Contacts of the strand formed by residues 130 - 137 (chain D) in PDB entry 5A0Q


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 SER 130 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23D  GLN*     5.2     0.2    +      -       -      -
     26D  VAL*     3.4    25.9    -      -       -      +
     74D  ALA*     3.0    27.4    +      -       -      +
    128D  GLY      4.1     0.6    +      -       -      -
    129D  ILE*     1.3    71.2    -      -       -      +
    131D  ALA*     1.3    62.2    +      -       -      +
    132D  LEU*     3.8     0.7    +      -       -      +
    147D  THR      3.1    15.9    -      -       -      -
    148D  ASP*     3.7     5.9    -      -       -      +
    149D  PRO*     3.3    21.8    -      -       -      +
    161D  ILE*     3.6    25.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 131 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71D  MET*     3.8    31.6    -      -       +      -
     73D  PHE*     3.9    10.1    -      -       +      +
    111D  ILE*     5.2     1.1    -      -       +      -
    115D  LYS*     3.5    14.6    -      -       -      +
    129D  ILE*     4.0     2.4    -      -       +      -
    130D  SER*     1.3    72.1    -      -       -      +
    132D  LEU*     1.4    58.1    +      -       -      +
    133D  ILE*     3.3    24.1    +      -       +      -
    146D  GLN*     3.7     1.6    -      -       -      -
    147D  THR*     3.0    30.1    +      -       -      -
    161D  ILE*     4.7     0.9    -      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
     32D  ALA*     3.4    34.8    -      -       +      +
     33D  VAL      4.1     2.7    -      -       -      +
     34D  GLY*     3.9    15.9    -      -       -      +
     43D  LEU*     5.9     0.4    -      -       +      -
     71D  MET*     3.8     0.2    -      -       -      -
     72D  ALA*     3.0    49.2    +      -       +      +
     74D  ALA*     4.9     0.4    -      -       +      -
    130D  SER      4.3     3.4    -      -       -      +
    131D  ALA*     1.4    69.3    -      -       -      +
    133D  ILE*     1.4    61.4    +      -       -      +
    134D  VAL*     3.4    14.1    +      -       +      +
    144D  LEU*     4.5    10.8    -      -       +      -
    145D  TYR      3.5    11.4    -      -       -      +
    159D  ASN*     3.6    26.2    -      -       +      +
    161D  ILE*     3.7    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 133 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65D  LEU*     5.1     2.0    -      -       +      -
     69D  VAL*     3.8    20.4    -      -       +      -
     70D  CYS      3.7    11.7    -      -       -      +
     71D  MET*     4.0    11.4    -      -       -      +
    104D  VAL*     4.1     5.4    -      -       +      -
    107D  ILE*     4.0     7.6    -      -       +      -
    108D  THR*     3.8    31.4    -      -       -      +
    111D  ILE*     3.5    32.3    -      -       +      -
    131D  ALA*     3.3    18.1    +      -       +      -
    132D  LEU*     1.4    69.1    -      -       -      +
    134D  VAL*     1.3    63.1    +      -       -      +
    145D  TYR*     3.1    34.7    +      -       +      +
    147D  THR*     3.5    22.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 134 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41D  VAL*     3.5    39.9    -      -       +      -
     43D  LEU*     3.8    21.5    -      -       +      -
     69D  VAL*     3.6     0.7    -      -       -      +
     70D  CYS*     2.8    42.2    +      -       -      +
    104D  VAL*     3.5    11.4    -      -       -      +
    132D  LEU*     3.4    16.8    -      -       +      +
    133D  ILE*     1.3    77.9    -      -       -      +
    135D  GLY*     1.3    62.6    +      -       -      +
    143D  ARG      3.4     7.6    -      -       -      +
    144D  LEU*     4.0    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 135 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41D  VAL*     4.5     3.1    -      -       -      +
     68D  ASN      3.2    15.3    -      -       -      -
     70D  CYS*     4.4     2.7    -      -       -      -
    104D  VAL*     3.4    16.4    -      -       -      +
    134D  VAL*     1.3    84.7    -      -       -      +
    136D  PHE*     1.3    68.2    +      -       -      -
    142D  PRO      3.9     0.2    -      -       -      -
    143D  ARG*     3.2    28.3    +      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
     39D  ASP      4.5     1.1    -      -       -      -
     40D  ILE*     3.0    51.4    -      -       +      -
     41D  VAL*     3.8    15.7    -      -       +      -
     68D  ASN*     3.4    27.7    +      -       +      +
    104D  VAL*     3.1    16.2    -      -       -      +
    135D  GLY*     1.3    74.7    -      -       -      -
    137D  ASP*     1.4    58.5    +      -       -      +
    140D  GLY      3.3    26.5    -      -       -      -
    141D  THR      3.8     5.4    -      -       -      -
    142D  PRO*     4.9     4.9    -      -       +      -
    211D  MET*     3.5    29.4    -      -       +      -
    212D  ARG      3.4    19.5    -      -       -      -
    213D  ARG*     3.4    36.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 137 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68D  ASN*     5.7     2.3    -      -       -      +
    103D  THR*     3.6    10.4    +      -       -      +
    104D  VAL*     3.8     3.5    -      -       -      +
    105D  GLU*     2.8    33.1    -      -       -      +
    136D  PHE*     1.4    75.1    -      -       -      +
    140D  GLY*     3.0    29.1    +      -       -      +
    141D  THR*     2.8    32.4    +      -       -      +
    143D  ARG*     3.1    22.9    +      -       -      +
    213D  ARG*     3.4    15.5    +      -       -      -
----------------------------------------------------------
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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