Contacts of the helix formed by residues 225 - 235 (chain B) in PDB entry 2JG7
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 GLY 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B GLN* 4.2 3.0 + - - -
189B LYS* 3.6 5.4 - - - +
192B PRO* 4.2 16.2 - - - -
224B GLY* 1.3 76.0 - - - +
226B ALA* 1.3 65.6 + - - -
227B ASP* 3.2 12.7 - - - +
228B ILE 3.3 2.1 + - - -
229B GLY 3.1 16.6 + - - -
1510B NAD 4.1 6.5 - - - -
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Residues in contact with ALA 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B GLY* 1.3 67.7 - - - -
227B ASP* 1.3 58.8 + - - +
229B GLY 3.0 0.9 + - - -
230B THR* 2.7 40.0 + - - +
1510B NAD 3.5 48.0 + - + +
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Residues in contact with ASP 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ALA 4.6 5.9 - - - +
55B THR* 5.8 0.3 - - - -
56B LEU* 3.3 27.8 + - - +
225B GLY* 4.1 13.3 + - - +
226B ALA* 1.3 76.4 - - - +
228B ILE* 1.3 73.8 - - - +
230B THR* 3.6 4.3 + - - -
231B ALA* 3.5 15.6 + - - +
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Residues in contact with ILE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ALA* 4.0 17.5 - - + +
55B THR 4.1 17.9 - - - +
56B LEU* 4.2 9.4 - - + +
59B TYR* 3.9 27.1 - - + -
189B LYS* 4.0 18.8 - - + -
222B THR* 3.6 22.4 - - - +
223B CYS 4.3 5.8 - - - +
224B GLY* 4.2 18.2 - - - -
225B GLY 3.3 2.2 + - - +
227B ASP* 1.3 94.7 - - - +
229B GLY* 1.3 66.7 + - - +
231B ALA* 3.0 17.3 + - - +
232B MET* 3.0 16.6 + - - +
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Residues in contact with GLY 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ILE* 3.7 13.1 - - - +
189B LYS* 3.5 14.6 - - - +
225B GLY 3.1 8.2 + - - -
226B ALA 3.0 5.3 + - - -
228B ILE* 1.3 77.1 - - - +
230B THR* 1.3 54.9 + - - +
232B MET* 3.4 6.6 + - - +
233B ALA* 3.1 24.1 + - - +
1510B NAD 3.2 25.9 - - - -
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Residues in contact with THR 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B ALA* 2.7 23.4 + - - +
227B ASP* 3.9 4.5 - - - -
229B GLY* 1.3 69.6 - - - +
231B ALA* 1.3 65.1 + - - +
233B ALA* 3.1 7.8 + - - +
234B LYS* 2.9 37.5 + - + +
256B MET* 3.7 23.9 - - + +
1510B NAD 3.1 24.6 + - - -
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Residues in contact with ALA 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 4.9 16.8 - - + -
59B TYR* 3.9 26.1 - - + -
227B ASP 3.5 10.4 + - - +
228B ILE* 3.0 13.1 + - - +
230B THR* 1.3 79.5 - - - +
232B MET* 1.3 56.2 + - - +
234B LYS* 3.3 6.7 + - - +
235B ASP* 2.9 31.0 + - - +
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Residues in contact with MET 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B TYR* 3.4 30.5 - - + +
160B GLY* 3.7 13.9 - - - -
161B ILE 3.6 30.3 - - - +
162B ILE* 3.7 24.9 - - + -
187B LEU* 3.9 20.0 - - + +
189B LYS* 3.9 22.0 - - + -
228B ILE* 3.0 18.4 + - - +
229B GLY* 3.5 7.2 - - - +
230B THR 3.2 0.2 - - - -
231B ALA* 1.3 75.9 - - - +
233B ALA* 1.3 62.8 + - - +
235B ASP* 3.1 13.9 + - - +
238B VAL* 3.8 12.4 - - + +
241B LEU* 4.0 8.2 - - + +
260B ARG* 3.5 11.1 + - - -
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B GLY 3.1 10.9 + - - +
230B THR* 3.1 12.2 + - - +
232B MET* 1.3 78.1 - - - +
234B LYS* 1.3 57.0 + - - +
241B LEU* 3.7 22.6 - - + +
253B VAL* 4.1 17.0 - - + +
256B MET* 3.8 25.3 - - + -
257B VAL* 3.4 14.8 + - - +
260B ARG* 2.9 21.0 + - - -
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Residues in contact with LYS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B THR* 2.9 30.6 + - + +
231B ALA* 3.9 5.6 - - - +
233B ALA* 1.3 74.3 - - - +
235B ASP* 1.3 63.1 + - - +
236B GLU* 3.3 6.1 + - - +
256B MET* 3.8 35.0 - - + +
260B ARG* 3.3 14.2 - - - +
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Residues in contact with ASP 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B TYR* 2.7 27.7 + - - +
63B VAL* 3.9 2.9 - - - +
231B ALA 2.9 16.9 + - - +
232B MET 3.1 7.3 + - - +
234B LYS* 1.3 75.1 - - - +
236B GLU* 1.3 64.3 + - - +
237B ARG* 3.0 61.8 + - - +
238B VAL* 3.1 13.2 + - + +
260B ARG* 2.9 21.8 + - - -
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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