Contacts of the strand formed by residues 125 - 131 (chain C) in PDB entry 4J2X


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 PRO 125 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101C  LEU*     3.9    22.2    -      -       +      -
    106C  TRP*     4.0    31.6    -      -       +      +
    110C  LYS*     6.0     0.9    -      -       +      +
    123C  SER      3.5     5.8    -      -       -      +
    124C  GLN*     1.4   118.6    +      -       -      +
    126C  CYS*     1.3    61.3    +      -       -      +
    143C  LEU*     3.8    10.9    +      -       +      +
    171C  MET*     5.6     0.7    -      -       -      -
    172C  PHE      3.7     5.6    -      -       -      +
    173C  TYR*     4.0    17.0    -      -       +      -
    179C  ILE*     4.6     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 126 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121C  GLN      5.7     0.2    -      -       -      -
    124C  GLN*     3.4    20.9    -      -       -      -
    125C  PRO*     1.3    75.2    -      -       -      +
    127C  ALA*     1.3    63.1    +      -       -      +
    128C  PHE*     5.1     4.9    -      -       +      -
    140C  GLN*     6.5     1.1    -      -       +      -
    141C  LEU      5.5     2.0    -      -       -      +
    143C  LEU*     4.1     4.3    -      -       -      -
    171C  MET*     3.1    25.2    -      -       -      +
    172C  PHE*     2.7    43.5    +      -       +      +
    173C  TYR      4.1     2.0    -      -       -      -
    174C  GLY*     3.8    16.8    -      -       -      -
    179C  ILE*     4.9     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 127 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99C  VAL*     5.1     2.7    -      -       +      -
    126C  CYS*     1.3    77.5    -      -       -      +
    128C  PHE*     1.3    66.6    +      -       -      +
    140C  GLN*     3.7     0.5    -      -       -      +
    141C  LEU*     2.9    51.5    +      -       +      +
    143C  LEU*     3.9    20.0    -      -       +      +
    169C  VAL*     4.1     9.6    -      -       +      -
    170C  LYS      3.4     6.1    -      -       -      +
    171C  MET*     3.7    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 128 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126C  CYS*     5.1     3.6    -      -       +      -
    127C  ALA*     1.3    80.8    -      -       -      +
    129C  ILE*     1.3    61.2    +      -       -      +
    138C  MET*     3.9    32.4    -      -       +      +
    139C  GLN      3.3     6.7    -      -       -      -
    140C  GLN*     3.5    42.8    -      -       +      -
    141C  LEU*     5.2     0.2    -      -       -      -
    168C  SER      3.7     0.7    -      -       -      +
    169C  VAL*     3.4     5.5    -      -       -      +
    170C  LYS*     3.0    37.2    +      -       +      +
    172C  PHE*     3.7    34.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 129 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76C  ILE*     5.2     1.8    -      -       +      -
     97C  PRO*     4.6     4.3    -      -       +      -
     99C  VAL*     4.3    12.8    -      -       +      -
    128C  PHE*     1.3    76.0    -      -       -      +
    130C  GLY*     1.3    66.6    +      -       -      +
    137C  GLU      4.9     0.2    -      -       -      +
    138C  MET*     3.4     4.3    -      -       -      -
    139C  GLN*     2.7    55.8    +      -       +      +
    141C  LEU*     3.8    26.2    -      -       +      -
    151C  ALA*     3.9    18.6    -      -       +      -
    154C  LEU*     4.0    23.4    -      -       +      +
    167C  LEU*     4.3    21.1    -      -       +      -
    168C  SER      3.4     8.1    -      -       -      +
    169C  VAL*     3.8    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 130 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129C  ILE*     1.3    76.4    -      -       -      +
    131C  ILE*     1.3    65.1    +      -       -      +
    137C  GLU      5.5     1.3    -      -       -      -
    138C  MET*     3.9    18.2    -      -       -      +
    154C  LEU*     4.5     7.2    -      -       -      -
    167C  LEU*     3.2    13.0    -      -       -      +
    168C  SER*     2.9    33.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 131 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93C  PHE*     3.7    24.5    -      -       +      -
    130C  GLY*     1.3    77.7    -      -       -      +
    132C  GLY*     1.3    51.1    +      -       -      +
    133C  ASN      2.5    22.3    +      -       -      +
    134C  SER*     3.3    28.0    +      -       -      +
    136C  GLN*     4.7     4.2    -      -       +      +
    154C  LEU*     5.1     6.7    -      -       +      -
    155C  TYR      3.3    29.8    -      -       -      +
    156C  ILE*     4.0    12.6    -      -       +      -
    160C  ASP*     4.1     2.5    -      -       -      +
    162C  ARG*     3.1    24.9    -      -       -      +
    165C  PHE*     3.8    22.2    -      -       +      -
    166C  MET      3.8     4.3    -      -       -      -
    167C  LEU*     4.4     5.2    -      -       +      -
    168C  SER*     5.3     3.8    -      -       -      -
----------------------------------------------------------
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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