Contacts of the strand formed by residues 135 - 140 (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 GLN 135 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133E  GLY      3.5     5.4    +      -       -      +
    134E  THR*     1.3    83.0    -      -       -      +
    136E  CYS*     1.3    63.9    +      -       -      +
    159E  LYS*     4.1    41.5    -      -       +      +
    160E  ALA      3.8     9.2    -      -       -      +
    161E  PRO*     4.1     5.4    -      -       +      -
    201E  CYS*     4.0     6.8    -      -       -      +
    202E  SER      4.8     1.6    +      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
    134E  THR      3.7    11.2    -      -       -      -
    135E  GLN*     1.3    77.2    -      -       -      +
    137E  LEU*     1.3    61.3    +      -       -      +
    138E  ILE*     4.9     2.9    -      -       +      -
    158E  LEU      3.5     0.5    -      -       -      +
    159E  LYS*     3.1     9.7    -      -       -      +
    160E  ALA*     2.9    37.1    +      -       -      +
    162E  ILE*     3.9    16.2    -      -       -      -
    199E  VAL*     4.0    16.6    -      -       +      -
    200E  VAL      3.3     8.1    -      -       -      +
    201E  CYS*     2.0    46.9    -      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
     20E  TYR*     3.6    24.7    -      -       -      +
     26E  THR      5.8     0.7    -      -       -      +
     27E  VAL*     4.3    19.5    -      -       +      -
     29E  TYR*     3.9    19.4    +      -       -      +
    136E  CYS*     1.3    73.3    -      -       -      +
    138E  ILE*     1.3    65.5    +      -       -      +
    139E  SER*     5.1     2.5    +      -       -      +
    157E  CYS*     3.9    16.6    -      -       +      -
    158E  LEU      3.5    13.9    -      -       -      +
    159E  LYS*     4.2    10.1    -      -       +      -
    198E  PRO*     3.6     2.3    -      -       -      +
    199E  VAL*     3.5     2.3    -      -       -      -
    200E  VAL*     2.8    45.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 138 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16E  ILE*     3.8    18.7    -      -       +      +
    136E  CYS*     4.8     0.9    -      -       +      +
    137E  LEU*     1.3    81.4    -      -       -      +
    139E  SER*     1.3    64.5    -      -       -      +
    157E  CYS*     3.3     5.4    -      -       -      +
    158E  LEU*     2.9    45.8    +      -       +      +
    160E  ALA*     3.8    29.4    -      -       +      +
    183E  ALA*     4.6     6.5    -      -       +      -
    190E  SER*     4.2     7.0    -      -       -      +
    198E  PRO      3.5     5.6    -      -       -      +
    199E  VAL*     4.0    16.6    -      -       +      -
    213E  VAL*     3.9    26.9    -      -       +      -
    228E  TYR*     3.7    26.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 139 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16E  ILE*     4.1     7.6    -      -       -      +
     22E  CYS*     4.3     1.6    -      -       -      -
     27E  VAL*     3.8    10.7    -      -       -      +
     29E  TYR*     5.0     1.4    +      -       -      -
     30E  GLN*     2.8    32.4    +      -       -      +
    137E  LEU*     5.1     2.6    +      -       -      +
    138E  ILE*     1.3    81.1    -      -       -      +
    140E  GLY*     1.3    60.5    +      -       -      +
    155E  LEU*     4.2     8.1    -      -       -      -
    156E  LYS      3.2    13.2    -      -       -      -
    157E  CYS*     4.2    13.7    -      -       -      -
    194E  ASP*     4.4     5.9    -      -       -      +
    197E  GLY*     4.5     6.1    -      -       -      -
    198E  PRO*     3.6    20.0    +      -       -      +
    213E  VAL*     5.0     0.3    -      -       -      +
----------------------------------------------------------
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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*     3.8     4.7    +      -       -      +
     30E  GLN*     4.3     7.0    -      -       -      -
     40E  HIS*     6.2     0.2    -      -       -      -
    139E  SER*     1.3    78.5    -      -       -      +
    141E  TRP*     1.3    58.8    +      -       -      -
    142E  GLY      3.3     7.0    +      -       -      -
    152E  PRO*     5.0     0.2    -      -       -      +
    155E  LEU*     3.5    14.2    -      -       -      +
    156E  LYS*     3.1    33.4    +      -       -      +
    193E  GLY      5.4     0.2    -      -       -      -
    194E  ASP*     3.3    14.5    -      -       -      +
----------------------------------------------------------
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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