Contacts of the helix formed by residues 1974 - 1984 (chain E) 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 ALA1974 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1937E ALA 3.5 23.8 - - - +
1940E SER* 3.3 27.6 - - - +
1969E ALA* 3.1 16.5 + - - +
1972E ALA* 3.1 8.9 - - + +
1973E ASP* 1.3 72.4 - - - +
1975E GLN* 1.4 64.7 + - - +
1976E GLY 3.0 4.5 + - - -
1977E VAL* 3.2 5.5 + - + -
1978E PHE* 3.0 22.7 + - - +
2011E MET* 3.7 0.8 - - - +
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Residues in contact with GLN1975 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1940E SER* 4.9 0.2 + - - -
1973E ASP 3.4 5.7 + - - -
1974E ALA* 1.4 71.2 - - - +
1976E GLY* 1.3 65.3 + - - +
1978E PHE* 3.3 30.5 - - - -
1979E GLN* 3.0 37.2 + - + +
2009E GLU 3.8 9.3 - - - +
2010E GLY* 4.6 3.6 - - - -
2011E MET* 4.5 5.8 + - - +
2014E ASP* 3.2 25.3 + - - +
22F ARG* 3.5 36.8 + - - +
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Residues in contact with GLY1976 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1940E SER* 5.1 2.8 + - - -
1942E SER* 3.7 22.2 - - - -
1974E ALA 3.0 2.6 + - - -
1975E GLN* 1.3 81.8 - - - +
1977E VAL* 1.3 59.9 + - - -
1979E GLN* 3.5 3.8 - - - +
1980E ILE* 3.2 23.4 + - - +
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Residues in contact with VAL1977 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1933E LEU* 5.4 1.6 - - + -
1936E ALA 3.5 20.0 - - - +
1937E ALA* 3.7 25.6 - - + +
1940E SER* 3.9 13.2 - - - -
1941E ARG 3.7 3.6 - - - +
1942E SER* 3.6 24.2 - - - +
1945E ALA* 3.7 21.5 - - + -
1969E ALA* 4.5 1.3 - - + -
1974E ALA* 3.2 5.9 + - + +
1976E GLY* 1.3 69.9 - - - +
1978E PHE* 1.3 71.8 + - - +
1980E ILE* 2.9 17.1 + - - +
1981E LEU* 2.9 31.5 + - + +
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Residues in contact with PHE1978 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1966E LEU* 3.7 19.1 - - + -
1969E ALA* 3.9 8.3 - - + +
1970E VAL* 4.2 9.2 - - + -
1974E ALA 3.0 19.2 + - - +
1975E GLN* 3.3 34.8 - - - +
1977E VAL* 1.3 80.1 - - - +
1979E GLN* 1.3 67.4 + - - +
1981E LEU* 2.7 29.7 + - - +
1982E ILE* 3.0 20.2 + - + +
2011E MET* 3.6 58.3 - - + -
2014E ASP* 4.0 8.1 - - + -
2015E LEU* 3.9 28.3 - - + -
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Residues in contact with GLN1979 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1975E GLN* 3.0 36.8 + - + +
1976E GLY* 3.5 6.1 - - - +
1978E PHE* 1.3 80.9 - - - +
1980E ILE* 1.3 68.2 + - + +
1982E ILE* 3.6 10.0 - - - +
1983E ARG* 3.1 67.1 + - - +
2014E ASP* 3.0 30.0 - - - +
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Residues in contact with ILE1980 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1942E SER* 3.8 22.7 - - - +
1945E ALA* 5.0 6.3 - - + -
1946E LYS* 4.6 29.6 - - + -
1949E LEU* 4.7 19.7 - - + -
1976E GLY 3.2 16.2 - - - +
1977E VAL* 2.9 16.8 + - + +
1979E GLN* 1.3 72.9 - - + +
1981E LEU* 1.3 71.6 + - + +
1983E ARG* 2.9 35.4 + - - +
1984E ASN* 3.0 13.5 + - + +
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Residues in contact with LEU1981 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1933E LEU* 3.5 31.0 - - + -
1949E LEU* 5.4 3.6 - - + -
1955E ALA* 4.8 11.7 - - + +
1965E PRO* 4.0 3.4 - - + +
1966E LEU* 3.9 28.7 - - + +
1969E ALA* 3.8 13.7 - - + -
1977E VAL* 2.9 43.7 - - + +
1978E PHE* 2.7 18.1 + - - +
1980E ILE* 1.3 82.3 - - + +
1982E ILE* 1.3 56.3 + - - +
1984E ASN* 3.1 17.0 + - - +
1987E THR* 2.9 38.1 + - + +
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Residues in contact with ILE1982 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1985B ARG* 2.9 30.3 + - - -
1966E LEU* 4.9 2.2 - - + -
1978E PHE* 3.0 41.0 + - + +
1979E GLN* 3.6 17.9 - - - +
1981E LEU* 1.3 70.1 - - - +
1983E ARG* 1.3 62.0 + - + +
1984E ASN 3.1 1.6 - - - -
1989E LEU* 4.2 18.8 - - + -
2014E ASP* 3.4 37.5 - - + +
2015E LEU* 4.0 10.1 - - + +
2018E SER* 3.3 30.0 + - - +
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Residues in contact with ARG1983 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1949B LEU* 4.6 17.4 + - - -
1950B GLU* 4.5 26.6 + - - +
1952B SER* 5.1 8.0 + - - +
1984B ASN* 3.5 19.4 - - - +
1985B ARG* 2.8 32.5 + - - -
1986B ALA 4.5 0.7 + - - +
1979E GLN* 3.1 57.6 + - - +
1980E ILE* 2.9 26.4 + - - +
1982E ILE* 1.3 78.7 - - + +
1984E ASN* 1.3 52.7 + - - +
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Residues in contact with ASN1984 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1983B ARG* 3.5 21.7 - - - +
1984B ASN* 4.8 0.2 - - - +
1985B ARG* 3.2 16.1 + - - -
1949E LEU* 3.3 30.7 - - + +
1955E ALA* 5.2 0.4 - - - +
1980E ILE* 3.0 12.0 + - + +
1981E LEU* 3.1 19.6 - - - +
1982E ILE 3.1 0.2 - - - -
1983E ARG* 1.3 78.1 - - - +
1985E ARG* 1.3 62.1 + - - +
1986E ALA* 2.9 26.0 + - - +
1987E THR* 2.6 27.8 + - - +
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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