Contacts of the helix formed by residues 1823 - 1840 (chain B) in PDB entry 3AU5


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.
For CSU analysis of other PDB entry

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 PRO1823 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1822B  ALA*     1.3    88.4    -      -       +      +
   1824B  GLU*     1.3    69.5    +      -       -      +
   1825B  GLU*     4.6     7.2    -      -       +      +
   1826B  ASN*     2.6    43.7    +      -       +      +
   1827B  LEU      3.4     1.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU1824 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1822B  ALA      3.5     3.4    +      -       -      -
   1823B  PRO*     1.3    68.4    -      -       -      +
   1825B  GLU*     1.3    66.8    +      -       -      +
   1827B  LEU*     2.9    26.4    +      -       -      +
   1828B  GLN*     2.6    42.2    +      -       -      +
   1855B  TYR*     2.4    34.2    +      -       -      -
   1859B  ARG*     5.0    11.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU1825 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1823B  PRO*     2.9     9.1    +      -       +      +
   1824B  GLU*     1.3    77.4    -      -       -      +
   1826B  ASN*     1.3    70.6    +      -       -      +
   1828B  GLN*     3.2    10.3    +      -       -      +
   1829B  VAL*     3.1    35.3    +      -       +      +
   1927B  LYS*     3.2    29.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN1826 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1820B  HIS*     5.6     2.0    +      -       -      -
   1822B  ALA*     3.9    21.1    -      -       +      +
   1823B  PRO*     2.6    33.6    +      -       +      +
   1825B  GLU*     1.3    81.9    -      -       -      +
   1827B  LEU*     1.3    62.9    +      -       +      +
   1829B  VAL*     3.3     7.9    +      -       -      +
   1830B  LEU*     3.0    29.9    +      -       +      +
   1946B  LEU*     3.1    39.4    +      -       +      +
   1949B  GLU*     4.1    12.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1827 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1815B  VAL*     4.3    21.0    -      -       +      +
   1820B  HIS*     4.0    23.6    -      -       +      +
   1822B  ALA*     4.0    36.3    -      -       +      +
   1823B  PRO      4.3     0.4    -      -       -      +
   1824B  GLU*     2.9    23.2    +      -       -      +
   1826B  ASN*     1.3    74.8    -      -       -      +
   1828B  GLN*     1.3    58.2    +      -       -      +
   1830B  LEU*     3.4     7.6    +      -       +      +
   1831B  ALA*     3.0    26.3    +      -       -      +
   1854B  VAL      4.9     0.7    -      -       -      +
   1855B  TYR*     4.3    20.6    -      -       +      -
   1856B  SER*     5.5    13.5    -      -       -      +
   1859B  ARG*     6.3     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN1828 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1824B  GLU*     2.6    50.9    +      -       -      +
   1825B  GLU*     3.7     5.2    -      -       -      +
   1827B  LEU*     1.3    72.4    -      -       -      +
   1829B  VAL*     1.3    66.2    +      -       -      +
   1831B  ALA*     3.1     9.5    +      -       -      +
   1832B  ALA*     2.9    22.7    +      -       -      +
   1855B  TYR*     3.9    12.6    +      -       +      +
   1920B  ALA*     5.0     5.6    -      -       -      +
   1923B  SER*     3.0    20.2    +      -       -      -
   1924B  ILE*     3.7    18.9    -      -       +      +
   1927B  LYS*     2.7    39.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL1829 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1825B  GLU*     3.1    30.6    +      -       +      +
   1826B  ASN*     3.6     7.6    -      -       -      +
   1828B  GLN*     1.3    76.0    -      -       -      +
   1830B  LEU*     1.3    57.5    +      -       -      +
   1832B  ALA*     3.1     6.5    +      -       -      +
   1833B  LEU*     2.9    31.8    +      -       +      +
   1927B  LYS*     3.6    21.5    -      -       +      -
   1931B  PHE*     4.0    19.7    -      -       +      -
   1946B  LEU*     3.6    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1830 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1812B  HIS*     5.9     0.2    -      -       -      -
   1815B  VAL*     4.5    10.1    -      -       +      -
   1820B  HIS*     4.2    16.2    -      -       +      +
   1826B  ASN*     3.0    26.2    +      -       +      +
   1827B  LEU*     3.6    13.7    -      -       +      +
   1829B  VAL*     1.3    77.3    -      -       -      +
   1831B  ALA*     1.3    61.6    +      -       -      +
   1833B  LEU*     3.4     2.6    +      -       +      +
   1834B  ARG*     3.1    19.4    +      -       -      +
   1854B  VAL      5.0     0.7    -      -       -      -
   1943B  TYR*     3.3    62.2    -      -       +      +
   1946B  LEU*     3.4    26.5    -      -       +      -
   1947B  ILE*     3.8    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA1831 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1827B  LEU      3.0    13.4    +      -       -      +
   1828B  GLN      3.1     9.4    +      -       -      +
   1830B  LEU*     1.3    76.7    -      -       -      +
   1832B  ALA*     1.3    58.2    +      -       -      +
   1834B  ARG*     3.3     4.5    +      -       -      +
   1835B  LEU*     2.9    32.2    +      -       -      +
   1854B  VAL*     3.3    32.5    +      -       +      +
   1855B  TYR*     4.4     2.0    -      -       +      -
   1924B  ILE*     3.4    31.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA1832 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1828B  GLN      2.9    11.6    +      -       -      +
   1829B  VAL      3.4     4.3    -      -       -      +
   1831B  ALA*     1.3    79.3    -      -       -      +
   1833B  LEU*     1.3    56.4    +      -       -      +
   1835B  LEU*     3.3     8.1    -      -       -      +
   1836B  GLN*     2.8    27.9    +      -       -      +
   1924B  ILE*     3.5    27.3    -      -       -      +
   1927B  LYS*     3.9     6.1    -      -       +      -
   1928B  TRP*     3.6    15.7    -      -       -      +
   1931B  PHE*     3.4    21.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1833 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1808B  PHE*     5.9     0.4    -      -       -      -
   1829B  VAL*     2.9    29.0    +      -       +      +
   1830B  LEU      3.8     4.9    -      -       -      +
   1831B  ALA      3.3     0.2    -      -       -      -
   1832B  ALA*     1.3    73.1    -      -       -      +
   1834B  ARG*     1.3    55.5    +      -       -      +
   1836B  GLN*     3.0     5.5    +      -       -      +
   1837B  TYR*     2.7    37.2    +      -       -      +
   1931B  PHE*     3.3    31.0    -      -       +      -
   1934B  MET*     3.8    24.7    -      -       +      -
   1939B  ALA*     4.0     9.3    -      -       -      +
   1942B  LYS*     3.8    15.3    -      -       +      +
   1943B  TYR*     3.5    44.2    -      -       +      +
   1946B  LEU*     4.5     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG1834 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1708B  GLY*     4.5     8.5    -      -       -      -
   1808B  PHE*     3.3    28.1    -      -       -      -
   1809B  GLU*     2.8    43.7    +      -       -      -
   1812B  HIS*     3.3    53.5    +      -       +      +
   1830B  LEU      3.1    13.1    +      -       -      +
   1831B  ALA*     3.5     9.4    -      -       -      +
   1833B  LEU*     1.3    75.0    -      -       -      +
   1835B  LEU*     1.3    54.4    +      -       -      +
   1837B  TYR*     3.2     5.9    +      -       -      +
   1838B  LEU*     2.7    76.5    +      -       +      +
   1853B  GLU      5.3     0.2    +      -       -      -
   1854B  VAL*     4.1     7.9    -      -       +      -
   1943B  TYR*     4.4     6.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1835 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1831B  ALA      2.9     8.0    +      -       -      +
   1832B  ALA      3.3     9.0    -      -       -      +
   1833B  LEU      3.1     0.2    -      -       -      -
   1834B  ARG*     1.3    77.8    -      -       -      +
   1836B  GLN*     1.3    61.4    +      -       -      +
   1838B  LEU*     4.6     4.9    -      -       +      -
   1839B  GLN*     3.1    32.1    +      -       -      +
   1840B  GLY      3.9     0.7    -      -       -      +
   1848B  ILE*     4.1    23.1    -      -       +      -
   1849B  PRO*     4.3    20.4    -      -       +      -
   1854B  VAL*     3.6    35.0    -      -       +      -
   1924B  ILE*     4.0    27.1    -      -       +      -
   1925B  ILE*     5.1     2.2    -      -       +      -
   1928B  TRP*     3.8    38.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN1836 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1832B  ALA      2.8    17.3    +      -       -      +
   1833B  LEU*     3.3    12.3    -      -       -      +
   1835B  LEU*     1.3    74.4    -      -       -      +
   1837B  TYR*     1.3    57.4    +      -       -      +
   1840B  GLY*     3.1    45.4    +      -       -      +
   1841B  ASP*     3.3    19.0    +      -       -      +
   1928B  TRP*     3.0    29.1    +      -       +      +
   1931B  PHE*     3.3    33.8    +      -       +      +
   1934B  MET*     2.9    41.8    +      -       +      +
   1936B  GLN*     5.1     4.2    +      -       -      +
   1939B  ALA*     4.4     3.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR1837 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1808B  PHE*     3.6    28.7    -      +       +      -
   1809B  GLU*     4.1    13.8    +      -       -      -
   1833B  LEU      2.7    17.7    +      -       -      +
   1834B  ARG*     3.6     6.7    -      -       -      +
   1836B  GLN*     1.3    74.4    -      -       -      +
   1838B  LEU*     1.3    84.3    +      -       +      +
   1840B  GLY      4.6     1.1    +      -       -      -
   1936B  GLN*     2.7    80.8    +      -       +      +
   1939B  ALA*     4.0    12.6    -      -       +      -
   1940B  MET*     3.5    32.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU1838 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1834B  ARG*     2.7    65.5    +      -       +      +
   1835B  LEU*     4.1     5.8    -      -       +      +
   1837B  TYR*     1.3    92.6    -      -       +      +
   1839B  GLN*     1.3    66.7    +      -       +      +
   1840B  GLY      3.8     0.2    -      -       -      -
   1849B  PRO*     5.3    10.3    -      -       +      -
   1853B  GLU      5.7     0.7    -      -       -      +
   1854B  VAL*     4.5    12.1    -      -       +      -
   1936B  GLN*     5.0     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN1839 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1835B  LEU*     3.1    15.2    +      -       -      +
   1838B  LEU*     1.3    81.4    -      -       +      +
   1840B  GLY*     1.3    64.0    +      -       -      +
   1841B  ASP      3.8     5.2    +      -       -      +
   1846B  ALA*     4.4     5.3    -      -       -      +
   1847B  ALA      2.9    25.2    +      -       -      +
   1848B  ILE*     4.7     1.6    -      -       -      -
   1849B  PRO*     3.4    30.0    -      -       -      +
   1928B  TRP*     3.3    29.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY1840 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1836B  GLN*     3.1    39.2    +      -       -      +
   1837B  TYR      4.6     1.0    +      -       -      -
   1838B  LEU      3.8     1.2    -      -       -      -
   1839B  GLN*     1.3    78.4    -      -       -      +
   1841B  ASP*     1.3    61.1    +      -       -      -
   1928B  TRP*     3.1    14.6    +      -       -      -
   1934B  MET      5.5     0.4    -      -       -      -
   1936B  GLN*     6.3     0.2    -      -       -      +
----------------------------------------------------------
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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
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
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