Contacts of the helix formed by residues 1946 - 1954 (chain B) in PDB entry 4JKE
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 ASN1946 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1942B ALA 2.9 8.6 + - - +
1945B VAL* 1.3 81.8 + - - +
1947B ASN* 1.3 64.8 + - - +
1948B ASP* 3.6 7.3 + - - +
1949B ARG* 3.0 32.9 + - - +
1950B ALA* 2.9 21.0 + - - +
1986B LEU* 3.8 19.3 - - + +
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Residues in contact with ASN1947 (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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1898B LYS* 3.6 33.1 + - + +
1943B LEU* 3.3 29.8 + - - +
1945B VAL 4.2 0.2 - - - -
1946B ASN* 1.3 72.9 + - - +
1948B ASP* 1.3 72.6 + - - +
1950B ALA* 3.3 1.9 + - - +
1951B LYS* 2.8 55.5 + - - +
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Residues in contact with ASP1948 (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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1946B ASN* 3.4 5.5 + - - +
1947B ASN* 1.3 85.6 + - - +
1949B ARG* 1.3 63.4 + - - +
1951B LYS* 3.3 8.4 + - - +
1952B VAL* 3.2 25.8 + - - +
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Residues in contact with ARG1949 (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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1946B ASN* 3.0 31.4 + - - +
1948B ASP* 1.3 74.0 - - - +
1950B ALA* 1.3 60.0 + - - +
1952B VAL* 3.2 41.8 + - - +
1953B ILE* 2.9 44.4 + - + +
1982B GLN* 3.8 21.0 + - - +
1986B LEU* 3.7 18.8 - - + -
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Residues in contact with ALA1950 (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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1942B ALA* 3.8 27.8 - - + +
1943B LEU* 3.9 16.4 - - + +
1946B ASN 2.9 18.6 + - - +
1947B ASN 3.5 4.9 - - - +
1949B ARG* 1.3 78.0 - - - +
1951B LYS* 1.3 56.2 + - - +
1953B ILE* 3.3 6.3 + - - +
1954B LEU* 2.9 36.8 + - + +
1983B LEU* 4.6 3.1 - - + +
1986B LEU* 3.6 9.5 - - + +
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Residues in contact with LYS1951 (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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1898B LYS 2.7 31.5 + - - -
1899B VAL* 4.5 4.1 - - - +
1900B GLU* 5.7 1.3 - - - +
1943B LEU* 3.8 13.0 - - + +
1947B ASN* 2.8 46.4 + - - +
1948B ASP* 3.7 8.3 - - - +
1949B ARG 3.3 0.4 - - - -
1950B ALA* 1.3 72.5 - - - +
1952B VAL* 1.3 64.8 + - + +
1954B LEU* 3.4 11.0 + - + +
1955B LYS* 3.3 22.7 + - - +
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Residues in contact with VAL1952 (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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1948B ASP 3.2 16.5 + - - +
1949B ARG* 3.2 34.3 - - - +
1951B LYS* 1.3 73.6 - - + +
1953B ILE* 1.3 65.1 + - - +
1955B LYS* 3.1 24.9 + - - +
1956B PRO* 4.8 0.9 - - - +
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Residues in contact with ILE1953 (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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1949B ARG* 2.9 49.9 + - + +
1950B ALA 3.6 6.1 - - - +
1952B VAL* 1.3 76.0 - - - +
1954B LEU* 1.3 59.9 + - - +
1955B LYS 3.3 1.0 + - - -
1956B PRO* 3.9 8.7 - - - +
1979B VAL* 3.6 36.6 - - + +
1982B GLN* 3.7 51.5 + - + +
1983B LEU* 3.6 22.2 - - + -
1986B LEU* 4.0 13.7 - - + -
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Residues in contact with LEU1954 (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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1939B ILE* 4.4 29.8 - - + +
1943B LEU* 4.7 11.7 - - + -
1950B ALA* 2.9 26.8 + - + +
1951B LYS* 3.8 10.3 - - + +
1952B VAL 3.2 0.4 - - - -
1953B ILE* 1.3 75.6 - - - +
1955B LYS* 1.3 57.3 + - - +
1956B PRO* 3.3 10.2 - - - +
1960B THR* 4.0 0.9 - - - +
1968B TRP* 5.0 8.7 - - + -
1969B PRO* 3.4 36.9 - - + +
1971B LEU* 4.6 0.7 - - - +
1976B TRP* 4.1 22.0 - - + -
1979B VAL* 4.0 23.3 - - + -
1983B LEU* 4.9 6.5 - - + -
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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