Contacts of the strand formed by residues 69 - 76 (chain A) 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 SER 69 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  PHE*     5.8     0.4    -      -       -      -
     25A  THR      3.3    14.6    -      -       -      -
     26A  THR*     4.8     0.2    -      -       -      -
     27A  ALA*     3.7     4.8    -      -       -      +
     68A  LYS*     1.3    79.6    -      -       -      +
     70A  ILE*     1.3    70.1    +      -       -      +
     71A  VAL*     4.9     0.2    -      -       -      +
    173A  ILE*     3.4     5.9    -      -       -      +
    174A  THR*     2.6    56.1    +      -       -      +
    176A  ILE      2.7    18.2    +      -       -      -
    178A  PHE*     3.4    27.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  PHE*     3.6     4.3    -      -       -      +
     25A  THR*     2.8    40.8    +      -       +      +
     26A  THR      3.5    17.3    -      -       -      +
     27A  ALA*     4.3     3.8    -      -       -      -
     30A  PHE*     4.0    19.5    -      -       +      -
     60A  PRO*     3.7    26.2    -      -       +      -
     69A  SER*     1.3    82.0    -      -       -      +
     71A  VAL*     1.3    66.0    +      -       -      +
     72A  ALA      3.8     0.5    +      -       -      -
    138A  LEU*     4.4     5.4    -      -       +      -
    143A  VAL*     3.7    26.7    -      -       +      -
    171A  GLU*     3.8    17.0    -      -       +      -
    172A  MET      3.4    12.8    -      -       -      +
    173A  ILE*     4.2    13.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  LEU*     4.0    15.5    -      -       +      -
     22A  ILE*     3.6    33.9    -      -       +      -
     23A  GLY      3.5     5.2    -      -       -      +
     24A  PHE*     3.6    25.1    -      -       +      -
     69A  SER*     4.9     0.2    -      -       -      +
     70A  ILE*     1.3    74.6    -      -       -      +
     72A  ALA*     1.3    60.5    +      -       -      +
     73A  ILE*     4.4     8.3    -      -       +      +
    113A  LEU*     5.2     0.4    -      -       +      +
    116A  LEU*     5.0     2.7    -      -       +      -
    171A  GLU*     3.0     5.0    -      -       -      -
    172A  MET*     2.7    62.1    +      -       +      +
    174A  THR*     4.6     4.0    -      -       +      -
    178A  PHE*     4.3    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  ILE*     3.2     6.1    -      -       -      +
     23A  GLY      2.8    33.9    +      -       -      +
     70A  ILE      3.8     1.4    +      -       -      -
     71A  VAL*     1.3    72.3    -      -       -      +
     73A  ILE*     1.3    63.8    +      -       -      +
    143A  VAL*     4.0    16.8    -      -       +      -
    144A  ALA*     4.3     7.0    -      -       +      -
    147A  ALA*     3.9    18.6    -      -       +      -
    149A  ILE*     3.7    22.7    -      -       +      +
    170A  ALA      3.6     7.0    -      -       -      +
    171A  GLU*     4.1     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  VAL*     3.7    25.4    -      -       +      -
     21A  LYS      3.3     4.3    -      -       -      -
     22A  ILE*     4.3     9.6    -      -       +      -
     71A  VAL*     4.4     4.9    -      -       +      +
     72A  ALA*     1.3    81.0    -      -       -      +
     74A  ALA*     1.3    62.7    +      -       -      +
     75A  LEU*     4.2    18.6    -      -       +      -
    109A  LEU*     4.3     6.3    -      -       +      +
    112A  LYS*     4.3    11.2    -      -       +      -
    113A  LEU*     3.9    27.1    -      -       +      +
    116A  LEU*     3.8    25.4    -      -       +      -
    144A  ALA*     6.1     0.2    -      -       -      +
    149A  ILE*     4.7     2.4    -      -       -      +
    169A  LEU*     3.5     5.7    -      -       -      +
    170A  ALA*     2.9    52.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  VAL*     3.8     0.2    -      -       -      +
     20A  ASP*     2.9    25.1    +      -       -      +
     21A  LYS*     2.8    23.0    +      -       +      +
     73A  ILE*     1.3    76.4    -      -       -      +
     75A  LEU*     1.3    66.5    +      -       -      +
     76A  ALA      4.3     0.2    -      -       -      -
    149A  ILE*     3.9    26.0    -      -       +      -
    160A  THR*     5.5     0.2    -      -       +      -
    163A  TYR*     6.5     0.2    -      -       +      -
    167A  VAL*     4.2    13.7    -      -       +      -
    168A  TYR      3.2    10.5    -      -       -      +
    169A  LEU*     3.9     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  GLY      3.7    13.7    -      -       -      +
     19A  VAL*     4.0    21.5    -      -       +      -
     20A  ASP*     3.3     4.5    -      -       -      +
     73A  ILE*     4.2     8.5    -      -       +      -
     74A  ALA*     1.3    81.2    -      -       -      +
     76A  ALA*     1.3    63.3    +      -       -      +
     77A  TYR      3.6     0.7    +      -       -      -
    108A  VAL*     4.2    16.6    -      -       +      -
    109A  LEU*     4.1    24.2    -      -       +      -
    112A  LYS*     4.5    11.2    -      -       +      -
    167A  VAL*     3.2     4.2    -      -       -      -
    168A  TYR*     2.9    35.1    +      -       -      +
    258A  HIS*     3.6    25.8    -      -       +      +
    261A  MET*     4.0    20.9    -      -       +      -
    505A  PO4      4.4     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  ASP*     2.7    17.8    +      -       -      +
     75A  LEU*     1.3    71.4    -      -       -      +
     77A  TYR*     1.3    61.2    +      -       -      +
     78A  PRO*     4.7     0.5    -      -       -      +
    163A  TYR*     3.5    41.1    -      -       +      -
    166A  TYR      3.4     8.7    -      -       -      +
    167A  VAL*     3.9     2.8    -      -       -      +
    255A  PHE*     4.0    20.9    -      -       +      +
    257A  LEU*     4.6     2.4    -      -       +      +
    258A  HIS*     3.2    25.5    -      -       -      -
    261A  MET*     3.8     0.9    -      -       -      +
----------------------------------------------------------
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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