Contacts of the strand formed by residues 167 - 174 (chain B) in PDB entry 5D0A


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 167 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74B  ALA*     4.2    13.2    -      -       +      -
     75B  LEU      3.3     7.2    -      -       -      +
     76B  ALA*     3.9    11.9    -      -       +      +
     77B  TYR*     3.4    10.8    +      -       -      -
    158B  ILE*     4.1     6.3    -      -       +      +
    160B  THR*     4.3    21.3    -      -       +      +
    163B  TYR*     3.7    28.7    -      -       +      -
    164B  GLY      4.4     0.7    -      -       -      +
    165B  SER      2.7    16.7    +      -       -      +
    166B  TYR*     1.3    79.5    -      -       -      +
    168B  TYR*     1.3    59.9    +      -       -      +
    169B  LEU*     4.0    13.5    -      -       +      -
    503B  B12      3.3    37.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 168 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74B  ALA*     3.2     7.3    -      -       -      +
     75B  LEU      2.8    35.3    +      -       -      +
     77B  TYR*     3.4    42.6    -      +       +      +
     98B  ARG      3.5     6.4    +      -       -      -
     99B  ALA*     3.2    37.0    +      -       +      -
    101B  TRP      4.2    10.6    +      -       -      -
    103B  LYS      5.5     2.2    +      -       -      -
    105B  TYR*     3.4    51.8    +      +       +      -
    109B  LEU*     3.7    21.3    -      -       +      +
    167B  VAL*     1.3    73.3    -      -       -      +
    169B  LEU*     1.3    60.1    +      -       -      +
    261B  MET*     3.9    30.0    -      -       +      +
    503B  B12      3.7     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 169 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73B  ILE      3.5     4.5    -      -       -      +
     74B  ALA*     3.9    18.2    -      -       +      -
    109B  LEU*     3.6     2.5    -      -       -      +
    133B  VAL*     3.5     9.2    -      -       -      +
    140B  ASP*     3.7    27.8    -      -       +      +
    141B  ARG*     4.0     1.3    -      -       -      -
    144B  ALA*     3.8    12.3    -      -       +      -
    149B  ILE*     4.2    14.1    -      -       +      -
    158B  ILE*     3.9    13.9    -      -       +      -
    167B  VAL*     4.0    14.8    -      -       +      -
    168B  TYR*     1.3    80.0    -      -       -      +
    170B  ALA*     1.3    65.4    +      -       -      +
    171B  GLU*     5.1     0.2    -      -       -      +
    503B  B12      2.7    72.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 170 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  ALA*     3.7     2.9    -      -       -      +
     73B  ILE*     3.0    35.3    +      -       +      +
    109B  LEU*     3.6    17.5    -      -       +      -
    113B  LEU*     3.9    11.9    -      -       +      -
    132B  MET      3.5    14.4    -      -       -      +
    133B  VAL*     3.6    16.4    -      -       +      +
    140B  ASP*     5.0     0.2    -      -       -      -
    169B  LEU*     1.3    77.6    -      -       -      +
    171B  GLU*     1.3    75.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 171 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70B  ILE*     3.8     3.4    -      -       +      -
     71B  VAL      3.2    14.1    -      -       -      +
    113B  LEU*     3.6     8.6    -      -       -      +
    130B  LYS      4.2     0.5    -      -       -      +
    131B  SER*     3.5     1.9    -      -       -      -
    132B  MET*     3.0    46.9    +      -       +      +
    138B  LEU*     3.8    28.7    -      -       +      +
    140B  ASP*     2.6    45.8    -      -       -      +
    143B  VAL*     3.8    25.6    -      -       +      +
    169B  LEU*     5.1     0.2    -      -       -      +
    170B  ALA*     1.3    93.7    +      -       -      +
    172B  MET*     1.3    61.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 172 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  LEU*     5.1     2.2    -      -       +      -
     70B  ILE*     4.1     1.8    -      -       -      -
     71B  VAL*     2.9    48.5    +      -       +      +
    113B  LEU*     4.1    13.0    -      -       +      +
    116B  LEU*     4.0    23.3    -      -       +      -
    117B  GLU*     4.0    19.7    -      -       -      -
    120B  LEU*     3.7    25.6    -      -       +      -
    129B  THR*     3.9    22.2    -      -       -      -
    130B  LYS      3.5     4.0    -      -       -      +
    131B  SER*     3.4    21.3    -      -       -      +
    171B  GLU*     1.3    76.5    -      -       -      +
    173B  ILE*     1.3    73.0    +      -       -      +
    174B  THR*     3.5    12.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 173 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  PRO*     4.0    11.0    -      -       +      +
     63B  LEU*     3.9    29.8    -      -       +      -
     64B  LEU*     3.7    13.9    -      -       +      -
     67B  ALA*     3.5    29.2    -      -       +      -
     69B  SER      3.7     9.0    -      -       -      +
     70B  ILE*     4.4    12.3    -      -       +      +
    129B  THR*     3.1     6.8    -      -       -      -
    130B  LYS*     2.8    41.1    +      -       +      +
    132B  MET*     4.2     9.2    -      -       +      -
    138B  LEU*     3.9    30.3    -      -       +      -
    171B  GLU*     5.7     0.4    -      -       +      -
    172B  MET*     1.3    73.3    -      -       -      +
    174B  THR*     1.3    63.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 174 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  LEU*     3.9     6.1    -      -       -      -
     67B  ALA*     3.5     3.5    -      -       -      -
     68B  LYS      2.8    21.1    +      -       -      -
     69B  SER*     2.6    42.1    +      -       -      +
     71B  VAL*     4.5     8.1    -      -       +      -
    120B  LEU*     4.3     9.0    -      -       +      -
    128B  ARG      3.4     9.4    -      -       -      -
    129B  THR*     3.9    15.5    -      -       +      -
    172B  MET*     3.5    24.7    +      -       +      +
    173B  ILE*     1.3    81.0    -      -       -      +
    175B  ASN*     1.3    58.9    +      -       -      +
    176B  ILE*     3.1    24.3    +      -       +      +
    178B  PHE*     4.2     0.5    -      -       -      -
----------------------------------------------------------
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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