Contacts of the strand formed by residues 133 - 141 (chain A) in PDB entry 4PTJ


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 TRP 133 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  LEU*     4.0    21.3    -      -       +      +
    107A  ALA*     3.6    24.0    -      -       +      -
    108A  GLN      3.6    11.9    -      -       -      -
    109A  LYS      3.8     2.9    -      -       -      -
    110A  LEU*     3.5    38.2    -      -       +      +
    129A  GLU*     3.1    33.3    +      -       -      +
    130A  PRO*     3.1    15.2    +      -       +      +
    131A  ASP      3.2     2.2    +      -       -      -
    132A  ASP*     1.3    89.3    +      -       +      +
    134A  GLU*     1.3    61.0    +      -       -      +
    135A  SER      3.9     1.6    +      -       -      -
    156A  LEU*     3.9    36.5    -      -       +      +
    157A  GLU      3.4     7.4    -      -       -      -
    158A  ARG*     3.3    37.7    -      -       +      -
    159A  ARG*     3.7    13.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  TRP*     1.3    72.8    -      -       -      +
    135A  SER*     1.3    73.2    +      -       -      +
    136A  VAL*     3.4    17.7    +      -       +      +
    156A  LEU*     3.2     3.8    -      -       -      -
    157A  GLU*     2.8    41.9    +      -       +      +
    159A  ARG*     3.0    50.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  TRP      3.9     1.6    +      -       -      -
    134A  GLU*     1.3    82.5    -      -       -      +
    136A  VAL*     1.3    59.1    +      -       -      +
    137A  PHE      3.6     7.0    +      -       -      -
    138A  SER*     4.5     5.2    -      -       -      -
    154A  GLU*     3.1    28.0    -      -       -      +
    155A  ILE      3.6     1.1    -      -       -      -
    156A  LEU*     3.5    19.0    -      -       -      +
    159A  ARG*     5.1     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  GLU*     3.4    21.0    +      -       +      +
    135A  SER*     1.3    75.3    -      -       -      +
    137A  PHE*     1.3    61.1    +      -       +      +
    155A  ILE*     2.9    34.3    +      -       +      +
    157A  GLU*     4.1    28.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  TRP*     4.0    32.3    -      +       -      -
    135A  SER*     3.6     1.6    +      -       -      -
    136A  VAL*     1.3    81.1    -      -       +      +
    138A  SER*     1.3    64.1    +      -       -      +
    139A  GLU*     3.7    43.7    -      -       +      -
    153A  PHE*     3.8     9.6    -      -       +      -
    154A  GLU*     3.2     8.0    -      -       -      +
    155A  ILE*     3.0    50.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 138 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  SER*     4.5     8.5    -      -       -      -
    137A  PHE*     1.3    79.2    -      -       -      +
    139A  GLU*     1.3    62.8    +      -       -      +
    140A  PHE*     4.3     3.0    +      -       -      +
    152A  CSD      5.2     6.2    -      -       -      +
    153A  PHE      3.2     7.7    +      -       -      -
    154A  GLU*     4.5     6.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 139 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  TRP*     5.4     1.2    -      -       -      -
    137A  PHE*     3.7    32.2    -      -       +      -
    138A  SER*     1.3    75.5    +      -       -      +
    140A  PHE*     1.3    61.8    +      -       -      +
    141A  HIS*     4.1    20.9    +      -       +      +
    151A  TYR      4.1     0.9    -      -       -      +
    152A  CSD      3.4     2.0    -      -       -      -
    153A  PHE*     2.9    60.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 140 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  ASP*     5.6     2.2    -      -       -      -
    138A  SER*     4.3     2.7    -      -       -      +
    139A  GLU*     1.3    75.7    -      -       -      +
    141A  HIS*     1.3    84.4    +      -       -      +
    142A  ASP*     3.7    35.7    -      -       -      -
    150A  SER*     4.5     9.0    -      -       -      -
    151A  TYR      3.6     8.3    -      -       -      +
    152A  CSD      4.1    17.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 141 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  ALA*     5.2     3.8    -      -       +      -
    139A  GLU*     4.1    26.4    +      -       +      +
    140A  PHE*     1.3    88.7    -      -       -      +
    142A  ASP*     1.3    65.6    +      -       -      +
    144A  ASP*     5.6     2.0    +      -       -      -
    150A  SER*     3.3     4.0    -      -       -      -
    151A  TYR*     2.7    75.7    +      +       +      +
    153A  PHE*     5.0     6.7    -      +       -      -
----------------------------------------------------------
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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