Contacts of the helix formed by residues 236 - 248 (chain B) in PDB entry 5IJ7
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 THR 236 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B SER* 3.7 11.3 + - - -
235B GLY* 1.3 73.9 - - - -
237B ALA* 1.4 58.6 + - - +
238B GLU* 3.6 16.2 - - + +
239B GLU* 3.1 42.7 + - + +
240B LEU* 3.0 30.2 + - - +
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Residues in contact with ALA 237 (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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221B ASP 5.5 0.2 - - - +
224B PHE* 3.7 18.9 - - + +
225B GLU* 3.8 35.7 - - + +
228B SER* 3.8 7.3 + - - -
236B THR* 1.4 75.1 + - - +
238B GLU* 1.4 59.0 + - - +
240B LEU* 4.0 1.1 + - - +
241B LYS* 3.5 28.3 + - + +
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Residues in contact with GLU 238 (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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236B THR* 3.2 14.2 - - + +
237B ALA* 1.4 75.5 - - - +
239B GLU* 1.4 63.3 + - - +
241B LYS* 3.0 28.3 + - + +
242B GLU* 3.1 33.9 + - + +
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Residues in contact with GLU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B GLY* 3.7 19.1 - - - -
236B THR* 3.1 35.4 + - + +
238B GLU* 1.4 81.5 - - + +
240B LEU* 1.4 53.5 + - + +
242B GLU* 3.4 19.8 - - - +
243B LYS* 2.8 48.8 + - - +
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Residues in contact with LEU 240 (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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171B PHE* 3.4 19.5 - - + -
224B PHE* 3.4 38.3 - - + +
227B ILE* 3.8 25.8 - - + -
228B SER* 3.9 12.6 - - - +
231B PHE* 5.6 2.0 - - + +
234B LYS* 4.1 40.2 - - + +
235B GLY* 4.4 2.9 - - - +
236B THR 3.0 20.3 + - - +
237B ALA 4.3 2.0 - - - +
239B GLU* 1.4 75.3 - - + +
241B LYS* 1.4 60.0 + - - +
243B LYS* 4.2 8.3 - - + -
244B TYR* 2.9 31.9 + - - +
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Residues in contact with LYS 241 (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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221B ASP* 3.2 35.1 + - + +
224B PHE* 3.6 31.9 - - + -
237B ALA 3.5 16.7 + - - +
238B GLU* 3.0 13.5 + - + +
240B LEU* 1.4 76.5 - - - +
242B GLU* 1.4 61.6 + - - +
244B TYR* 3.9 2.1 - - - +
245B LYS* 3.1 45.6 + - + +
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Residues in contact with GLU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLU* 3.1 41.7 + - + +
239B GLU* 3.4 21.6 - - - +
241B LYS* 1.4 77.2 - - + +
243B LYS* 1.4 61.8 + - + +
245B LYS* 3.5 16.6 + - - +
246B GLU* 3.1 20.6 + - - +
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Residues in contact with LYS 243 (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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168B ASP* 4.9 8.7 - - - +
171B PHE* 4.2 11.0 - - + -
234B LYS* 3.4 45.8 + - - +
239B GLU* 2.8 36.9 + - - +
240B LEU* 4.0 10.3 - - + +
241B LYS 3.5 0.2 - - - -
242B GLU* 1.4 71.8 - - + +
244B TYR* 1.3 61.3 - - - +
246B GLU* 3.3 27.8 - - - +
247B LEU* 3.4 23.7 + - + +
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Residues in contact with TYR 244 (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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171B PHE* 3.7 9.8 - + + -
172B VAL* 4.2 20.9 - - + -
175B VAL* 3.6 29.5 - - + +
176B ASN* 3.1 33.4 + - - -
219B PRO* 3.6 27.1 - - + +
224B PHE* 3.6 23.1 - + + -
240B LEU 2.9 20.3 + - - +
241B LYS 3.9 2.0 - - - +
243B LYS* 1.3 75.6 - - - +
245B LYS* 1.4 57.9 + - + +
247B LEU* 3.5 4.6 + - - +
248B THR* 2.9 58.4 + - + -
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Residues in contact with LYS 245 (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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241B LYS* 3.1 37.7 + - - +
242B GLU* 3.7 9.7 - - - +
243B LYS 3.4 0.4 - - - -
244B TYR* 1.4 78.2 - - + +
246B GLU* 1.3 65.9 + - - +
248B THR* 3.4 24.7 + - + +
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Residues in contact with GLU 246 (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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242B GLU 3.1 18.9 - - - +
243B LYS* 3.3 26.3 - - - +
245B LYS* 1.3 75.5 - - - +
247B LEU* 1.4 77.0 + - - +
248B THR 3.3 4.9 + - - -
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Residues in contact with LEU 247 (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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168B ASP* 3.7 42.2 - - + +
171B PHE* 4.4 7.9 - - + -
172B VAL* 3.8 28.1 - - + +
243B LYS* 3.4 26.1 + - + +
244B TYR 3.8 3.1 - - - +
245B LYS 3.4 0.2 - - - -
246B GLU* 1.4 86.3 - - - +
248B THR* 1.4 59.6 + - - +
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Residues in contact with THR 248 (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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172B VAL* 5.2 6.5 - - - +
176B ASN* 5.4 0.3 + - - -
244B TYR* 2.9 49.1 + - + +
245B LYS* 3.4 26.7 - - + +
246B GLU 3.3 4.9 - - - -
247B LEU* 1.4 79.2 - - - +
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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