Contacts of the helix formed by residues 213 - 234 (chain E) in PDB entry 5MGX
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 THR 213 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211E MET 3.8 0.8 + - - -
212E LEU* 1.3 75.9 - - - +
214E GLY* 1.3 54.3 + - - +
215E GLN* 3.6 11.2 + - + +
216E GLU* 3.0 46.8 + - + +
217E ARG* 2.8 34.9 + - - +
257E VAL* 4.5 6.4 - - - +
263E GLU* 5.3 1.4 + - - -
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Residues in contact with GLY 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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213E THR* 1.3 74.2 + - - +
215E GLN* 1.4 56.5 + - - +
217E ARG* 3.3 5.3 + - - +
218E VAL* 3.0 33.4 + - - +
257E VAL* 5.0 0.6 - - - +
259E MET* 3.8 35.1 - - - +
263E GLU* 3.8 20.1 + - - -
267E LEU* 4.2 0.5 - - - +
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Residues in contact with GLN 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 THR* 3.3 10.0 - - + +
214E GLY* 1.4 74.7 - - - +
216E GLU* 1.4 57.1 + - + +
218E VAL* 3.6 11.5 + - + +
219E ALA* 3.2 26.2 + - - +
263E GLU* 3.7 11.3 + - - +
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Residues in contact with GLU 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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211E MET 4.7 1.2 - - - +
212E LEU* 3.8 26.1 - - + +
213E THR* 3.0 40.1 + - + +
215E GLN* 1.4 74.0 - - + +
217E ARG* 1.4 55.9 + - - +
219E ALA* 3.4 7.2 + - - +
220E LEU* 2.9 35.5 + - - +
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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
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209E LEU 2.8 25.1 + - - -
210E GLU 4.1 5.9 + - - -
212E LEU* 3.0 41.4 + - + +
213E THR 2.8 13.4 + - - +
214E GLY* 3.4 7.9 - - - +
216E GLU* 1.4 74.1 - - - +
218E VAL* 1.3 58.9 + - - +
220E LEU* 4.2 1.4 - - - +
221E ALA* 3.1 30.7 + - - +
250E ALA* 2.9 38.5 + - - +
251E ILE 3.6 13.9 - - - -
253E SER* 2.8 32.0 + - - -
254E SER* 4.0 13.0 - - - +
257E VAL* 4.3 4.4 - - - +
259E MET* 4.0 11.9 - - - -
267E LEU* 3.9 24.5 - - + -
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Residues in contact with VAL 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 GLY 3.0 21.9 + - - +
215E GLN* 3.6 11.7 - - + +
216E GLU 3.3 0.2 - - - -
217E ARG* 1.3 76.2 - - - +
219E ALA* 1.4 57.9 + - - +
221E ALA* 3.9 1.6 - - - +
222E ASN* 2.9 49.1 + - - +
263E GLU* 5.0 3.1 - - + +
266E GLN* 3.9 39.9 - - + +
267E LEU* 3.8 25.6 - - + -
270E LEU* 3.9 7.4 - - + +
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Residues in contact with ALA 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 GLN 3.2 17.7 + - - +
216E GLU* 3.7 7.9 - - - +
218E VAL* 1.4 75.6 - - - +
220E LEU* 1.3 63.4 + - - +
222E ASN* 3.8 5.4 + - - +
223E ARG* 3.2 22.9 + - - +
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Residues in contact with LEU 220 (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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146E THR* 5.4 4.9 - - - +
207E PRO* 4.5 14.1 - - + -
209E LEU* 3.7 29.8 - - + -
212E LEU* 4.0 15.3 - - + -
216E GLU 2.9 20.5 + - - +
217E ARG 4.2 3.1 - - - +
219E ALA* 1.3 70.0 - - - +
221E ALA* 1.4 65.5 + - - +
223E ARG* 3.2 12.1 + - + +
224E LYS* 3.0 51.7 + - + +
249E LYS* 5.5 2.2 - - - +
250E ALA* 4.1 12.6 - - + -
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Residues in contact with ALA 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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217E ARG 3.1 18.8 + - - +
218E VAL 3.9 2.2 - - - +
220E LEU* 1.4 75.3 - - - +
222E ASN* 1.3 57.6 + - - +
224E LYS 3.4 0.3 + - - -
225E ARG* 3.0 28.8 + - - +
247E ALA* 3.4 23.7 - - - +
250E ALA* 4.5 3.8 - - + +
251E ILE* 3.6 34.1 - - + -
270E LEU* 3.8 12.9 - - + +
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Residues in contact with ASN 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 VAL* 2.9 34.5 + - - +
219E ALA* 4.1 5.6 - - - +
221E ALA* 1.3 73.8 - - - +
223E ARG* 1.3 60.8 + - - +
225E ARG* 2.9 39.4 + - - +
226E GLU* 2.9 42.3 + - - +
266E GLN* 5.9 0.6 - - - +
270E LEU* 3.6 20.8 - - - +
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Residues in contact with ARG 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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143E LEU* 4.3 17.6 - - - +
144E VAL 3.8 22.3 + - - +
151E ASP* 5.1 5.8 + - - +
152E VAL* 4.3 10.3 - - - +
219E ALA 3.2 18.7 + - - +
220E LEU* 3.2 12.9 + - + +
222E ASN* 1.3 74.4 - - - +
224E LYS* 1.3 64.3 + - + +
226E GLU* 3.3 22.7 + - - +
227E CYS* 3.0 58.4 + - - +
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Residues in contact with LYS 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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146E THR* 3.4 10.7 + - - -
149E ASP* 2.8 29.4 + - - -
151E ASP* 2.8 39.9 + - - +
220E LEU* 3.0 39.8 + - + +
222E ASN 3.4 0.2 - - - -
223E ARG* 1.3 79.2 - - + +
225E ARG* 1.4 52.1 + - - +
227E CYS* 3.2 6.8 + - + +
228E GLY* 2.9 30.1 + - - -
243E SER* 3.6 17.8 - - - +
246E LEU* 4.4 16.6 - - + +
247E ALA* 3.6 31.4 - - + +
249E LYS* 5.2 4.9 - - - +
250E ALA* 5.6 0.7 - - + -
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Residues in contact with ARG 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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709C ASP* 3.1 41.9 + - - +
221E ALA 3.0 18.4 + - - +
222E ASN* 2.9 29.0 + - - +
223E ARG 3.3 0.2 - - - -
224E LYS* 1.4 75.3 - - - +
226E GLU* 1.3 82.1 + - - +
228E GLY 3.5 0.3 + - - -
229E ASN* 3.0 50.4 + - - +
244E TYR* 3.7 10.6 - - + -
247E ALA* 3.9 2.5 - - - +
270E LEU* 4.4 6.0 - - - +
273E LYS* 4.6 12.0 - - - +
274E CYS* 4.0 23.6 - - - -
277E ASN* 4.1 9.4 - - - +
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Residues in contact with GLU 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 ASN* 2.9 29.1 + - - +
223E ARG* 3.3 22.9 + - - +
225E ARG* 1.3 95.5 + - - +
227E CYS* 1.3 64.2 + - - +
229E ASN* 3.5 8.9 + - - +
230E ALA* 3.2 22.0 + - - +
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Residues in contact with CYS 227 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151E ASP* 3.3 45.5 - - - +
223E ARG* 3.0 52.5 + - - -
224E LYS* 3.4 11.0 - - - +
226E GLU* 1.3 73.4 - - - +
228E GLY* 1.3 64.9 + - - +
230E ALA* 3.1 17.6 + - - +
231E HIS* 3.1 18.9 + - - -
243E SER* 4.1 9.4 - - - +
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Residues in contact with GLY 228 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224E LYS 2.9 10.7 + - - -
225E ARG 3.5 0.2 + - - -
227E CYS* 1.3 74.4 - - - +
229E ASN* 1.4 56.5 + - - +
231E HIS* 3.3 1.4 + - - -
232E TYR 2.9 24.3 + - - -
240E ALA* 3.4 15.2 - - - +
243E SER* 3.5 20.3 - - - -
244E TYR* 3.3 25.3 + - - -
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Residues in contact with ASN 229 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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708C VAL* 3.5 14.3 + - - +
709C ASP 3.1 20.4 + - - -
225E ARG* 3.0 35.9 + - - +
226E GLU* 3.7 9.6 - - - +
227E CYS 3.2 0.2 - - - -
228E GLY* 1.4 74.5 - - - +
230E ALA* 1.4 55.3 + - - +
232E TYR* 3.2 2.1 + - - +
233E GLN* 3.0 43.0 + - - +
244E TYR* 2.7 25.2 + - - -
277E ASN* 3.1 16.3 + - - -
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Residues in contact with ALA 230 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151E ASP 6.0 0.9 - - - +
226E GLU 3.2 13.1 + - - +
227E CYS* 3.1 11.3 + - - +
229E ASN* 1.4 76.5 - - - +
231E HIS* 1.3 61.3 + - + +
233E GLN* 3.7 15.2 + - - +
234E ARG* 3.7 26.6 + - - +
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Residues in contact with HIS 231 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150E CYS 2.8 27.5 + - - -
151E ASP 3.6 10.4 + - - -
152E VAL 3.3 25.4 - - - -
227E CYS 3.1 17.6 + - - -
228E GLY* 3.3 6.5 + - - +
230E ALA* 1.3 73.2 - - + +
232E TYR* 1.3 58.0 + - - +
234E ARG* 2.9 32.5 + - - +
235E ALA 3.5 3.1 + - - -
236E ASP* 2.8 38.1 + - + +
239E LEU* 3.5 29.2 - - + +
240E ALA 3.5 13.9 - - - +
243E SER* 3.2 22.6 + - - -
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Residues in contact with TYR 232 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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705C MET 5.0 0.2 + - - -
706C GLU* 3.0 37.6 + - + -
708C VAL* 3.7 29.6 - - + -
228E GLY 2.9 16.6 + - - +
229E ASN* 3.5 5.4 - - - +
231E HIS* 1.3 74.3 - - - +
233E GLN* 1.4 67.6 + - - +
235E ALA* 3.0 20.8 + - - +
236E ASP 4.3 1.3 - - - -
237E PHE* 3.5 32.5 - + - -
240E ALA* 3.7 6.9 - - + +
244E TYR* 3.8 7.6 - - - +
280E ALA* 3.8 33.7 + - + +
281E SER* 3.5 20.0 - - - -
284E LYS* 4.5 12.7 + - - -
311E ARG* 5.0 0.5 + - - -
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Residues in contact with GLN 233 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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707C GLU* 6.0 3.6 - - - +
708C VAL* 3.4 24.5 - - - +
182E GLN* 4.5 6.6 - - - +
185E SER* 5.4 12.6 - - - +
229E ASN* 3.0 32.5 + - - +
230E ALA* 3.9 9.4 - - - +
231E HIS 3.5 0.2 - - - -
232E TYR* 1.4 80.9 - - - +
234E ARG* 1.3 58.3 + - + +
235E ALA* 3.3 1.4 + - - +
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Residues in contact with ARG 234 (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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152E VAL 3.7 11.2 + - - -
153E ILE* 5.4 0.2 - - - +
178E CYS 4.3 9.5 + - - -
179E TYR* 3.2 56.8 - - - +
181E PRO* 6.1 0.3 - - - +
182E GLN* 3.6 21.6 + - - +
183E GLY 3.2 22.7 - - - +
184E ARG* 4.9 5.2 - - - +
230E ALA* 3.7 15.0 + - - +
231E HIS* 2.9 52.9 + - - +
232E TYR 3.3 0.6 - - - -
233E GLN* 1.3 75.0 - - + +
235E ALA* 1.4 64.2 + - - +
236E ASP* 3.5 26.6 + - + +
239E LEU* 4.6 2.4 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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