Contacts of the strand formed by residues 148 - 154 (chain G) in PDB entry 5T0J


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 GLY 148 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143G  ILE*     4.0     8.2    -      -       -      +
    144G  ASP      3.8    10.4    +      -       -      +
    146G  GLU*     3.5     4.2    -      -       -      +
    147G  GLN*     1.3    76.7    -      -       -      +
    149G  PRO*     1.3    67.2    -      -       -      +
    150G  GLN*     2.3    28.9    +      -       -      +
    222G  VAL*     5.0     7.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 149 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43G  ARG*     2.7    49.8    +      -       +      -
     45G  LYS      3.5    18.6    -      -       -      +
     46G  ASP*     3.5    33.0    -      -       -      +
     47G  CYS*     3.5    14.1    -      -       -      +
     48G  ALA*     4.3     4.0    -      -       +      +
    142G  GLY      4.8     0.4    -      -       -      +
    143G  ILE*     3.8    15.7    -      -       +      -
    147G  GLN      3.7     2.8    -      -       -      +
    148G  GLY*     1.3    87.7    -      -       -      +
    150G  GLN*     1.3    58.4    +      -       -      +
    220G  VAL*     4.3     9.4    -      -       +      +
    222G  VAL*     5.2     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 150 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43G  ARG*     3.5    11.4    -      -       -      +
     48G  ALA*     4.4     4.0    -      -       -      +
    110G  PRO      4.8     4.5    -      -       -      +
    141G  ILE*     3.7    21.1    -      -       -      +
    142G  GLY*     2.9    28.9    +      -       -      +
    143G  ILE      3.2     0.9    +      -       -      -
    144G  ASP*     3.1    26.3    +      -       +      +
    147G  GLN*     3.2    28.3    -      -       +      +
    148G  GLY      2.3    28.0    +      -       -      -
    149G  PRO*     1.3    75.2    +      -       -      +
    151G  VAL*     1.3    70.7    +      -       -      +
    152G  TYR*     3.5    31.4    -      -       +      +
    220G  VAL*     4.8     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 151 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41G  ALA*     3.6    33.7    -      -       +      +
     42G  VAL      4.5     3.1    -      -       -      +
     43G  ARG*     3.7    28.0    -      -       +      +
     48G  ALA*     3.8    12.6    -      -       +      -
     50G  ILE*     4.9     0.9    -      -       +      -
    140G  LEU      3.7     7.0    -      -       -      +
    141G  ILE*     4.4     6.5    -      -       +      -
    150G  GLN*     1.3    82.7    -      -       -      +
    152G  TYR*     1.3    72.7    +      -       -      +
    153G  LYS*     6.1     0.2    -      -       +      -
    162G  GLY*     3.1    20.4    -      -       -      -
    163G  PHE      3.4    22.7    +      -       -      +
    164G  LYS      3.9     4.3    -      -       -      +
    166G  THR*     4.4    13.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 152 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110G  PRO      4.7     1.6    +      -       -      -
    111G  VAL*     3.5    29.4    -      -       +      -
    112G  ASP*     2.9    44.1    +      -       +      +
    115G  CYS*     3.5    25.8    -      -       +      -
    139G  ILE*     3.3     9.2    -      -       -      +
    140G  LEU*     2.4    51.1    +      -       +      +
    141G  ILE*     4.9     0.9    -      -       -      -
    150G  GLN*     3.5    31.6    -      -       +      +
    151G  VAL*     1.3    79.9    -      -       -      +
    153G  LYS*     1.3    57.8    +      -       -      +
    160G  TYR*     5.2     2.2    -      +       -      -
    161G  CYS      3.2    23.6    -      -       -      +
    162G  GLY*     3.6    16.8    -      -       -      -
    166G  THR*     6.5     0.2    -      -       -      -
     61H  SER*     5.7     4.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 153 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39G  SER      4.5     4.8    +      -       -      -
     41G  ALA*     4.9     1.0    -      -       -      +
    115G  CYS*     5.8     0.2    -      -       -      -
    137G  CYS*     5.2     0.4    -      -       -      -
    138G  MET      3.5     5.2    -      -       -      +
    139G  ILE*     3.5    33.2    -      -       +      +
    140G  LEU*     4.2     2.5    -      -       -      -
    151G  VAL*     6.1     0.2    -      -       +      -
    152G  TYR*     1.3    76.2    -      -       -      +
    154G  CYS*     1.3    63.7    +      -       -      +
    155G  ASP*     3.8    16.6    -      -       -      +
    159G  TYR*     4.9     0.3    -      -       -      -
    161G  CYS*     2.9    44.0    +      -       -      +
    162G  GLY*     4.7     0.2    -      -       -      -
    166G  THR*     3.5    34.9    +      -       +      +
    167G  ALA*     3.4    10.4    -      -       -      +
    168G  ALA*     3.2    50.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 154 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115G  CYS*     4.7     7.4    -      -       +      +
    118G  ILE*     4.9    10.3    -      -       +      -
    119G  ALA*     3.8    24.9    -      -       -      -
    122G  SER*     4.9     3.6    -      -       -      -
    138G  MET*     2.5    48.3    +      -       +      +
    140G  LEU*     4.1    12.7    -      -       +      +
    153G  LYS*     1.3    75.0    -      -       -      +
    155G  ASP*     1.3    81.8    +      -       -      +
    158G  GLY*     4.8     0.2    -      -       -      -
    159G  TYR*     3.4    24.2    -      -       -      +
    161G  CYS*     5.5     0.2    -      -       -      -
----------------------------------------------------------
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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