Contacts of the helix formed by residues 237 - 248 (chain B) in PDB entry 5O9Z
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 LEU 237 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B MET* 1.3 76.2 - - - +
238B ASN* 1.3 56.9 + - - +
240B GLU* 3.7 8.3 - - - +
241B ARG* 2.9 31.7 + - - +
835B GLU* 5.2 15.5 - - + +
898B LEU* 6.3 3.6 - - + -
900B VAL* 6.0 5.4 - - + -
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Residues in contact with ASN 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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136B GLY 4.3 18.4 - - - +
137B HIS* 5.0 7.9 - - + -
207B GLY* 5.0 11.7 - - - +
212B SER* 6.2 4.0 - - - -
236B MET* 3.1 5.8 - - + +
237B LEU* 1.3 79.6 - - - +
239B THR* 1.3 57.3 + - - +
241B ARG* 4.1 3.2 - - - +
242B LEU* 2.9 32.6 + - - +
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Residues in contact with THR 239 (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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136B GLY 6.2 0.2 - - - -
227B LEU* 5.4 12.3 - - - -
228B PHE 5.9 2.2 - - - -
229B ILE* 5.7 5.6 - - - -
235B VAL* 4.4 12.8 - - - -
236B MET 3.3 17.9 + - - +
238B ASN* 1.3 79.4 - - - +
240B GLU* 1.3 58.3 + - - +
242B LEU* 3.9 4.6 - - - +
243B ILE* 2.9 31.4 + - - +
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Residues in contact with GLU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B VAL* 6.0 0.2 - - - +
236B MET 3.3 10.3 + - - +
237B LEU* 3.8 11.0 - - - +
238B ASN 3.3 0.4 - - - -
239B THR* 1.3 77.0 - - - +
241B ARG* 1.3 59.8 + - - +
243B ILE* 3.4 4.3 + - - +
244B LYS* 2.9 30.3 + - - +
288B LEU* 6.4 3.1 - - + -
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Residues in contact with ARG 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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237B LEU 2.9 17.8 + - - +
238B ASN* 4.1 4.3 - - - +
240B GLU* 1.3 75.7 - - - +
242B LEU* 1.3 57.6 + - - +
244B LYS* 3.4 5.1 + - - +
245B HIS* 2.9 32.4 + - - +
583B ASN* 5.5 4.8 - - + +
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Residues in contact with LEU 242 (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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135B CYS* 5.1 15.5 - - + -
212B SER* 6.6 0.2 - - - -
238B ASN 2.9 20.2 + - - +
239B THR* 4.2 4.0 - - - +
241B ARG* 1.3 76.1 - - - +
243B ILE* 1.3 57.8 + - - +
245B HIS* 4.4 3.8 - - - +
246B ALA* 2.8 33.1 + - - +
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Residues in contact with ILE 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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239B THR 2.9 21.3 + - - +
240B GLU* 3.8 4.9 - - - +
241B ARG 3.2 0.2 - - - -
242B LEU* 1.3 76.3 - - - +
244B LYS* 1.3 59.9 + - - +
246B ALA* 4.5 3.1 - - - -
247B VAL* 2.9 32.7 + - - +
288B LEU* 5.7 9.2 - - + -
289B ILE* 6.2 3.1 - - + +
292B TYR* 5.3 0.2 - - - +
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Residues in contact with LYS 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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240B GLU 2.9 17.7 + - - +
241B ARG* 3.9 5.2 - - - +
243B ILE* 1.3 76.8 - - - +
245B HIS* 1.3 58.6 + - - +
247B VAL* 3.9 2.3 - - - +
248B GLN* 2.9 30.8 + - - +
292B TYR* 5.5 6.0 - - - +
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Residues in contact with HIS 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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216B THR* 6.1 4.5 - - - -
241B ARG 2.9 17.7 + - - +
242B LEU* 4.4 3.4 - - - +
244B LYS* 1.3 74.1 - - - +
246B ALA* 1.3 65.9 + - - +
248B GLN* 3.5 6.5 + - - +
249B GLU* 3.1 23.4 + - - +
583B ASN* 4.1 24.2 - - + -
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Residues in contact with ALA 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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225B VAL* 4.7 19.1 - - + -
242B LEU 2.8 24.1 + - - +
243B ILE* 4.2 3.4 - - - +
245B HIS* 1.3 75.2 - - - +
247B VAL* 1.3 63.8 + - - +
249B GLU* 3.3 9.4 + - - +
251B LEU* 3.2 39.4 + - + +
253B VAL* 5.0 9.4 - - + -
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Residues in contact with VAL 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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243B ILE 2.9 20.8 + - - +
244B LYS 4.2 0.7 - - - +
246B ALA* 1.3 75.5 - - - +
248B GLN* 1.3 62.9 + - - +
250B ARG* 3.2 12.7 + - - +
251B LEU 4.5 6.1 - - - +
289B ILE* 5.4 7.4 - - + +
292B TYR* 3.7 28.9 - - + -
293B SER* 5.2 9.9 - - - -
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Residues in contact with GLN 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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244B LYS 2.9 21.3 + - - +
245B HIS* 3.8 7.9 - - - +
246B ALA 3.3 0.2 - - - -
247B VAL* 1.3 76.9 - - - +
249B GLU* 1.3 57.3 + - - +
250B ARG* 3.3 1.9 + - - +
292B TYR* 5.4 1.0 - - - +
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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