Contacts of the helix formed by residues 225 - 243 (chain B) in PDB entry 2E9D
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 ASP 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ARG* 3.8 19.3 - - - +
223B ASP 3.6 9.7 - - - +
224B PHE* 1.3 78.6 - - - +
226B GLU* 1.3 68.2 + - - +
227B GLN* 2.8 15.3 + - - +
228B ASP* 2.7 38.1 + - - +
229B PHE* 2.8 36.1 + - - +
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Residues in contact with GLU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ARG* 3.3 40.6 + - + +
56B PHE* 3.4 38.5 - - + -
225B ASP* 1.3 84.8 - - - +
227B GLN* 1.3 54.1 - - - +
229B PHE* 3.8 2.9 - - - -
230B GLU* 3.0 28.4 + - - +
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Residues in contact with GLN 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ASP* 2.8 14.9 + - - +
226B GLU* 1.3 74.7 + - - +
228B ASP* 1.3 70.9 + - - +
229B PHE 3.2 1.1 - - - -
230B GLU* 3.5 7.4 + - + +
231B GLY* 3.2 18.9 + - - -
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Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TYR* 4.6 6.1 + - - -
217B THR* 5.8 1.3 - - - +
219B VAL* 3.9 22.3 - - + +
223B ASP 3.1 7.3 - - - +
224B PHE* 3.0 35.0 - - + -
225B ASP* 2.7 37.1 + - - +
227B GLN* 1.3 79.2 - - - +
229B PHE* 1.3 63.2 + - - +
231B GLY* 3.4 1.4 + - - -
232B ALA* 3.2 20.8 + - - +
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Residues in contact with PHE 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B VAL* 4.2 13.5 - - + -
23B ILE* 4.2 21.5 - - + -
53B ALA* 3.6 24.7 - - - -
56B PHE* 3.1 38.8 - + + -
57B ALA* 4.3 2.0 - - + -
62B ILE* 4.3 12.3 - - + -
65B LEU* 4.4 6.1 - - + -
193B ILE* 4.1 21.5 - - + -
224B PHE* 3.6 19.2 - + + -
225B ASP 2.8 16.4 + - - +
226B GLU* 3.6 7.2 - - - +
228B ASP* 1.3 76.3 - - - +
230B GLU* 1.3 64.1 + - - +
232B ALA* 2.9 12.9 + - - +
233B LEU* 2.9 30.6 + - + +
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B PHE* 3.8 15.0 - - + -
226B GLU 3.0 19.0 + - - +
227B GLN* 3.8 8.5 - - + +
228B ASP 3.5 0.2 - - - -
229B PHE* 1.3 75.3 - - - +
231B GLY* 1.3 58.2 + - - +
233B LEU* 3.4 6.6 + - - +
234B ASN* 2.8 60.8 + - - +
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Residues in contact with GLY 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B TYR* 4.1 9.4 + - - -
227B GLN 3.2 12.1 + - - -
228B ASP 3.9 3.6 - - - -
229B PHE 3.1 0.8 - - - -
230B GLU* 1.3 77.7 - - - +
232B ALA* 1.3 60.5 + - - +
234B ASN* 3.7 11.1 - - - +
235B ALA* 2.9 28.8 + - - +
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B LEU* 3.9 8.2 - - + +
193B ILE* 3.6 31.6 - - + -
215B TYR* 3.8 35.0 + - + -
224B PHE* 5.3 0.2 - - + -
228B ASP 3.2 8.9 + - - +
229B PHE 2.9 9.2 + - - +
231B GLY* 1.3 72.2 - - - +
233B LEU* 1.3 68.4 + - - +
235B ALA* 3.2 4.2 + - - +
236B PHE* 2.9 22.9 + - - +
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B CYS* 3.6 39.7 - - + -
21B VAL* 4.2 8.1 - - + -
56B PHE* 3.6 33.2 - - + -
60B ASN* 5.5 3.8 - - + -
62B ILE* 4.0 14.8 - - + -
191B LEU* 4.1 8.5 - - + -
229B PHE* 2.9 26.8 + - + +
230B GLU* 3.7 5.2 - - - +
232B ALA* 1.3 79.4 - - - +
234B ASN* 1.3 62.3 + - - +
236B PHE* 3.1 9.1 + - + +
237B ALA* 3.0 20.8 + - - +
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Residues in contact with ASN 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B GLU* 2.8 57.6 + - - +
231B GLY* 3.7 8.9 - - - +
232B ALA 3.3 0.2 - - - -
233B LEU* 1.3 71.3 - - - +
235B ALA* 1.3 67.0 + - - +
237B ALA* 2.8 19.8 + - - +
238B ASN* 2.9 25.0 + - - +
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B GLU* 6.4 0.2 - - + -
215B TYR* 3.7 25.8 - - + -
231B GLY 2.9 19.6 + - - +
232B ALA 3.3 6.1 - - - +
234B ASN* 1.3 77.6 - - - +
236B PHE* 1.3 62.5 + - - +
238B ASN* 3.3 8.5 + - - +
239B ARG* 3.1 41.2 + - - +
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Residues in contact with PHE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ARG* 5.8 3.6 - - - -
17B GLY 4.8 1.1 - - - -
18B CYS* 3.7 33.0 - - + -
190B ASP* 3.5 44.2 - - + -
191B LEU* 4.1 16.4 - - + -
213B GLU* 3.6 34.1 - - + +
232B ALA 2.9 13.0 + - - +
233B LEU* 3.2 11.2 - - - +
235B ALA* 1.3 74.2 - - - +
237B ALA* 1.3 60.1 + - + +
239B ARG* 3.4 2.1 + - - +
240B GLU* 2.7 75.0 + - + +
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Residues in contact with ALA 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B LEU 3.0 11.0 + - - +
234B ASN* 2.8 14.3 + - - +
236B PHE* 1.3 79.1 - - + +
238B ASN* 1.3 60.5 + - - +
240B GLU* 3.2 13.8 + - - +
241B ARG* 2.9 54.5 + - - +
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Residues in contact with ASN 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B ASN* 2.9 30.0 + - - +
235B ALA* 3.9 7.0 - - - +
237B ALA* 1.3 72.2 - - - +
239B ARG* 1.3 58.9 + - + +
241B ARG* 3.2 29.4 + - - +
242B ARG* 2.9 34.8 + - - +
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Residues in contact with ARG 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A GLY 3.0 23.6 + - - -
199A HIS* 3.4 37.2 + - - +
200A ARG* 3.7 3.6 + - - -
218A ASP* 5.3 3.4 + - - -
213B GLU* 3.0 37.2 + - - +
215B TYR* 6.0 1.6 - - - -
235B ALA* 3.1 29.1 + - - +
236B PHE 3.9 1.1 - - - +
238B ASN* 1.3 71.9 - - + +
240B GLU* 1.3 61.8 + - - +
241B ARG 3.0 1.8 - - - -
242B ARG* 3.8 26.1 - - - +
243B PHE* 2.9 54.0 + - + +
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Residues in contact with GLU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ARG* 3.9 15.7 - - - +
17B GLY 3.3 25.2 + - - +
236B PHE* 2.7 58.6 + - + +
237B ALA* 3.4 11.1 - - - +
239B ARG* 1.3 78.7 - - - +
241B ARG* 1.3 60.5 + - + +
243B PHE 3.7 12.5 - - - -
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Residues in contact with ARG 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ALA* 2.9 38.4 + - - +
238B ASN* 3.2 32.3 + - - +
240B GLU* 1.3 80.1 - - + +
242B ARG* 1.3 59.7 + - - +
243B PHE* 4.8 0.7 - - - -
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Residues in contact with ARG 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ARG* 6.2 0.4 - - - +
197A GLY* 5.2 3.8 + - - -
218A ASP* 5.7 3.6 + - - -
238B ASN* 2.9 18.7 + - - +
239B ARG* 3.4 40.0 + - - +
241B ARG* 1.3 76.1 - - - +
243B PHE* 1.3 99.3 + - + +
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Residues in contact with PHE 243 (chain B).
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* 6.0 0.4 - - - -
30A ARG* 4.2 17.9 - - - -
196A GLY 3.9 16.2 - - - -
197A GLY* 3.7 18.8 - - - -
198A GLU* 3.4 41.1 - - + +
200A ARG* 3.6 22.9 + - - +
213B GLU* 6.0 0.2 - - - -
239B ARG* 2.9 46.6 + - + +
240B GLU 3.7 17.3 - - - -
241B ARG 4.8 0.4 - - - -
242B ARG* 1.3 118.4 - - + +
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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