Contacts of the helix formed by residues 231 - 236 (chain C) in PDB entry 5AEW
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 MET 231 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C SER 3.7 3.0 + - - -
230C ASP* 1.3 73.5 - - - +
232C TYR* 1.3 65.7 + - - +
233C HIS* 3.2 2.5 - - - -
234C ALA* 2.9 24.2 + - - -
235C GLY 2.9 10.0 + - - -
275C GLY 3.9 0.7 - - - +
276C TRP* 3.7 21.1 - - - +
277C TYR* 3.3 39.0 - - + +
321C GLY* 3.6 28.5 - - - +
322C GLN* 4.5 0.7 - - - +
323C HIS* 3.5 32.6 + - + +
432C VAL* 3.7 25.5 + - + +
433C TYR* 3.7 4.1 - - + -
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Residues in contact with TYR 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C SER 5.1 0.9 + - - +
230C ASP* 3.3 11.0 - - - +
231C MET* 1.3 77.0 - - - +
233C HIS* 1.3 56.2 + - - +
235C GLY 3.2 1.0 + - - -
236C THR* 2.7 57.5 + - + +
413C MET* 3.6 44.9 - - + -
432C VAL 4.9 0.8 + - - -
433C TYR* 3.5 28.6 - + + -
434C ALA 5.5 1.3 - - - +
435C GLU* 5.5 2.0 - - - -
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Residues in contact with HIS 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C GLN* 3.3 25.7 + - + +
230C ASP* 2.6 53.7 + - - +
231C MET* 3.2 0.6 - - - -
232C TYR* 1.3 74.1 - - - +
234C ALA* 1.3 70.4 + - + +
236C THR* 3.6 9.5 + - - -
237C THR 3.6 0.3 + - - -
238C THR* 3.2 56.1 + - + +
239C HIS* 3.3 11.0 + + - -
388C ASP* 2.8 26.9 + - - -
391C ASN* 5.3 0.7 - - - +
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Residues in contact with ALA 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C MET* 2.9 21.9 + - - +
233C HIS* 1.3 87.0 - - + +
235C GLY* 1.3 60.3 + - - +
236C THR* 3.2 8.3 + - - +
239C HIS* 4.0 28.1 + - + +
243C ILE* 4.3 13.7 - - - +
258C ILE* 3.9 10.6 - - - +
277C TYR* 4.6 3.6 - - + +
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Residues in contact with GLY 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C MET 2.9 10.6 + - - -
232C TYR 3.2 3.1 + - - -
234C ALA* 1.3 77.5 - - - +
236C THR* 1.3 66.4 + - - +
258C ILE* 3.8 22.8 - - - +
277C TYR* 3.8 2.4 + - - -
433C TYR* 3.4 28.3 + - - -
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Residues in contact with THR 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C TYR* 2.7 50.6 + - + +
233C HIS* 3.6 7.6 + - - -
234C ALA 3.2 3.5 - - - +
235C GLY* 1.3 85.6 - - - +
237C THR* 1.3 78.2 + - - +
238C THR 4.0 0.2 - - - -
239C HIS 5.4 0.4 - - - -
240C LEU* 3.5 21.7 + - - +
258C ILE* 5.8 1.9 - - - +
433C TYR* 6.3 0.9 - - + -
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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
------------------------------------------------------------
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