Contacts of the strand formed by residues 121 - 126 (chain D) in PDB entry 2X4O


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 LYS 121 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117D  ALA*     3.1     6.9    -      -       -      +
    118D  TYR*     2.9    33.5    +      -       +      +
    119D  ASP      4.5     0.7    -      -       -      +
    120D  GLY*     1.3    80.3    -      -       -      +
    122D  ASP*     1.3    96.0    +      -       -      +
    136D  ALA*     4.2    12.7    -      -       -      +
    137D  ASP*     5.1     9.2    -      -       -      +
      1E  ILE*     3.5    19.5    -      -       +      -
     60E  TRP*     4.5     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 122 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115D  GLN*     5.5     1.2    -      -       -      +
    116D  TYR      4.0     3.9    -      -       -      +
    118D  TYR*     5.9     0.2    -      -       -      +
    121D  LYS*     1.3    98.5    +      -       -      +
    123D  TYR*     1.3    60.1    +      -       -      +
    124D  ILE      5.4     0.2    -      -       -      +
    136D  ALA*     3.2    20.8    -      -       +      +
    137D  ASP*     5.1     1.2    -      -       -      +
     60E  TRP*     2.9    31.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 123 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81D  LEU*     3.5    20.6    -      -       +      +
     84D  TYR*     3.4    14.6    -      -       -      -
     85D  TYR*     3.3    28.0    -      -       -      -
    116D  TYR*     3.1    18.6    +      -       +      +
    117D  ALA*     4.0     1.8    -      -       -      -
    118D  TYR*     4.0    22.7    -      -       +      +
    122D  ASP*     1.3    78.0    -      -       -      +
    124D  ILE*     1.3    72.6    +      -       +      +
    136D  ALA*     2.8    29.8    +      -       -      +
    137D  ASP*     4.6     1.8    -      -       -      -
    139D  ALA*     3.2    16.1    +      -       +      -
    140D  ALA*     3.2    32.9    -      -       +      +
    143D  THR*     3.0    32.4    +      -       -      -
      9F  LEU*     4.0    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 124 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114D  HIS      4.4     0.2    -      -       -      +
    115D  GLN*     3.6     0.5    -      -       -      -
    116D  TYR*     2.9    36.5    +      -       +      +
    122D  ASP*     6.4     0.2    -      -       -      -
    123D  TYR*     1.3   101.9    -      -       +      +
    125D  ALA*     1.3    65.9    +      -       -      +
    133D  TRP*     3.9    17.5    -      -       +      -
    134D  THR      3.2    18.2    -      -       -      +
    135D  ALA*     4.5     2.2    -      -       +      -
    140D  ALA*     4.4     2.0    -      -       +      +
    143D  THR*     3.9     4.0    -      -       +      -
    144D  LYS*     3.8    33.0    -      -       +      +
    147D  TRP*     3.8    42.2    -      -       +      -
      9F  LEU*     4.6     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 125 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114D  HIS      3.6     5.8    -      -       -      -
    115D  GLN*     4.1    24.7    -      -       +      +
    122D  ASP*     6.0     2.7    -      -       -      +
    124D  ILE*     1.3    76.5    -      -       -      +
    126D  LEU*     1.3    67.0    +      -       -      +
    133D  TRP*     3.4    10.5    -      -       -      -
    134D  THR*     2.9    40.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 126 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113D  TYR*     4.8     4.1    -      -       -      +
    114D  HIS*     2.9    37.6    +      -       +      +
    115D  GLN*     5.6     2.8    +      -       -      +
    125D  ALA*     1.3    77.4    -      -       -      +
    127D  LYS*     1.3    70.2    +      -       -      +
    128D  GLU      4.0     0.2    +      -       -      -
    130D  LEU*     3.4    47.6    -      -       +      +
    131D  ARG      4.2     0.2    -      -       -      +
    132D  SER      3.4    16.8    -      -       -      +
    133D  TRP*     3.7    29.9    -      -       +      -
    153D  ALA*     4.4     5.2    -      -       +      -
    156D  LEU*     4.3    12.8    -      -       +      -
    157D  ARG      5.4     0.4    -      -       -      +
    160D  LEU*     3.9    16.8    -      -       +      -
----------------------------------------------------------
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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