Contacts of the strand formed by residues 133 - 146 (chain E) in PDB entry 1PPF


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 133 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132E  ASN*     1.3    75.5    +      -       -      +
    134E  VAL*     1.3    68.4    +      -       -      +
    135E  GLN*     3.4    14.9    +      -       -      +
    161E  THR*     3.6    11.0    -      -       -      -
    162E  VAL      2.8    17.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 134 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130E  LEU*     4.1    22.7    -      -       +      -
    131E  GLY      2.9    34.6    +      -       -      +
    132E  ASN      4.8     0.7    -      -       -      +
    133E  GLY*     1.3    77.0    -      -       -      +
    135E  GLN*     1.3    70.1    +      -       -      +
    136E  CYS*     3.7     9.3    +      -       -      -
    161E  THR*     3.4     4.9    -      -       -      -
    162E  VAL*     2.9    40.0    +      -       +      +
    201E  CYS*     4.5     0.4    -      -       +      -
    202E  ASN*     4.2    16.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 135 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  NAG      3.6    24.4    +      -       -      +
      8A  FUC      2.7    37.1    +      -       -      +
    133E  GLY      3.4    14.3    +      -       -      +
    134E  VAL*     1.3    78.3    -      -       -      +
    136E  CYS*     1.3    56.0    +      -       -      +
    159E  ASN*     4.8     9.9    -      -       -      +
    160E  VAL      3.8     7.2    +      -       -      -
    161E  THR*     2.7    28.7    +      -       -      +
    202E  ASN*     4.8     2.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 136 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  NAG      5.3     1.3    -      -       -      -
      8A  FUC      3.8     4.9    -      -       -      -
    134E  VAL*     4.0     3.4    -      -       -      -
    135E  GLN*     1.3    77.0    -      -       -      +
    137E  LEU*     1.3    62.0    +      -       -      +
    159E  ASN*     3.5     9.3    +      -       -      +
    160E  VAL*     2.8    35.0    +      -       +      +
    162E  VAL*     3.7    23.6    -      -       -      -
    199E  LEU*     3.7    15.5    -      -       +      -
    200E  VAL      3.2     8.3    -      -       -      +
    201E  CYS*     2.0    49.8    -      -       -      -
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Residues in contact with LEU 137 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  NAG      4.0    16.8    -      -       -      +
      8A  FUC      4.1    14.8    -      -       +      -
     20E  ARG*     3.8    11.9    -      -       -      +
     27E  TRP*     3.2    43.1    -      -       +      +
    136E  CYS*     1.3    77.3    -      -       -      +
    138E  ALA*     1.3    68.7    +      -       -      +
    139E  MET*     4.3     6.3    -      -       +      +
    157E  GLU*     4.1    12.1    -      -       +      +
    158E  LEU      3.4    20.2    -      -       -      +
    159E  ASN*     3.7    24.2    -      -       -      +
    198E  PRO      4.1     0.2    -      -       -      +
    199E  LEU*     3.7     5.6    -      -       -      -
    200E  VAL*     3.0    34.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 138 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16E  ILE*     4.6     1.6    -      -       +      -
    136E  CYS      4.3     0.2    +      -       -      -
    137E  LEU*     1.3    76.0    -      -       -      +
    139E  MET*     1.3    67.6    +      -       -      +
    157E  GLU*     3.1     3.9    -      -       -      +
    158E  LEU*     2.7    42.9    +      -       +      +
    160E  VAL*     4.3    16.3    -      -       +      +
    190E  VAL*     4.5    12.1    -      -       +      -
    198E  PRO      3.9     6.3    -      -       -      +
    199E  LEU*     4.4    11.0    -      -       +      -
    228E  PHE*     4.4    15.7    -      -       +      -
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Residues in contact with MET 139 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16E  ILE*     3.7    12.7    -      -       -      +
     27E  TRP*     3.7    50.7    -      -       +      +
     29E  PHE*     4.2     1.8    -      -       +      -
     30E  MET*     4.1    19.1    -      -       -      +
    137E  LEU*     4.3    11.9    -      -       +      +
    138E  ALA*     1.3    83.0    -      -       -      +
    140E  GLY*     1.3    60.7    +      -       -      +
    155E  LEU*     4.5     4.7    -      -       +      -
    156E  GLN      3.1    15.5    -      -       -      +
    157E  GLU*     4.1     4.5    -      -       +      -
    190E  VAL*     5.8     0.9    -      -       -      +
    194E  ASP*     4.3     0.9    -      -       -      +
    197E  SER*     3.0    23.9    -      -       -      -
    198E  PRO*     3.8    25.0    +      -       +      +
    200E  VAL*     3.6    30.1    -      -       +      -
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Residues in contact with GLY 140 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16E  ILE*     3.7     3.3    -      -       -      +
     30E  MET*     3.9    10.1    -      -       -      -
    139E  MET*     1.3    77.0    -      -       -      +
    141E  TRP*     1.3    59.6    +      -       -      -
    155E  LEU*     3.5    14.9    -      -       -      +
    156E  GLN*     3.1    35.2    +      -       -      +
    194E  ASP*     2.9    18.1    -      -       -      +
    197E  SER*     4.0     3.4    -      -       -      -
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Residues in contact with TRP 141 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30E  MET*     3.9    37.0    -      -       +      +
     31E  VAL      3.8    13.7    -      -       -      -
     32E  SER*     3.5    21.3    -      -       -      -
     40E  HIS*     3.8    29.5    +      +       +      +
     70E  ALA*     3.9    37.5    -      -       +      -
     71E  HIS      3.1    27.7    +      -       -      -
     73E  LEU*     3.6    23.5    -      -       +      +
    140E  GLY*     1.3    73.1    -      -       -      -
    142E  GLY*     1.3    64.2    +      -       -      +
    151E  ILE*     3.2    19.5    -      -       -      +
    152E  ALA*     3.5    14.5    +      -       -      +
    153E  SER      3.4    22.1    +      -       -      -
    154E  VAL      3.9     0.7    -      -       -      -
    155E  LEU*     3.1    28.6    -      -       +      +
    193E  GLY      4.3     5.9    +      -       -      -
    194E  ASP*     3.2     0.6    +      -       -      -
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Residues in contact with GLY 142 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16E  ILE      3.3     8.7    +      -       -      +
    140E  GLY      3.4     1.2    +      -       -      +
    141E  TRP*     1.3    76.6    -      -       -      +
    143E  LEU*     1.3    68.4    +      -       -      +
    144E  LEU*     3.6     1.2    +      -       -      +
    151E  ILE*     4.1     4.7    -      -       -      -
    152E  ALA*     3.4    15.9    +      -       -      +
    192E  PHE      3.2    14.6    -      -       -      -
    193E  GLY*     3.6    11.2    +      -       -      -
    194E  ASP*     2.7    25.0    +      -       -      -
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Residues in contact with LEU 143 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16E  ILE      3.0    22.6    +      -       -      +
     17E  VAL*     3.8     0.2    -      -       -      +
    142E  GLY*     1.3    71.9    -      -       -      -
    144E  LEU*     1.3    59.5    +      -       -      +
    145E  GLY      3.1    24.9    +      -       -      +
    146E  ARG*     5.0     1.8    -      -       -      -
    147E  ASN*     4.7    13.2    -      -       -      +
    150E  GLY*     3.4    11.2    -      -       -      +
    151E  ILE*     3.5    31.2    -      -       +      +
    191E  CYS*     3.7    27.0    -      -       -      +
    192E  PHE*     2.9    35.5    +      -       +      +
     20I  TYR*     3.9    17.9    -      -       +      +
     30I  THR*     5.6     1.3    -      -       +      +
     32I  GLY*     4.9     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 144 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16E  ILE      3.5    17.9    -      -       -      +
     17E  VAL*     3.8    13.1    -      -       -      +
     18E  GLY      4.6     1.6    +      -       -      -
    142E  GLY      3.9     2.5    -      -       -      +
    143E  LEU*     1.3    73.2    -      -       -      +
    145E  GLY*     1.3    58.2    +      -       -      +
    148E  ARG*     3.3    37.2    +      -       +      +
    150E  GLY      2.7    21.4    +      -       -      +
    151E  ILE      4.5     2.2    -      -       -      +
    152E  ALA*     3.5    36.3    -      -       +      -
    156E  GLN*     3.8    23.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 145 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17E  VAL*     3.6    17.1    -      -       -      +
    143E  LEU*     3.1    21.4    +      -       -      +
    144E  LEU*     1.3    85.4    -      -       -      +
    146E  ARG*     1.3    65.3    +      -       -      -
    147E  ASN      2.8    10.0    +      -       -      -
    148E  ARG*     3.1    23.1    +      -       -      -
    191E  CYS*     5.2     1.8    -      -       -      -
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Residues in contact with ARG 146 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17E  VAL*     5.0     0.8    -      -       -      +
    143E  LEU*     5.0     4.0    -      -       -      -
    145E  GLY*     1.3    67.6    -      -       -      -
    147E  ASN*     1.3    84.3    +      -       -      +
    148E  ARG*     4.3    23.6    -      -       -      +
    187E  GLN*     5.9     2.4    -      -       -      +
    191E  CYS*     5.4     3.4    -      -       -      -
    220E  CYS*     5.9     6.6    -      -       +      +
     29I  LYS*     5.7     5.4    -      -       -      +
----------------------------------------------------------
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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