Contacts of the strand formed by residues 129 - 136 (chain O) in PDB entry 2AXT


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 PHE 129 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329C  GLY      4.4     5.6    -      -       -      -
    330C  SER*     3.2    22.9    -      -       -      -
    331C  ALA      3.7    16.8    -      -       -      -
    332C  GLN*     3.7    24.0    -      -       +      -
    336C  GLY      3.5    22.7    -      -       -      -
    337C  LEU      4.1     4.3    -      -       -      -
    338C  GLY*     3.8    10.8    -      -       -      -
    341C  LEU      5.5     2.7    -      -       -      -
    104O  LEU*     3.9     3.3    -      -       -      +
    127O  ILE*     3.4     8.6    +      -       +      +
    128O  ASP*     1.3    84.4    -      -       -      +
    130O  GLN*     1.3    80.3    +      -       -      +
    131O  PRO*     4.4     2.5    -      -       +      -
    145O  LEU*     3.8    19.7    -      -       +      -
    146O  PHE      3.4     9.9    -      -       -      -
    147O  THR*     3.7    13.9    -      -       -      +
    149O  LYS*     3.4    24.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 130 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337C  LEU*     5.7     2.2    +      -       -      +
    342C  MET*     5.2     5.3    -      -       -      +
    343C  ARG*     3.6    24.8    +      -       -      +
    101O  THR*     3.3    38.7    +      -       -      +
    102O  THR*     3.7    14.6    -      -       -      +
    103O  SER      3.5    20.4    -      -       -      +
    104O  LEU*     4.0     3.6    -      -       +      -
    127O  ILE*     3.5    24.1    -      -       +      +
    129O  PHE*     1.3    83.0    -      -       -      +
    131O  PRO*     1.3    77.0    -      -       -      +
    132O  VAL*     3.2     4.1    +      -       +      +
    145O  LEU*     4.4     3.3    -      -       -      +
    146O  PHE*     2.9    34.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 131 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ARG*     3.4    26.0    +      -       +      +
    335C  THR      5.3     0.2    -      -       -      +
    336C  GLY      3.0    29.6    -      -       -      +
    337C  LEU*     3.2    30.7    -      -       +      +
     98O  THR*     5.3     0.3    -      -       -      +
    101O  THR      4.7     3.3    -      -       -      +
    129O  PHE*     4.4     6.3    -      -       +      +
    130O  GLN*     1.3    91.1    -      -       +      +
    132O  VAL*     1.3    60.2    +      -       -      +
    144O  LEU      3.7     7.4    -      -       -      +
    145O  LEU*     4.2     4.5    -      -       +      -
    177O  TYR*     3.6    26.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 132 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ARG*     5.8     0.2    -      -       -      -
     76O  PHE*     3.9    26.0    -      -       +      -
     96O  LEU*     3.9    21.3    -      -       +      -
     98O  THR*     4.5     4.0    -      -       -      +
    101O  THR      4.6     1.8    -      -       -      +
    102O  THR*     3.8    28.0    -      -       +      -
    130O  GLN*     3.2    11.6    +      -       +      +
    131O  PRO*     1.3    76.9    -      -       -      +
    133O  THR*     1.3    67.2    +      -       -      +
    134O  VAL*     4.0     6.3    -      -       +      -
    143O  PRO*     3.2     2.9    -      -       -      +
    144O  LEU*     2.8    51.1    +      -       +      +
    146O  PHE*     4.3     8.7    -      -       +      -
    177O  TYR*     4.7     0.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 133 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ARG*     4.9     4.3    +      -       -      +
    107A  TYR*     3.9    24.2    +      -       +      +
     96O  LEU*     3.6     3.1    -      -       -      +
     97O  VAL*     3.2    42.8    +      -       +      +
     98O  THR*     3.5    13.5    +      -       -      -
    131O  PRO      4.4     0.2    +      -       -      -
    132O  VAL*     1.3    74.8    -      -       -      +
    134O  VAL*     1.3    64.5    +      -       -      +
    141O  ARG*     4.4    19.1    -      -       +      -
    142O  ILE      3.6     5.2    -      -       -      +
    143O  PRO*     3.3    25.1    -      -       +      +
    177O  TYR*     3.6     9.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 134 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76O  PHE*     4.2    20.6    -      -       +      -
     78O  VAL*     4.6     5.4    -      -       +      -
     94O  THR*     3.4    30.3    -      -       +      +
     95O  LYS      3.2    14.6    -      -       -      +
     96O  LEU*     4.1    10.8    -      -       +      -
    132O  VAL*     4.0    17.7    -      -       +      -
    133O  THR*     1.3    80.0    -      -       -      +
    135O  GLN*     1.3    59.4    +      -       -      +
    136O  MET      3.6     0.9    +      -       -      -
    141O  ARG*     4.4     1.6    -      -       -      -
    142O  ILE*     2.7    55.4    +      -       +      +
    144O  LEU*     4.8     4.5    -      -       +      -
    259O  VAL*     6.3     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 135 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  PRO*     5.2     8.9    -      -       -      +
    103A  ASP*     2.7    40.5    +      -       +      +
    106A  LEU*     6.0     0.4    -      -       -      +
    489C  UNK      5.4     5.9    -      -       -      +
     94O  THR*     3.6     0.8    -      -       -      -
     95O  LYS*     2.7    45.9    +      -       +      +
     97O  VAL*     3.9    15.5    -      -       +      +
    134O  VAL*     1.3    69.9    -      -       -      +
    136O  MET*     1.3    66.6    +      -       -      +
    139O  GLY*     3.5    12.2    +      -       -      +
    140O  GLU      3.4    13.9    -      -       -      +
    141O  ARG*     2.8    40.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 136 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78O  VAL*     4.1    28.0    -      -       +      +
     80O  GLU*     5.8     8.3    -      -       +      -
     92O  VAL*     6.1     5.6    -      -       +      -
     93O  PRO      5.0     0.7    -      -       -      +
     94O  THR*     3.5    24.9    -      -       +      -
    134O  VAL      3.6     1.6    +      -       -      -
    135O  GLN*     1.3    78.8    -      -       -      +
    137O  ALA*     1.3    83.6    +      -       +      +
    138O  GLY*     3.1    15.4    +      -       -      +
    139O  GLY*     3.4    13.9    +      -       -      +
    140O  GLU*     2.9    29.1    +      -       +      +
    142O  ILE*     3.8    23.3    -      -       +      -
    257O  HIS*     4.7     4.0    -      -       +      -
   5076b  SER      4.7     0.3    -      -       -      +
----------------------------------------------------------
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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