Contacts of the helix formed by residues 226 - 248 (chain A) in PDB entry 3ETL
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 LYS 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A GLU 5.0 4.9 + - - +
221A PHE* 3.9 34.8 - - + +
223A GLY* 3.3 15.7 + - - +
225A GLY* 1.3 72.3 - - - +
227A LEU* 1.3 58.7 + - - +
228A ALA* 3.1 7.6 + - - +
229A GLU* 3.5 41.9 + - + +
230A ARG* 3.6 10.0 + - - +
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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
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221A PHE 5.7 1.3 - - - +
223A GLY 4.6 1.8 - - - -
224A ARG* 4.1 33.0 - - + +
225A GLY 3.0 5.3 + - - +
226A LYS* 1.3 75.3 - - - +
228A ALA* 1.3 63.8 + - + +
229A GLU 3.5 0.2 - - - -
230A ARG* 3.7 33.8 - - - +
231A GLN* 3.5 32.9 + - + +
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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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225A GLY 4.4 3.7 + - - +
226A LYS* 3.1 1.3 - - - +
227A LEU* 1.3 82.0 - - + +
229A GLU* 1.3 63.5 + - - +
230A ARG 3.2 1.6 - - - -
231A GLN* 3.5 6.0 + - - +
232A GLN* 3.1 22.7 + - - +
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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
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221A PHE* 3.6 18.7 - - + -
226A LYS* 3.5 40.2 + - + +
227A LEU 3.5 0.2 - - - -
228A ALA* 1.3 77.1 - - - +
230A ARG* 1.3 65.5 + - - +
232A GLN* 3.5 11.8 + - - +
233A LYS* 3.1 25.4 + - + +
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Residues in contact with ARG 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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214A THR* 5.0 7.1 + - - +
217A PHE* 4.3 22.7 + - + +
218A ARG* 4.0 42.2 - - - +
221A PHE* 3.9 50.5 + - + -
224A ARG* 5.8 4.4 - - - +
226A LYS 3.6 5.5 + - - +
227A LEU* 3.7 31.7 - - - +
229A GLU* 1.3 75.8 - - - +
231A GLN* 1.3 65.2 + - + +
232A GLN 3.2 0.3 + - - -
233A LYS* 3.2 3.9 + - - +
234A LEU* 2.9 40.6 + - + +
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Residues in contact with GLN 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 LEU* 3.5 33.8 + - + +
228A ALA* 3.9 6.7 - - - +
229A GLU 3.5 0.2 - - - -
230A ARG* 1.3 82.7 + - + +
232A GLN* 1.3 58.0 + - - +
234A LEU* 4.4 15.9 - - - +
235A GLY* 2.8 25.5 + - - -
279A GLY 3.1 43.7 + - - +
280A HIS* 5.1 0.9 - - - +
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Residues in contact with GLN 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 3.1 17.1 + - - +
229A GLU* 3.7 13.4 - - - +
230A ARG 3.1 0.4 - - - -
231A GLN* 1.3 75.2 - - - +
233A LYS* 1.3 66.0 + - - +
235A GLY* 3.2 1.9 + - - -
236A ARG* 3.0 47.8 + - + +
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Residues in contact with LYS 233 (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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185A SER* 2.6 28.7 + - - -
186A ASP* 2.8 30.3 + - - +
189A MET* 3.5 33.5 - - - +
217A PHE* 3.8 10.3 - - + -
220A GLU* 4.1 3.8 + - - -
221A PHE* 3.8 21.9 - - + -
229A GLU* 3.1 16.1 + - + +
230A ARG* 3.7 3.8 - - - +
232A GLN* 1.3 77.5 + - - +
234A LEU* 1.3 65.0 + - - +
236A ARG* 3.2 23.7 + - - +
237A HIS 3.1 17.0 + - - -
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Residues in contact with LEU 234 (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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213A LEU* 4.1 24.7 - - + +
214A THR* 4.1 18.8 - - + -
217A PHE* 3.4 47.3 - - + -
230A ARG* 2.9 26.8 + - + +
231A GLN* 4.2 13.5 - - - +
233A LYS* 1.3 78.0 - - - +
235A GLY* 1.3 62.5 + - - +
237A HIS* 3.3 4.8 + - - +
238A MET* 3.0 32.0 + - + +
279A GLY 6.0 0.2 - - - -
280A HIS* 4.3 24.9 - - + +
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Residues in contact with GLY 235 (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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231A GLN 2.8 21.5 + - - -
232A GLN* 3.6 2.9 - - - -
233A LYS 3.1 0.4 - - - -
234A LEU* 1.3 77.6 - - - +
236A ARG* 1.3 59.4 + - - +
238A MET* 3.6 8.7 + - - +
239A ALA* 3.3 20.8 + - - +
280A HIS* 6.4 0.4 - - - -
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Residues in contact with ARG 236 (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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189A MET* 3.2 23.5 - - + +
193A GLU* 4.9 5.5 + - - -
232A GLN* 3.0 34.8 + - + +
233A LYS* 3.2 29.5 + - - +
235A GLY* 1.3 74.1 - - - +
237A HIS* 1.3 67.2 + - - +
239A ALA* 3.2 7.2 + - - +
240A THR* 3.0 27.2 + - - +
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Residues in contact with HIS 237 (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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188A GLN* 2.8 43.5 + - + +
189A MET* 3.8 36.2 - - + +
192A ALA* 3.9 23.0 - - + +
210A ILE* 4.2 7.1 - - + +
213A LEU* 3.5 24.2 - - + +
217A PHE* 4.2 6.6 - - + -
233A LYS 3.1 9.8 + - - +
234A LEU* 3.5 13.0 - - - +
236A ARG* 1.3 80.2 - - - +
238A MET* 1.3 56.1 + - - +
240A THR* 3.3 8.1 + - - -
241A LEU* 3.1 42.6 + - + +
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Residues in contact with MET 238 (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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100A VAL* 4.2 21.8 - - + -
213A LEU* 3.8 35.9 - - + -
234A LEU* 3.0 22.5 + - + +
235A GLY* 3.7 7.9 - - - +
236A ARG 3.2 0.2 - - - -
237A HIS* 1.3 73.9 - - - +
239A ALA* 1.3 58.2 + - - +
241A LEU* 3.4 10.4 + - + +
242A ASN* 2.9 40.3 + - - +
254A VAL* 5.7 0.2 - - + -
280A HIS* 3.8 20.4 - - + -
281A ALA* 2.9 43.3 - - + +
282A ALA* 4.7 0.4 - - + -
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Residues in contact with ALA 239 (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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235A GLY 3.3 11.0 + - - +
236A ARG* 3.2 10.3 + - - +
238A MET* 1.3 76.0 - - - +
240A THR* 1.3 60.8 + - - +
242A ASN* 3.8 5.0 - - - +
243A LYS* 2.8 32.1 + - - +
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Residues in contact with THR 240 (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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189A MET* 5.6 0.7 - - - +
192A ALA* 4.2 26.0 - - + +
193A GLU* 4.3 27.4 + - + +
236A ARG* 3.0 13.8 + - - +
237A HIS* 3.4 12.6 - - - +
239A ALA* 1.3 78.0 - - - +
241A LEU* 1.3 57.9 + - - +
243A LYS* 3.7 5.2 - - - +
244A LEU* 3.0 33.5 + - + +
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Residues in contact with LEU 241 (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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100A VAL* 4.5 4.0 - - + -
192A ALA* 4.2 22.9 - - + -
208A VAL* 4.6 4.7 - - + -
210A ILE* 3.9 31.4 - - + -
213A LEU* 4.3 5.8 - - + -
237A HIS* 3.1 37.7 + - + +
238A MET* 3.6 25.4 - - + +
239A ALA 3.2 0.2 - - - -
240A THR* 1.3 73.9 - - - +
242A ASN* 1.3 65.2 + - - +
244A LEU* 3.4 17.1 + - + +
245A ALA* 3.1 23.0 + - - +
252A VAL* 3.7 18.0 - - + +
254A VAL* 4.3 8.3 - - + -
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Residues in contact with ASN 242 (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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98A GLN 5.4 1.2 + - - -
99A SER* 4.8 5.3 - - - +
100A VAL* 3.3 33.3 - - - +
238A MET* 2.9 25.7 + - - +
239A ALA* 3.9 6.4 - - - +
241A LEU* 1.3 76.2 - - - +
243A LYS* 1.3 62.4 + - - +
245A ALA* 3.3 3.8 + - - +
246A ASP* 3.1 32.7 + - - +
281A ALA* 4.5 16.1 - - - +
282A ALA* 5.1 1.8 + - - +
283A THR* 5.0 5.7 - - - +
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Residues in contact with LYS 243 (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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29A LYS* 5.4 12.0 + - - +
32A THR* 4.0 31.9 + - - -
33A ALA* 5.2 0.2 - - - +
37A GLU* 4.1 14.6 + - - -
239A ALA 2.8 18.8 + - - +
240A THR* 3.7 6.3 - - - +
242A ASN* 1.3 77.7 - - - +
244A LEU* 1.3 58.3 + - - +
246A ASP* 3.2 8.3 + - + +
247A LEU* 2.9 49.9 + - + +
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Residues in contact with LEU 244 (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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192A ALA 3.7 23.3 - - - +
195A ILE* 4.1 21.8 - - + -
196A GLU* 5.9 4.9 - - + -
208A VAL* 3.9 15.9 - - + -
240A THR* 3.0 21.8 + - + +
241A LEU* 3.5 22.0 - - + +
243A LYS* 1.3 76.5 - - - +
245A ALA* 1.3 62.2 + - - +
246A ASP 3.3 0.2 - - - -
247A LEU* 4.1 2.2 - - - -
248A TYR* 3.3 38.6 + - + -
250A CYS* 3.4 25.8 - - - -
252A VAL* 3.9 9.4 - - + -
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Residues in contact with ALA 245 (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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98A GLN* 3.2 16.6 - - - -
99A SER* 3.8 21.8 - - - +
241A LEU 3.1 16.4 + - - +
242A ASN* 3.7 6.7 - - - +
243A LYS 3.2 0.2 - - - -
244A LEU* 1.3 77.2 - - - +
246A ASP* 1.3 63.0 + - - +
249A ASN* 3.3 16.5 + - - -
250A CYS* 3.3 25.8 + - - +
252A VAL* 3.6 14.6 - - + -
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Residues in contact with ASP 246 (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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28A MET* 6.1 0.9 - - - +
98A GLN* 3.2 17.6 - - - +
242A ASN* 3.1 14.8 + - - +
243A LYS* 3.6 8.9 - - + +
245A ALA* 1.3 80.2 - - - +
247A LEU* 1.3 64.7 + - + +
248A TYR 3.6 0.2 + - - -
249A ASN* 3.7 6.8 + - - +
502A MG 2.0 32.7 - - - -
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Residues in contact with LEU 247 (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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26A ASP* 5.4 6.7 - - - +
28A MET* 4.0 37.1 - - + +
29A LYS* 3.9 35.9 - - + +
32A THR* 4.0 19.3 - - + +
196A GLU* 4.8 2.0 - - - +
243A LYS* 2.9 36.4 + - + +
244A LEU* 5.7 0.2 - - - -
246A ASP* 1.3 81.3 - - + +
248A TYR* 1.3 87.5 + - + +
249A ASN* 3.8 0.5 + - - +
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Residues in contact with TYR 248 (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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26A ASP* 5.3 16.4 - - + +
29A LYS* 4.0 10.6 - - - +
195A ILE* 6.3 0.7 - - + -
196A GLU* 3.0 42.6 + - + +
199A ILE* 3.5 46.9 - - + -
205A ILE 4.4 2.6 - - - +
206A LYS* 3.5 19.0 + - - +
244A LEU* 3.3 33.5 + - + +
247A LEU* 1.3 98.8 - - + +
249A ASN* 1.3 70.6 + - - +
250A CYS* 3.2 11.9 + - - +
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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