Contacts of the strand formed by residues 73 - 79 (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 GLY 73 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  ARG      3.8     2.0    +      -       -      -
     72A  LEU*     1.3    75.5    -      -       -      +
     74A  VAL*     1.3    62.8    +      -       -      +
     75A  GLY      4.3     0.2    -      -       -      -
    131A  ILE      3.7     0.2    -      -       -      +
    132A  LEU*     3.6     3.1    -      -       -      -
    133A  VAL*     2.8    41.3    +      -       -      -
    144A  LEU*     4.2     3.7    -      -       -      +
    148A  LEU*     4.1    20.0    -      -       -      -
    168A  PHE*     4.4     5.4    -      -       -      -
    169A  SER      3.7     6.7    -      -       -      -
    170A  CYS*     4.2     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ILE*     4.1    18.4    -      -       +      -
     55A  LEU*     3.8    20.9    -      -       +      -
     72A  LEU*     4.1    12.8    -      -       +      +
     73A  GLY*     1.3    79.1    -      -       -      +
     75A  GLY*     1.3    61.9    +      -       -      +
     76A  MET      4.1     0.3    +      -       -      -
    130A  GLN*     4.1    14.6    -      -       +      -
    131A  ILE      3.4     2.7    -      -       -      +
    132A  LEU*     3.8    26.7    -      -       +      -
    167A  SER*     3.7     2.9    +      -       -      +
    168A  PHE*     3.4     6.2    +      -       -      -
    169A  SER      2.9    31.7    +      -       -      +
    172A  THR      4.8     3.7    -      -       -      +
    173A  ILE*     3.8    28.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  VAL*     1.3    73.6    -      -       -      +
     76A  MET*     1.3    61.5    +      -       -      -
     77A  VAL*     3.7     7.7    +      -       -      +
    130A  GLN*     3.0     9.5    -      -       -      -
    131A  ILE*     2.8    45.0    +      -       -      -
    167A  SER      3.2     8.3    -      -       -      -
    168A  PHE*     3.5    17.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  VAL*     4.1     1.2    -      -       -      +
     75A  GLY*     1.3    70.7    -      -       -      -
     77A  VAL*     1.3    58.4    +      -       -      +
     78A  PHE*     5.2     0.9    -      -       +      -
    110A  VAL*     4.0     2.9    -      -       +      -
    128A  ILE*     3.7    32.1    -      -       +      -
    129A  GLU      3.9     0.7    -      -       -      -
    130A  GLN*     3.5    25.4    -      -       -      +
    165A  VAL*     3.7     3.1    -      -       -      -
    166A  CYS*     2.9    39.3    +      -       +      +
    167A  SER*     2.9    27.0    +      -       -      +
    173A  ILE*     4.1    10.1    -      -       +      -
    174A  VAL      3.3    21.5    -      -       -      +
    175A  TYR*     3.7    35.2    -      -       +      -
    188A  TYR*     3.7    15.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  GLY*     3.7    16.6    -      -       -      +
     76A  MET*     1.3    79.6    -      -       -      +
     78A  PHE*     1.3    78.5    +      -       -      +
     79A  LEU*     3.8    21.7    -      -       +      +
     93A  VAL*     4.6    11.9    -      -       +      -
    107A  TRP*     4.1    21.5    -      -       +      -
    127A  HIS      3.6     0.9    -      -       -      +
    128A  ILE*     3.5     5.4    -      -       -      +
    129A  GLU      2.8    37.3    +      -       -      +
    131A  ILE*     4.3     8.3    -      -       +      -
    163A  PHE*     4.7     3.4    -      -       +      -
    164A  TYR      3.7     8.7    -      -       -      +
    165A  VAL*     4.4    21.1    -      -       +      -
    168A  PHE*     6.2     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  MET*     5.2     2.7    -      -       +      -
     77A  VAL*     1.3    79.9    -      -       -      +
     79A  LEU*     1.3    60.4    +      -       -      +
    126A  PRO*     3.6    20.6    -      -       +      -
    127A  HIS      3.7     2.7    -      -       -      -
    128A  ILE*     3.7    28.5    -      -       +      -
    161A  GLU      5.2     1.3    -      -       -      +
    162A  ASP      3.8     4.3    -      -       -      +
    163A  PHE*     3.3     5.7    -      -       -      -
    164A  TYR*     2.8    55.3    +      +       +      +
    166A  CYS*     3.3    26.5    -      -       -      -
    176A  LYS*     3.6    24.5    -      -       +      -
    188A  TYR*     3.8    15.3    -      -       -      -
    215A  TRP*     3.7    40.2    -      +       +      -
    216A  PRO*     4.1     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  VAL*     3.8    22.2    -      -       +      +
     78A  PHE*     1.3    73.3    -      -       -      +
     80A  PRO*     1.3    67.9    -      -       +      +
     81A  GLN      3.5     0.3    +      -       -      -
     86A  ARG*     4.2    17.5    -      -       +      +
     89A  ALA*     3.8    25.1    -      -       +      -
     90A  ARG*     4.1    19.3    -      -       +      +
     93A  VAL*     4.9     0.4    -      -       +      -
    107A  TRP*     4.0    23.8    -      -       +      -
    126A  PRO*     3.6     5.2    -      -       -      +
    127A  HIS*     2.6    45.8    +      -       +      +
    129A  GLU*     4.1    30.5    -      -       +      +
    162A  ASP*     3.0     7.3    -      -       -      +
    163A  PHE*     4.2     7.0    -      -       +      -
----------------------------------------------------------
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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