Contacts of the helix formed by residues 2074 - 2084 (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 SER2074 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2037E ALA 2.7 26.2 + - - -
2038E ALA 4.2 5.3 + - - -
2040E ASN* 2.9 39.7 + - - +
2069E ALA* 3.3 10.9 + - - +
2072E GLU* 3.2 5.9 + - - +
2073E GLY* 1.3 73.8 - - - +
2075E TYR* 1.3 61.9 + - - +
2076E GLU 3.5 2.2 - - - -
2077E THR* 4.5 0.3 - - - -
2078E ALA* 3.4 21.0 + - - +
2110E ILE* 3.8 0.4 - - - -
33F HIS* 5.5 2.2 - - - -
40F ARG* 4.1 8.3 - - - +
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Residues in contact with TYR2075 (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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2073E GLY 2.8 11.2 + - - +
2074E SER* 1.3 71.1 - - - +
2076E GLU* 1.3 86.4 + - + +
2078E ALA* 3.2 3.0 - - - +
2079E LYS* 2.9 44.1 + - + +
2109E ASP* 4.0 31.9 - - + -
2110E ILE* 3.7 20.9 - - + -
2112E ARG* 4.6 8.6 + - - -
2113E LEU* 3.9 40.3 - - + +
40F ARG* 6.0 0.4 - - - +
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Residues in contact with GLU2076 (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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2040E ASN* 2.7 30.0 + - - +
2042E VAL* 3.4 20.4 - - + +
2074E SER 3.5 0.2 - - - -
2075E TYR* 1.3 95.0 + - + +
2077E THR* 1.3 68.0 + - - +
2078E ALA 3.0 1.6 + - - -
2079E LYS* 3.1 16.6 + - - +
2080E VAL* 3.2 14.6 + - - +
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Residues in contact with THR2077 (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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2036E ALA 3.5 1.7 + - - +
2037E ALA* 3.5 35.7 - - + -
2040E ASN* 2.6 30.2 + - - -
2041E ASN 3.1 21.3 + - - -
2042E VAL* 3.2 16.9 + - - +
2045E ALA* 4.1 15.7 - - + -
2069E ALA* 4.8 0.7 - - + -
2074E SER 4.3 3.6 - - - -
2076E GLU* 1.3 72.4 - - - +
2078E ALA* 1.3 55.6 - - - +
2080E VAL* 3.1 17.7 + - - +
2081E LEU* 2.8 28.8 - - + +
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Residues in contact with ALA2078 (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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2066E LEU* 4.2 9.9 - - + -
2069E ALA* 4.1 11.4 - - + -
2070E ALA* 5.1 1.1 - - + +
2074E SER 3.4 14.9 + - - +
2075E TYR* 3.2 13.4 + - - +
2076E GLU 3.0 0.6 - - - -
2077E THR* 1.3 75.7 - - - +
2079E LYS* 1.3 64.2 + - - +
2081E LEU* 3.1 13.1 + - - +
2082E LEU* 3.0 28.0 + - + +
2110E ILE* 4.3 10.5 - - + -
2113E LEU* 4.3 9.6 - - + -
2114E LEU* 6.1 1.6 - - + -
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Residues in contact with LYS2079 (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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2075E TYR* 2.9 32.7 + - + +
2076E GLU* 3.5 11.7 - - - +
2078E ALA* 1.3 72.3 - - - +
2080E VAL* 1.3 58.9 + - + +
2082E LEU* 3.6 5.4 + - - +
2083E ASP* 2.9 39.4 + - - +
2113E LEU* 3.7 18.9 - - + +
2117E TYR* 3.6 42.9 + - + +
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Residues in contact with VAL2080 (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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2042E VAL* 3.9 24.2 - - + -
2045E ALA* 4.3 9.9 - - + -
2046E VAL* 4.0 22.4 - - + -
2049E LEU* 3.6 22.9 - - + -
2076E GLU 3.2 7.7 + - - +
2077E THR* 3.1 14.1 + - - +
2078E ALA 3.1 1.0 - - - -
2079E LYS* 1.3 78.1 - - + +
2081E LEU* 1.3 62.2 + - + +
2083E ASP* 2.9 29.3 - - + +
2084E HIS* 3.1 16.1 + - + -
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Residues in contact with LEU2081 (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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2033E LEU* 3.9 35.0 - - + -
2037E ALA* 4.8 6.5 - - + -
2045E ALA* 5.6 0.4 - - + -
2049E LEU* 4.8 10.1 - - + -
2055E LYS* 4.6 6.5 - - + +
2065E PRO* 4.2 17.3 - - + -
2066E LEU* 4.0 20.6 - - + +
2069E ALA* 4.8 0.4 - - + -
2077E THR* 2.8 41.7 - - + +
2078E ALA* 3.1 13.0 + - - +
2080E VAL* 1.3 74.1 - - + +
2082E LEU* 1.3 59.5 + - - +
2083E ASP 2.7 9.5 + - - -
2084E HIS* 2.8 11.4 + - - +
2086E ALA* 2.8 38.6 + - + -
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Residues in contact with LEU2082 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2066E LEU* 3.3 42.6 - - + -
2078E ALA* 3.0 16.9 + - + +
2079E LYS* 3.7 7.4 - - - +
2081E LEU* 1.3 76.1 - - - +
2083E ASP* 1.3 53.3 + - - +
2085E PHE* 3.5 7.3 + - - -
2086E ALA 4.3 8.1 - - - +
2088E ARG* 3.0 53.8 - - + +
2113E LEU* 4.8 11.0 - - + +
2114E LEU* 3.6 12.6 - - + -
2117E TYR* 3.7 20.0 - - + +
2118E ASN* 2.5 34.5 + - - +
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Residues in contact with ASP2083 (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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2079E LYS* 2.9 23.1 + - - +
2080E VAL* 2.9 26.8 - - + +
2081E LEU 2.7 1.0 - - - -
2082E LEU* 1.3 76.8 - - - +
2084E HIS* 1.3 66.3 - - + +
2085E PHE* 3.0 21.2 + - - -
2117E TYR* 2.7 31.2 + - - -
2118E ASN* 4.3 5.1 + - - +
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Residues in contact with HIS2084 (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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2046E VAL* 4.9 9.4 - - + -
2049E LEU* 3.1 48.9 - - + +
2050E LYS* 4.5 22.7 - - + +
2055E LYS* 3.0 23.6 + - + -
2080E VAL* 3.1 13.0 + - + +
2081E LEU 2.8 6.8 + - - +
2083E ASP* 1.3 85.7 - - + +
2085E PHE* 1.3 83.4 - - - +
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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