Contacts of the helix formed by residues 227 - 241 (chain B) in PDB entry 2ACX
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 GLY 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197B PHE* 4.6 15.7 - - - -
222B ILE* 3.0 20.4 + - - +
225B ARG* 3.3 5.0 + - - +
226B LYS* 1.3 70.9 - - - +
228B GLU* 1.3 58.6 + - - +
229B ALA 3.6 1.6 - - - -
230B MET* 3.8 15.2 - - - +
231B ALA* 2.8 32.6 + - - +
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Residues in contact with GLU 228 (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 ILE* 3.0 28.7 - - + +
223B LYS* 3.2 18.5 + - - +
226B LYS* 3.1 35.8 + - - +
227B GLY* 1.3 74.1 - - - +
229B ALA* 1.3 67.8 + - - +
231B ALA* 3.1 1.2 + - - -
232B LEU* 2.9 26.6 + - - +
494B THR* 6.1 4.0 - - + -
495B ASP* 5.1 8.6 - - - +
498B PHE* 3.4 42.1 - - + -
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Residues in contact with ALA 229 (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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226B LYS 5.2 0.4 + - - -
228B GLU* 1.3 79.5 + - - +
230B MET* 1.3 57.4 + - - +
232B LEU* 3.7 11.3 - - - +
233B ASN* 3.0 28.8 + - - +
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Residues in contact with MET 230 (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 PHE* 4.3 25.4 - - + -
217B LEU* 6.2 0.7 - - + -
227B GLY* 3.6 13.8 + - - +
228B GLU 3.1 0.4 - - - -
229B ALA* 1.3 79.0 - - - +
231B ALA* 1.3 74.2 + - + +
233B ASN* 3.4 6.7 + - + +
234B GLU* 3.2 33.6 + - - +
331B GLY* 3.7 30.4 - - - +
332B LEU* 6.0 3.6 - - + -
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Residues in contact with ALA 231 (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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217B LEU* 3.7 29.2 - - + +
222B ILE* 3.9 10.3 - - + -
227B GLY 2.8 21.6 + - - +
228B GLU 3.8 2.2 - - - +
230B MET* 1.3 79.8 - - + +
232B LEU* 1.3 66.3 + - - +
234B GLU* 3.3 7.7 + - - +
235B LYS* 3.2 21.7 + - - +
259B LEU* 5.5 0.2 - - + -
261B LEU* 5.6 1.6 - - - +
498B PHE* 4.6 8.7 - - + -
502B PHE* 4.2 7.4 - - + -
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Residues in contact with LEU 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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228B GLU 2.9 16.7 + - - +
229B ALA* 3.7 9.0 - - - +
231B ALA* 1.3 76.7 - - - +
233B ASN* 1.3 55.7 + - - +
235B LYS* 3.3 7.6 + - + +
236B GLN* 2.9 65.9 + - + +
498B PHE* 4.1 16.8 - - + -
501B LYS* 4.2 36.3 - - + +
502B PHE* 4.6 13.2 - - + +
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Residues in contact with ASN 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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229B ALA 3.0 19.4 + - - +
230B MET* 3.6 9.8 - - + +
231B ALA 3.2 0.2 - - - -
232B LEU* 1.3 73.6 - - - +
234B GLU* 1.3 67.1 + - - +
236B GLN* 3.4 8.0 + - - +
237B ILE* 3.1 49.3 + - - +
330B LEU 5.1 0.4 + - - -
331B GLY 4.7 7.1 + - - -
333B ALA 3.0 27.7 + - - +
334B VAL* 4.4 11.0 - - - +
335B HIS* 5.4 1.6 + - - +
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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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215B LYS* 2.4 37.4 + - - +
217B LEU* 6.0 2.3 - - - +
230B MET* 3.2 20.8 + - - +
231B ALA* 3.3 10.4 + - - +
233B ASN* 1.3 78.9 - - - +
235B LYS* 1.3 58.8 + - - +
237B ILE* 3.8 3.3 - - - +
238B LEU* 3.0 48.4 + - + +
261B LEU* 3.9 14.3 - - + +
263B LEU* 6.0 0.5 - - - +
329B ASP* 4.2 2.6 - - - +
330B LEU* 3.9 19.6 + - + +
331B GLY* 3.6 33.8 - - - +
577B ANP 4.7 0.2 + - - -
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Residues in contact with LYS 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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231B ALA 3.2 12.8 + - - +
232B LEU* 3.6 8.3 - - + +
234B GLU* 1.3 77.8 - - - +
236B GLN* 1.3 72.8 + - + +
238B LEU* 3.2 5.5 + - - +
239B GLU* 2.7 55.8 + - - +
249B LEU* 3.9 10.8 - - + +
252B ALA* 4.1 9.9 - - + -
261B LEU* 3.8 30.7 - - + +
501B LYS 4.1 5.1 + - - -
502B PHE* 3.4 33.3 + - + +
504B THR* 3.4 34.9 + - - +
507B VAL* 6.0 0.2 - - - -
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Residues in contact with GLN 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 LEU* 2.9 55.9 + - + +
233B ASN* 4.1 6.9 - - - +
235B LYS* 1.3 80.4 - - + +
237B ILE* 1.3 62.6 + - + +
239B GLU* 3.2 23.2 - - - +
240B LYS* 3.1 24.4 + - - +
501B LYS* 4.8 8.7 + - - +
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Residues in contact with ILE 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 ASN* 3.1 48.3 + - - +
234B GLU* 3.8 3.8 - - - +
236B GLN* 1.3 76.0 - - + +
238B LEU* 1.3 66.2 + - - +
239B GLU 3.2 0.2 + - - -
240B LYS* 3.2 2.9 + - - +
241B VAL* 3.1 25.6 + - + +
307B ILE* 3.8 34.3 - - + -
330B LEU* 3.8 28.3 - - + +
333B ALA* 3.8 24.2 - - + +
334B VAL* 4.2 7.6 - - - +
335B HIS* 4.9 3.1 - - + +
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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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234B GLU* 3.0 45.3 + - + +
235B LYS* 3.2 5.4 + - - +
237B ILE* 1.3 76.7 - - - +
239B GLU* 1.3 61.8 + - - +
241B VAL* 3.2 19.3 + - - +
246B VAL* 4.6 1.6 - - + -
247B VAL* 3.4 31.5 - - + +
248B SER* 5.0 0.3 - - - -
249B LEU* 3.8 25.2 + - + +
261B LEU* 4.4 9.2 - - + -
263B LEU* 4.0 24.7 - - + -
330B LEU* 3.8 33.2 - - + +
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Residues in contact with GLU 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 LYS* 2.7 46.7 + - - +
236B GLN* 3.2 28.9 - - - +
238B LEU* 1.3 76.9 - - - +
240B LYS* 1.3 63.8 + - + +
241B VAL 3.8 4.0 - - - +
242B ASN* 5.9 0.7 + - - +
249B LEU* 4.0 15.9 - - + +
504B THR* 4.5 4.9 + - - -
507B VAL* 4.1 30.9 - - + +
508B PRO* 6.0 0.7 - - - +
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Residues in contact with LYS 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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59B ARG* 5.3 4.7 + - - -
236B GLN 3.1 17.7 + - - +
237B ILE* 4.0 4.5 - - - +
239B GLU* 1.3 80.5 - - + +
241B VAL* 1.3 61.7 + - + +
242B ASN* 3.7 2.8 + - - +
305B GLU* 2.9 66.5 + - - +
307B ILE* 4.4 9.3 - - + +
335B HIS* 4.2 18.4 + - - +
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Residues in contact with VAL 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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237B ILE* 3.1 22.4 + - + +
238B LEU* 3.2 16.2 - - - +
239B GLU 3.8 3.6 - - - +
240B LYS* 1.3 76.2 - - - +
242B ASN* 1.3 67.6 + - - +
243B SER* 3.9 23.6 - - - +
246B VAL* 4.0 24.5 - - + +
247B VAL 5.6 0.9 - - - +
248B SER* 5.5 5.2 - - - -
301B ASP* 5.4 4.7 - - + +
302B LEU* 3.8 24.5 - - + -
305B GLU* 4.1 14.1 - - + -
307B ILE* 4.0 17.5 - - + -
330B LEU* 5.4 0.9 - - + -
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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