Contacts of the helix formed by residues 231 - 247 (chain B) in PDB entry 3B0A
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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205B LYS* 3.0 34.9 - - - +
228B TYR* 4.4 2.5 + - - -
229B GLN 3.6 2.4 + - - -
230B PRO* 1.3 75.1 - - - +
232B GLU* 1.3 65.2 + - + +
233B GLU* 3.1 13.0 + - - +
234B GLU* 2.8 28.9 + - - +
235B ARG* 2.9 19.8 + - - +
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Residues in contact with GLU 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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230B PRO 4.7 0.2 - - - -
231B ASP* 1.3 75.3 - - - +
233B GLU* 1.3 59.9 + - + +
235B ARG* 3.7 8.9 - - - +
236B ALA* 2.9 31.5 + - - +
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Residues in contact with GLU 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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139A LYS* 2.9 35.9 + - - -
140A GLU* 5.0 1.8 - - - -
205B LYS* 5.5 6.5 + - - -
231B ASP* 3.1 9.9 + - - +
232B GLU* 1.3 84.3 - - + +
234B GLU* 1.3 56.7 + - - +
236B ALA* 3.4 6.1 + - - +
237B ARG* 2.9 27.3 + - + +
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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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140A GLU* 6.0 0.3 - - - +
205B LYS* 3.9 20.5 - - + +
207B THR* 2.7 33.9 + - - +
208B ARG* 3.9 7.5 + - - +
228B TYR* 4.0 10.5 - - - +
230B PRO* 4.0 8.3 - - + -
231B ASP* 2.8 29.1 + - - +
233B GLU* 1.3 70.3 - - - +
235B ARG* 1.3 67.7 + - - +
237B ARG* 2.8 46.5 + - - +
238B LEU* 2.9 26.1 + - + +
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Residues in contact with ARG 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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229B GLN* 4.0 11.7 - - - +
230B PRO* 3.2 54.6 + - + +
231B ASP 2.9 16.7 + - - +
232B GLU* 3.7 7.5 - - - +
234B GLU* 1.3 76.8 - - - +
236B ALA* 1.3 56.4 - - - +
238B LEU* 3.3 5.8 + - + +
239B ALA* 2.8 33.0 + - + +
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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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232B GLU 2.9 18.4 + - - +
233B GLU* 3.8 6.3 - - - +
235B ARG* 1.3 72.2 - - - +
237B ARG* 1.3 66.3 + - - +
239B ALA* 3.3 8.4 + - - +
240B GLY* 2.9 19.9 + - - -
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Residues in contact with ARG 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 4.0 22.4 - - - -
140A GLU* 3.7 39.8 + - + +
142A THR* 4.5 4.9 + - - -
207B THR 3.2 19.0 + - - -
208B ARG* 4.0 3.6 - - - +
209B PRO* 3.8 13.9 - - - +
233B GLU* 2.9 15.2 + - + +
234B GLU* 2.8 46.3 + - - +
236B ALA* 1.3 75.9 - - - +
238B LEU* 1.3 76.7 + - - +
240B GLY* 3.0 11.7 + - - -
241B GLU* 3.1 34.9 + - - +
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Residues in contact with LEU 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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207B THR* 3.8 35.9 - - + +
230B PRO* 4.7 13.7 - - + -
234B GLU* 2.9 26.9 + - + +
235B ARG* 3.7 4.5 - - - +
237B ARG* 1.3 100.4 - - - +
239B ALA* 1.3 56.4 + - - +
241B GLU* 3.1 13.2 + - + +
242B GLU* 2.9 28.6 + - - +
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Residues in contact with ALA 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 ARG* 2.8 19.7 + - + +
236B ALA* 3.6 9.6 - - - +
238B LEU* 1.3 77.1 - - - +
240B GLY* 1.3 57.3 + - - +
242B GLU* 3.3 13.6 + - - +
243B GLU* 2.9 32.0 + - + +
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Residues in contact with GLY 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 14.1 + - - -
237B ARG* 3.0 5.3 + - - -
239B ALA* 1.3 73.4 - - - +
241B GLU* 1.3 67.4 + - - +
243B GLU* 3.0 18.3 + - - +
244B ALA* 3.1 13.3 + - - +
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Residues in contact with GLU 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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140A GLU 4.9 1.7 - - - +
141A SER* 5.3 0.7 - - - -
142A THR* 3.4 43.4 + - - +
144A HIS* 5.0 4.7 + - - -
237B ARG* 3.1 33.3 + - - +
238B LEU* 3.1 15.2 + - + +
240B GLY* 1.3 75.8 - - - +
242B GLU* 1.3 63.4 + - - +
244B ALA* 3.1 18.7 + - - +
245B LEU* 3.3 16.9 + - - +
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Residues in contact with GLU 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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238B LEU 2.9 16.0 + - - +
239B ALA* 3.6 11.0 - - - +
240B GLY 3.2 0.2 - - - -
241B GLU* 1.3 76.0 - - - +
243B GLU* 1.3 63.9 + - - +
245B LEU* 3.5 20.8 + - + +
246B ARG* 3.4 46.6 + - + +
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Residues in contact with GLU 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 ALA* 2.9 17.4 + - + +
240B GLY* 3.0 13.4 + - - +
242B GLU* 1.3 78.3 - - + +
244B ALA* 1.3 63.3 + - - +
246B ARG* 3.3 17.5 + - - +
247B GLN* 3.0 46.0 + - - +
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Residues in contact with ALA 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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122A ALA* 6.4 2.2 - - - -
144A HIS* 5.9 4.9 - - - +
240B GLY 3.1 11.1 + - - +
241B GLU* 3.1 14.1 + - - +
243B GLU* 1.3 76.8 - - - +
245B LEU* 1.3 64.2 + - + +
247B GLN* 3.1 26.2 + - - +
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Residues in contact with LEU 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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144A HIS* 6.5 1.8 - - + -
241B GLU 3.3 12.6 + - - +
242B GLU* 3.8 15.5 - - + +
243B GLU 3.3 0.4 - - - -
244B ALA* 1.3 80.2 - - + +
246B ARG* 1.3 64.7 + - + +
247B GLN 3.2 4.7 + - - -
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Residues in contact with ARG 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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242B GLU* 3.4 41.3 + - + +
243B GLU* 3.3 12.2 + - - +
244B ALA 3.2 1.2 - - - -
245B LEU* 1.3 78.1 - - + +
247B GLN* 1.3 62.4 + - + +
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Residues in contact with GLN 247 (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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243B GLU* 3.0 39.0 + - - +
244B ALA* 3.1 18.5 + - - +
245B LEU 4.2 4.0 - - - -
246B ARG* 1.3 83.0 - - + +
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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