Contacts of the strand formed by residues 125 - 129 (chain D) in PDB entry 2XTJ


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 125 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6D  GLN*     2.8    25.5    +      -       -      +
      7D  SER*     3.1    18.8    +      -       -      +
      8D  GLY      3.2    29.8    -      -       -      +
      9D  ALA      5.2     0.4    -      -       -      +
     10D  GLU*     4.8     1.3    -      -       +      +
     20D  VAL*     3.3    31.4    -      -       +      +
     93D  VAL*     3.3     4.7    -      -       -      +
     94D  TYR*     2.7    37.5    +      -       -      +
    124D  GLY*     1.3    72.5    -      -       -      -
    126D  LEU*     1.3    68.0    +      -       -      +
    127D  VAL*     3.5     5.8    +      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
      9D  ALA*     3.3    17.7    -      -       +      +
     10D  GLU      2.9    26.5    +      -       -      +
     41D  PRO*     5.5     7.6    -      -       +      -
     91D  THR*     5.2     5.4    -      -       +      -
     92D  ALA*     3.7    19.3    -      -       -      +
     93D  VAL*     3.9    20.8    -      -       +      +
    124D  GLY      4.3     0.4    -      -       -      -
    125D  THR*     1.3    71.5    -      -       -      +
    127D  VAL*     1.3    63.4    +      -       -      +
    128D  THR*     4.0    18.4    -      -       -      +
    166E  GLU*     4.1    33.7    -      -       +      +
    167E  PRO*     5.2     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 127 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10D  GLU*     3.6    11.9    -      -       +      -
     12D  LYS*     4.8     5.2    -      -       +      -
     18D  VAL*     4.1    31.0    -      -       +      -
     20D  VAL*     4.1    23.1    -      -       +      -
     86D  LEU*     5.2     2.2    -      -       +      -
     90D  ASP      5.2     0.2    -      -       -      +
     91D  THR*     3.3     7.1    -      -       -      +
     92D  ALA      3.0    29.7    +      -       -      +
     94D  TYR*     3.6    30.7    -      -       +      -
    125D  THR*     3.5     7.6    +      -       +      +
    126D  LEU*     1.3    77.9    -      -       -      +
    128D  THR*     1.3    69.7    +      -       -      +
    129D  VAL*     4.6    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 128 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10D  GLU      3.0    12.9    +      -       -      -
     11D  VAL*     3.3    10.8    -      -       -      +
     12D  LYS*     2.8    27.0    +      -       -      +
     91D  THR*     3.9    11.0    -      -       +      +
    126D  LEU*     4.0    20.8    -      -       -      +
    127D  VAL*     1.3    75.4    +      -       -      +
    129D  VAL*     1.3    67.2    +      -       -      +
    130D  SER*     4.1     1.7    +      -       -      -
    164E  PHE*     3.7    29.6    -      -       +      -
    165E  PRO*     4.1    11.8    -      -       +      +
    166E  GLU*     5.1     1.2    +      -       -      +
    194E  TYR*     4.1    17.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 129 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12D  LYS*     3.3    13.2    -      -       +      +
     13D  LYS      4.2     0.2    -      -       -      -
     14D  PRO*     3.9    16.8    -      -       +      -
     86D  LEU*     3.7    30.3    -      -       +      -
     87D  ARG      3.4    33.2    -      -       -      +
     88D  SER*     3.8    14.7    +      -       -      +
     90D  ASP*     4.0    11.4    -      -       +      +
     91D  THR*     3.0    28.9    +      -       -      +
    127D  VAL*     4.6     8.3    -      -       +      -
    128D  THR*     1.3    77.3    -      -       -      +
    130D  SER*     1.3    63.9    +      -       -      +
----------------------------------------------------------
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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