Contacts of the helix formed by residues 2031 - 2039 (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 SER2031 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2001E ILE* 3.6 1.3 - - - -
2022E VAL 4.8 4.0 - - - -
2023E ASN 4.3 3.8 - - - -
2024E ALA 3.9 11.0 - - - -
2025E VAL* 3.9 5.2 - - - +
2030E LYS* 1.3 75.4 - - - +
2032E ALA* 1.3 62.0 + - - +
2033E LEU* 3.5 11.6 + - - +
2034E HIS* 2.7 51.5 + - - +
2035E TRP* 3.0 6.4 + - - -
2057E MET* 3.8 34.1 - - - +
2065E PRO* 4.9 1.2 - - - +
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Residues in contact with ALA2032 (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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2000E LEU* 3.3 47.1 - - + +
2001E ILE* 3.1 19.8 - - + +
2004E ALA* 3.7 11.6 - - + +
2022E VAL 4.8 3.9 + - - +
2024E ALA 4.5 1.8 + - - -
2031E SER* 1.3 72.6 - - - +
2033E LEU* 1.3 55.9 + - - +
2035E TRP* 4.5 2.5 - - - -
2036E ALA* 2.8 31.7 + - - +
2048E LEU* 4.1 8.5 - - + -
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Residues in contact with LEU2033 (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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2031E SER* 3.0 11.5 + - - +
2032E ALA* 1.3 75.2 - - - +
2034E HIS* 1.3 68.6 + - - +
2036E ALA* 3.7 1.9 - - + -
2037E ALA* 2.9 19.2 + - - +
2045E ALA* 3.9 38.4 - - + +
2048E LEU* 3.6 23.9 - - + +
2049E LEU* 4.2 11.9 - - + -
2053E ALA* 4.8 6.1 - - + -
2054E ASN 3.9 7.0 - - - +
2055E LYS* 3.8 29.4 - - - -
2057E MET* 6.1 0.2 - - + -
2065E PRO* 3.8 16.8 - - + -
2081E LEU* 3.9 16.6 - - + -
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Residues in contact with HIS2034 (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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2029E GLY 4.2 0.4 - - - -
2030E LYS* 3.4 19.7 - - + -
2031E SER* 2.7 38.6 + - - +
2033E LEU* 1.3 72.6 - - - +
2035E TRP* 1.3 54.9 + - - +
2037E ALA* 2.6 27.4 + - - +
2038E ALA* 2.9 9.7 + - - +
2057E MET* 3.2 31.1 + - + -
2058E GLN 3.8 10.3 - - - -
2059E ASN* 4.0 5.4 - - + -
2063E GLU 2.5 28.3 + - - -
2064E THR 3.7 0.4 - - - -
2065E PRO* 3.0 43.0 - - + +
2068E LEU* 4.0 17.7 - - + +
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Residues in contact with TRP2035 (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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360D THR* 5.2 3.8 - - + -
383D CYS* 4.3 16.2 - - - -
385D GLU* 4.6 15.9 - - + -
386D SER* 4.0 20.0 - - - -
1997E THR* 4.9 0.7 - - + -
2001E ILE* 3.4 25.4 - - + +
2004E ALA* 4.7 3.1 - - + -
2005E ARG* 3.2 58.8 - - + -
2026E ASP* 3.1 28.1 + - - -
2030E LYS* 3.7 36.8 - - + +
2031E SER 3.0 16.6 + - - -
2032E ALA* 3.9 6.7 - - - +
2034E HIS* 1.3 73.2 - - - +
2036E ALA* 1.3 53.6 + - - +
2038E ALA* 2.6 29.1 + - + +
2039E VAL* 2.7 21.7 + - + +
2068E LEU* 4.9 1.5 - - + +
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Residues in contact with ALA2036 (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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2004E ALA* 4.3 6.9 - - + +
2032E ALA 2.8 24.4 + - - +
2033E LEU* 3.7 6.7 - - - +
2035E TRP* 1.3 71.0 - - - +
2037E ALA* 1.3 57.6 + - - +
2039E VAL* 4.0 2.9 - - - +
2040E ASN 3.4 0.3 + - - -
2041E ASN* 2.8 38.8 + - + -
2044E ALA* 3.9 28.7 - - + -
2045E ALA* 4.2 11.0 - - - +
2048E LEU* 4.9 0.9 - - + -
2077E THR* 3.5 4.8 + - - -
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Residues in contact with ALA2037 (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* 2.9 11.7 + - + +
2034E HIS 2.6 18.0 + - - +
2036E ALA* 1.3 72.1 - - - +
2038E ALA* 1.3 57.2 + - - -
2039E VAL 3.3 0.2 - - - -
2040E ASN 3.8 0.7 - - - -
2065E PRO* 3.6 28.7 - - + +
2069E ALA* 3.4 13.1 - - + -
2074E SER* 2.7 28.4 + - - -
2077E THR* 3.5 24.0 - - + -
2081E LEU* 4.8 3.6 - - + -
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Residues in contact with ALA2038 (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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382D ARG 4.4 0.7 - - - +
383D CYS* 3.6 28.0 - - + +
385D GLU* 4.8 2.7 - - + +
2034E HIS 2.9 9.3 + - - +
2035E TRP* 2.6 25.2 + - + +
2037E ALA* 1.3 75.2 - - - +
2039E VAL* 1.3 56.8 + - + +
2040E ASN 3.2 3.3 + - - -
2068E LEU* 4.2 22.6 - - + +
2072E GLU* 3.5 31.1 - - + +
2074E SER* 4.2 1.7 + - - -
33F HIS* 5.1 1.6 + - - -
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Residues in contact with VAL2039 (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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382D ARG* 3.8 54.1 + - + +
383D CYS* 4.0 14.8 - - + -
386D SER* 4.5 0.2 - - - +
2004E ALA 3.7 15.0 - - - +
2005E ARG* 4.0 18.6 - - + +
2035E TRP* 2.7 23.8 + - + +
2036E ALA* 4.0 0.4 - - - -
2038E ALA* 1.3 74.7 - - + +
2040E ASN* 1.3 70.1 + - - +
2041E ASN* 3.0 24.8 + - + -
33F HIS* 3.8 13.3 + - - -
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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