Contacts of the helix formed by residues 213 - 233 (chain E) in PDB entry 1UW9
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 ARG 213 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E SER* 3.5 14.2 + - - +
209E GLN* 3.4 29.2 + - - +
210E PRO* 3.5 20.9 + - - +
212E MET* 1.3 75.0 - - - +
214E TRP* 1.3 67.8 + - + +
215E ARG* 3.3 3.4 + - + +
216E ASP* 3.3 24.2 + - - +
217E ARG* 3.2 18.4 + - - +
146H LYS* 5.1 0.2 - - - +
149H VAL 5.3 5.6 + - - -
152H PRO 5.6 0.7 - - - +
285H ARG* 3.6 45.4 - - - +
372H PRO* 6.0 3.8 - - - +
109K GLU* 5.4 0.8 - - - +
110K GLU* 2.8 43.6 + - - -
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Residues in contact with TRP 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E ASN 3.5 18.6 - - - +
208E SER* 3.0 27.8 + - - -
212E MET 3.9 0.4 + - - -
213E ARG* 1.3 72.9 - - + +
215E ARG* 1.3 92.8 + - + +
217E ARG* 3.1 20.1 + - - +
218E PHE* 2.8 50.2 + + + -
241E ASN 5.5 0.2 - - - +
249E GLU* 3.9 8.3 + - - -
252E LYS* 3.8 28.2 - - + +
253E ARG* 3.5 50.0 - - + +
256E SMC 3.6 40.6 - - + -
285H ARG* 6.4 0.2 - - - +
286H ASP* 5.2 11.2 + - - -
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Residues in contact with ARG 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E ARG* 3.4 2.5 - - + +
214E TRP* 1.3 111.4 - - + +
216E ASP* 1.3 67.2 + - - +
218E PHE* 3.4 2.3 + - - +
219E LEU* 3.1 47.7 + - + +
256E SMC 3.8 29.2 - - - +
161H LYS* 5.0 2.9 - - - +
258H LYS* 4.6 3.2 - - - +
285H ARG* 3.7 22.2 - - - +
286H ASP* 3.0 26.2 + - - +
287H ASN* 3.4 20.8 + - - +
288H GLY* 3.5 20.0 - - - +
63J VAL* 3.8 27.1 + - - +
65J CYS* 4.9 2.4 + - - +
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Residues in contact with ASP 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E ALA* 3.6 19.5 - - + -
213E ARG* 3.3 25.4 + - - +
214E TRP 3.3 0.2 - - - -
215E ARG* 1.3 78.5 - - - +
217E ARG* 1.3 61.9 + - - +
219E LEU* 3.3 3.6 + - - +
220E PHE* 3.1 29.4 + - + -
152H PRO 4.9 3.9 - - - +
153H HIS* 3.4 12.3 + - - -
157H VAL* 3.5 31.9 - - + +
161H LYS* 3.0 32.9 + - - +
285H ARG* 6.1 1.5 - - - -
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Residues in contact with ARG 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E ALA* 3.6 10.2 - - - +
185E TYR* 3.7 13.2 - - + -
202E ASP* 2.7 40.2 + - - -
206E VAL* 3.4 20.6 + - - +
207E ASN* 2.7 33.7 + - - +
212E MET* 3.6 39.8 + - - +
213E ARG 3.2 3.8 + - - +
214E TRP* 3.1 18.4 + - - +
216E ASP* 1.3 77.5 - - - +
218E PHE* 1.3 84.1 + - - +
220E PHE 3.8 0.2 - - - -
221E VAL* 2.8 43.3 + - + +
240E LEU* 4.6 2.0 - - + +
241E ASN 4.1 4.8 + - - -
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Residues in contact with PHE 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E TRP* 2.8 58.4 + + + +
215E ARG* 3.7 6.1 - - - +
216E ASP 3.4 0.2 - - - -
217E ARG* 1.3 88.4 - - - +
219E LEU* 1.3 53.8 + - - +
221E VAL* 3.9 1.0 - - - +
222E THR* 2.7 39.3 + - - -
240E LEU* 3.6 48.7 - - + +
241E ASN 3.4 27.4 - - - -
242E ALA* 4.9 0.7 - - - -
253E ARG* 3.3 28.0 - - + -
256E SMC 3.8 21.1 - - - -
257E ALA* 4.3 7.9 - - + -
260E LEU* 4.1 5.2 - - + -
265E ILE* 5.3 0.9 - - + -
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Residues in contact with LEU 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E ARG* 3.1 44.4 + - - +
216E ASP* 3.6 9.2 - - - +
218E PHE* 1.3 78.0 - - - +
220E PHE* 1.3 64.7 + - + +
222E THR* 3.2 7.2 + - - -
223E GLU* 3.1 18.2 + - - +
256E SMC 4.5 2.9 - - + -
260E LEU* 4.0 28.5 - - + -
161H LYS* 4.9 13.9 - - - +
63J VAL 4.7 3.6 - - - +
65J CYS 3.5 24.9 - - - +
66J LEU 3.9 17.0 - - - +
67J TYR* 4.0 20.7 - - + -
71J ARG* 5.1 2.6 + - - +
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Residues in contact with PHE 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E ALA* 3.6 19.7 - - + +
183E LYS* 3.5 30.5 - - + -
186E GLY* 4.2 2.5 - - - -
216E ASP* 3.1 26.6 + - + +
217E ARG 4.1 0.9 - - - +
219E LEU* 1.3 75.1 - - + +
221E VAL* 1.3 65.6 + - - +
223E GLU* 3.3 3.8 + - - -
224E ALA* 3.1 18.4 + - - +
157H VAL* 5.1 4.0 - - + -
160H ASP* 3.6 44.9 - - + -
161H LYS* 3.7 24.2 - - + -
71J ARG* 4.3 24.2 - - + -
72J TYR* 3.3 41.2 - + - +
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Residues in contact with VAL 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E TYR* 4.2 15.9 - - + -
186E GLY* 4.4 7.0 - - - +
189E VAL* 4.2 12.8 - - + -
217E ARG* 2.8 36.4 + - + +
218E PHE 3.9 2.2 - - - +
220E PHE* 1.3 76.0 - - - +
222E THR* 1.3 58.8 + - - +
224E ALA* 3.1 8.7 + - - +
225E ILE* 2.8 35.4 + - + +
238E HIS* 3.5 40.6 - - + +
240E LEU* 3.8 14.8 - - + -
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Residues in contact with THR 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E PHE 2.7 24.0 + - - -
219E LEU* 3.2 8.3 + - - -
221E VAL* 1.3 76.5 - - - +
223E GLU* 1.3 62.8 + - - +
225E ILE* 3.3 10.3 + - - +
226E TYR* 3.1 51.6 + - + -
240E LEU* 4.8 3.3 - - - +
260E LEU* 3.4 19.2 - - + +
262E VAL* 3.5 17.3 - - + +
60J PHE* 4.1 12.1 - - + -
67J TYR* 4.1 10.3 - - + -
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Residues in contact with GLU 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E LEU 3.1 10.1 + - - +
220E PHE* 3.3 10.9 + - - +
222E THR* 1.3 75.5 - - - +
224E ALA* 1.3 57.6 + - - +
226E TYR* 3.5 1.6 + - - +
227E LYS* 3.0 31.5 + - + +
67J TYR* 3.4 24.9 + - + +
68J TYR 3.2 17.9 - - - +
69J ASP* 4.4 6.1 - - - +
70J ASN 3.6 4.8 + - - +
71J ARG* 2.9 45.1 + - - +
72J TYR* 2.9 46.7 + - + +
1141J EDO 5.3 0.8 - - - -
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Residues in contact with ALA 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E GLY 3.2 27.8 - - - +
189E VAL* 3.8 8.7 - - + -
190E TYR* 3.6 23.4 - - + +
193E LEU* 4.4 2.2 - - - +
220E PHE 3.1 10.4 + - - +
221E VAL 3.1 10.1 + - - +
223E GLU* 1.3 73.4 - - - +
225E ILE* 1.3 65.1 + - - +
227E LYS* 3.4 3.3 + - - +
228E ALA* 3.0 26.2 + - - +
72J TYR* 4.4 5.3 - - + -
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Residues in contact with ILE 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E VAL* 4.9 0.4 - - + -
193E LEU* 3.9 13.9 - - + +
221E VAL* 2.8 30.1 + - + +
222E THR* 3.3 5.1 + - - +
224E ALA* 1.3 73.5 - - - +
226E TYR* 1.3 75.1 + - + +
228E ALA* 3.4 2.1 + - - +
229E GLN* 2.9 30.4 + - - +
236E LYS* 3.5 30.2 - - + +
237E GLY* 4.3 1.1 - - - -
238E HIS* 3.7 42.0 - - + +
240E LEU* 5.3 1.1 - - + -
262E VAL* 4.0 28.0 - - + -
263E PRO* 4.7 4.7 - - + -
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Residues in contact with TYR 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E THR* 3.1 37.4 + - + +
223E GLU 4.1 1.8 - - - +
225E ILE* 1.3 90.9 - - + +
227E LYS* 1.3 66.3 + - - +
229E GLN* 3.9 18.0 - - - +
230E ALA* 3.1 18.4 + - - +
260E LEU 2.7 23.8 + - - -
261E GLY 3.2 12.5 - - - -
262E VAL* 3.6 8.2 + - + -
263E PRO* 5.7 0.7 - - + -
54F ASN* 5.8 2.0 - - - -
68F TYR* 5.4 3.6 - + - -
56J SER* 3.6 34.8 - - - +
59J ARG* 3.0 39.3 + - - -
60J PHE* 4.0 9.2 - + - -
67J TYR* 3.8 3.6 - - - +
69J ASP* 4.7 0.2 - - - +
1141J EDO 3.4 14.6 - - - -
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Residues in contact with LYS 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E TYR* 3.5 45.6 + - + -
223E GLU* 3.0 23.1 + - + +
224E ALA* 3.8 4.9 - - - +
226E TYR* 1.3 76.8 - - - +
228E ALA* 1.3 55.9 + - - +
230E ALA* 3.3 3.6 + - - +
231E GLU* 3.0 34.0 + - - +
49J LYS* 4.1 31.7 + - - +
70J ASN* 4.8 5.8 + - - +
72J TYR* 3.3 40.0 + - + +
73J TRP* 4.3 6.7 - - - +
74J THR* 4.5 2.9 + - - -
1141J EDO 3.7 20.3 + - - +
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Residues in contact with ALA 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E TYR* 3.9 12.5 - - + -
193E LEU* 3.5 31.2 - - + -
194E ARG* 3.8 14.4 - - - +
224E ALA 3.0 17.4 + - - +
225E ILE 3.9 2.7 - - - +
227E LYS* 1.3 74.8 - - - +
229E GLN* 1.3 58.1 + - - +
231E GLU* 3.7 4.9 - - - +
232E THR* 2.8 36.8 + - - +
236E LYS* 4.1 4.0 - - + -
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Residues in contact with GLN 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E ILE* 2.9 21.6 + - - +
226E TYR* 3.9 16.7 - - - +
228E ALA* 1.3 76.3 - - - +
230E ALA* 1.3 57.1 + - - +
233E GLY* 2.8 30.3 + - - -
234E GLU 3.2 22.7 - - - +
235E VAL* 3.4 14.0 - - - +
236E LYS* 3.0 37.0 + - + +
52F VAL* 3.4 26.0 - - + +
54F ASN* 4.9 4.5 + - - +
68F TYR* 3.5 23.0 + - - -
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Residues in contact with ALA 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E TYR 3.1 18.2 + - - +
227E LYS 3.8 3.1 - - - +
229E GLN* 1.3 78.6 - - - +
231E GLU* 1.3 62.4 + - - +
233E GLY* 4.0 1.0 + - - -
10F LYS* 3.2 25.5 + - - -
49J LYS* 4.3 10.5 - - - +
1141J EDO 3.8 23.3 - - - +
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Residues in contact with GLU 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E TYR* 2.6 29.3 + - - -
194E ARG* 2.9 44.2 + - - +
227E LYS* 3.0 20.7 + - + +
228E ALA* 3.7 5.2 - - - +
229E GLN 3.3 0.2 - - - -
230E ALA* 1.3 79.9 - - - +
232E THR* 1.3 62.7 + - + +
4F TRP* 5.2 0.5 - - - -
5F THR 4.3 1.3 - - - +
6F PRO* 3.3 35.6 - - + +
9F ASN* 4.2 7.0 + - + +
10F LYS* 3.9 23.1 + - - +
49J LYS* 6.2 2.0 - - - +
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Residues in contact with THR 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E ARG* 3.5 35.7 - - + +
228E ALA 2.8 21.0 + - - +
231E GLU* 1.3 81.8 - - + +
233E GLY* 1.3 62.6 + - - +
234E GLU* 3.2 17.3 + - - -
236E LYS* 3.2 22.8 - - - +
9F ASN 4.7 3.8 - - - +
10F LYS* 3.6 6.2 - - - +
11F MET* 2.7 39.5 + - + +
17F TYR* 4.8 6.1 - - - +
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Residues in contact with GLY 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E GLN* 2.8 15.6 + - - -
230E ALA 4.0 2.3 + - - -
231E GLU 3.6 1.4 - - - -
232E THR* 1.3 77.5 - - - +
234E GLU* 1.3 60.4 + - - +
10F LYS* 4.1 5.8 - - - +
11F MET 4.7 2.7 - - - +
12F PHE* 6.0 0.2 - - - -
13F GLU* 5.9 0.3 - - - +
51F TYR* 3.9 32.2 - - - -
52F VAL* 4.8 15.8 + - - +
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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
------------------------------------------------------------
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