Contacts of the helix formed by residues 231 - 244 (chain B) in PDB entry 1EJD
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 231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B ILE* 3.5 1.6 - - - +
19B SER* 2.9 21.1 + - - +
20B GLY 4.0 3.8 - - - +
21B ALA* 3.6 26.1 - - - +
22B LYS* 4.7 3.8 + - - +
230B PRO* 1.3 69.2 - - - +
232B ARG* 1.3 58.9 + - - +
233B ILE* 3.1 11.8 + - - +
234B GLU* 2.9 36.9 + - + +
235B THR* 2.8 30.0 + - - -
371B ARG* 4.9 8.7 + - - -
398B GLY 4.4 12.1 - - - +
399B TYR* 5.8 0.5 - - - -
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Residues in contact with ARG 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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21B ALA* 5.2 0.2 - - - +
188B GLU* 3.6 20.2 - - - +
189B PRO* 3.7 20.0 - - - +
190B GLU* 2.9 42.3 + - - +
229B LEU* 6.1 0.9 - - + -
230B PRO* 3.2 7.8 + - - +
231B ASP* 1.3 72.9 + - - +
233B ILE* 1.3 77.6 + - + +
235B THR* 3.4 8.7 + - - -
236B GLY* 2.9 22.5 + - - -
258B THR* 3.6 35.7 + - - +
259B LEU* 3.6 22.0 - - + +
299B HIS* 4.0 17.4 + - - +
303B PRO* 4.2 23.0 - - - +
305B ASP* 5.8 1.6 + - - -
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Residues in contact with ILE 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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231B ASP* 3.1 8.2 + - - +
232B ARG* 1.3 101.7 - - + +
234B GLU* 1.3 61.5 + - - +
236B GLY* 3.2 1.2 + - - -
237B THR* 2.8 31.8 + - - +
259B LEU* 5.6 1.1 - - + -
303B PRO* 4.2 13.0 - - + -
305B ASP* 3.5 45.1 - - + +
306B MET* 3.7 20.5 - - + +
309B GLN* 3.9 6.5 - - - +
371B ARG* 3.5 35.0 - - - +
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Residues in contact with GLU 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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18B ILE* 3.4 10.4 - - + +
19B SER* 2.8 35.7 + - - +
231B ASP* 2.9 26.8 + - - +
233B ILE* 1.3 75.0 - - - +
235B THR* 1.3 64.8 + - - +
237B THR* 3.1 1.7 + - - -
238B PHE* 3.0 47.2 + - + -
371B ARG* 4.6 1.2 - - - +
399B TYR* 4.0 29.5 - - + +
400B GLU 4.6 7.7 + - - +
402B ILE* 6.0 0.5 - - - -
405B LYS* 2.6 30.2 + - - +
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Residues in contact with THR 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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18B ILE* 3.3 25.9 - - - +
230B PRO* 5.0 1.2 - - - +
231B ASP 2.8 19.7 + - - -
232B ARG* 3.5 10.3 - - - -
234B GLU* 1.3 78.8 - - - +
236B GLY* 1.3 62.6 + - - +
238B PHE* 3.2 2.4 + - - +
239B LEU* 3.0 31.8 + - + +
251B CYS* 4.3 16.8 - - + -
254B ALA* 4.4 8.4 - - + +
255B GLN 5.4 0.9 + - - +
259B LEU* 3.5 21.1 - - + -
280B ILE* 3.8 20.0 - - + -
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Residues in contact with GLY 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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232B ARG 2.9 13.9 + - - -
233B ILE 3.2 2.7 + - - -
235B THR* 1.3 77.5 - - - +
237B THR* 1.3 56.0 + - - +
239B LEU* 3.3 12.3 + - - +
240B VAL* 2.9 35.0 + - - +
259B LEU* 4.2 1.7 - - - +
262B VAL* 4.6 9.4 - - - +
306B MET* 3.4 21.3 - - - -
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Residues in contact with THR 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 ILE 2.8 19.1 + - - -
234B GLU 3.1 8.7 + - - -
236B GLY* 1.3 77.2 - - - +
238B PHE* 1.3 60.7 + - + +
240B VAL* 3.3 3.5 + - - +
241B ALA* 3.0 24.6 + - - +
306B MET* 3.9 4.2 - - - +
309B GLN* 3.2 18.6 + - + +
374B ALA* 4.7 6.3 - - + -
378B LEU* 3.7 22.9 - - + +
399B TYR* 2.8 39.5 + - + +
402B ILE* 4.7 11.0 - - + -
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Residues in contact with PHE 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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16B VAL* 4.0 17.0 - - + -
18B ILE* 4.2 4.5 - - + -
234B GLU* 3.0 56.9 + - + +
235B THR 3.9 2.7 - - - +
237B THR* 1.3 76.5 - - + +
239B LEU* 1.3 66.2 + - - +
241B ALA* 3.2 14.4 + - + +
242B ALA* 3.2 10.4 + - - +
249B ILE* 3.9 22.1 - - + +
251B CYS* 4.3 4.0 - - - -
378B LEU* 6.1 0.4 - - + -
399B TYR* 5.1 1.8 - + - -
402B ILE* 3.9 22.2 - - + -
405B LYS* 3.5 35.9 - - + -
406B LEU* 3.8 26.7 - - + -
409B LEU* 3.8 21.5 - - + -
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Residues in contact with LEU 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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235B THR* 3.0 36.8 + - + +
236B GLY* 3.3 8.3 + - - +
238B PHE* 1.3 75.2 - - - +
240B VAL* 1.3 63.8 + - - +
242B ALA* 3.3 2.6 + - - +
243B ALA* 3.0 22.6 + - - +
249B ILE* 4.3 6.7 - - + -
251B CYS* 3.8 20.9 - - - -
259B LEU* 4.5 3.4 - - + -
262B VAL* 5.1 0.9 - - + -
263B LEU* 3.7 29.6 - - + -
266B LEU* 3.8 18.6 - - + -
273B ILE* 6.0 0.2 - - + -
280B ILE* 4.0 18.4 - - + +
282B LEU* 3.7 32.4 - - + +
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Residues in contact with VAL 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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236B GLY 2.9 21.1 + - - +
237B THR 3.7 3.8 - - - +
239B LEU* 1.3 73.1 - - + +
241B ALA* 1.3 65.8 + - - +
243B ALA* 3.0 6.8 + - - -
244B ILE* 2.9 42.3 + - + +
266B LEU* 4.3 6.3 - - + -
306B MET* 3.9 6.3 - - + -
309B GLN* 3.6 31.2 - - + +
310B PHE* 3.7 36.6 - - + -
312B LEU* 5.4 0.4 - - + -
313B LEU* 4.6 4.3 - - + -
378B LEU* 4.4 10.1 - - + -
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Residues in contact with ALA 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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12B LEU* 3.7 26.5 - - + +
237B THR 3.0 14.6 + - - +
238B PHE* 3.2 17.0 + - + +
240B VAL* 1.3 78.0 - - - +
242B ALA* 1.3 59.2 + - - +
244B ILE* 3.5 9.2 - - - +
245B SER* 2.8 24.0 + - - -
249B ILE* 5.9 0.2 - - + -
378B LEU* 3.7 21.5 - - + +
406B LEU* 4.7 5.8 - - + -
409B LEU* 5.4 2.5 - - + -
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Residues in contact with ALA 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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12B LEU* 4.0 15.2 - - + +
238B PHE 3.2 4.3 + - - +
239B LEU 3.8 4.5 - - - +
241B ALA* 1.3 78.7 - - - +
243B ALA* 1.3 64.1 + - - +
245B SER* 3.2 9.3 + - - -
246B GLY 3.3 0.5 + - - -
247B GLY 2.9 31.5 + - - -
249B ILE* 3.7 36.8 - - + +
282B LEU* 4.0 9.6 - - + -
284B MET* 3.6 4.0 - - - +
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Residues in contact with ALA 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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239B LEU 3.0 17.5 + - - +
240B VAL* 3.0 9.6 + - - +
242B ALA* 1.3 78.7 - - - +
244B ILE* 1.3 59.1 + - - +
245B SER 3.8 0.2 + - - -
246B GLY 4.4 1.4 + - - -
266B LEU* 4.1 18.2 - - + -
269B ALA* 6.1 1.3 - - + -
271B ALA* 5.2 0.7 - - + -
282B LEU* 4.0 5.1 - - + +
284B MET* 3.5 40.8 - - + +
289B PRO* 3.6 13.5 - - + +
313B LEU* 4.2 9.6 - - + -
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Residues in contact with ILE 244 (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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12B LEU* 6.1 0.7 - - + -
240B VAL* 2.9 27.3 + - + +
241B ALA* 3.5 12.6 - - - +
243B ALA* 1.3 77.9 - - - +
245B SER* 1.3 57.2 + - - +
246B GLY 3.6 1.3 - - - -
289B PRO* 4.4 10.6 - - - +
312B LEU* 3.6 28.7 - - + -
313B LEU* 3.7 39.9 - - + +
316B VAL* 4.0 15.0 - - + +
378B LEU* 4.1 19.5 - - + +
382B ILE* 3.8 32.8 - - + +
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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
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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