Contacts of the strand formed by residues 1858 - 1865 (chain A) in PDB entry 2HC2


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 ARG1858 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1790A  VAL      4.5     0.6    +      -       -      -
   1791A  TRP*     2.8    71.0    +      -       +      +
   1794A  ASN*     3.4    35.8    +      -       -      +
   1795A  VAL      5.4     1.5    +      -       -      -
   1796A  HIS*     4.6    13.9    -      -       -      +
   1847A  LYS*     3.4     5.2    -      -       -      +
   1848A  ILE*     2.9    42.9    +      -       +      +
   1857A  HIS*     1.3    81.3    -      -       -      +
   1859A  LEU*     1.3    65.3    +      -       -      +
   1860A  ILE*     4.1    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1859 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1796A  HIS*     3.6    20.0    +      -       -      +
   1833A  LEU*     3.7    29.2    -      -       +      -
   1845A  GLU*     3.9    22.9    -      -       -      +
   1846A  PHE      3.3     7.2    -      -       -      +
   1847A  LYS*     4.2    14.6    -      -       +      -
   1858A  ARG*     1.3    74.4    -      -       -      +
   1860A  ILE*     1.3    71.8    +      -       -      +
   1861A  ARG*     5.8     2.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE1860 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1787A  TRP*     4.9     4.3    -      -       +      -
   1790A  VAL*     4.4     9.4    -      -       +      -
   1795A  VAL      3.2    26.0    -      -       -      +
   1796A  HIS*     3.4    16.4    -      -       +      +
   1798A  ILE*     3.7    25.8    -      -       +      -
   1845A  GLU*     3.3     5.3    -      -       -      +
   1846A  PHE*     2.8    49.9    +      -       +      +
   1848A  ILE*     4.1    17.9    -      -       +      -
   1858A  ARG*     4.1    20.0    -      -       +      -
   1859A  LEU*     1.3    89.5    -      -       -      +
   1861A  ARG*     1.3    76.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG1861 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1796A  HIS      2.9     7.4    +      -       -      +
   1797A  ASN*     3.4    11.4    -      -       -      +
   1798A  ILE*     2.9    25.6    +      -       -      +
   1843A  ILE*     4.6    10.7    -      -       -      +
   1844A  ARG      3.4     7.4    -      -       -      +
   1845A  GLU*     3.4    36.2    +      -       +      +
   1859A  LEU*     5.8     1.7    -      -       -      +
   1860A  ILE*     1.3    82.1    -      -       -      +
   1862A  HIS*     1.3    62.6    +      -       -      +
   1863A  PHE*     3.7    20.1    -      -       +      -
   1890A  TYR*     3.5    43.9    +      -       -      -
   1894A  SER*     6.0     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS1862 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1798A  ILE*     3.3    27.1    -      -       +      -
   1800A  MET*     3.8    31.0    -      -       +      +
   1815A  TYR*     2.8    35.4    +      +       -      -
   1816A  TRP*     4.3     9.1    -      +       -      -
   1842A  THR      3.6     1.4    -      -       -      +
   1843A  ILE*     3.3     7.4    -      -       -      +
   1844A  ARG*     2.9    52.9    +      -       +      +
   1846A  PHE*     3.5    33.0    -      +       +      -
   1861A  ARG*     1.3    76.5    -      -       -      +
   1863A  PHE*     1.3    61.4    +      -       -      +
   1864A  HIS*     4.1    11.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE1863 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1797A  ASN*     3.4    25.1    -      -       +      -
   1798A  ILE      2.8    22.3    +      -       -      +
   1799A  VAL*     3.4     3.3    -      -       +      -
   1800A  MET      2.8    27.6    +      -       -      +
   1841A  TRP*     6.0     0.4    -      +       -      -
   1842A  THR      3.7     2.5    -      -       -      -
   1843A  ILE*     4.0    28.5    -      -       +      -
   1861A  ARG*     3.7    22.2    -      -       +      -
   1862A  HIS*     1.3    72.9    -      -       -      +
   1864A  HIS*     1.3    59.9    +      -       -      +
   1883A  PHE*     3.6    24.8    -      +       +      -
   1886A  THR*     4.9     3.4    -      -       +      -
   1887A  VAL*     3.7    29.4    -      -       +      -
   1890A  TYR*     3.4    51.4    -      +       +      -
----------------------------------------------------------
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Residues in contact with HIS1864 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1800A  MET*     3.4    35.2    -      -       +      +
   1802A  THR      2.8    30.1    +      -       -      -
   1803A  GLN*     4.1    18.9    +      -       -      -
   1804A  CYS*     5.3     2.5    -      -       -      -
   1816A  TRP*     4.6     6.2    -      +       -      -
   1841A  TRP*     3.1     6.1    -      -       -      -
   1842A  THR*     2.8    45.3    +      -       -      +
   1844A  ARG*     3.6    28.3    +      -       -      +
   1862A  HIS*     4.1     7.9    -      -       +      -
   1863A  PHE*     1.3    70.8    -      -       -      +
   1865A  TYR*     1.3    69.3    +      -       -      +
   1866A  THR*     3.3    13.4    -      -       +      +
   1883A  PHE*     4.2     1.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR1865 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1800A  MET      2.9    13.5    +      -       -      +
   1801A  VAL*     4.1    12.3    -      -       +      -
   1802A  THR      4.6     2.6    -      -       -      +
   1803A  GLN*     4.5     1.4    +      -       -      -
   1840A  GLU      3.7    12.3    -      -       -      -
   1841A  TRP*     4.0     3.4    -      +       -      -
   1864A  HIS*     1.3    82.4    +      -       -      +
   1866A  THR*     1.3    59.7    +      -       -      +
   1867A  VAL*     3.5    11.1    -      -       +      +
   1868A  TRP*     3.5    56.9    +      +       +      +
   1874A  PRO*     3.5    21.2    -      -       +      +
   1879A  SER*     3.2    47.4    +      -       -      -
   1880A  LEU*     3.7    14.3    +      -       +      -
   1883A  PHE*     3.7    40.7    -      +       +      -
----------------------------------------------------------
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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