Contacts of the helix formed by residues 227 - 238 (chain A) in PDB entry 2J2M
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 SER 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A ARG* 5.6 0.2 - - - -
183A ASP* 3.7 22.5 + - - -
186A ILE* 4.8 0.7 - - - -
225A ASN 4.4 0.2 + - - -
226A LEU* 1.3 76.0 - - - +
228A ALA* 1.3 64.8 + - - +
229A ASP* 3.4 7.0 + - - +
230A GLU* 3.1 35.9 + - - +
231A ALA* 3.0 20.4 + - - +
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Residues in contact with ALA 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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108A ARG* 4.5 8.2 - - - +
183A ASP* 4.6 4.4 + - - -
186A ILE* 4.6 7.3 - - + +
227A SER* 1.3 73.4 - - - +
229A ASP* 1.3 63.0 + - - +
231A ALA* 3.4 8.6 + - - +
232A THR* 3.1 30.6 + - - -
442A ASN* 4.2 17.5 + - - +
445A ASN* 5.9 4.3 - - - +
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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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227A SER* 3.3 6.9 + - - +
228A ALA* 1.3 78.7 - - - +
230A GLU* 1.3 61.9 + - + +
232A THR* 3.5 7.8 + - - +
233A GLU* 3.1 27.8 + - - +
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Residues in contact with GLU 230 (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 4.0 5.4 - - - +
226A LEU* 3.5 23.0 - - + +
227A SER* 3.1 39.1 + - - +
229A ASP* 1.3 77.0 - - + +
231A ALA* 1.3 57.5 + - - +
233A GLU* 3.2 13.4 + - - +
234A VAL* 2.9 36.9 + - + +
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Residues in contact with ALA 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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106A THR* 3.5 29.6 - - - +
186A ILE* 3.7 24.5 - - + -
226A LEU* 4.1 11.2 - - + +
227A SER 3.0 14.0 + - - +
228A ALA 3.5 8.7 - - - +
230A GLU* 1.3 76.7 - - - +
232A THR* 1.3 56.2 + - - +
234A VAL 3.4 0.5 + - - -
235A GLN* 2.9 32.6 + - - +
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Residues in contact with THR 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 ALA 3.1 15.5 + - - -
229A ASP* 3.7 12.1 + - - -
230A GLU 3.3 0.2 - - - -
231A ALA* 1.3 72.5 - - - +
233A GLU* 1.3 67.5 + - - +
235A GLN* 3.3 2.9 + - - +
236A GLY* 3.2 18.0 + - - -
236B GLY* 3.4 34.7 + - - +
237B LYS* 4.0 27.7 + - + +
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Residues in contact with GLU 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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229A ASP 3.1 15.5 + - - +
230A GLU* 3.5 16.5 - - - +
232A THR* 1.3 78.2 - - - +
234A VAL* 1.3 68.6 + - + +
236A GLY* 3.4 6.9 + - - -
237A LYS* 3.6 26.4 + - + +
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Residues in contact with VAL 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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106A THR* 3.7 11.2 - - + -
226A LEU* 4.4 15.3 - - + -
230A GLU* 2.9 23.4 + - + +
231A ALA* 3.9 4.0 - - - +
233A GLU* 1.3 81.3 - - + +
235A GLN* 1.3 53.9 + - - +
237A LYS* 3.0 7.3 + - - +
238A ASP* 2.8 35.3 + - + +
241A HIS* 3.7 39.5 - - + -
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Residues in contact with GLN 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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104A PRO* 4.1 18.6 - - + -
106A THR* 2.7 36.1 + - - +
107A LEU* 3.3 23.2 - - - +
231A ALA 2.9 15.0 + - - +
232A THR* 3.6 6.2 - - - +
234A VAL* 1.3 76.0 - - - +
236A GLY* 1.3 58.5 + - - +
237A LYS 3.4 0.7 + - - -
238A ASP 3.6 11.0 + - - -
239A PHE* 4.0 2.2 + - + +
235B GLN* 3.0 43.6 - - + +
236B GLY* 3.4 14.7 + - - +
237B LYS 4.6 1.2 - - - -
238B ASP* 4.5 1.6 + - - -
239B PHE* 4.1 17.2 + - - +
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Residues in contact with GLY 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 THR 3.2 7.6 + - - -
233A GLU 3.4 4.0 + - - -
234A VAL 3.2 1.0 - - - -
235A GLN* 1.3 79.0 - - - +
237A LYS* 1.3 57.3 + - - +
232B THR* 3.4 48.1 + - - +
235B GLN* 3.5 13.0 - - - +
236B GLY* 3.5 12.9 - - - -
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Residues in contact with LYS 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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233A GLU* 3.6 26.2 + - + +
234A VAL* 3.0 7.9 + - - +
235A GLN 4.2 0.2 - - - -
236A GLY* 1.3 80.5 - - - +
238A ASP* 1.3 61.9 + - + +
232B THR* 3.7 22.0 - - + +
235B GLN* 4.6 3.0 - - - +
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Residues in contact with ASP 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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106A THR* 4.5 1.2 - - - +
234A VAL* 2.8 26.3 + - + +
235A GLN* 3.6 6.6 + - - +
237A LYS* 1.3 77.7 - - + +
239A PHE* 1.3 61.3 + - - +
240A ASN* 2.8 38.4 + - - +
241A HIS* 3.5 32.7 + - + +
244A ASN* 3.2 25.5 + - - +
157B ILE* 5.6 0.2 - - - +
235B GLN* 5.0 0.4 - - - -
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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