Contacts of the helix formed by residues 1941 - 1951 (chain B) in PDB entry 3NBN
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 ARG1941 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1936B ALA* 3.0 14.9 + - + +
1939B TYR* 3.7 49.2 + - + +
1940B SER* 1.3 74.1 + - - +
1942B SER* 1.3 64.7 + - - +
1943B ASP* 3.3 4.0 - - - +
1944B ALA* 3.2 24.6 - - + +
1945B ALA* 3.1 17.7 + - - +
1977B VAL* 3.7 7.5 - - - +
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Residues in contact with SER1942 (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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1940B SER 3.1 8.9 + - - -
1941B ARG* 1.3 72.7 - - - +
1943B ASP* 1.3 63.6 + - - +
1945B ALA* 3.8 2.9 - - - +
1946B LYS* 3.8 10.2 + - - +
1976B GLY* 3.6 33.2 - - - -
1977B VAL* 3.6 10.8 - - - +
1980B ILE* 3.8 20.8 - - - +
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Residues in contact with ASP1943 (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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1941B ARG* 4.7 1.4 - - - +
1942B SER* 1.3 79.7 + - - +
1944B ALA* 1.3 75.0 + - - +
1945B ALA 3.0 1.3 - - - -
1946B LYS* 2.9 33.8 + - + +
1947B ARG* 2.9 44.7 + - - +
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Residues in contact with ALA1944 (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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1936B ALA* 4.2 8.3 - - + -
1941B ARG* 3.2 34.1 - - + +
1943B ASP* 1.3 87.7 + - - +
1945B ALA* 1.3 61.2 + - - +
1947B ARG* 3.6 22.8 - - - +
1948B LEU* 3.5 20.4 - - - +
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Residues in contact with ALA1945 (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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1933B LEU* 4.1 20.4 - - + -
1936B ALA* 4.1 7.8 - - + +
1941B ARG 3.1 10.0 + - - +
1942B SER 3.8 6.5 - - - +
1943B ASP 3.0 0.2 - - - -
1944B ALA* 1.3 78.4 - - - +
1946B LYS* 1.3 62.8 - - - +
1948B LEU* 3.2 5.9 + - - +
1949B LEU* 3.1 25.7 + - + +
1977B VAL* 3.7 31.4 - - + -
1980B ILE* 5.0 8.5 - - + -
1981B LEU* 6.1 0.4 - - + -
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Residues in contact with LYS1946 (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 SER 3.8 2.5 + - - +
1943B ASP* 2.9 29.0 + - + +
1945B ALA* 1.3 78.2 - - - +
1947B ARG* 1.3 58.0 + - - +
1949B LEU* 2.9 12.3 + - + +
1950B GLU* 2.9 35.2 + - - +
1980B ILE* 4.4 28.9 - - + +
1946E LYS* 3.5 32.7 - - - +
1950E GLU* 2.7 32.8 + - - +
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Residues in contact with ARG1947 (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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1943B ASP* 2.9 52.7 + - - +
1944B ALA* 3.6 17.0 - - - +
1946B LYS* 1.3 71.9 - - - +
1948B LEU* 1.3 58.1 + - + +
1949B LEU 3.0 5.2 - - - -
1950B GLU* 3.1 16.8 + - + +
1951B ALA* 2.8 33.1 + - - +
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Residues in contact with LEU1948 (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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1932B ALA* 3.4 44.4 - - + +
1933B LEU* 3.4 18.4 - - + +
1936B ALA* 5.7 1.8 - - + -
1944B ALA 3.5 16.5 + - - +
1945B ALA* 3.2 10.9 + - - +
1947B ARG* 1.3 81.7 - - + +
1949B LEU* 1.3 60.2 + - - +
1951B ALA* 2.8 18.6 - - + +
1953B ALA* 2.9 27.5 - - + +
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Residues in contact with LEU1949 (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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1933B LEU* 3.9 28.5 - - + -
1945B ALA* 3.1 14.6 + - + +
1946B LYS* 2.9 14.5 + - + +
1948B LEU* 1.3 78.3 - - - +
1950B GLU* 1.3 63.2 - - - +
1951B ALA 2.7 12.8 - - - +
1952B SER* 4.1 3.2 + - - -
1953B ALA 4.3 13.9 - - - +
1955B ALA* 4.5 15.0 - - + -
1980B ILE* 4.8 16.8 - - + -
1981B LEU* 5.5 4.5 - - + -
1984B ASN* 3.3 32.5 - - + +
1986B ALA* 6.0 1.6 - - + -
1983E ARG* 4.6 15.2 + - - -
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Residues in contact with GLU1950 (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 LYS* 2.9 25.5 + - - +
1947B ARG* 3.1 27.4 + - + +
1949B LEU* 1.3 79.0 - - - +
1951B ALA* 1.3 61.2 + - - +
1952B SER* 3.2 8.0 + - - -
1946E LYS* 2.6 31.7 + - - +
1983E ARG* 4.5 24.8 + - - +
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Residues in contact with ALA1951 (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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1947B ARG 2.8 14.8 + - - +
1948B LEU* 2.8 21.9 - - + +
1949B LEU* 2.7 17.3 - - - +
1950B GLU* 1.3 74.0 - - - +
1952B SER* 1.3 51.4 + - - +
1953B ALA* 2.4 24.3 + - + +
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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