Contacts of the strand formed by residues 204 - 216 (chain E) in PDB entry 1PPE


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 LYS 204 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121E  ILE*     4.4     1.1    -      -       -      -
    122E  SER*     3.4    27.2    +      -       -      +
    123E  LEU      4.0    11.8    +      -       -      +
    124E  PRO*     3.9    26.9    -      -       +      -
    125E  THR*     5.0    11.8    -      -       -      +
    200E  VAL*     3.4     5.4    -      -       -      +
    201E  CYS      2.9    27.2    +      -       -      +
    202E  SER*     3.7    14.6    -      -       -      +
    203E  GLY*     1.3    87.6    -      -       -      +
    209E  LEU*     1.3    59.7    +      -       -      +
    210E  GLN*     3.1    14.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 209 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45E  SER*     3.6    24.2    -      -       -      +
     47E  ILE*     4.3    10.5    -      -       +      -
     53E  VAL*     3.4    32.5    -      -       +      -
    121E  ILE*     4.0     9.9    -      -       +      +
    122E  SER      2.8    19.2    +      -       -      +
    123E  LEU*     4.5     4.7    -      -       +      -
    124E  PRO*     3.2    21.4    -      -       -      +
    198E  PRO*     3.7    18.8    -      -       +      -
    199E  VAL      3.8     6.1    -      -       -      +
    200E  VAL*     4.2     5.4    -      -       +      -
    204E  LYS*     1.3    69.4    -      -       -      +
    210E  GLN*     1.3    58.2    +      -       -      +
    211E  GLY      3.4    23.1    -      -       -      +
    212E  ILE*     5.3     1.3    -      -       +      -
    231E  VAL*     3.5    22.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 210 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124E  PRO*     3.4    22.4    -      -       -      +
    127E  SER      3.1    25.3    +      -       -      +
    128E  CYS*     3.8     0.4    -      -       -      +
    129E  ALA*     3.7    30.0    -      -       +      +
    162E  ILE*     5.0     0.7    -      -       +      -
    181E  PHE*     3.4    16.9    -      -       +      -
    199E  VAL      3.0     5.9    +      -       -      -
    201E  CYS*     3.7    38.0    -      -       +      +
    204E  LYS*     3.1    11.1    +      -       -      +
    209E  LEU*     1.3    74.1    -      -       -      +
    211E  GLY*     1.3    57.8    +      -       -      +
    230E  LYS*     4.0     1.0    -      -       -      +
    231E  VAL*     3.1    24.4    +      -       -      -
    232E  CYS*     3.8    13.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 211 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181E  PHE*     3.7    10.3    -      -       -      -
    198E  PRO      3.8     0.3    -      -       -      -
    199E  VAL*     3.0    41.0    +      -       -      +
    209E  LEU*     3.4    13.9    -      -       -      +
    210E  GLN*     1.3    77.8    -      -       -      +
    212E  ILE*     1.3    63.8    +      -       -      +
    228E  TYR*     4.6     0.4    -      -       -      -
    229E  THR      3.2     9.4    -      -       -      -
    231E  VAL*     3.8     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 212 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53E  VAL*     3.7    19.3    -      -       +      -
     54E  SER      3.6    16.2    -      -       -      +
     55E  ALA*     3.6    16.6    -      -       +      +
    102E  ASP      4.2     5.4    -      -       -      +
    103E  ILE*     3.7    31.0    -      -       +      -
    196E  GLY*     3.5    34.1    -      -       -      +
    197E  GLY      3.4     4.9    -      -       -      +
    209E  LEU*     5.3     1.6    -      -       +      -
    211E  GLY*     1.3    75.4    -      -       -      +
    213E  VAL*     1.3    69.2    +      -       -      +
    214E  SER*     3.9     0.7    -      -       -      -
    228E  TYR*     3.1     8.3    -      -       -      -
    229E  THR*     2.9    35.6    +      -       -      +
    231E  VAL*     3.6    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 213 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55E  ALA*     4.0     3.5    -      -       -      +
    138E  ILE*     3.9    20.9    -      -       +      -
    139E  SER      5.0     1.3    -      -       -      +
    190E  SER*     3.6    21.1    -      -       -      +
    194E  ASP*     3.3    40.2    -      -       +      +
    195E  SER*     3.6     6.8    +      -       -      +
    196E  GLY*     2.9    24.3    +      -       -      +
    197E  GLY*     2.9    24.1    +      -       -      +
    199E  VAL*     4.5     1.8    -      -       +      +
    211E  GLY      4.3     0.2    -      -       -      -
    212E  ILE*     1.3    72.5    -      -       -      +
    214E  SER*     1.3    63.8    +      -       -      +
    228E  TYR*     3.6    22.5    -      -       +      -
      5I  ARG*     4.1    12.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 214 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57E  HIS*     3.2    15.1    +      -       -      -
     99E  LEU*     4.5     1.9    +      -       -      +
    102E  ASP*     2.6    30.3    +      -       -      +
    195E  SER*     4.3     0.4    -      -       -      -
    212E  ILE      3.2     7.8    +      -       -      -
    213E  VAL*     1.3    80.0    -      -       -      +
    215E  TRP*     1.3    78.6    +      -       -      +
    227E  VAL      3.1    17.6    +      -       -      -
    228E  TYR      4.5     0.7    -      -       -      -
    229E  THR*     3.9    13.0    -      -       -      -
      4I  PRO*     3.3     0.3    -      -       -      +
      5I  ARG*     3.1    24.6    +      -       -      +
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Residues in contact with TRP 215 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98E  THR      4.9     2.0    -      -       -      -
     99E  LEU*     3.4    30.8    -      -       +      +
    172E  TYR*     3.7    41.5    -      +       -      -
    175E  GLN*     3.9    29.8    -      -       +      -
    176E  ILE*     3.9    20.2    -      -       +      -
    180E  MET*     3.9    16.6    -      -       +      +
    214E  SER*     1.3    96.5    -      -       -      +
    216E  GLY*     1.3    72.0    +      -       -      +
    226E  GLY      3.8     0.5    -      -       -      -
    227E  VAL*     2.8    54.8    +      -       +      +
      1I  ARG      4.0     1.8    -      -       -      -
      2I  VAL*     3.8    37.7    -      -       +      -
      3I  CYS      3.4    15.9    -      -       -      +
      4I  PRO*     3.7     1.1    -      -       +      -
      5I  ARG*     3.6    14.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 216 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172E  TYR*     3.6    12.1    -      -       -      -
    192E  GLN*     5.5     0.3    +      -       -      -
    215E  TRP*     1.3    81.2    -      -       -      +
    217E  SER*     1.3    61.5    +      -       -      -
    219E  GLY      3.8     5.3    +      -       -      +
    225E  PRO      4.3     2.5    -      -       -      -
    227E  VAL      4.8     0.2    -      -       -      -
      1I  ARG      3.3    11.9    -      -       -      +
      3I  CYS*     3.3    20.8    +      -       -      +
      5I  ARG*     3.5    19.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 217 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172E  TYR*     3.2    22.6    +      -       -      -
    216E  GLY*     1.3    71.8    -      -       -      -
    219E  GLY*     1.3    60.7    +      -       -      +
    220E  CYS      3.8     0.7    +      -       -      -
    221E  GLN*     4.0     8.5    -      -       -      +
    224E  LYS*     3.7    34.8    -      -       -      +
      1I  ARG*     2.8    46.8    +      -       -      +
      3I  CYS*     5.4     0.2    -      -       -      -
      5I  ARG*     4.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 219 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192E  GLN*     4.8     4.4    +      -       -      -
    216E  GLY      3.8     4.8    +      -       -      +
    217E  SER*     1.3    72.9    -      -       -      +
    220E  CYS*     1.3    69.3    +      -       -      -
    221E  GLN*     3.8     8.3    -      -       -      -
      1I  ARG*     3.7    22.4    -      -       -      +
      3I  CYS*     5.3     1.6    -      -       -      +
      5I  ARG*     3.1    20.7    +      -       -      -
     29I  GLY*     4.6     8.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 220 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17E  VAL*     4.0     9.4    -      -       +      -
    146E  SER*     3.2    16.4    +      -       -      +
    189E  ASP*     3.7     5.4    -      -       -      -
    190E  SER      3.9     5.2    -      -       -      +
    191E  CYS*     2.0    59.0    -      -       +      -
    192E  GLN*     3.3    14.6    -      -       -      -
    217E  SER      5.1     0.2    -      -       -      -
    219E  GLY*     1.3    80.2    -      -       -      -
    221E  GLN*     1.3    93.6    +      -       -      +
      5I  ARG*     4.6     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 221 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17E  VAL*     3.9    19.5    -      -       +      -
    146E  SER*     4.0     5.8    -      -       -      -
    187E  GLY*     3.1     5.6    -      -       -      -
    188E  GLY*     2.8    49.9    +      -       -      +
    189E  ASP*     2.8    36.4    +      -       +      +
    220E  CYS*     1.3    75.4    -      -       -      +
    221E  GLN*     1.3    64.7    +      -       -      +
    222E  LYS      3.8     0.3    +      -       -      -
    224E  LYS      4.8     0.6    +      -       -      -
----------------------------------------------------------
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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