Contacts of the strand formed by residues 132 - 136 (chain R) in PDB entry 3L73


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 132 (chain R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78R  LEU*     3.0    64.3    -      -       +      +
     81R  ILE*     3.4    36.8    -      -       +      -
     98R  VAL*     4.4    10.3    -      -       +      -
     99R  ARG      3.5     9.6    -      -       -      -
    100R  HIS*     3.2    37.5    -      +       +      -
    127R  VAL*     3.2    17.8    -      -       -      +
    129R  LYS*     2.6    42.4    +      -       +      +
    130R  PRO      2.7     3.2    +      -       -      +
    131R  GLU*     1.3   104.1    +      -       +      +
    133R  VAL*     1.3    60.1    +      -       -      +
    134R  ILE*     4.3     4.9    -      -       +      -
    185R  TYR*     5.2     1.6    +      -       -      -
    187R  PHE*     3.8    26.7    -      +       +      -
----------------------------------------------------------
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Residues in contact with VAL 133 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97R  PHE      3.6     1.2    -      -       -      +
     98R  VAL*     3.3     4.3    -      -       -      +
     99R  ARG*     3.0    54.7    +      -       +      +
    101R  ARG*     4.1    18.8    -      -       +      +
    126R  ARG*     6.0     0.9    -      -       +      +
    127R  VAL*     3.8    16.8    -      -       +      -
    132R  TRP*     1.3    74.8    -      -       -      +
    134R  ILE*     1.3    64.3    +      -       -      +
    135R  LEU*     4.1    26.0    -      -       +      -
    156R  TYR*     4.4     7.0    -      -       -      +
    167R  ALA      4.5    10.3    -      -       -      +
    168R  SER*     4.4    14.1    -      -       -      +
    182R  VAL*     6.2     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 134 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78R  LEU*     5.6     0.9    -      -       +      -
     96R  LEU*     4.1    13.9    -      -       +      -
     97R  PHE      3.0     6.5    -      -       -      +
     98R  VAL*     3.8    26.7    -      -       +      -
    127R  VAL*     4.9     1.2    -      -       -      +
    132R  TRP*     5.3     3.6    -      -       +      -
    133R  VAL*     1.3    82.3    -      -       -      +
    135R  LEU*     1.3    63.2    +      -       -      +
    182R  VAL*     3.5    26.4    -      -       -      +
    183R  PRO*     3.6    11.1    -      -       +      +
    185R  TYR*     3.2    44.5    +      -       +      -
    187R  PHE*     5.1     5.2    -      -       +      -
    193R  VAL*     3.7    20.6    -      -       +      -
    195R  VAL*     4.1    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 135 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96R  LEU*     3.2    10.0    -      -       -      +
     97R  PHE*     2.7    46.4    +      -       +      -
    126R  ARG*     3.4    18.6    -      -       -      +
    133R  VAL*     4.1    14.1    -      -       +      -
    134R  ILE*     1.3    74.8    -      -       -      +
    136R  VAL*     1.3    62.2    +      -       -      +
    137R  GLY      3.7     0.2    -      -       -      -
    156R  TYR*     3.8    22.2    -      -       +      +
    168R  SER      4.2     4.7    -      -       -      +
    169R  GLY*     3.7    16.2    -      -       -      +
    180R  LEU*     3.5    39.7    -      -       +      +
    181R  GLU      3.3     3.1    -      -       -      +
    182R  VAL*     3.4    29.8    -      -       +      -
    183R  PRO*     4.2     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 136 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91R  TRP*     4.7    14.8    -      -       +      -
     94R  LYS*     4.9    13.2    -      -       +      -
     95R  PRO      3.9     9.2    -      -       -      +
     96R  LEU*     4.6     2.7    -      -       +      -
    135R  LEU*     1.3    71.5    -      -       -      +
    137R  GLY*     1.3    53.6    +      -       -      +
    138R  VAL*     2.6    40.9    +      -       +      +
    180R  LEU*     4.2    10.6    -      -       -      +
    181R  GLU*     2.7    50.6    +      -       +      +
    183R  PRO*     3.5    28.9    -      -       +      -
----------------------------------------------------------
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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