Contacts of the helix formed by residues 209 - 232 (chain A) in PDB entry 3HPD
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 GLU 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A THR* 1.3 79.5 + - - +
210A PRO* 1.3 71.4 - - + +
211A LEU* 3.4 3.4 - - + +
212A LYS* 3.2 14.1 + - + +
213A ALA 2.8 30.7 + - - -
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Residues in contact with PRO 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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88A PRO* 6.2 0.2 - - + -
115A ASP* 3.6 32.1 - - + +
116A VAL* 4.0 3.6 - - + -
161A THR* 3.4 18.6 - - - +
205A VAL* 4.0 22.2 - - + -
208A THR 3.6 1.8 - - - +
209A GLU* 1.3 100.8 - - + +
211A LEU* 1.3 62.3 + - - +
213A ALA* 4.2 0.4 - - + -
214A THR* 2.8 31.3 + - - -
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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
----------------------------------------------------------
161A THR* 3.5 11.2 + - + +
171A VAL* 3.6 39.4 - - + +
172A SER* 3.9 11.0 - - - -
173A ASP* 3.8 20.4 - - + +
175A ARG* 5.1 0.2 - - - +
176A ARG* 3.6 39.5 - - + +
178A PHE* 3.8 25.8 - - + -
209A GLU* 3.3 3.3 + - + +
210A PRO* 1.3 79.6 - - - +
212A LYS* 1.3 65.1 + - + +
215A THR* 2.8 29.8 + - - -
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Residues in contact with LYS 212 (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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3A PHE* 3.7 54.8 - - + +
7A ALA* 6.2 0.2 - - + -
176A ARG* 4.5 18.8 - - - +
178A PHE* 5.5 2.7 - - + -
208A THR* 3.8 21.3 - - + +
209A GLU* 3.2 10.5 + - + +
211A LEU* 1.3 79.6 - - + +
213A ALA* 1.3 57.5 + - - +
215A THR* 4.4 0.2 - - - -
216A SER* 2.6 38.4 + - - -
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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
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201A THR* 4.7 1.8 - - - +
204A PHE* 3.4 19.0 - - + +
205A VAL* 3.5 39.5 - - + +
208A THR* 3.6 12.3 - - + +
209A GLU 2.8 18.2 + - - +
210A PRO* 3.8 4.0 - - + +
211A LEU 3.3 0.2 - - - -
212A LYS* 1.3 77.9 - - - +
214A THR* 1.3 58.2 + - - +
216A SER* 3.3 2.2 + - - -
217A ALA* 3.0 24.7 + - - +
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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
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116A VAL* 3.3 34.2 - - + +
118A LYS* 5.4 4.0 - - + -
161A THR* 3.9 1.9 - - + +
163A ALA* 3.7 29.8 - - + -
171A VAL* 3.8 13.9 - - + -
201A THR* 3.7 17.8 - - - +
210A PRO 2.8 18.2 + - - -
213A ALA* 1.3 72.3 - - - +
215A THR* 1.3 66.6 + - - +
217A ALA* 3.2 3.1 + - - +
218A LEU* 3.0 28.5 + - + +
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Residues in contact with THR 215 (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 21.3 - - + -
4A ILE* 4.7 1.3 - - + -
171A VAL* 3.8 22.6 - - - +
178A PHE* 3.8 20.8 - - + +
180A VAL* 4.2 6.5 - - + -
211A LEU 2.8 23.1 + - - -
212A LYS 3.9 3.6 - - - -
214A THR* 1.3 75.4 - - - +
216A SER* 1.3 63.5 + - - +
218A LEU* 3.3 4.4 + - - +
219A VAL* 3.0 25.2 + - + +
260A VAL* 4.0 26.9 - - + -
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Residues in contact with SER 216 (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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3A PHE* 3.7 6.8 - - - -
4A ILE* 3.5 35.7 - - - +
7A ALA* 3.7 7.3 - - - +
204A PHE* 3.8 24.5 - - - -
212A LYS 2.6 23.6 + - - -
213A ALA 3.5 4.7 - - - -
215A THR* 1.3 78.4 - - - +
217A ALA* 1.3 56.2 + - - +
219A VAL* 3.4 1.0 + - - +
220A THR* 2.9 35.9 + - - -
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Residues in contact with ALA 217 (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 VAL* 4.2 7.7 - - + +
200A LEU* 4.3 6.2 - - + +
201A THR* 3.3 33.4 - - - +
204A PHE* 3.7 23.7 - - + -
213A ALA 3.0 12.8 + - - +
214A THR 3.2 5.6 + - - +
216A SER* 1.3 77.0 - - - +
218A LEU* 1.3 57.2 - - - +
220A THR* 3.9 0.9 - - - -
221A PHE* 2.9 32.2 + - - +
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Residues in contact with LEU 218 (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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118A LYS* 5.3 0.7 - - + -
163A ALA* 4.2 8.3 - - + -
165A THR* 4.0 14.8 - - + -
169A ASP* 3.8 32.2 - - + +
171A VAL* 3.4 34.5 - - + -
180A VAL* 4.1 19.6 - - + +
182A ASN 5.1 0.2 - - - +
197A VAL* 3.8 27.4 - - + -
214A THR* 3.0 25.4 + - + +
215A THR 3.7 4.0 - - - +
217A ALA* 1.3 74.4 - - - +
219A VAL* 1.3 60.0 + - - +
221A PHE* 4.2 2.3 - - - +
222A GLY* 2.9 27.0 + - - -
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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
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4A ILE* 3.7 35.9 - - + -
180A VAL* 4.0 18.6 - - + -
182A ASN* 3.8 10.8 - - - +
215A THR 3.0 21.0 + - - +
216A SER 3.9 2.9 - - - +
218A LEU* 1.3 72.4 - - - +
220A THR* 1.3 68.6 + - - +
222A GLY* 3.3 0.3 + - - -
223A ILE* 2.9 49.0 + - + +
254A ILE* 5.0 1.1 - - + -
258A ALA* 4.1 9.9 - - + -
260A VAL* 3.9 22.4 - - + -
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Residues in contact with THR 220 (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 ILE* 4.3 10.0 - - - +
8A LEU* 4.7 5.5 - - + +
37A LEU* 4.0 26.9 - - + -
200A LEU* 5.7 1.3 - - + -
204A PHE* 3.7 15.2 - - + -
216A SER 2.9 21.4 + - - -
217A ALA 3.9 2.7 - - - -
219A VAL* 1.3 79.7 - - - +
221A PHE* 1.3 58.2 + - - +
223A ILE* 3.8 2.4 - - - +
224A ALA* 3.0 25.8 + - - +
246A LEU* 4.2 8.1 - - + -
249A ILE* 3.8 34.2 - - + +
254A ILE* 4.8 4.3 - - - +
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Residues in contact with PHE 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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187A LEU* 3.8 41.3 - - + -
193A THR* 3.9 14.4 - - + -
196A MET* 3.8 35.4 - - + -
197A VAL* 3.4 29.2 - - + -
200A LEU* 3.7 22.2 - - + -
217A ALA 2.9 18.8 + - - +
218A LEU 4.2 2.0 - - - +
220A THR* 1.3 76.1 - - - +
222A GLY* 1.3 62.3 + - - +
224A ALA* 3.2 6.0 + - + +
225A ALA* 2.9 25.1 + - - +
242A LEU* 4.3 13.7 - - + -
246A LEU* 4.2 17.9 - - + -
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Residues in contact with GLY 222 (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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182A ASN* 3.8 6.3 - - - -
183A GLY* 3.3 35.4 + - - -
187A LEU* 5.7 0.9 - - - -
218A LEU 2.9 20.1 + - - -
219A VAL 3.8 0.4 - - - -
221A PHE* 1.3 80.7 - - - +
223A ILE* 1.3 61.1 + - - +
225A ALA* 3.3 5.0 + - - +
226A GLU* 3.1 17.3 + - - +
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Residues in contact with ILE 223 (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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182A ASN* 3.8 18.6 - - - +
219A VAL* 2.9 36.5 + - + +
220A THR 3.8 4.0 - - - +
222A GLY* 1.3 73.0 - - - +
224A ALA* 1.3 67.4 + - - +
226A GLU* 3.1 9.3 + - - +
227A LYS* 2.9 27.5 + - + +
249A ILE* 3.9 13.0 - - + -
253A VAL* 3.7 27.4 - - + -
254A ILE* 4.0 19.1 - - + -
257A TYR* 3.8 13.0 - - + -
258A ALA* 3.7 23.6 - - - +
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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
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220A THR 3.0 15.4 + - - +
221A PHE* 3.2 9.6 + - + +
223A ILE* 1.3 77.3 - - - +
225A ALA* 1.3 57.0 + - - +
227A LYS* 3.4 2.2 + - - +
228A ALA* 2.8 31.2 + - - +
242A LEU* 4.1 9.9 - - + +
245A TRP* 3.9 28.7 - - + +
246A LEU* 3.9 26.7 - - + +
249A ILE* 4.9 2.0 - - + +
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Residues in contact with ALA 225 (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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183A GLY* 4.3 0.2 - - - -
184A HIS* 4.1 14.0 - - + +
187A LEU* 3.9 37.2 - - + -
221A PHE 2.9 12.4 + - - +
222A GLY 3.4 10.5 - - - +
223A ILE 3.1 0.2 - - - -
224A ALA* 1.3 74.5 - - - +
226A GLU* 1.3 65.7 + - - +
229A TYR* 3.0 21.0 + - - +
238A PHE* 3.3 10.2 - - + -
242A LEU* 3.7 11.8 - - + +
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Residues in contact with GLU 226 (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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181A TYR 4.7 0.3 - - - +
182A ASN* 2.9 32.6 + - - +
183A GLY 2.9 36.6 + - - +
184A HIS* 4.6 8.7 - - + -
222A GLY 3.1 6.7 + - - +
223A ILE* 3.1 9.5 + - - +
225A ALA* 1.3 76.1 - - - +
227A LYS* 1.3 62.6 + - - +
229A TYR* 3.3 5.6 + - - +
230A GLU* 3.1 27.3 + - - +
257A TYR* 3.7 27.5 - - + +
259A LYS* 4.6 12.5 - - - +
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Residues in contact with LYS 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 ILE* 2.9 31.6 + - + +
224A ALA* 3.7 2.0 - - - +
226A GLU* 1.3 72.5 - - - +
228A ALA* 1.3 65.7 + - - +
230A GLU* 2.9 39.8 + - - +
231A GLU* 3.5 6.1 + - - +
245A TRP* 3.4 68.7 + - + -
253A VAL* 4.4 5.8 - - + +
257A TYR* 3.2 41.6 + - + -
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Residues in contact with ALA 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 2.8 19.0 + - - +
225A ALA 3.7 4.3 - - - +
226A GLU 3.3 0.2 - - - -
227A LYS* 1.3 76.0 - - - +
229A TYR* 1.3 59.2 + - - +
231A GLU* 3.0 5.4 + - - +
232A ALA* 2.8 29.3 + - - +
238A PHE* 3.7 17.7 - - + +
241A LYS* 3.5 37.4 - - + +
242A LEU* 3.9 6.5 - - + -
245A TRP* 3.9 4.2 - - - +
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Residues in contact with TYR 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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184A HIS* 3.2 47.7 - + + -
186A LEU* 3.7 21.1 - - + -
225A ALA 3.0 17.2 + - - +
226A GLU 3.7 5.2 - - - +
228A ALA* 1.3 76.2 - - - +
230A GLU* 1.3 64.8 + - + +
231A GLU 3.1 0.7 + - - -
232A ALA 3.3 18.9 + - - +
233A LYS* 2.9 64.1 + - + +
238A PHE* 3.7 5.5 - - + -
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Residues in contact with GLU 230 (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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226A GLU* 3.1 17.7 + - - +
227A LYS* 2.9 37.9 + - - +
228A ALA 3.2 0.6 - - - -
229A TYR* 1.3 78.0 - - + +
231A GLU* 1.3 60.5 + - + +
233A LYS* 3.0 17.7 + - - +
257A TYR* 2.6 33.3 + - - -
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Residues in contact with GLU 231 (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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227A LYS 3.5 6.2 + - - +
228A ALA 3.0 7.2 + - - +
230A GLU* 1.3 84.9 - - + +
232A ALA* 1.3 58.6 + - - +
233A LYS* 4.4 2.7 - - - -
241A LYS* 3.0 43.1 + - + +
244A ASP* 5.3 1.2 - - - +
245A TRP* 2.7 36.3 + - + +
248A ARG* 4.2 9.2 + - - -
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Residues in contact with ALA 232 (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 2.8 11.2 + - - +
229A TYR* 3.3 25.3 + - - -
231A GLU* 1.3 78.5 - - - +
233A LYS* 1.3 61.6 + - - +
234A TYR* 3.4 0.8 + - - -
237A SER* 3.5 23.3 - - - +
238A PHE* 3.5 36.2 - - - +
241A LYS* 4.0 7.2 - - + -
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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
------------------------------------------------------------
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