Contacts of the helix formed by residues 233 - 248 (chain B) in PDB entry 3KDO
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 ALA* 1.3 77.6 - - - +
234B LEU* 1.3 68.2 + - - +
235B LEU* 3.3 1.8 - - + +
236B GLU* 3.1 21.8 + - - +
237B MET* 3.0 18.5 + - - +
99G ALA 3.0 27.0 - - - +
100G ASN* 4.2 3.3 + - - -
101G LEU* 4.5 2.6 + - - +
102G PRO* 3.7 19.6 - - - +
261G TRP 4.3 7.1 - - - +
262G GLY 3.8 4.2 - - - +
265G ARG* 4.1 36.4 + - + +
266G TYR 6.2 0.2 - - - +
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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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233B ASP* 1.3 73.2 - - - +
235B LEU* 1.3 66.4 + - + +
237B MET* 3.1 13.9 + - + +
238B GLU* 3.0 32.5 + - + +
263B ALA* 4.3 8.1 - - + -
266B TYR* 4.0 15.7 - - + -
267B ILE* 3.8 25.4 - - + -
234G LEU* 3.1 31.6 - - + -
262G GLY 2.8 18.6 + - - +
263G ALA* 4.4 3.6 - - + -
266G TYR* 3.5 43.6 - - + +
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Residues in contact with LEU 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* 3.3 1.6 - - + +
234B LEU* 1.3 78.2 - - + +
236B GLU* 1.3 68.7 + - - +
238B GLU* 3.1 25.3 + - - +
239B GLN* 3.0 35.3 + - - +
266G TYR* 4.1 35.4 - - + -
269G ASP* 6.1 0.7 - - - +
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Residues in contact with GLU 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 ALA* 3.7 17.5 - - + -
233B ASP* 3.1 31.1 + - - +
235B LEU* 1.3 79.2 - - - +
237B MET* 1.3 60.9 + - - +
239B GLN* 3.3 17.9 + - - +
240B ARG* 2.9 57.9 + - - +
97G GLU* 4.9 2.9 - - - +
99G ALA* 5.0 5.9 - - - +
100G ASN* 6.6 0.2 - - + -
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Residues in contact with MET 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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230B ILE* 3.3 41.9 - - + +
231B THR* 4.3 3.8 - - - -
232B ALA 3.3 35.0 - - - +
233B ASP 3.0 6.7 + - - +
234B LEU* 3.4 21.8 - - + +
236B GLU* 1.3 76.2 - - - +
238B GLU* 1.3 57.3 + - - +
240B ARG* 3.3 3.1 + - - +
241B LEU* 2.9 36.1 + - - +
254B VAL* 5.0 2.2 - - - -
259B THR* 4.1 28.5 - - + -
263B ALA* 5.4 0.9 - - + -
267B ILE* 3.6 33.0 - - + -
262G GLY* 4.4 6.1 - - - +
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Residues in contact with GLU 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 LEU* 3.0 25.9 + - + +
235B LEU* 3.1 27.5 + - - +
237B MET* 1.3 76.5 - - - +
239B GLN* 1.3 64.4 + - + +
241B LEU* 3.2 4.9 + - - +
242B GLU* 3.1 21.5 + - - +
266B TYR* 2.5 39.3 + - + -
267B ILE* 5.2 0.9 - - + -
270B LEU* 4.0 25.1 - - + +
274B TYR* 5.0 1.7 + - - -
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Residues in contact with GLN 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 LEU* 3.0 18.8 + - - +
236B GLU* 3.3 24.5 + - - +
238B GLU* 1.3 78.1 - - + +
240B ARG* 1.3 60.1 + - + +
242B GLU* 3.3 14.4 + - - +
243B VAL* 3.1 31.8 + - + +
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Residues in contact with ARG 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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195B THR* 4.3 3.6 - - - +
196B SER* 3.6 21.9 + - - +
202B PHE* 3.4 43.3 - - + +
229B ASN 5.0 1.2 + - - -
230B ILE* 3.9 21.6 + - + +
231B THR 3.9 7.7 + - - -
232B ALA* 3.8 14.7 - - - +
236B GLU* 2.9 44.1 + - - +
237B MET 3.8 3.4 - - - +
239B GLN* 1.3 78.1 + - + +
241B LEU* 1.3 63.4 + - - +
243B VAL* 3.5 4.4 + - + -
244B LEU* 3.2 28.2 + - - +
97G GLU* 2.5 43.2 + - - -
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Residues in contact with LEU 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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230B ILE* 3.9 22.0 - - + -
237B MET 2.9 21.2 + - - +
238B GLU 3.2 4.5 + - - +
240B ARG* 1.3 73.8 - - - +
242B GLU* 1.3 66.3 + - - +
244B LEU* 3.2 7.2 + - - +
245B ALA* 2.9 23.7 + - - +
252B ALA* 3.8 29.6 - - + -
267B ILE* 4.2 16.8 - - + +
270B LEU* 3.5 33.7 - - + -
271B ALA* 4.4 13.0 - - + -
274B TYR* 3.9 14.1 - - + -
276B LEU* 3.9 14.5 - - + +
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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 GLU 3.1 11.8 + - - +
239B GLN* 3.5 15.8 - - - +
241B LEU* 1.3 77.6 - - - +
243B VAL* 1.3 56.2 + - + +
245B ALA* 3.1 2.5 + - - +
246B ASP* 2.8 54.4 + - - +
274B TYR* 3.9 26.4 + - + +
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Residues in contact with VAL 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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202B PHE* 4.1 19.3 - - + -
203B GLU* 4.5 17.0 - - + +
206B ALA* 4.1 9.9 - - + -
207B GLU* 6.1 0.2 - - + -
239B GLN* 3.1 19.1 + - + +
240B ARG* 3.6 11.2 - - + +
242B GLU* 1.3 76.9 - - - +
244B LEU* 1.3 63.3 + - - +
246B ASP* 3.3 5.9 + - - +
247B LEU* 3.2 40.3 + - + +
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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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202B PHE* 3.4 29.4 - - + -
206B ALA* 4.6 2.0 - - + -
226B TRP* 3.8 2.9 - - + -
228B ALA* 3.7 14.1 - - + -
230B ILE* 4.0 8.3 - - + -
240B ARG 3.2 14.3 + - - +
241B LEU* 3.2 7.7 + - - +
243B VAL* 1.3 78.8 - - - +
245B ALA* 1.3 63.2 + - - +
247B LEU* 3.3 2.3 + - - -
248B GLY 3.3 3.1 + - - -
249B LEU* 3.1 54.6 + - + +
251B HIS 3.6 21.8 - - - +
252B ALA* 3.8 19.7 - - + -
276B LEU* 3.9 16.8 - - + -
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Residues in contact with ALA 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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241B LEU 2.9 11.6 + - - +
242B GLU 3.6 3.8 - - - +
244B LEU* 1.3 77.0 - - - +
246B ASP* 1.3 66.2 + - - +
248B GLY* 3.3 12.2 + - - -
249B LEU 5.2 0.9 - - - +
274B TYR* 3.4 52.3 - - + +
276B LEU* 4.4 7.1 - - - +
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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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242B GLU* 2.8 40.5 + - - +
243B VAL* 3.8 6.6 - - - +
244B LEU 3.3 0.4 - - - -
245B ALA* 1.3 80.4 - - - +
247B LEU* 1.3 63.6 + - + +
274B TYR* 6.0 0.5 - - - -
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Residues in contact with LEU 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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206B ALA* 3.8 41.7 - - + +
207B GLU* 3.8 28.0 - - + +
210B ALA* 4.3 19.5 - - + +
243B VAL* 3.2 23.8 + - + +
244B LEU 3.3 4.2 + - - +
245B ALA 3.2 0.2 - - - -
246B ASP* 1.3 82.0 - - + +
248B GLY* 1.3 60.7 + - - +
249B LEU* 3.3 13.3 + - + +
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Residues in contact with GLY 248 (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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244B LEU 3.3 2.8 + - - -
245B ALA 3.3 12.2 + - - -
246B ASP 3.3 1.0 + - - -
247B LEU* 1.3 78.7 - - - +
249B LEU* 1.3 68.6 + - - +
250B LYS* 4.2 9.2 - - - +
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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