Contacts of the strand formed by residues 164 - 169 (chain A) in PDB entry 1OFD


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 TYR 164 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  VAL*     3.7     1.9    -      -       -      -
     78A  PHE*     2.8    42.4    +      +       +      +
    155A  ILE*     6.1     1.1    -      -       -      -
    159A  LEU*     3.5    20.2    -      -       +      -
    160A  ALA      4.1     1.6    -      -       -      +
    163A  PHE*     1.3    78.7    -      -       -      +
    165A  VAL*     1.3    72.3    +      -       -      +
    166A  CYS*     3.6    24.3    +      -       -      -
    176A  LYS*     3.1    36.7    +      -       -      -
    216A  PRO*     3.7    40.5    +      -       +      -
    221A  MET*     4.6     7.6    -      -       -      -
    222A  ARG*     3.4    37.0    +      -       -      -
    272A  TYR*     4.1    21.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  MET      3.7     7.4    -      -       -      +
     77A  VAL*     4.4    20.6    -      -       +      +
     93A  VAL*     5.3     1.6    -      -       +      -
    152A  ARG*     3.9    17.9    -      -       +      +
    155A  ILE*     3.7    41.5    -      -       +      +
    163A  PHE*     5.8     0.2    -      -       +      -
    164A  TYR*     1.3    78.1    -      -       -      +
    166A  CYS*     1.3    58.0    +      -       -      +
    167A  SER      3.4    29.2    -      -       -      +
    168A  PHE*     4.0    10.1    -      -       +      -
    222A  ARG*     2.7    40.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  MET*     2.9    28.6    +      -       +      +
     78A  PHE*     3.3    49.6    -      -       -      -
    164A  TYR*     3.6    19.9    +      -       +      -
    165A  VAL*     1.3    71.7    -      -       -      +
    167A  SER*     1.3    63.0    +      -       -      +
    174A  VAL*     4.1    16.2    -      -       +      +
    176A  LYS*     4.1    13.3    +      -       -      +
    221A  MET*     4.2     6.1    -      -       -      +
    222A  ARG*     3.5    24.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  VAL      3.7     1.4    +      -       -      +
     75A  GLY*     3.2     2.8    -      -       -      -
     76A  MET*     2.9    37.6    +      -       -      +
    165A  VAL*     3.4     8.8    -      -       -      +
    166A  CYS*     1.3    80.5    -      -       -      +
    168A  PHE*     1.3    60.6    +      -       -      +
    172A  THR*     4.3    10.7    +      -       -      -
    173A  ILE*     3.5    12.8    -      -       -      +
    174A  VAL*     3.1    35.6    +      -       -      -
    222A  ARG*     4.4    12.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  GLY      4.4     1.1    -      -       -      -
     74A  VAL      3.4    11.7    -      -       -      -
     75A  GLY*     3.5    25.4    -      -       -      -
     77A  VAL*     6.2     0.4    -      -       +      -
     93A  VAL*     4.9     2.0    -      -       +      -
     97A  VAL*     3.7    30.5    -      -       +      -
    131A  ILE*     3.7    20.6    -      -       +      -
    133A  VAL*     3.9    13.9    -      -       +      -
    145A  ASP*     4.7     1.4    -      -       -      +
    148A  LEU*     3.4    51.2    -      -       +      +
    151A  ALA*     4.6     8.5    -      -       +      -
    152A  ARG*     3.4    43.1    +      -       +      +
    155A  ILE*     4.6    11.7    -      -       +      -
    165A  VAL*     4.0     8.3    -      -       +      -
    167A  SER*     1.3    74.4    -      -       -      +
    169A  SER*     1.3    62.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ILE*     3.8     7.0    -      -       -      +
     74A  VAL*     2.9    30.5    +      -       -      +
    145A  ASP*     2.7    29.7    +      -       -      -
    148A  LEU*     3.9     5.4    -      -       -      -
    152A  ARG*     5.8     1.1    -      -       -      -
    168A  PHE*     1.3    78.1    -      -       -      +
    170A  CYS*     1.3    56.7    +      -       -      +
    171A  ARG*     2.7    21.7    +      -       -      +
    172A  THR*     3.0    37.6    +      -       -      +
    283A  ARG*     5.5     3.4    -      -       -      -
----------------------------------------------------------
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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