Contacts of the helix formed by residues 231 - 246 (chain B) in PDB entry 3D8U
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 SER 231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A SER* 5.5 11.4 - - - -
288A MSE 6.0 1.1 - - - -
229B ALA 3.6 7.1 + - - -
230B PRO* 1.3 77.6 - - - +
232B SER* 1.3 61.6 + - - +
233B GLN* 3.3 10.1 + - - +
234B LEU* 2.8 39.0 + - - +
235B GLY 3.4 4.2 + - - -
258B GLU* 3.9 11.7 - - - +
259B ILE* 3.7 10.3 - - - +
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Residues in contact with SER 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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287A SER 3.6 9.4 + - - -
288A MSE 3.3 35.7 + - - +
291A HIS* 3.9 9.9 + - - +
231B SER* 1.3 72.5 - - - +
233B GLN* 1.3 67.1 + - - +
235B GLY 3.1 0.9 + - - -
236B ALA* 3.0 22.3 + - - +
258B GLU* 3.3 23.5 + - - +
261B ILE* 4.5 7.2 - - - -
262B GLY* 3.1 20.5 - - - -
265B PHE* 5.9 0.7 - - - -
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Residues in contact with GLN 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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287A SER* 4.9 3.2 + - - +
291A HIS* 3.4 50.7 + - + +
231B SER* 3.2 8.1 + - - +
232B SER* 1.3 81.0 + - - +
234B LEU* 1.3 63.2 + - - +
236B ALA* 3.4 1.9 + - - +
237B GLU* 2.9 56.8 + - - +
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Residues in contact with LEU 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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193B ILE* 3.8 21.1 - - + -
194B GLY 4.7 4.5 - - - +
195B ALA* 3.9 18.4 - - + -
224B LEU* 5.5 7.0 - - + +
226B THR* 3.5 36.8 - - + +
228B GLU* 5.7 1.1 - - + -
229B ALA 4.3 10.3 - - - +
230B PRO* 4.8 0.7 - - + -
231B SER* 2.8 25.3 + - - +
232B SER 3.1 0.2 - - - -
233B GLN* 1.3 79.9 - - - +
235B GLY* 1.3 52.2 + - - +
237B GLU* 4.3 4.4 - - + +
238B GLY* 2.6 34.1 + - - +
241B LYS* 6.2 2.7 - - - +
259B ILE* 4.8 5.4 - - + -
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Residues in contact with GLY 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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193B ILE* 4.2 3.3 - - - +
231B SER 3.4 5.1 + - - -
232B SER 3.1 5.1 + - - -
234B LEU* 1.3 73.2 - - - +
236B ALA* 1.3 66.9 + - - +
238B GLY* 4.3 1.8 - - - -
239B LEU* 2.9 23.2 + - - +
259B ILE* 3.3 35.1 - - - +
263B ALA* 3.7 14.4 - - - +
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Residues in contact with ALA 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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291A HIS* 5.0 13.9 - - + +
232B SER 3.0 12.7 + - - +
233B GLN* 3.6 10.8 - - - +
235B GLY* 1.3 75.1 - - - +
237B GLU* 1.3 67.8 + - + +
239B LEU* 2.9 6.9 + - - +
240B ALA* 2.9 21.0 + - - +
262B GLY* 3.6 6.2 - - - +
266B GLU* 3.8 39.3 - - + +
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Residues in contact with GLU 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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291A HIS* 4.8 3.9 + - + -
233B GLN* 2.9 55.1 + - + +
234B LEU* 4.3 3.5 + - + +
236B ALA* 1.3 81.2 - - + +
238B GLY* 1.3 63.6 + - - +
240B ALA* 3.0 11.2 + - + +
241B LYS* 2.8 47.4 + - + +
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Residues in contact with GLY 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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193B ILE* 3.6 21.5 - - - -
224B LEU* 3.7 17.1 - - - +
234B LEU* 2.6 28.5 + - - +
237B GLU* 1.3 74.1 - - - +
239B LEU* 1.3 63.9 + - - +
241B LYS* 3.2 1.6 + - - +
242B LEU* 3.1 22.7 + - - +
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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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193B ILE* 3.6 7.1 - - - +
235B GLY 2.9 14.4 + - - +
236B ALA 3.3 8.1 - - - +
238B GLY* 1.3 74.5 - - - +
240B ALA* 1.3 65.1 + - - +
242B LEU* 3.2 2.7 + - - +
243B LEU* 2.9 46.8 + - + +
249B LEU* 3.8 24.0 - - + -
252B LEU* 3.9 21.5 - - + -
263B ALA* 4.1 3.4 - - - +
266B GLU* 3.9 22.7 - - + -
267B CYS* 4.0 28.5 - - - +
270B ARG* 4.5 2.7 - - - -
272B LEU* 5.3 1.3 - - + -
278B ILE* 4.0 8.3 - - + -
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Residues in contact with ALA 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 ALA 2.9 10.9 + - - +
237B GLU* 3.0 13.9 + - + +
239B LEU* 1.3 79.5 - - - +
241B LYS* 1.3 65.6 + - + +
243B LEU* 3.1 11.2 + - - +
244B LEU* 3.0 21.2 + - - +
270B ARG* 3.4 30.9 - - - +
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Residues in contact with LYS 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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224B LEU* 4.1 25.3 - - + +
234B LEU* 6.2 2.0 - - - +
237B GLU* 2.8 41.3 + - + +
238B GLY* 4.0 3.1 - - - +
240B ALA* 1.3 74.1 - - + +
242B LEU* 1.3 58.6 + - - +
244B LEU* 3.1 14.1 + - + +
245B ARG* 2.8 30.4 + - - +
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Residues in contact with LEU 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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191B GLY* 3.8 28.0 - - - -
192B PHE 4.1 5.2 - - - +
193B ILE* 4.2 11.2 - - + -
222B HIS* 4.0 28.3 - - + +
223B PHE 4.3 5.4 - - - +
224B LEU* 3.9 20.6 - - + -
238B GLY 3.1 14.2 + - - +
239B LEU 3.6 7.2 - - - +
241B LYS* 1.3 74.1 - - - +
243B LEU* 1.3 60.0 + - - +
244B LEU 3.0 0.3 + - - -
245B ARG* 3.0 14.1 + - + +
246B ASP* 2.8 31.8 + - - +
249B LEU* 4.2 14.6 - - + -
252B LEU* 3.8 18.6 - - + -
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Residues in contact with LEU 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* 2.9 37.1 + - + +
240B ALA* 3.2 8.7 - - - +
242B LEU* 1.3 75.3 - - - +
244B LEU* 1.3 59.5 + - - +
246B ASP 4.0 3.1 - - - -
247B SER* 3.5 34.1 + - - +
249B LEU* 3.6 31.6 - - + +
270B ARG* 3.9 31.6 - - - +
272B LEU* 4.7 13.0 - - + -
278B ILE* 4.0 11.0 - - + -
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Residues in contact with LEU 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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240B ALA 3.0 11.8 + - - +
241B LYS* 3.6 15.5 - - + +
242B LEU 3.0 0.4 - - - -
243B LEU* 1.3 75.0 - - + +
245B ARG* 1.3 68.4 + - - +
246B ASP 3.2 0.4 - - - -
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Residues in contact with ARG 245 (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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221B ASP 4.4 8.0 + - - -
222B HIS* 3.4 36.6 + - + +
223B PHE 5.9 2.0 - - - +
224B LEU* 5.9 4.3 - - - -
241B LYS 2.8 12.8 + - - +
242B LEU* 3.2 21.5 - - - +
244B LEU* 1.3 80.4 - - - +
246B ASP* 1.3 60.0 + - - +
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Residues in contact with ASP 246 (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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222B HIS* 4.2 28.5 + - + +
242B LEU 2.8 15.0 + - - +
243B LEU* 3.5 4.2 - - - +
244B LEU 3.2 2.2 - - - -
245B ARG* 1.3 81.1 - - + +
247B SER* 1.3 61.3 + - - +
248B SER* 2.6 33.0 + - - -
249B LEU* 3.4 17.3 + - + +
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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