Contacts of the helix formed by residues 2068 - 2075 (chain A) in PDB entry 5DZZ
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 THR2068 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1972A ARG* 4.0 29.8 - - - +
2058A ILE* 4.9 0.2 - - - -
2066A LYS 4.3 1.1 + - - +
2067A LEU* 1.3 77.3 - - - +
2069A VAL* 1.3 60.0 + - - +
2070A ASP* 3.7 10.1 + - - +
2071A SER* 3.1 26.5 + - - +
2072A ALA* 2.8 26.3 + - - +
2090A GLU* 3.8 10.5 - - - -
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Residues in contact with VAL2069 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2053A ALA* 4.7 2.2 - - + -
2058A ILE* 4.6 6.3 - - + -
2067A LEU 4.0 0.2 + - - -
2068A THR* 1.3 74.3 - - - +
2070A ASP* 1.3 62.4 + - - +
2072A ALA* 3.2 7.4 + - - +
2073A ILE* 3.0 27.6 + - + +
2078A ILE* 4.2 14.4 - - + -
2083A ARG 4.7 2.5 - - - +
2086A ILE* 3.8 25.6 - - + +
2087A TYR* 3.6 35.7 - - + +
2090A GLU* 3.4 44.4 + - + +
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Residues in contact with ASP2070 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2068A THR* 3.2 10.0 + - - +
2069A VAL* 1.3 79.9 - - - +
2071A SER* 1.3 62.7 + - - +
2073A ILE* 3.4 5.1 + - - +
2074A ALA* 3.2 20.3 + - - +
2087A TYR* 3.0 30.7 + - - -
2090A GLU* 5.2 0.4 + - - -
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Residues in contact with SER2071 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2067A LEU* 4.1 26.2 - - - +
2068A THR* 3.1 22.0 + - - +
2070A ASP* 1.3 77.8 - - - +
2072A ALA* 1.3 63.0 + - - +
2074A ALA* 3.2 10.5 + - - +
2075A ARG* 3.1 29.8 + - - +
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Residues in contact with ALA2072 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2058A ILE* 3.7 25.1 - - + -
2067A LEU* 4.5 8.5 - - + -
2068A THR 2.8 16.0 + - - +
2069A VAL 3.5 4.9 - - - +
2070A ASP 3.2 0.2 - - - -
2071A SER* 1.3 75.5 - - - +
2073A ILE* 1.3 63.7 + - - +
2075A ARG* 3.4 0.9 + - - -
2076A ASP 3.2 3.1 + - - -
2077A LEU* 2.9 34.2 + - + +
2078A ILE* 3.6 25.3 + - + -
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Residues in contact with ILE2073 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2069A VAL* 3.0 22.3 + - + +
2070A ASP* 3.7 7.0 - - - +
2072A ALA* 1.3 75.8 - - - +
2074A ALA* 1.3 63.3 + - - +
2076A ASP* 3.2 18.9 + - - +
2078A ILE* 3.6 37.5 - - + +
2083A ARG* 3.3 61.9 + - + +
2087A TYR* 4.4 7.9 - - - +
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Residues in contact with ALA2074 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2070A ASP 3.2 10.1 + - - +
2071A SER* 3.2 14.1 + - - +
2072A ALA 3.2 0.8 - - - -
2073A ILE* 1.3 80.4 - - - +
2075A ARG* 1.3 60.8 + - + +
2076A ASP* 3.4 5.4 + - - +
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Residues in contact with ARG2075 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2060A ASP* 3.5 17.1 + - - -
2063A ARG* 3.0 25.9 - - - +
2065A GLU* 2.5 27.7 + - - -
2067A LEU* 3.4 37.4 - - + +
2071A SER* 3.1 16.1 + - - +
2072A ALA 3.4 0.4 + - - -
2073A ILE 3.2 0.2 - - - -
2074A ALA* 1.3 81.1 - - + +
2076A ASP* 1.3 71.6 + - - +
2077A LEU* 3.2 23.0 + - + +
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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