Contacts of the helix formed by residues 736 - 738 (chain B) in PDB entry 3E0D
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 GLU 736 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447B GLY* 5.7 1.9 - - - -
686B ARG* 5.6 3.3 + - - -
688B GLU* 5.6 5.9 - - - +
708B TYR* 5.7 0.5 + - - -
732B PRO 5.1 3.4 + - - +
733B ILE 4.2 12.0 + - - +
735B ASP* 1.3 76.7 - - - +
737B THR* 1.3 66.3 + - + +
738B TYR* 3.7 8.8 - - - -
743B TYR* 4.3 16.0 + - + -
746B GLN* 5.0 2.2 - - - +
815B LYS* 3.9 22.7 + - - -
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Residues in contact with THR 737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B ALA* 4.8 5.9 - - - +
696B LEU* 4.8 0.2 - - - +
708B TYR* 4.3 11.3 - - - -
733B ILE 4.7 0.2 - - - +
734B LEU* 3.5 10.1 - - - +
735B ASP 2.7 5.7 + - - -
736B GLU* 1.3 81.7 - - + +
738B TYR* 1.3 73.1 + - - +
740B ILE* 2.8 40.7 + - - +
742B VAL* 3.3 20.3 - - - +
743B TYR* 4.9 5.4 - - - -
746B GLN* 2.9 29.6 - - - +
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Residues in contact with TYR 738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708B TYR* 3.8 41.7 - + + -
711B ARG* 2.7 65.5 + - + -
712B HIS* 4.3 22.7 + - - -
718B VAL* 3.5 22.7 - - + -
734B LEU 3.7 0.4 - - - -
735B ASP 2.9 14.5 + - - -
736B GLU 4.8 7.2 - - - -
737B THR* 1.3 81.8 - - - +
739B GLY* 1.3 51.9 + - - +
740B ILE* 3.1 12.1 + - + +
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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
------------------------------------------------------------
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