Contacts of the strand formed by residues 57 - 64 (chain C) in PDB entry 2B2T


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 GLU 57 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  ARG      3.4     0.2    -      -       -      +
     24C  ILE*     3.0     6.8    -      -       -      -
     25C  GLY      2.7    40.6    +      -       -      +
     27C  LYS*     2.9    63.4    +      -       +      +
     28C  GLY      3.4     8.5    +      -       -      -
     30C  THR*     4.3     4.2    +      -       -      +
     56C  GLY*     1.3    74.3    -      -       -      +
     58C  ILE*     1.3    62.7    +      -       -      +
     59C  GLN*     3.5    18.0    +      -       +      +
     76C  THR*     3.8    24.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 58 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  CYS*     3.8    27.1    -      -       -      -
     23C  ARG      3.1     8.1    -      -       -      +
     24C  ILE*     4.3    10.7    -      -       +      +
     57C  GLU*     1.3    71.4    -      -       -      +
     59C  GLN*     1.3    59.5    +      -       -      +
     60C  TYR*     3.5    31.5    -      -       +      +
     75C  GLU      4.4     0.3    -      -       -      +
     76C  THR*     3.3    14.9    +      -       -      +
     77C  GLU      5.4     0.3    +      -       -      -
     95C  LYS*     5.9     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 59 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  CYS*     3.5     5.9    -      -       -      -
     23C  ARG*     2.7    64.0    +      -       -      +
     25C  GLY*     3.6    14.4    +      -       -      -
     26C  ARG      3.0    27.0    +      -       -      -
     29C  ALA*     3.2    11.2    +      -       -      +
     30C  THR*     3.2    23.5    -      -       +      +
     57C  GLU*     3.5    16.3    +      -       +      +
     58C  ILE*     1.3    77.9    -      -       -      +
     60C  TYR*     1.3    65.7    +      -       -      +
     74C  TRP*     3.6    13.9    -      -       +      -
     75C  GLU      3.1    13.9    -      -       -      +
     76C  THR*     3.9     9.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 60 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19C  PHE*     3.8    28.7    -      +       +      -
     21C  ASP      3.6     3.8    -      -       -      +
     22C  CYS*     3.4    31.4    -      -       +      -
     58C  ILE*     3.5    31.9    -      -       +      +
     59C  GLN*     1.3    72.7    -      -       -      +
     61C  LEU*     1.3    60.0    -      -       -      +
     62C  ILE*     3.1    13.9    +      -       +      +
     73C  THR      3.4     0.2    -      -       -      +
     74C  TRP*     3.6     3.4    -      -       -      -
     75C  GLU      2.7    44.8    +      -       -      +
     76C  THR*     4.9     2.2    -      -       -      -
     77C  GLU*     4.6    16.8    +      -       +      -
     80C  LEU*     5.0     6.3    -      -       +      -
     91C  LEU*     4.1    14.4    -      -       +      -
     94C  TYR*     3.8    25.4    -      +       -      -
     95C  LYS*     3.3    29.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 61 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  ARG*     5.7     3.1    -      -       +      -
    106B  LYS*     5.2    11.7    -      -       -      +
     19C  PHE*     3.9     2.1    -      -       -      -
     20C  MSE      2.9    47.7    +      -       +      +
     21C  ASP*     3.2    36.9    +      -       +      +
     34C  THR      5.8     0.2    -      -       -      +
     60C  TYR*     1.3    67.9    -      -       -      +
     62C  ILE*     1.3    61.0    +      -       -      +
     72C  ASN*     4.2    22.9    -      -       +      +
     73C  THR      3.7    12.6    -      -       -      +
     74C  TRP*     3.3    39.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 62 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16C  ILE*     3.3    45.1    -      -       +      -
     18C  ARG      3.6     5.6    -      -       -      +
     19C  PHE*     4.5     9.6    -      -       +      -
     20C  MSE      4.7     0.4    -      -       -      -
     60C  TYR*     3.7    14.6    -      -       +      +
     61C  LEU*     1.3    74.4    -      -       -      +
     63C  LYS*     1.3    69.2    +      -       -      +
     64C  TRP*     3.5    24.3    -      -       +      -
     72C  ASN*     3.1    28.4    -      -       -      -
     73C  THR      2.8    18.9    +      -       -      +
     75C  GLU*     3.9    10.3    -      -       +      -
     80C  LEU*     3.3    34.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 63 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17C  GLU*     3.0    56.8    +      -       +      +
     18C  ARG*     3.0    16.7    +      -       +      +
     20C  MSE      3.8    24.2    -      -       +      -
     61C  LEU      4.0     0.6    +      -       -      -
     62C  ILE*     1.3    72.8    -      -       -      +
     64C  TRP*     1.3    66.8    +      -       -      +
     66C  GLY      5.9     0.2    -      -       -      +
     67C  TRP      2.9    27.1    -      -       -      +
     68C  SER*     4.3     2.5    -      -       -      +
     69C  HIS*     3.7    35.3    +      -       +      +
     72C  ASN*     3.0    26.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 64 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14C  GLU*     4.2    15.0    -      -       +      +
     15C  THR      3.3    27.6    -      -       -      +
     16C  ILE*     3.3    28.3    -      -       +      -
     17C  GLU*     4.2     1.8    -      -       -      +
     62C  ILE*     3.5    24.6    +      -       +      +
     63C  LYS*     1.3    84.5    -      -       -      +
     65C  LYS*     1.3    61.2    +      -       -      +
     66C  GLY      3.5     0.9    +      -       -      -
     67C  TRP*     3.2    43.1    +      +       +      +
     71C  HIS*     3.7    20.6    +      -       +      -
     72C  ASN*     3.8     4.0    +      -       -      -
     73C  THR*     3.1    20.8    +      -       -      +
     75C  GLU*     3.8    24.9    -      -       +      -
     80C  LEU*     3.8     8.7    -      -       +      -
     83C  GLN*     4.9     6.7    -      -       -      -
     85C  VAL*     3.6    29.4    -      -       +      -
----------------------------------------------------------
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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