Contacts of the strand formed by residues 1783 - 1790 (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 LYS1783 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1705B  TYR*     3.5    51.9    -      -       +      -
   1745B  PHE      3.5     0.9    -      -       -      +
   1746B  GLU*     4.2     0.3    -      -       -      -
   1747B  TYR      2.9    35.4    +      -       -      +
   1768B  PHE*     3.9    11.9    -      -       -      -
   1781B  PRO*     4.0    26.1    -      -       +      +
   1782B  TRP*     1.3    84.9    -      -       -      +
   1784B  PHE*     1.3    63.7    +      -       -      +
   1785B  TYR*     3.4    19.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE1784 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1702B  SER*     4.0    12.6    -      -       -      -
   1703B  THR      3.4    22.9    +      -       -      +
   1704B  VAL*     4.1    11.0    -      -       +      -
   1705B  TYR*     2.7    38.4    +      -       -      -
   1714B  ILE*     4.7     6.5    -      -       +      -
   1744B  LEU*     4.2    16.8    -      -       +      -
   1745B  PHE      3.7     4.3    -      -       -      -
   1755B  ILE*     4.0    19.7    -      -       +      -
   1761B  VAL*     3.6    38.4    -      -       +      -
   1764B  VAL*     3.5    29.4    -      -       +      -
   1765B  LEU*     3.3    32.5    -      -       +      -
   1768B  PHE*     4.1     9.4    -      +       -      -
   1783B  LYS*     1.3    71.7    -      -       -      +
   1785B  TYR*     1.3    54.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR1785 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1704B  VAL*     4.4     0.7    -      -       -      -
   1705B  TYR*     3.1    34.8    -      +       +      +
   1706B  CYS*     4.1     2.0    -      -       -      -
   1707B  HIS*     3.7    49.8    -      +       -      -
   1743B  ALA      3.8     0.5    -      -       -      +
   1744B  LEU*     3.4     9.7    -      -       -      +
   1745B  PHE*     3.0    35.6    +      -       +      +
   1747B  TYR*     3.5    41.7    -      +       +      -
   1783B  LYS*     3.7    26.0    +      -       +      -
   1784B  PHE*     1.3    80.1    -      -       -      +
   1786B  PHE*     1.3    59.5    +      -       -      +
   1787B  LYS*     3.9    16.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE1786 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1704B  VAL*     3.8    18.6    -      -       +      -
   1705B  TYR      2.7    10.8    +      -       -      +
   1706B  CYS*     3.9    12.6    -      -       +      +
   1707B  HIS*     5.0     1.9    +      -       -      -
   1726B  VAL*     4.4     9.6    -      -       +      -
   1729B  LEU*     3.5    32.5    -      -       +      -
   1730B  ILE*     3.7    20.9    -      -       +      -
   1733B  LEU*     3.8    23.3    -      -       +      -
   1735B  MET*     3.9    11.2    -      -       +      -
   1742B  PHE*     3.6    35.9    -      +       +      -
   1743B  ALA      3.8    15.0    -      -       -      -
   1744B  LEU*     4.8     1.6    -      -       +      -
   1785B  TYR*     1.3    73.7    -      -       -      +
   1787B  LYS*     1.3    65.3    +      -       -      +
   1806B  PHE*     3.7    28.6    -      +       -      -
----------------------------------------------------------
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Residues in contact with LYS1787 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1707B  HIS*     3.0    43.4    +      -       +      +
   1742B  PHE*     3.4    11.6    -      -       -      -
   1743B  ALA      3.2    28.4    +      -       -      -
   1745B  PHE*     3.4    28.8    -      -       +      -
   1747B  TYR*     3.8    16.7    -      -       -      -
   1752B  ASP*     2.9    31.3    +      -       -      +
   1785B  TYR*     3.9    15.1    -      -       +      +
   1786B  PHE*     1.3    79.6    -      -       -      +
   1788B  LEU*     1.3    67.0    +      -       -      +
   1806B  PHE*     5.0     4.3    -      -       +      -
   1810B  GLN*     3.2    26.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU1788 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1740B  ASN*     3.4    23.3    -      -       +      +
   1741B  MET      3.8     3.6    -      -       -      +
   1742B  PHE*     3.2    43.9    -      -       +      -
   1745B  PHE*     3.8     7.4    -      -       -      -
   1787B  LYS*     1.3    72.1    -      -       -      +
   1789B  TYR*     1.3    63.0    +      -       -      +
   1790B  CYS      3.2    32.1    -      -       -      +
   1791B  PHE*     3.7    29.9    -      -       +      -
   1803B  GLU*     4.8     1.1    -      -       +      +
   1806B  PHE*     5.2     3.8    -      -       +      -
   1807B  MET*     4.6    15.7    -      -       +      +
   1810B  GLN*     2.9    38.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR1789 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1741B  MET*     2.5    23.2    +      -       +      +
   1742B  PHE      4.4     0.4    -      -       -      -
   1743B  ALA*     4.3    18.2    -      -       +      -
   1745B  PHE*     3.3    28.0    -      +       +      -
   1754B  ALA*     3.4    31.8    -      -       +      +
   1787B  LYS      3.3     1.0    +      -       -      -
   1788B  LEU*     1.3    75.7    -      -       -      +
   1790B  CYS*     1.3    67.9    +      -       -      +
   1791B  PHE*     4.2     4.6    +      -       -      -
   1956B  THR*     4.5     7.1    +      -       -      -
   2028B  ASP*     4.2     2.9    +      -       -      +
   2031B  LYS*     3.6    10.4    -      -       +      +
   2032B  LEU*     3.3    59.7    +      -       +      +
   2035B  ALA*     4.3    15.5    -      -       +      -
   2036B  TYR*     4.1     4.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS1790 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1740B  ASN*     3.0    26.2    -      -       -      +
   1741B  MET*     3.0    31.6    +      -       +      -
   1788B  LEU*     3.2     3.0    -      -       -      +
   1789B  TYR*     1.3    93.4    -      -       -      +
   1791B  PHE*     1.3    60.0    +      -       -      +
   1792B  LEU*     3.3     9.1    +      -       +      -
   2032B  LEU*     4.1     8.3    -      -       -      -
   2035B  ALA*     3.7    32.1    -      -       -      -
   2036B  TYR*     3.8    20.6    -      -       +      -
   2039B  MET*     5.2     2.2    -      -       -      -
----------------------------------------------------------
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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