Contacts of the strand formed by residues 131 - 136 (chain D) in PDB entry 1MQ8


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 ASP 131 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130D  VAL*     1.3    68.7    -      -       -      +
    132D  LEU*     1.3    63.1    +      -       -      +
    167D  GLN*     2.9    40.9    +      -       -      +
    183D  PHE*     3.9    20.1    -      -       +      -
    220D  PHE*     3.7    10.6    -      -       +      -
    226D  ALA*     4.2     6.5    -      -       +      +
    227D  ARG      2.7    43.4    +      -       -      +
    230D  ALA*     3.2    10.1    -      -       -      +
    231D  THR      2.7    10.7    +      -       -      +
    232D  LYS*     3.2    11.0    -      -       +      -
    233D  VAL      3.0    17.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 132 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130D  VAL*     3.3     5.2    +      -       +      -
    131D  ASP*     1.3    74.8    -      -       -      +
    133D  VAL*     1.3    84.4    +      -       -      +
    134D  PHE*     3.4    38.1    -      -       +      +
    157D  VAL*     5.8     2.2    -      -       +      -
    166D  TYR*     4.9     6.3    -      -       +      +
    167D  GLN      2.9     6.5    +      -       -      -
    168D  PHE*     3.0    57.9    -      -       +      -
    169D  ALA      3.3     0.2    +      -       -      -
    183D  PHE*     4.0     1.2    -      -       -      -
    233D  VAL*     3.6    37.0    -      -       +      -
    235D  ILE*     3.7     6.7    -      -       +      -
    302D  LEU*     3.9    26.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 133 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132D  LEU*     1.3    84.5    -      -       -      +
    134D  PHE*     1.3    71.4    +      -       -      +
    135D  LEU      4.5     0.2    -      -       -      +
    169D  ALA*     3.5    25.4    -      -       +      -
    171D  VAL*     4.1     9.9    -      -       +      -
    183D  PHE*     4.6     1.3    -      -       +      -
    215D  VAL*     3.4    26.0    -      -       +      -
    219D  VAL*     4.2     3.8    -      -       +      -
    220D  PHE*     3.2    34.8    -      -       +      -
    233D  VAL      2.9    14.2    +      -       -      +
    234D  LEU*     4.7     4.0    -      -       +      -
    235D  ILE*     2.5    38.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 134 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132D  LEU*     3.4    24.0    -      -       +      -
    133D  VAL*     1.3    73.4    -      -       -      +
    135D  LEU*     1.3    59.5    +      -       -      +
    136D  PHE      3.8     1.3    -      -       -      -
    153D  PHE*     5.2     3.4    -      +       -      -
    154D  MET*     3.8    52.9    -      -       +      -
    157D  VAL*     4.4    11.7    -      -       +      -
    158D  MET*     3.3    54.3    -      -       +      -
    168D  PHE*     4.6     6.3    -      +       +      -
    169D  ALA      3.1    15.3    +      -       -      +
    170D  ALA*     3.2     4.2    -      -       +      -
    171D  VAL*     3.0    28.2    +      -       -      +
    181D  PHE*     5.2     0.7    -      +       -      -
    235D  ILE*     3.3    35.2    -      -       +      +
    237D  ILE*     4.7     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 135 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133D  VAL*     4.9     2.5    -      -       +      -
    134D  PHE*     1.3    73.6    -      -       -      +
    136D  PHE*     1.3    53.7    +      -       -      +
    171D  VAL*     3.3    35.9    -      -       +      +
    173D  PHE*     3.8    18.3    -      -       +      -
    177D  TYR*     6.0     0.4    -      -       +      -
    208D  THR      5.1     0.2    -      -       -      +
    211D  ALA*     3.9    16.2    -      -       +      +
    212D  ILE*     3.9    22.4    -      -       +      +
    215D  VAL*     3.9    19.1    -      -       +      -
    234D  LEU*     4.7     3.8    -      -       +      -
    235D  ILE      2.4    15.3    +      -       -      +
    236D  ILE*     3.2    33.1    -      -       +      +
    237D  ILE*     2.5    34.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 136 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134D  PHE      4.3     2.0    -      -       -      -
    135D  LEU*     1.3    72.3    -      -       -      +
    137D  ASP*     1.3    54.7    +      -       -      +
    147D  PHE*     4.1    22.9    -      +       -      -
    150D  ILE*     4.0     9.9    -      -       +      -
    151D  LEU*     4.4    12.6    -      -       +      -
    154D  MET*     4.2    20.9    -      -       +      -
    170D  ALA*     3.8     9.6    -      -       +      -
    171D  VAL      3.2    18.1    +      -       -      -
    172D  GLN*     3.1    40.5    -      -       +      -
    173D  PHE*     2.9    34.1    +      -       -      -
    180D  GLU*     3.1    35.9    -      -       +      -
    196D  LEU*     5.5     3.4    -      -       +      -
    199D  VAL*     5.0     2.5    -      -       +      -
    237D  ILE*     3.3    28.7    -      -       +      -
----------------------------------------------------------
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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