Contacts of the helix formed by residues 233 - 247 (chain B) in PDB entry 3ADB
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 233 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B VAL* 1.3 77.2 - - - +
234B ALA* 1.3 64.5 + - - +
235B ASP* 3.6 23.5 - - - +
236B ARG* 3.2 49.8 + - - +
237B VAL* 2.7 33.8 + - - +
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Residues in contact with ALA 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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186B ILE* 5.8 5.9 - - + +
189B LYS* 5.3 16.6 - - + -
190B ILE* 5.3 10.1 - - + -
193B GLU* 5.7 0.2 - - + -
232B VAL* 4.2 1.4 + - - +
233B ASP* 1.3 74.3 + - - +
235B ASP* 1.3 60.4 + - - +
236B ARG 3.2 0.2 + - - -
237B VAL* 3.2 4.4 + - - -
238B LEU* 2.6 63.4 + - + +
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Residues in contact with ASP 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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233B ASP* 3.4 16.0 - - - +
234B ALA* 1.3 80.1 - - - +
236B ARG* 1.3 63.3 + - + +
238B LEU* 4.2 6.2 - - - +
239B LYS* 3.2 23.9 + - - +
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Residues in contact with ARG 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 VAL* 6.2 0.8 - - - +
233B ASP* 3.3 42.6 + - + +
234B ALA 3.2 0.2 - - - -
235B ASP* 1.3 79.2 - - + +
237B VAL* 1.3 63.0 + - + +
239B LYS* 3.4 4.9 - - - +
240B GLU* 3.0 30.7 + - - +
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Residues in contact with VAL 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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190B ILE* 4.9 2.7 - - + -
222B PHE* 3.1 36.3 - - + -
226B ILE* 3.2 26.5 - - + -
229B MSE 4.6 5.2 - - + -
232B VAL* 3.1 27.8 - - + -
233B ASP 2.7 20.8 + - - +
234B ALA* 3.9 3.8 - - - +
236B ARG* 1.3 73.2 - - + +
238B LEU* 1.3 64.7 + - + +
239B LYS 3.0 1.6 - - - -
240B GLU* 2.9 36.6 + - - +
241B PHE 2.9 10.0 + - - -
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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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190B ILE* 4.4 27.6 - - + +
193B GLU* 3.4 51.4 - - + +
194B THR* 4.7 7.4 - - + -
197B ILE* 3.7 14.6 - - + +
222B PHE* 5.3 0.7 - - + -
234B ALA* 2.6 45.5 + - + +
235B ASP* 4.4 5.4 - - - +
237B VAL* 1.3 74.1 - - + +
239B LYS* 1.3 55.8 + - - +
241B PHE* 3.6 7.4 - - - +
242B LYS* 3.1 26.9 + - - +
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Residues in contact with LYS 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 ASP 3.2 20.1 + - - +
236B ARG* 3.4 6.1 - - - +
237B VAL 3.0 0.4 - - - -
238B LEU* 1.3 75.8 - - - +
240B GLU* 1.3 65.8 - - + +
242B LYS* 2.8 42.4 + - - +
243B ASP* 2.9 47.7 + - - +
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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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222B PHE* 4.4 10.7 - - + -
229B MSE 5.6 3.3 - - - +
236B ARG* 3.0 19.1 - - - +
237B VAL* 2.9 30.8 + - - +
239B LYS* 1.3 77.8 - - + +
241B PHE* 1.3 58.5 + - - +
243B ASP* 3.4 7.6 + - - +
244B LEU* 2.9 30.1 + - - +
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Residues in contact with PHE 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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194B THR* 3.9 16.2 - - + -
197B ILE* 3.5 44.2 - - + -
198B VAL* 4.1 7.9 - - + -
215B VAL 4.9 0.4 - - - -
218B LEU* 4.2 9.2 - - + -
219B ARG* 3.6 46.0 - - + -
222B PHE* 3.3 47.5 - + + -
237B VAL 2.9 6.0 + - - +
238B LEU* 3.6 10.5 - - - +
240B GLU* 1.3 75.1 - - - +
242B LYS* 1.3 65.6 + - - +
244B LEU* 3.1 7.6 + - + +
245B LEU* 3.0 42.6 + - + +
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Residues in contact with LYS 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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197B ILE* 4.5 21.5 - - + -
200B GLU* 5.6 9.6 - - - +
238B LEU 3.1 12.1 + - - +
239B LYS* 2.8 45.8 - - - +
241B PHE* 1.3 79.1 - - - +
243B ASP* 1.3 64.2 + - - +
245B LEU* 3.4 5.2 + - + +
246B ASN* 3.1 45.0 + - - +
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Residues in contact with ASP 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 LYS* 2.9 54.1 + - - +
240B GLU* 3.8 6.7 + - - +
242B LYS* 1.3 77.4 - - - +
244B LEU* 1.3 65.6 + - - +
246B ASN* 3.1 18.9 + - - +
247B SER* 3.2 12.5 + - - -
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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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218B LEU* 3.5 36.6 - - + +
222B PHE* 5.3 14.6 - - + -
240B GLU 2.9 17.5 + - - +
241B PHE* 3.1 7.8 + - + +
243B ASP* 1.3 75.7 - - - +
245B LEU* 1.3 60.1 + - - +
247B SER* 2.5 31.8 + - - +
248B TYR* 3.2 21.7 - - + +
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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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197B ILE* 3.6 32.8 - - + +
198B VAL* 4.8 0.2 - - - -
201B TYR* 3.4 45.8 + - + -
215B VAL* 3.5 35.9 - - + -
218B LEU* 4.0 19.5 - - + -
241B PHE* 3.0 29.2 + - + +
242B LYS* 3.4 10.5 - - + +
244B LEU* 1.3 78.5 - - - +
246B ASN* 1.3 62.5 + - - +
247B SER 3.1 0.2 - - - -
248B TYR* 3.2 19.6 + - + +
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Residues in contact with ASN 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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201B TYR* 3.8 22.0 - - - -
205B LYS* 4.1 17.7 + - - +
242B LYS* 3.1 39.9 + - - +
243B ASP* 3.1 12.2 + - - +
245B LEU* 1.3 72.2 - - - +
247B SER* 1.3 59.1 + - - +
248B TYR* 3.1 7.6 + - - +
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Residues in contact with SER 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 ASP 3.2 9.7 + - - -
244B LEU* 2.5 31.1 + - - +
245B LEU 3.1 0.2 - - - -
246B ASN* 1.3 76.6 - - - +
248B TYR* 1.3 69.7 + - - +
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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