Contacts of the helix formed by residues 225 - 240 (chain N) in PDB entry 5GJQ
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 225 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199N ARG* 2.8 37.9 + - - +
220N LEU* 3.4 21.0 + - + +
223N LEU* 2.9 35.5 - - + +
224N ASP* 1.3 76.5 - - - +
226N PRO* 1.3 64.8 - - - +
227N GLN* 3.3 4.4 + - + +
228N ALA* 3.4 22.7 + - + +
229N VAL 3.5 0.3 + - - -
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Residues in contact with PRO 226 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220N LEU* 5.4 0.2 - - + -
224N ASP 3.5 6.3 - - - +
225N ASP* 1.3 69.0 - - - +
227N GLN* 1.3 55.4 + - - +
229N VAL* 3.1 6.5 + - + +
230N SER* 2.5 42.2 + - - +
260N PHE* 5.9 4.0 - - + +
263N SER* 4.7 15.9 - - - -
264N VAL* 4.1 25.3 - - + +
267N ASN* 5.0 7.6 - - - -
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Residues in contact with GLN 227 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225N ASP* 3.3 3.6 - - + -
226N PRO* 1.3 77.5 - - - +
228N ALA* 1.3 51.7 + - - +
230N SER* 2.8 8.7 + - - -
231N ASP* 2.2 50.4 + - - -
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Residues in contact with ALA 228 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202N VAL* 4.8 17.9 - - + -
220N LEU* 4.7 11.2 - - + -
223N LEU* 6.0 4.0 - - + -
225N ASP* 3.4 20.5 + - + +
226N PRO 3.3 0.2 - - - -
227N GLN* 1.3 77.1 - - - +
229N VAL* 1.3 51.7 + - - +
231N ASP* 3.2 9.6 - - - +
232N ILE* 2.3 39.6 + - - +
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Residues in contact with VAL 229 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220N LEU* 4.1 20.9 - - + +
225N ASP 3.5 2.2 + - - -
226N PRO* 3.1 9.8 + - + +
228N ALA* 1.3 76.6 - - - +
230N SER* 1.3 52.2 + - - +
232N ILE* 2.9 12.4 - - + +
233N LEU* 2.3 45.7 + - + +
252N LEU* 5.8 7.6 - - + -
264N VAL* 4.4 16.6 - - + -
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Residues in contact with SER 230 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226N PRO* 2.5 28.3 + - - +
227N GLN* 2.8 13.2 + - - -
229N VAL* 1.3 67.7 - - - +
231N ASP* 1.3 54.8 + - - -
233N LEU* 3.2 12.3 - - - +
234N GLU* 2.5 43.5 + - - +
264N VAL* 5.1 4.2 - - - +
267N ASN* 4.1 22.9 - - - +
268N LEU 5.4 0.5 + - - -
271N VAL* 5.4 11.3 - - - +
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Residues in contact with ASP 231 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206N MET* 5.0 15.9 - - - -
227N GLN* 2.2 46.9 + - - +
228N ALA* 3.2 9.6 - - - +
230N SER* 1.3 64.9 - - - +
232N ILE* 1.3 53.8 + - - +
234N GLU* 3.3 8.7 + - - +
235N LYS* 2.6 41.1 + - - +
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Residues in contact with ILE 232 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213N PHE* 5.3 7.2 - - + -
216N VAL* 6.3 4.9 - - + -
228N ALA 2.3 28.0 + - - +
229N VAL* 2.9 17.9 - - - +
231N ASP* 1.3 65.9 - - - +
233N LEU* 1.3 53.1 + - + +
235N LYS* 2.8 26.4 + - - +
236N LEU* 2.1 39.3 + - + -
248N ILE* 4.2 33.9 - - + -
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Residues in contact with LEU 233 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229N VAL* 2.3 46.0 + - + +
230N SER* 2.9 13.9 + - - +
232N ILE* 1.3 67.3 - - + +
234N GLU* 1.3 50.9 + - - +
236N LEU* 3.0 20.9 - - + +
237N VAL* 2.3 45.0 + - + +
248N ILE* 5.7 3.6 - - + -
252N LEU* 6.3 2.9 - - + -
264N VAL* 6.3 3.6 - - + -
268N LEU* 4.8 23.1 - - + -
271N VAL* 6.3 2.5 - - + -
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Residues in contact with GLU 234 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230N SER* 2.5 24.0 + - - +
231N ASP* 3.5 9.0 - - - +
233N LEU* 1.3 69.2 - - - +
235N LYS* 1.3 52.2 + - - +
237N VAL* 2.7 11.8 + - - +
238N LYS* 2.3 46.6 + - + +
271N VAL* 5.1 15.0 - - + -
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Residues in contact with LYS 235 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202N VAL* 6.3 1.8 - - - -
206N MET* 3.8 37.5 - - + +
208N LEU* 3.8 26.8 - - + +
211N PRO* 4.9 5.5 - - - +
213N PHE* 5.3 7.9 - - - -
216N VAL* 6.3 0.6 - - - +
231N ASP 2.6 21.4 + - - +
232N ILE* 3.2 25.6 + - - +
234N GLU* 1.3 71.7 - - - +
236N LEU* 1.3 51.9 + - - +
238N LYS* 3.1 12.4 - - + +
239N GLU* 2.4 55.3 + - + +
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Residues in contact with LEU 236 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232N ILE* 2.1 33.0 + - + +
233N LEU* 3.0 22.9 - - + +
235N LYS* 1.3 66.8 - - - +
237N VAL* 1.3 57.4 + - + +
239N GLU* 2.6 11.6 + - - +
240N ASP* 2.5 47.5 + - - -
244N MET* 4.2 5.8 - - + -
245N ALA* 3.4 48.9 - - + +
248N ILE* 3.8 31.9 - - + -
268N LEU* 6.3 1.6 - - + -
325N MET* 5.1 8.7 - - + -
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Residues in contact with VAL 237 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233N LEU* 2.3 41.3 + - + +
234N GLU* 2.7 11.0 + - - +
236N LEU* 1.3 74.1 - - + +
238N LYS* 1.3 59.9 + - + +
240N ASP* 3.2 25.5 - - - +
268N LEU* 5.7 7.0 - - + -
321N GLN* 4.6 22.7 - - - +
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Residues in contact with LYS 238 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234N GLU* 2.3 39.6 + - + +
235N LYS* 3.1 16.4 - - + +
237N VAL* 1.3 69.9 - - + +
239N GLU* 1.3 62.7 + - - +
240N ASP 3.2 3.0 + - - -
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Residues in contact with GLU 239 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208N LEU* 6.2 3.8 - - + +
235N LYS* 2.4 51.5 + - + +
236N LEU* 2.6 9.4 + - - +
238N LYS* 1.3 73.4 - - - +
240N ASP* 1.3 64.9 + - - +
241N ASN* 3.2 7.2 + - - +
244N MET* 4.9 12.9 - - + +
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Residues in contact with ASP 240 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236N LEU* 2.5 20.1 + - - +
237N VAL* 3.2 25.8 - - - +
238N LYS 3.2 4.2 + - - -
239N GLU* 1.3 74.1 - - - +
241N ASN* 1.3 69.9 + - - +
242N LEU* 5.1 0.4 - - - -
245N ALA* 5.1 5.6 - - - -
321N GLN 5.6 7.0 - - - -
322N THR* 5.7 6.1 - - - -
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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