Contacts of the strand formed by residues 1841 - 1850 (chain A) in PDB entry 2H03


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 TRP1841 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1838A  LEU*     2.9    60.1    +      -       +      +
   1840A  GLU*     1.3   114.4    -      -       +      +
   1842A  THR*     1.3    64.7    +      -       -      +
   1843A  ILE*     4.1    14.5    -      -       +      +
   1863A  PHE*     5.4     1.3    -      +       -      -
   1864A  HIS      3.1    17.9    -      -       -      +
   1865A  TYR*     3.8    13.9    -      +       -      -
   1866A  THR*     4.1     3.4    -      -       -      -
   1879A  SER*     3.6    17.5    -      -       -      -
   1882A  GLN*     3.7    17.0    -      -       +      -
   1883A  PHE*     3.4    53.4    -      +       +      -
   1886A  THR*     4.1    26.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR1842 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1835A  GLU*     4.0    18.2    -      -       +      -
   1836A  SER      3.3    13.9    -      -       -      +
   1837A  VAL*     3.7    23.1    -      -       +      +
   1838A  LEU      4.8     0.2    +      -       -      -
   1841A  TRP*     1.3    77.4    +      -       -      +
   1843A  ILE*     1.3    65.3    +      -       -      +
   1844A  ARG*     3.6    37.0    +      -       +      +
   1862A  HIS      3.6     1.9    -      -       -      +
   1863A  PHE*     3.8     0.5    -      -       -      -
   1864A  HIS*     2.8    36.9    +      -       -      +
   1866A  THR*     4.3    11.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1843 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1834A  SER*     4.2     2.3    +      -       -      +
   1835A  GLU*     3.6     1.0    +      -       -      -
   1836A  SER*     2.9    46.2    +      -       -      +
   1838A  LEU*     4.0    21.3    -      -       +      -
   1841A  TRP*     4.1    16.2    -      -       +      +
   1842A  THR*     1.3    76.5    -      -       -      +
   1844A  ARG*     1.3    66.2    +      -       -      +
   1861A  ARG*     3.4    36.1    -      -       -      +
   1862A  HIS      3.3     9.0    -      -       -      +
   1863A  PHE*     3.9    31.0    -      -       +      -
   1886A  THR*     5.3     2.5    -      -       +      -
   1890A  TYR*     4.2    12.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG1844 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1814A  HIS*     5.8     0.4    +      -       -      -
   1816A  TRP*     3.5    39.3    -      -       -      +
   1832A  MET*     4.0     6.7    -      -       -      -
   1834A  SER*     3.2     9.0    -      -       -      +
   1835A  GLU*     2.9    42.0    +      -       +      -
   1837A  VAL*     6.1     0.2    -      -       -      +
   1842A  THR*     3.6    19.2    -      -       +      +
   1843A  ILE*     1.3    84.2    -      -       -      +
   1845A  GLU*     1.3    60.6    +      -       -      +
   1846A  PHE*     3.9    21.3    -      -       +      -
   1861A  ARG*     3.5     3.1    -      -       -      -
   1862A  HIS*     2.8    42.3    +      -       +      +
   1864A  HIS*     3.4    36.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU1845 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1832A  MET*     3.6     5.2    -      -       -      +
   1833A  LEU*     2.7    45.0    +      -       +      -
   1834A  SER*     3.0    26.9    +      -       -      +
   1844A  ARG*     1.3    74.4    -      -       -      +
   1846A  PHE*     1.3    65.1    +      -       -      +
   1859A  LEU*     3.4    31.0    -      -       +      +
   1860A  ILE      3.3     9.6    -      -       -      +
   1861A  ARG*     3.2    37.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE1846 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1787A  TRP*     4.6     7.4    -      +       -      -
   1816A  TRP*     3.6    45.1    -      +       +      -
   1817A  PRO*     4.0     7.0    -      -       +      -
   1830A  LEU*     4.0    21.1    -      -       +      -
   1831A  GLN      3.2     8.7    -      -       -      +
   1832A  MET*     3.6    35.7    -      -       +      -
   1833A  LEU*     4.1     4.9    -      -       -      +
   1844A  ARG*     3.9    17.5    -      -       +      -
   1845A  GLU*     1.3    77.3    -      -       -      +
   1847A  LYS*     1.3    60.8    +      -       -      +
   1859A  LEU*     3.4     5.4    -      -       -      +
   1860A  ILE*     2.9    52.2    +      -       +      -
   1862A  HIS*     3.6    34.3    -      +       +      -
----------------------------------------------------------
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Residues in contact with LYS1847 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1829A  ILE      3.8     0.7    -      -       -      +
   1830A  LEU*     3.5     4.9    -      -       -      +
   1831A  GLN*     2.9    48.5    +      -       +      +
   1833A  LEU*     3.9    28.7    -      -       +      +
   1846A  PHE*     1.3    75.6    -      -       -      +
   1848A  ILE*     1.3    62.5    +      -       -      +
   1849A  CYS*     4.3    13.8    -      -       -      -
   1857A  HIS*     3.8    45.7    +      -       +      +
   1858A  ARG      3.4     4.3    -      -       -      -
   1859A  LEU*     4.4     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE1848 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1787A  TRP*     4.1    22.0    -      -       +      +
   1790A  VAL*     4.9     4.0    -      -       +      -
   1791A  TRP*     3.7    23.4    -      -       +      -
   1828A  LEU*     4.0    26.9    -      -       +      -
   1829A  ILE      3.3     3.4    -      -       -      +
   1830A  LEU*     3.4    34.5    -      -       +      -
   1847A  LYS*     1.3    76.3    -      -       -      +
   1849A  CYS*     1.3    63.2    +      -       -      +
   1857A  HIS*     3.3     3.3    -      -       -      -
   1858A  ARG*     2.9    50.8    +      -       +      +
   1860A  ILE*     3.7    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS1849 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1791A  TRP*     4.3     2.7    -      -       -      -
   1828A  LEU*     3.4     8.9    -      -       -      +
   1829A  ILE*     2.9    46.0    +      -       +      +
   1847A  LYS*     4.3    17.0    -      -       -      -
   1848A  ILE*     1.3    76.7    -      -       -      +
   1850A  GLY*     1.3    66.1    +      -       -      +
   1854A  LEU*     4.1    35.0    -      -       +      +
   1856A  ALA      4.7     1.1    -      -       -      -
   1857A  HIS*     4.0    19.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY1850 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1791A  TRP*     3.7    24.1    -      -       -      -
   1827A  ASP      3.9     0.9    -      -       -      -
   1828A  LEU*     3.7    15.5    -      -       -      -
   1849A  CYS*     1.3    72.3    -      -       -      +
   1851A  GLU*     1.3    65.7    +      -       -      -
   1852A  GLU      3.1     2.9    -      -       -      -
   1853A  GLN*     3.0    29.1    +      -       -      +
   1854A  LEU*     3.7     3.5    +      -       -      +
----------------------------------------------------------
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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