Contacts of the helix formed by residues 1941 - 1951 (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 ARG1941 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1936E ALA* 3.0 14.9 + - + +
1939E TYR* 3.7 47.1 + - + +
1940E SER* 1.3 77.3 + - - +
1942E SER* 1.3 62.0 + - - +
1943E ASP* 3.4 4.5 - - - +
1944E ALA* 3.2 23.8 - - + -
1945E ALA* 3.2 17.3 + - - +
1977E VAL* 3.7 7.0 - - - +
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Residues in contact with SER1942 (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 3.1 9.1 + - - -
1941E ARG* 1.3 71.5 - - - +
1943E ASP* 1.3 64.5 + - - +
1945E ALA* 3.9 2.8 - - - +
1946E LYS* 3.8 10.4 + - - +
1976E GLY* 3.7 31.9 - - - -
1977E VAL* 3.6 11.0 - - - -
1980E ILE* 3.8 21.5 - - - +
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Residues in contact with ASP1943 (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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1941E ARG* 4.8 1.2 - - - +
1942E SER* 1.3 80.3 + - - +
1944E ALA* 1.3 74.6 + - - +
1945E ALA 3.1 1.1 - - - -
1946E LYS* 3.0 31.7 + - + +
1947E ARG* 2.8 46.0 + - - +
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Residues in contact with ALA1944 (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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1936E ALA* 4.1 9.4 - - + -
1941E ARG* 3.2 34.1 - - + -
1943E ASP* 1.3 87.5 + - - +
1945E ALA* 1.3 61.3 + - - +
1947E ARG* 3.5 24.7 - - - +
1948E LEU* 3.5 19.1 - - - +
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Residues in contact with ALA1945 (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* 4.1 19.5 - - + -
1936E ALA* 4.1 7.8 - - + +
1941E ARG 3.2 13.4 + - - +
1942E SER 3.9 6.5 - - - +
1944E ALA* 1.3 79.5 - - - +
1946E LYS* 1.3 62.3 - - - +
1948E LEU* 3.2 5.7 + - - +
1949E LEU* 3.1 25.3 + - + +
1977E VAL* 3.7 27.6 - - + -
1980E ILE* 5.0 8.3 - - + -
1981E LEU* 6.0 0.2 - - + -
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Residues in contact with LYS1946 (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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1946B LYS* 3.5 32.6 - - - +
1950B GLU* 2.6 33.1 + - - +
1942E SER 3.8 2.1 + - - +
1943E ASP* 3.0 29.8 + - + +
1945E ALA* 1.3 77.6 - - - +
1947E ARG* 1.3 57.0 + - - +
1949E LEU* 2.9 12.0 + - + +
1950E GLU* 2.9 36.9 + - - +
1980E ILE* 4.6 26.7 - - + +
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Residues in contact with ARG1947 (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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1943E ASP* 2.8 51.6 + - - +
1944E ALA* 3.5 18.9 - - - +
1946E LYS* 1.3 71.1 - - - +
1948E LEU* 1.3 63.7 + - + +
1949E LEU 3.0 5.4 - - - -
1950E GLU* 3.2 16.2 + - + +
1951E ALA* 2.9 28.8 + - - +
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Residues in contact with LEU1948 (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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1932E ALA* 3.4 45.5 - - + +
1933E LEU* 3.4 18.6 - - + +
1936E ALA* 5.7 1.8 - - + -
1944E ALA 3.5 16.3 + - - +
1945E ALA 3.2 9.6 + - - +
1947E ARG* 1.3 83.9 - - + +
1949E LEU* 1.3 60.4 + - - +
1951E ALA* 2.7 19.7 - - + +
1953E ALA* 3.0 21.2 - - + +
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Residues in contact with LEU1949 (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* 4.4 14.8 + - - -
1933E LEU* 3.8 29.4 - - + -
1945E ALA* 3.1 14.3 + - + +
1946E LYS* 2.9 14.3 + - + +
1948E LEU* 1.3 78.9 - - - +
1950E GLU* 1.3 63.5 + - - +
1951E ALA 2.8 13.8 - - - +
1952E SER* 4.4 2.6 - - - -
1953E ALA 4.4 13.0 - - - +
1955E ALA* 4.5 15.3 - - + -
1980E ILE* 4.7 16.4 - - + -
1981E LEU* 5.4 4.0 - - + -
1984E ASN* 3.3 32.1 - - + +
1986E ALA* 6.0 1.3 - - + -
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Residues in contact with GLU1950 (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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1946B LYS* 2.7 33.0 + - - +
1983B ARG* 4.4 27.4 + - - +
1946E LYS* 2.9 26.4 + - - +
1947E ARG* 3.2 26.1 + - + +
1949E LEU* 1.3 76.4 - - - +
1951E ALA* 1.3 64.6 + - - +
1952E SER* 3.2 7.4 + - - -
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Residues in contact with ALA1951 (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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1947E ARG 2.9 14.2 + - - +
1948E LEU* 2.7 25.0 - - + +
1949E LEU* 2.8 13.0 - - - +
1950E GLU* 1.3 73.1 - - - +
1952E SER* 1.3 51.8 + - - +
1953E ALA* 2.4 24.7 + - + +
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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