Contacts of the helix formed by residues 229 - 245 (chain B) in PDB entry 5E9W
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 ALA 229 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B ASP* 2.8 12.7 + - - +
228B ILE* 1.3 80.6 - - + +
230B ASP* 1.3 65.7 + - - +
231B VAL* 3.3 2.5 - - + +
232B SER* 3.1 20.6 + - - +
233B VAL* 3.1 23.5 + - - +
501B SAH 4.1 7.6 - - - +
194D LYS 5.0 10.8 - - - +
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Residues in contact with ASP 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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228B ILE 3.5 4.8 + - - -
229B ALA* 1.3 71.8 - - - +
231B VAL* 1.3 61.0 + - + +
233B VAL* 3.3 1.6 + - - +
234B LYS* 3.0 61.1 + - - +
259B THR* 2.6 39.7 + - + +
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Residues in contact with VAL 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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208B LYS* 4.9 1.1 - - - -
229B ALA* 3.3 2.8 - - + +
230B ASP* 1.3 79.4 - - + +
232B SER* 1.3 58.4 + - - +
234B LYS* 3.4 8.1 + - + +
235B GLN* 2.9 48.1 + - + +
194D LYS 5.4 1.6 - - - +
195D LYS* 3.2 28.5 - - - +
196D LYS* 3.8 16.2 - - + +
197D ARG* 4.0 18.6 - - + -
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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
----------------------------------------------------------
207B GLY* 3.3 33.5 - - - +
208B LYS* 3.2 29.3 + - - +
227B ASP* 4.4 4.4 + - - -
229B ALA* 3.1 25.2 + - - +
231B VAL* 1.3 76.1 - - - +
233B VAL* 1.3 54.7 + - - +
235B GLN* 3.1 1.9 + - - +
236B CYS 2.7 31.7 + - - -
501B SAH 4.8 2.6 + - - -
194D LYS 5.3 2.3 + - - -
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B CYS* 5.0 2.9 - - - -
207B GLY 4.6 1.6 - - - -
225B CYS 4.8 2.7 - - - +
226B THR 4.7 0.9 - - - -
227B ASP* 3.6 35.2 - - + +
229B ALA 3.1 15.1 + - - +
230B ASP* 3.6 7.0 - - - +
232B SER* 1.3 74.3 - - - +
234B LYS* 1.3 61.9 + - + +
236B CYS* 3.2 7.5 + - - +
237B GLN* 2.8 29.1 + - + +
257B PHE* 3.9 27.2 - - + +
258B ILE 4.0 12.3 - - - +
259B THR* 3.5 22.4 - - - +
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Residues in contact with LYS 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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230B ASP* 3.0 49.6 + - - +
231B VAL* 3.8 7.6 - - + +
233B VAL* 1.3 80.8 - - + +
235B GLN* 1.3 57.0 + - + +
237B GLN* 3.3 19.3 + - - +
238B GLN* 2.9 28.4 + - - +
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Residues in contact with GLN 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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208B LYS* 3.0 46.6 - - + +
231B VAL* 2.9 32.4 + - + +
232B SER 3.6 4.0 - - - +
234B LYS* 1.3 74.0 - - - +
236B CYS* 1.3 65.2 + - - +
238B GLN* 3.2 6.4 + - - +
239B ARG* 2.9 26.7 + - - +
196D LYS* 4.2 7.3 - - - +
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Residues in contact with CYS 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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206B CYS* 4.1 5.8 - - - -
207B GLY 3.6 11.7 - - - +
208B LYS 3.3 12.2 + - - -
209B GLY* 3.7 20.4 - - - -
212B LEU* 3.5 11.8 - - - +
225B CYS* 3.8 33.9 - - - -
232B SER 2.7 19.5 + - - +
233B VAL* 3.4 7.9 - - - +
235B GLN* 1.3 73.8 - - - +
237B GLN* 1.3 62.0 + - - +
239B ARG* 3.2 1.5 + - - -
240B TYR* 3.0 19.4 + - - +
257B PHE* 4.0 6.5 - - + -
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Residues in contact with GLN 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 VAL* 2.8 21.1 + - - +
234B LYS* 3.5 20.7 + - - +
236B CYS* 1.3 73.6 - - - +
238B GLN* 1.3 57.3 + - - +
240B TYR* 3.2 4.2 + - - +
241B GLU* 3.0 37.1 + - + +
257B PHE* 3.5 47.7 - - + +
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Residues in contact with GLN 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 LYS 2.9 16.1 + - - +
235B GLN* 3.2 8.0 + - - +
237B GLN* 1.3 75.2 - - - +
239B ARG* 1.3 60.8 + - - +
241B GLU* 3.2 15.0 + - - +
242B ASP* 2.6 60.5 + - - +
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Residues in contact with ARG 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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208B LYS* 3.5 26.8 + - - +
209B GLY 2.9 28.5 + - - -
210B GLY* 3.5 15.0 + - - +
212B LEU* 3.7 11.0 - - + +
235B GLN 2.9 14.2 + - - +
236B CYS 3.2 8.0 + - - +
238B GLN* 1.3 75.8 - - - +
240B TYR* 1.3 59.0 + - - +
242B ASP* 3.3 10.6 + - + +
243B MET* 3.0 35.4 + - + +
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Residues in contact with TYR 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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212B LEU* 3.7 12.5 - - + +
236B CYS 3.0 9.6 + - - +
237B GLN 3.5 6.7 - - - +
238B GLN 3.2 0.2 - - - -
239B ARG* 1.3 78.9 - - - +
241B GLU* 1.3 75.9 + - - +
243B MET* 3.2 8.2 + - - +
244B LYS* 3.1 60.2 + - + +
252B ILE* 3.7 18.4 - - + -
253B PHE* 2.6 57.6 + + - -
254B SER* 3.6 7.6 - - - -
255B ALA* 3.7 15.1 + - + -
257B PHE* 3.6 31.2 - + + -
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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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237B GLN* 3.0 26.9 + - + +
238B GLN* 3.2 23.1 + - - +
240B TYR* 1.3 95.9 - - + +
242B ASP* 1.3 57.3 + - - +
244B LYS* 3.2 12.8 + - - +
245B ASN* 2.9 55.5 + - - +
257B PHE* 5.7 0.7 - - - -
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Residues in contact with ASP 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 GLN* 2.6 51.1 + - - +
239B ARG* 3.6 10.0 - - - +
241B GLU* 1.3 75.3 - - - +
243B MET* 1.3 62.5 + - + +
245B ASN* 3.8 6.1 + - - +
246B ARG* 3.3 25.8 + - - +
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Residues in contact with MET 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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212B LEU* 3.8 39.0 - - + +
213B LEU* 4.3 12.1 - - + -
216B LYS* 3.7 44.2 + - + +
239B ARG* 3.0 22.6 + - + +
240B TYR* 3.5 9.9 - - - +
242B ASP* 1.3 77.8 - - + +
244B LYS* 1.3 61.0 + - - +
246B ARG* 3.4 23.3 + - - +
249B SER* 3.2 14.0 + - - -
252B ILE* 3.8 14.8 - - + -
253B PHE* 4.7 4.0 - - + -
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Residues in contact with LYS 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 TYR* 3.1 42.8 + - + +
241B GLU* 3.4 20.8 + - - +
243B MET* 1.3 79.0 - - - +
245B ASN* 1.3 66.0 + - - +
246B ARG 3.2 2.9 + - - +
249B SER* 3.6 18.7 - - - -
252B ILE* 3.3 33.6 - - + +
253B PHE 5.0 0.2 - - - -
254B SER* 5.6 2.4 - - - +
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Residues in contact with ASN 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 GLU* 2.9 41.7 + - - +
242B ASP* 3.5 7.0 + - - +
243B MET 3.3 0.2 - - - -
244B LYS* 1.3 82.9 - - - +
246B ARG* 1.3 61.8 + - - +
247B ARG 3.6 1.2 + - - -
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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