Contacts of the strand formed by residues 112 - 118 (chain C) in PDB entry 4BC1


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 THR 112 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108C  PRO*     3.3    26.1    -      -       +      +
    110C  SER      3.5     1.0    +      -       -      -
    111C  PRO*     1.3    75.9    -      -       -      +
    113C  PRO*     1.3    80.6    -      -       +      +
    114C  VAL*     3.5     3.5    +      -       -      +
    143C  GLY      3.2    27.6    -      -       -      +
    144C  ALA*     4.6     0.4    -      -       -      -
    145C  VAL*     3.6    12.9    -      -       +      +
    191C  GLY      2.8    16.3    +      -       -      -
    192C  GLY*     3.6     1.4    -      -       -      -
    193C  ASP*     2.9    25.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 113 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111C  PRO      4.3     3.1    -      -       -      +
    112C  THR*     1.3    97.9    -      -       +      +
    114C  VAL*     1.3    60.6    +      -       -      +
    115C  LEU*     4.1     2.5    +      -       +      +
    144C  ALA*     4.5     5.5    -      -       -      +
    145C  VAL      3.7    16.3    +      -       -      -
    193C  ASP*     4.2     2.9    -      -       +      +
    196C  SER*     3.5    31.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 114 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112C  THR      3.6    13.9    -      -       -      +
    113C  PRO*     1.3    72.7    -      -       -      +
    115C  LEU*     1.3    67.1    +      -       -      +
    116C  ILE*     4.1     8.9    +      -       +      -
    145C  VAL*     3.2    19.5    -      -       +      +
    147C  VAL*     4.0    22.4    -      -       +      -
    183C  VAL*     4.7     4.7    -      -       +      -
    187C  ILE*     3.9    15.7    -      -       +      -
    192C  GLY*     3.8    10.3    -      -       -      -
    193C  ASP      3.6    22.9    -      -       -      +
    196C  SER      2.9     9.3    +      -       -      +
    197C  VAL*     3.5    10.4    -      -       +      -
    198C  THR*     2.9    27.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 115 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113C  PRO*     4.1     2.6    +      -       +      +
    114C  VAL*     1.3    74.3    -      -       -      +
    116C  ILE*     1.3    60.8    +      -       -      +
    117C  TRP      4.0     0.2    -      -       -      -
    138C  LEU*     4.6    14.8    -      -       +      -
    144C  ALA*     4.6    16.4    -      -       +      -
    145C  VAL      3.1     7.9    +      -       -      +
    146C  LEU*     3.4    23.2    -      -       +      +
    147C  VAL      2.9    24.9    +      -       -      -
    198C  THR*     3.4    34.8    -      -       +      +
    200C  PHE*     3.9    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 116 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114C  VAL*     4.4     8.7    -      -       +      -
    115C  LEU*     1.3    75.9    -      -       -      +
    117C  TRP*     1.3    63.0    +      -       -      +
    118C  ILE*     3.8     1.8    +      -       +      +
    147C  VAL*     3.2    19.3    -      -       +      +
    149C  MET*     3.7    28.5    -      -       +      -
    179C  ALA      5.7     0.2    -      -       -      -
    180C  LEU*     4.1    13.2    -      -       +      -
    183C  VAL*     3.8    29.4    -      -       +      -
    197C  VAL*     3.8    28.9    -      -       +      -
    198C  THR      3.0     7.7    +      -       -      -
    199C  LEU*     3.5    23.1    -      -       +      +
    200C  PHE*     2.8    30.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 117 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115C  LEU      4.0     0.6    +      -       -      -
    116C  ILE*     1.3    74.7    -      -       -      +
    118C  ILE*     1.3    73.1    +      -       -      +
    119C  TYR*     3.4    23.5    -      +       +      +
    120C  GLY      5.1     0.2    -      -       -      -
    128C  ALA*     5.6     0.9    -      -       -      -
    133C  TYR*     3.3    62.0    -      +       +      +
    146C  LEU*     4.6     7.6    -      -       +      +
    147C  VAL      3.0    10.5    +      -       -      +
    148C  SER*     3.8    29.6    -      -       -      -
    149C  MET*     3.9     9.0    +      -       -      +
    200C  PHE*     3.2    64.8    -      +       +      -
    201C  GLY*     3.7    12.6    -      -       -      -
    202C  GLU*     3.6    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 118 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116C  ILE*     4.8     7.4    -      -       +      +
    117C  TRP*     1.3    82.2    -      -       -      +
    119C  TYR*     1.3    68.4    +      -       -      +
    149C  MET*     4.1    16.4    -      -       +      -
    151C  TYR*     3.6    12.1    -      -       +      -
    176C  GLN*     3.3    48.7    -      -       +      +
    180C  LEU*     5.1     6.1    -      -       +      -
    199C  LEU*     5.2    16.8    -      -       +      -
    200C  PHE      3.1     9.3    +      -       -      +
    201C  GLY*     3.3    21.4    -      -       -      -
    202C  GLU      3.9     0.5    +      -       -      -
    205C  GLY*     3.5    16.1    -      -       -      +
    208C  SER*     4.7    13.9    -      -       -      -
----------------------------------------------------------
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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