 - - + -
208A ALA 3.0 17.5 + - - +
209A ARG* 3.6 6.1 - - - +
211A LEU* 1.3 77.6 - - - +
213A GLU* 1.3 62.6 - - + +
215A SER* 3.5 4.9 + - - +
216A ARG* 3.0 40.1 + - + +
182B HIS* 5.4 0.9 - - - +
220B ALA* 5.1 2.7 - - - +
223B LEU* 3.6 34.3 - - + -
224B GLU* 3.5 45.1 - - + +
227B VAL* 3.9 16.8 - - + -
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Residues in contact with GLU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ARG* 2.9 57.8 + - - +
210A LEU* 4.1 8.3 + - + +
212A LEU* 1.3 80.2 - - + +
214A THR* 1.3 62.7 + - - +
215A SER 3.5 0.5 + - - -
216A ARG* 3.8 22.5 + - - +
217A PHE 5.0 1.2 + - - -
140B HIS* 3.5 21.4 + - + -
224B GLU* 5.0 3.3 - - - +
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Residues in contact with THR 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 2.7 39.8 + - - +
213A GLU* 1.3 76.7 - - - +
215A SER* 1.3 58.2 + - - +
217A PHE 5.3 0.6 + - - -
218A PHE* 4.7 3.5 + - - +
128B VAL* 4.3 14.0 - - + +
140B HIS* 3.7 45.3 + - + +
141B SER 5.5 1.1 - - - +
142B ILE* 4.9 6.5 - - + -
165B VAL* 5.5 4.0 - - + +
175B PHE* 4.0 9.8 - - + -
179B LEU* 3.8 28.3 - - + -
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Residues in contact with SER 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU 2.8 21.3 + - - -
212A LEU* 3.5 5.2 + - - +
214A THR* 1.3 79.6 - - - +
216A ARG* 1.3 67.2 + - - +
217A PHE 3.4 1.6 - - - -
218A PHE* 3.3 7.5 + - - +
219A VAL* 2.9 33.3 + - - +
128B VAL* 5.5 0.7 - - - -
179B LEU* 3.5 16.4 - - - -
182B HIS* 3.5 26.8 + - - -
183B ALA* 4.4 8.5 - - - -
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Residues in contact with ARG 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LEU* 3.0 25.8 + - + +
213A GLU* 3.8 16.2 + - - +
214A THR 3.6 1.6 - - - -
215A SER* 1.3 76.8 - - - +
217A PHE* 1.3 72.2 + - - +
219A VAL* 3.9 3.5 - - - +
220A ALA* 3.0 32.4 + - + +
138B GLU* 3.6 24.5 + - - +
140B HIS* 5.8 3.2 + - - -
163B HIS* 6.0 2.4 + - - -
220B ALA* 6.5 0.7 - - - -
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Residues in contact with PHE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLU 5.0 1.6 + - - -
214A THR 5.3 0.4 + - - -
215A SER 3.4 0.2 - - - -
216A ARG* 1.3 90.2 - - - +
218A PHE* 1.3 64.0 + - - +
220A ALA* 4.5 5.6 - - + -
221A ASP* 2.8 62.0 + - + +
128B VAL 6.2 0.2 - - - -
133B ASN* 4.1 20.6 - - + -
136B HIS* 3.7 33.2 - + - -
138B GLU* 3.7 54.5 - - + +
139B SER* 4.1 13.9 - - - -
140B HIS* 5.6 3.1 - - + -
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Residues in contact with PHE 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A THR 4.7 2.6 + - - +
215A SER* 3.3 10.8 + - - +
217A PHE* 1.3 84.4 - - - +
219A VAL* 1.3 58.5 + - - +
221A ASP* 4.0 3.7 - - - +
222A ALA* 3.0 30.1 + - - +
128B VAL* 3.4 40.8 - - + +
129B ALA* 3.8 20.4 - - - -
130B TYR* 3.5 43.0 - + - -
180B HIS* 5.0 5.4 - + - -
183B ALA* 3.8 31.2 - - + -
184B PHE* 4.0 25.1 - + - -
187B MSE 4.7 6.7 - - - -
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Residues in contact with VAL 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A SER* 2.9 26.6 + - - +
216A ARG* 3.9 3.4 - - - +
218A PHE* 1.3 74.8 - - + +
220A ALA* 1.3 62.4 + - - +
222A ALA* 3.0 6.4 + - - +
223A LEU* 2.8 50.4 + - + +
182B HIS* 5.0 5.4 - - - +
183B ALA* 3.7 40.4 - - + +
186B ALA* 4.3 18.6 - - + -
187B MSE 5.1 3.6 - - + -
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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
----------------------------------------------------------
216A ARG* 3.0 23.4 + - + +
217A PHE* 3.9 6.3 - - + +
219A VAL* 1.3 78.0 - - - +
221A ASP* 1.3 58.5 + - - +
223A LEU* 3.5 8.5 + - - +
224A GLU* 3.0 42.9 + - - +
212B LEU* 5.2 0.6 - - - +
216B ARG* 5.1 10.0 + - + +
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Residues in contact with ASP 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A PHE* 2.8 44.3 + - + +
218A PHE* 4.0 3.8 - - - +
220A ALA* 1.3 69.5 - - - +
222A ALA* 1.3 65.6 + - - +
224A GLU* 3.3 12.9 + - - +
225A GLU* 3.0 22.2 + - - +
130B TYR* 5.0 1.7 - - - -
132B ARG* 2.8 33.7 + - - -
133B ASN* 3.0 30.7 + - - +
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Residues in contact with ALA 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A PHE 3.0 19.8 + - - +
219A VAL 3.0 4.0 + - - +
221A ASP* 1.3 78.4 + - - +
223A LEU* 1.3 57.5 + - - +
225A GLU* 3.4 2.1 + - - +
226A ALA* 3.0 29.0 + - - +
130B TYR* 4.2 15.7 - - + -
132B ARG* 4.1 9.9 - - - +
187B MSE 3.8 36.3 - - + +
191B PHE* 6.3 0.2 - - - -
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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
----------------------------------------------------------
182A HIS* 4.6 17.3 - - + +
219A VAL* 2.8 38.9 + - + +
220A ALA* 4.0 4.9 - - - +
222A ALA* 1.3 72.9 - - - +
224A GLU* 1.3 56.2 + - - +
226A ALA* 3.5 5.0 + - - +
227A VAL* 3.0 33.1 + - - +
186B ALA* 4.6 1.1 - - + +
187B MSE 3.9 26.0 - - + +
190B PHE* 3.7 34.9 - - + -
191B PHE* 5.3 3.1 - - + -
212B LEU* 3.7 31.9 - - + -
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Residues in contact with GLU 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 29.4 + - - +
221A ASP* 3.3 10.6 + - - +
223A LEU* 1.3 73.9 - - - +
225A GLU* 1.3 56.6 + - - +
227A VAL* 3.4 4.8 + - - +
228A ARG* 3.1 26.3 + - - +
209B ARG* 5.1 3.5 + - - -
212B LEU* 4.0 19.9 - - + +
216B ARG* 3.8 20.3 + - - +
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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 ASP* 3.0 17.1 + - - +
222A ALA 3.7 3.1 - - - +
224A GLU* 1.3 73.8 - - - +
226A ALA* 1.3 61.1 + - - +
228A ARG* 2.7 50.5 + - - +
229A ARG* 2.8 51.3 + - - +
239A GLN* 5.5 1.7 + - - -
285A ASP* 5.7 1.1 - - - +
132B ARG* 3.6 39.3 + - - +
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Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ALA 3.0 17.7 + - - +
223A LEU* 3.6 8.3 - - - +
225A GLU* 1.3 77.3 - - - +
227A VAL* 1.3 57.0 + - - +
229A ARG* 3.3 4.7 + - - +
230A LEU* 2.9 37.8 + - + +
285A ASP* 5.4 0.4 - - - -
286A ILE* 6.3 0.4 - - + -
287A ALA* 4.1 13.6 - - + +
187B MSE 6.3 0.2 - - + -
190B PHE* 5.0 3.6 - - + -
191B PHE* 3.7 32.3 - - + -
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A LEU 3.0 20.5 + - - +
224A GLU* 3.6 7.0 - - - +
225A GLU 3.3 0.2 - - - -
226A ALA* 1.3 72.1 - - - +
228A ARG* 1.3 57.1 + - - +
230A LEU* 3.1 5.8 + - - +
231A GLU* 2.8 42.2 + - + +
190B PHE* 3.7 18.8 - - + -
208B ALA* 3.7 26.0 - - + +
209B ARG* 3.7 46.0 - - + +
212B LEU* 4.1 12.3 - - + -
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Residues in contact with ARG 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A GLU 3.1 14.3 + - - +
225A GLU* 2.7 45.6 + - - +
227A VAL* 1.3 75.7 - - - +
229A ARG* 1.3 79.6 + - - +
231A GLU* 3.4 11.6 + - - +
232A THR* 3.0 45.2 + - + +
234A ASP* 4.4 10.3 + - - -
209B ARG* 5.0 6.3 - - - +
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Residues in contact with ARG 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLU* 2.8 44.3 + - - +
226A ALA* 3.7 6.3 - - - +
228A ARG* 1.3 88.9 - - - +
230A LEU* 1.3 52.6 + - - +
232A THR* 3.8 5.4 - - - -
233A GLN* 2.7 32.1 + - - -
234A ASP* 3.0 51.5 + - - +
235A PHE* 4.9 4.3 - - + -
236A LYS 3.0 24.6 + - - +
238A ASP* 3.2 29.5 + - - -
239A GLN* 4.2 11.5 - - - +
285A ASP* 3.5 35.0 + - - +
287A ALA* 4.7 7.4 - - + -
----------------------------------------------------------
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Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ALA* 2.9 34.7 + - + +
227A VAL 3.1 4.0 + - - +
229A ARG* 1.3 72.3 - - - +
231A GLU* 1.3 59.6 + - - +
233A GLN* 2.9 25.4 + - - +
235A PHE* 3.8 28.7 - - + -
287A ALA* 3.9 8.1 - - + +
290A THR* 3.8 26.7 - - + +
190B PHE* 4.5 11.2 - - + -
191B PHE* 5.1 1.1 - - + -
194B VAL* 4.2 5.8 - - + -
204B VAL* 3.6 27.4 - - + +
205B SER* 3.6 11.1 + - - -
208B ALA* 3.8 25.6 - - + -
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Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A VAL* 2.8 24.4 + - + +
228A ARG* 3.8 8.3 - - - +
230A LEU* 1.3 78.8 - - + +
232A THR* 1.3 60.2 + - - +
233A GLN* 3.3 5.7 + - - +
205B SER* 3.4 33.2 - - - +
208B ALA* 5.7 1.1 - - + -
209B ARG* 2.9 66.2 + - + +
----------------------------------------------------------
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Residues in contact with THR 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ARG* 3.0 39.3 + - - +
229A ARG* 3.5 7.2 - - - +
231A GLU* 1.3 76.2 - - - +
233A GLN* 1.3 68.7 + - - +
234A ASP* 3.2 30.5 + - + +
----------------------------------------------------------
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Residues in contact with GLN 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ARG 2.7 10.1 + - - -
230A LEU* 2.9 30.3 + - - +
231A GLU 3.3 5.1 - - - +
232A THR* 1.3 80.3 - - - +
234A ASP* 1.3 56.7 + - - +
235A PHE* 3.7 35.3 + - - -
291A LYS* 5.5 1.0 - - - -
204B VAL* 5.2 7.3 - - - +
205B SER* 4.7 8.4 - - - +
----------------------------------------------------------
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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).
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