Contacts of the helix formed by residues 228 - 244 (chain N) in PDB entry 5DSV
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 PRO 228 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215N TRP* 3.4 19.7 - - + +
225N GLU* 6.2 0.2 - - - +
226N ILE* 3.5 10.5 - - + +
227N VAL* 1.4 90.8 - - + +
229N LYS* 1.3 59.7 + - - +
230N ASP* 3.4 19.1 - - - +
231N ILE* 3.1 25.5 + - + +
232N ARG* 3.3 7.8 + - - +
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Residues in contact with LYS 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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60N GLU* 6.2 0.2 - - - -
227N VAL 3.8 0.2 + - - -
228N PRO* 1.3 69.8 - - - +
230N ASP* 1.3 70.6 + - - +
231N ILE 3.1 1.1 - - - -
232N ARG* 3.9 29.1 - - - +
233N GLU* 3.0 53.0 + - + +
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Residues in contact with ASP 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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228N PRO* 3.8 17.3 - - - +
229N LYS* 1.3 78.8 + - - +
231N ILE* 1.3 75.5 + - + +
233N GLU* 3.9 3.9 + - - +
234N GLU* 2.9 29.4 + - - +
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Residues in contact with ILE 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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187N ARG* 3.4 47.1 - - - +
190N VAL* 4.6 13.7 - - + -
215N TRP* 4.6 9.6 - - + -
227N VAL* 3.7 16.4 - - + -
228N PRO* 3.1 21.2 + - + +
230N ASP* 1.3 96.8 - - + +
232N ARG* 1.3 58.0 + - - +
234N GLU* 3.3 9.3 - - - +
235N ALA* 2.8 37.4 + - + +
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Residues in contact with ARG 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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211N LEU 3.4 26.2 + - - -
212N GLU* 5.6 0.2 - - - +
213N LEU* 4.1 30.0 - - + +
226N ILE* 4.4 17.2 - - - +
227N VAL* 2.7 36.4 + - + +
228N PRO 3.3 3.7 + - - +
229N LYS* 3.9 35.2 - - - +
231N ILE* 1.3 75.0 - - - +
233N GLU* 1.3 60.2 + - + +
235N ALA* 2.9 2.5 + - - -
236N GLU* 2.5 61.3 + - + +
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Residues in contact with GLU 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 LYS* 3.0 49.0 + - + +
230N ASP* 3.9 3.0 + - - +
232N ARG* 1.3 78.1 - - + +
234N GLU* 1.3 56.8 + - - +
236N GLU* 3.5 14.7 - - - +
237N LYS* 2.9 30.7 + - - +
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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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187N ARG* 3.9 24.3 + - - -
191N LYS* 3.6 29.5 + - - +
230N ASP 2.9 19.2 + - - +
231N ILE* 3.3 9.5 - - - +
233N GLU* 1.3 77.2 - - - +
235N ALA* 1.3 71.8 + - - +
237N LYS* 3.5 8.9 + - - +
238N TYR* 3.0 25.6 + - - +
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Residues in contact with ALA 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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190N VAL* 4.1 13.7 - - + +
191N LYS* 3.9 29.4 - - + +
194N ALA* 4.1 8.1 - - + +
213N LEU* 5.2 1.1 - - + -
231N ILE* 2.8 25.0 + - + +
232N ARG* 2.9 3.1 + - - +
234N GLU* 1.3 76.7 + - - +
236N GLU* 1.3 59.4 + - - +
238N TYR* 3.3 11.8 + - - +
239N ALA* 3.0 28.1 + - - +
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Residues in contact with GLU 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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194N ALA* 4.6 2.8 - - - +
198N TYR* 3.1 24.8 + - - +
209N PHE 5.7 0.3 - - - +
210N GLU* 5.7 1.2 - - - +
211N LEU* 3.9 33.4 + - + +
213N LEU* 5.9 0.2 - - - +
232N ARG* 2.5 47.7 + - + +
233N GLU* 3.5 13.4 - - - +
235N ALA* 1.3 68.8 - - - +
237N LYS* 1.3 65.6 + - - +
239N ALA* 3.2 8.7 + - - +
240N LYS* 3.0 42.0 + - - +
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Residues in contact with LYS 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 GLU 2.9 20.9 + - - +
234N GLU* 3.5 9.0 - - - +
236N GLU* 1.3 72.4 - - - +
238N TYR* 1.3 62.5 + - - +
240N LYS* 3.1 16.5 + - + +
241N GLU* 3.0 48.0 + - + +
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Residues in contact with TYR 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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191N LYS* 3.5 63.0 - - + -
192N GLU* 2.9 26.5 + - - -
195N LYS* 3.9 21.4 + - + +
234N GLU 3.0 15.1 + - - +
235N ALA 3.3 8.5 + - - +
237N LYS* 1.3 75.6 - - - +
239N ALA* 1.3 56.5 + - - +
241N GLU* 3.6 10.3 + - + +
242N SER* 2.6 53.5 + - - -
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Residues in contact with ALA 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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194N ALA* 3.4 27.4 - - + +
195N LYS* 3.5 18.2 - - - +
198N TYR* 3.7 17.4 - - + +
235N ALA 3.0 10.4 + - - +
236N GLU 3.2 9.4 + - - +
238N TYR* 1.3 77.4 - - - +
240N LYS* 1.3 65.2 + - - +
241N GLU 3.1 0.3 + - - -
242N SER* 3.5 5.1 + - - -
243N LEU* 2.9 25.8 + - - +
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Residues in contact with LYS 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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198N TYR* 3.2 38.5 - - + -
236N GLU* 3.0 31.3 + - - +
237N LYS* 3.5 15.0 - - + +
239N ALA* 1.3 74.4 - - - +
241N GLU* 1.3 59.4 + - + +
243N LEU* 3.2 27.9 - - + +
244N LYS* 3.6 25.5 + - - +
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Residues in contact with GLU 241 (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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237N LYS* 3.0 52.0 + - + +
238N TYR* 3.9 9.7 - - + +
240N LYS* 1.3 76.1 - - + +
242N SER* 1.3 60.7 + - - +
243N LEU 3.1 1.6 - - - -
244N LYS* 3.1 40.4 + - - +
245N GLU* 4.8 0.3 - - - +
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Residues in contact with SER 242 (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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195N LYS* 4.0 31.1 + - - +
238N TYR* 2.6 43.5 + - - -
239N ALA* 3.5 6.9 + - - -
241N GLU* 1.3 74.7 - - - +
243N LEU* 1.3 63.5 + - - +
245N GLU* 2.9 28.7 - - - +
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Residues in contact with LEU 243 (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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195N LYS* 6.1 0.6 - - - +
198N TYR* 4.2 38.4 - - + +
199N ILE* 4.6 13.5 - - + +
203N GLU* 4.2 20.9 - - - +
239N ALA 2.9 13.6 + - - +
240N LYS* 3.2 23.8 - - + +
242N SER* 1.3 78.7 - - - +
244N LYS* 1.3 66.7 + - + +
245N GLU* 3.1 12.1 + - - +
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Residues in contact with LYS 244 (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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240N LYS* 3.6 24.4 + - - +
241N GLU* 3.1 26.4 + - - +
243N LEU* 1.3 74.8 - - + +
245N GLU* 1.3 72.1 + - - +
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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