Contacts of the strand formed by residues 134 - 142 (chain O) in PDB entry 3SDI


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 VAL 134 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31O  VAL*     3.5     7.6    -      -       -      +
     78O  TYR*     3.8    17.5    -      -       +      -
     79O  SER      3.5     4.9    -      -       -      +
     81O  MET      3.2    34.3    -      -       -      +
     84O  ASP*     4.2     4.5    -      -       +      -
     85O  TYR*     4.0     7.2    -      -       +      +
     88O  LEU*     3.5    32.3    -      -       +      -
    120O  MET*     3.7     8.7    -      -       +      +
    132O  PHE*     3.2    12.3    +      -       +      -
    133O  GLY*     1.3    82.3    -      -       -      +
    135O  SER*     1.3    62.3    +      -       -      +
    136O  LEU*     4.4     8.7    -      -       +      -
    153O  PRO*     3.1    24.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 135 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28O  LEU*     4.8     2.1    -      -       -      +
     31O  VAL*     3.5    24.3    -      -       -      +
     78O  TYR*     3.2     5.0    -      -       -      +
     79O  SER      2.9    31.1    +      -       -      -
    134O  VAL*     1.3    75.1    +      -       -      +
    136O  LEU*     1.3    63.7    +      -       -      +
    150O  GLN*     4.7     1.1    +      -       -      -
    151O  VAL      3.1     8.2    +      -       -      -
    152O  ASP*     2.7    26.2    +      -       -      -
    153O  PRO*     3.7     4.0    -      -       -      +
    165O  ILE*     3.4    20.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 136 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76O  ALA*     5.3     3.1    -      -       +      -
     77O  VAL      3.3     3.4    -      -       -      +
     78O  TYR*     3.7     7.9    -      -       +      -
     85O  TYR*     3.3    39.5    -      -       +      -
     88O  LEU*     4.2    18.2    -      -       +      -
     89O  VAL*     6.0     0.2    -      -       +      -
    116O  VAL*     3.7    29.4    -      -       +      -
    120O  MET*     4.3     7.2    -      -       -      -
    134O  VAL*     4.4    11.9    -      -       +      -
    135O  SER*     1.3    75.9    -      -       -      +
    137O  LEU*     1.3    65.7    +      -       -      +
    138O  ILE*     4.0    22.2    -      -       +      -
    149O  TYR      3.6     0.5    -      -       -      +
    150O  GLN*     3.2     7.1    -      -       -      +
    151O  VAL*     2.9    39.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 137 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37O  SER      3.9     8.5    -      -       -      +
     38O  LEU*     3.4    41.5    -      -       -      +
     39O  GLY*     3.5     4.9    -      -       -      +
     48O  ILE*     4.4     9.2    -      -       +      +
     75O  GLY      4.2     0.2    -      -       -      +
     76O  ALA*     3.3     3.5    -      -       -      -
     77O  VAL*     2.7    48.3    +      -       +      +
    135O  SER      4.3     0.2    +      -       -      -
    136O  LEU*     1.3    82.9    -      -       -      +
    138O  ILE*     1.3    61.3    +      -       -      +
    139O  ALA      4.2     0.5    +      -       -      -
    148O  LEU*     4.5     5.8    -      -       +      -
    149O  TYR      3.3     4.3    -      -       -      +
    150O  GLN*     3.6    27.8    -      -       +      +
    163O  THR*     3.9    20.4    -      -       +      +
    165O  ILE*     3.8    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 138 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70O  LEU*     4.3    13.7    -      -       +      -
     74O  ILE*     3.6    20.2    -      -       +      -
     75O  GLY      3.4     9.9    -      -       -      +
     76O  ALA*     3.8    13.2    -      -       +      -
    109O  THR*     4.4     4.3    -      -       +      +
    112O  LEU*     5.9     1.6    -      -       +      -
    113O  VAL*     3.6    28.7    -      -       +      +
    116O  VAL*     4.3    15.0    -      -       +      -
    136O  LEU*     4.1    27.6    -      -       +      -
    137O  LEU*     1.3    77.4    -      -       -      +
    139O  ALA*     1.3    61.5    +      -       -      +
    140O  GLY      4.2     0.2    +      -       -      -
    147O  SER      4.2     0.2    -      -       -      +
    148O  LEU*     3.5     3.5    -      -       -      -
    149O  TYR*     2.8    42.3    +      -       +      +
    151O  VAL*     4.2    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 139 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46O  VAL*     3.7    27.6    -      -       +      -
     48O  ILE*     3.9    25.1    -      -       +      -
     74O  ILE*     3.4     4.2    -      -       -      +
     75O  GLY      2.8    36.9    +      -       -      +
    109O  THR*     4.6     0.7    -      -       -      -
    137O  LEU      4.1     1.2    +      -       -      -
    138O  ILE*     1.3    74.5    -      -       -      +
    140O  GLY*     1.3    59.6    +      -       -      +
    147O  SER      3.5     4.5    -      -       -      -
    148O  LEU*     4.0     2.5    -      -       +      -
    215O  ILE*     3.5    15.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 140 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46O  VAL*     4.4     1.1    -      -       -      +
     73O  ASP      3.2    12.3    -      -       -      -
     74O  ILE*     4.2     2.0    -      -       -      -
    109O  THR*     3.2    21.0    -      -       -      +
    139O  ALA*     1.3    74.3    -      -       -      +
    141O  HIS*     1.3    61.2    +      -       -      -
    147O  SER*     2.8    43.8    +      -       -      +
    215O  ILE*     3.9     9.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 141 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73O  ASP*     3.1    28.3    +      -       +      +
     74O  ILE*     4.8     3.1    -      -       -      +
    107O  PRO      5.4     1.0    -      -       -      +
    109O  THR*     3.4     4.9    +      -       -      -
    140O  GLY*     1.3    74.3    -      -       -      +
    142O  ASP*     1.3    90.7    +      -       -      +
    143O  GLU*     4.1     9.3    +      -       +      -
    146O  GLY*     3.3    32.8    -      -       -      -
    147O  PHE*     3.9    31.6    -      +       +      -
    215O  ILE*     3.9     5.2    -      -       +      -
    220O  ARG*     3.1    51.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 142 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73O  ASP*     5.5     1.6    -      -       -      -
    107O  PRO      5.0     1.3    -      -       -      +
    108O  PRO*     3.4    29.2    -      -       +      +
    109O  THR*     3.3    23.7    +      -       -      -
    110O  LYS*     4.9     1.2    +      -       -      +
    141O  HIS*     1.3    85.3    -      -       -      +
    143O  GLU*     1.3    67.0    +      -       -      +
    144O  PHE*     3.3     4.2    +      -       -      +
    145O  ASN*     2.8    49.6    +      -       -      +
    146O  GLY*     2.9    27.5    +      -       -      +
    147O  SER*     4.8     0.7    -      -       -      +
----------------------------------------------------------
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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