Contacts of the helix formed by residues 225 - 233 (chain E) in PDB entry 5BOU
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49E LYS* 3.2 25.0 + - - +
210E LEU 3.5 2.3 - - - +
211E SER* 2.8 27.0 + - - -
223E ILE* 3.5 21.5 + - - +
224E TYR* 1.3 76.5 - - - +
226E GLY* 1.3 67.8 + - - +
227E GLU 3.7 0.3 + - - -
228E ALA* 3.5 15.4 + - - +
229E VAL* 4.3 4.5 - - - -
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Residues in contact with GLY 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E LYS* 5.2 2.0 - - - +
207E VAL* 3.2 30.4 + - - +
208E ASP* 5.3 3.3 - - - +
210E LEU 4.8 0.8 + - - -
225E ASP* 1.3 71.0 - - - +
227E GLU* 1.3 62.7 + - - -
228E ALA 3.1 6.3 + - - -
229E VAL* 3.2 21.7 - - - +
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Residues in contact with GLU 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E VAL* 3.9 17.2 - - + +
225E ASP 3.7 0.4 + - - -
226E GLY* 1.3 70.4 - - - -
228E ALA* 1.3 59.8 + - - +
229E VAL 3.2 1.2 + - - -
230E ALA* 3.3 19.5 + - + +
231E LYS* 4.5 2.6 + - - -
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Residues in contact with ALA 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E TYR* 4.2 29.7 - - + +
225E ASP 3.5 15.9 + - - +
226E GLY 3.1 1.4 - - - -
227E GLU* 1.3 78.6 - - - +
229E VAL* 1.3 60.4 + - - +
231E LYS* 3.8 20.9 + - - +
232E TYR* 4.2 8.7 - - - -
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Residues in contact with VAL 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E VAL* 3.9 12.3 - - - +
210E LEU* 3.9 38.9 - - + +
212E ILE* 3.9 19.3 - - + -
224E TYR* 3.4 42.4 - - + +
225E ASP* 4.3 0.2 - - - -
226E GLY 3.2 17.7 + - - +
228E ALA* 1.3 74.8 - - - +
230E ALA* 1.3 64.7 + - - +
231E LYS 3.2 3.4 - - - -
232E TYR* 3.0 20.4 + - + +
233E ILE* 3.3 13.1 + - + +
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Residues in contact with ALA 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E VAL* 4.1 16.6 - - + -
226E GLY 4.0 0.4 + - - -
227E GLU* 3.3 20.1 + - + +
229E VAL* 1.3 78.9 - - - +
231E LYS* 1.3 62.9 + - - +
232E TYR 3.2 0.5 + - - -
233E ILE* 3.2 31.0 + - + +
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Residues in contact with LYS 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E ASP* 4.5 11.4 - - - +
190E LYS* 5.3 6.6 + - - +
227E GLU 4.5 2.8 + - - +
228E ALA* 3.8 18.8 + - - +
230E ALA* 1.3 80.2 - - - +
232E TYR* 1.3 91.9 + - + +
233E ILE 4.6 2.4 - - - +
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Residues in contact with TYR 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E ASP* 3.2 39.7 + - + -
189E ILE* 3.4 45.5 - - + +
190E LYS* 4.6 20.4 - - + +
193E VAL* 3.8 32.8 - - + +
210E LEU* 4.7 2.0 - - + -
212E ILE* 4.0 17.3 - - + -
224E TYR* 5.5 9.1 - + - -
228E ALA 4.2 9.6 - - - -
229E VAL* 3.0 19.2 + - + +
231E LYS* 1.3 101.9 - - + +
233E ILE* 1.3 64.8 + - - +
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Residues in contact with ILE 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E VAL* 5.7 1.3 - - - -
205E LEU* 3.4 26.7 - - + +
206E THR* 3.4 34.5 - - - +
207E VAL* 3.5 13.7 - - + +
210E LEU* 4.3 11.2 - - + -
229E VAL* 3.3 10.7 + - + +
230E ALA* 3.2 28.7 + - + +
231E LYS 4.6 2.6 - - - +
232E TYR* 1.3 81.8 - - - +
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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