Contacts of the strand formed by residues 132 - 136 (chain C) in PDB entry 5D4E


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 ALA 132 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128C  ILE*     4.2     1.5    -      -       -      +
    129C  ILE      3.0    31.3    +      -       -      +
    130C  ASN      3.4     2.0    -      -       -      +
    131C  GLY*     1.3    80.4    -      -       -      +
    133C  ASP*     1.3    65.4    +      -       -      +
    134C  ARG*     3.5     7.9    +      -       +      +
    394C  PHE*     3.9    32.1    -      -       +      -
    632C  ASN*     4.7     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 133 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84C  ARG*     3.0    48.0    +      -       -      +
    126C  SER*     4.7     2.9    +      -       -      +
    127C  PHE      3.3    11.4    -      -       -      +
    128C  ILE*     4.2     2.6    -      -       -      +
    131C  GLY      4.6     0.9    -      -       -      +
    132C  ALA*     1.3    75.4    -      -       -      +
    134C  ARG*     1.3    62.6    +      -       -      +
    394C  PHE*     4.1     1.7    -      -       -      -
    395C  LYS*     3.1    49.7    +      -       +      +
    397C  GLU*     4.3    11.8    -      -       -      +
    632C  ASN*     3.4    19.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 134 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126C  SER*     3.3     6.2    -      -       -      -
    127C  PHE*     2.9    38.3    +      -       +      +
    129C  ILE*     3.8    36.0    +      -       +      +
    132C  ALA*     3.6    10.2    -      -       +      +
    133C  ASP*     1.3    79.7    -      -       -      +
    135C  VAL*     1.3    65.2    +      -       -      +
    136C  ILE*     6.0     1.6    -      -       +      -
    386C  PHE*     4.0     3.5    +      -       +      -
    387C  SER*     3.8    20.5    +      -       -      +
    392C  SER*     2.9    52.6    +      -       -      +
    393C  GLN      3.3    18.4    -      -       -      +
    394C  PHE*     4.1    26.9    -      -       +      +
    395C  LYS*     3.8     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 135 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  GLN*     4.6     3.1    -      -       -      +
    125C  GLY      5.2     0.4    -      -       -      +
    126C  SER*     4.0    11.7    -      -       -      +
    127C  PHE*     5.2     0.2    -      -       -      -
    134C  ARG*     1.3    81.0    -      -       -      +
    136C  ILE*     1.3    77.1    +      -       -      +
    137C  VAL*     3.6     1.9    +      -       -      +
    391C  LEU      3.3     2.3    -      -       -      +
    393C  GLN*     2.9    34.5    +      -       -      +
    395C  LYS*     3.7    24.8    -      -       +      +
    406C  HIS*     3.8    41.3    -      -       +      +
    407C  LYS*     3.8    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 136 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  GLN*     3.0    30.3    +      -       -      +
    127C  PHE*     3.7    28.1    -      -       +      -
    134C  ARG*     6.0     1.6    -      -       +      -
    135C  VAL*     1.3    73.9    -      -       -      +
    137C  VAL*     1.3    62.9    +      -       -      +
    336C  VAL*     3.7    35.5    +      -       +      +
    339C  LEU*     4.1    12.1    -      -       +      -
    385C  PHE*     4.0    31.2    -      -       +      -
    386C  PHE*     4.1    12.6    -      -       +      -
    391C  LEU      3.2     5.6    -      -       -      +
    392C  SER*     3.6    32.8    -      -       -      +
----------------------------------------------------------
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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