Contacts of the helix formed by residues 227 - 239 (chain A) in PDB entry 5I2Y
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 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ARG* 2.9 45.9 + - + -
151A HIS* 4.5 14.1 + - - +
223A GLY 4.1 1.2 + - - -
224A CYS 3.3 16.9 + - - +
225A ASN 3.2 1.0 - - - -
226A GLN* 1.3 77.1 - - - +
228A LEU* 1.3 61.0 + - - +
229A ASP 3.1 16.5 + - - -
230A VAL* 3.2 15.1 + - + +
231A GLN* 2.9 30.8 + - - +
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A GLN 3.7 2.2 + - - -
227A ASP* 1.3 75.8 + - - +
229A ASP* 1.3 62.8 + - - +
231A GLN* 3.5 21.7 + - + +
232A LYS* 3.1 55.7 + - + +
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Residues in contact with ASP 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ARG* 3.0 26.0 + - - +
104A LEU* 3.4 23.2 - - + +
227A ASP* 3.1 8.8 + - - +
228A LEU* 1.3 80.0 - - - +
230A VAL* 1.3 63.9 + - - +
232A LYS* 3.7 13.5 + - - +
233A LYS* 3.2 16.8 + - - +
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Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG* 3.9 21.8 - - + -
103A ILE* 4.1 15.0 - - + -
104A LEU* 4.0 13.9 - - + -
202A PHE* 3.5 27.8 - - + -
224A CYS* 3.4 29.8 - - + +
225A ASN* 4.0 12.1 - - - +
227A ASP* 3.2 18.0 + - + +
228A LEU 3.3 0.2 - - - -
229A ASP* 1.3 75.2 - - - +
231A GLN* 1.3 54.6 + - - +
233A LYS* 3.0 5.2 + - - +
234A LEU* 2.8 31.7 + - - +
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Residues in contact with GLN 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ASN* 3.1 27.9 + - - +
226A GLN* 3.3 26.3 + - - +
227A ASP 2.9 14.5 + - - +
228A LEU* 3.7 24.3 - - + +
229A ASP 3.4 0.2 - - - -
230A VAL* 1.3 76.4 - - - +
232A LYS* 1.3 64.1 + - + +
234A LEU* 3.1 14.4 + - + +
235A TYR* 3.1 29.6 + - + +
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Residues in contact with LYS 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LEU* 3.1 44.7 + - + +
229A ASP* 3.8 15.3 + - - +
231A GLN* 1.3 78.7 - - + +
233A LYS* 1.3 61.1 + - - +
235A TYR* 3.5 6.2 + - - +
236A ASP* 3.1 28.0 + - - +
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Residues in contact with LYS 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ILE* 3.0 29.4 + - + +
104A LEU* 3.2 32.3 + - + +
105A GLY 3.5 9.9 + - - -
106A SER* 4.4 8.7 - - - +
202A PHE* 3.9 11.7 - - + -
229A ASP 3.2 10.7 + - - +
230A VAL 3.0 8.3 + - - +
232A LYS* 1.3 75.8 - - - +
234A LEU* 1.3 65.5 + - - +
236A ASP* 3.2 14.1 + - + +
237A CYS* 3.0 38.0 + - - -
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A VAL* 3.9 27.1 - - + -
200A ALA* 3.5 36.8 - - + +
201A GLU* 3.8 19.3 - - - +
202A PHE* 3.4 23.5 - - + -
225A ASN* 4.2 9.0 - - - +
230A VAL 2.8 16.0 + - - +
231A GLN* 3.1 17.0 + - + +
233A LYS* 1.3 70.4 - - - +
235A TYR* 1.3 72.3 + - + +
237A CYS* 3.0 7.1 + - - +
238A LEU* 3.0 31.1 + - + +
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Residues in contact with TYR 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ALA* 5.9 1.6 - - + -
231A GLN* 3.1 19.5 + - + +
232A LYS* 4.0 5.6 - - - +
233A LYS 3.3 0.2 - - - -
234A LEU* 1.3 90.1 - - + +
236A ASP* 1.3 64.8 + - - +
238A LEU* 3.9 24.4 - - + +
239A GLU* 3.3 30.9 + - + +
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Residues in contact with ASP 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A LYS* 3.1 21.8 + - - +
233A LYS* 3.4 19.4 - - + +
234A LEU 3.2 0.4 - - - -
235A TYR* 1.3 76.7 - - - +
237A CYS* 1.3 64.0 + - - +
239A GLU* 3.3 24.3 + - - +
240A GLU* 3.8 7.8 - - - +
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Residues in contact with CYS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A VAL* 4.0 21.3 - - + -
202A PHE* 3.8 20.9 - - - -
233A LYS* 3.0 39.0 + - - -
234A LEU 3.0 8.1 + - - +
236A ASP* 1.3 76.4 - - - +
238A LEU* 1.3 67.6 + - - +
239A GLU 3.3 0.5 + - - -
240A GLU* 3.7 24.9 - - - +
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Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A VAL* 4.1 22.2 - - + -
193A VAL* 4.2 20.4 - - + -
200A ALA* 4.2 23.1 - - + -
234A LEU* 3.0 19.5 + - + +
235A TYR* 3.9 37.5 - - + +
237A CYS* 1.3 76.8 - - - +
239A GLU* 1.3 58.6 + - + +
240A GLU 2.8 13.7 + - - +
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Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A TYR* 3.3 18.4 - - + +
236A ASP* 3.3 10.1 + - - +
237A CYS 3.2 1.2 - - - -
238A LEU* 1.3 72.9 - - + +
240A GLU* 1.3 79.1 + - - +
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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