Contacts of the strand formed by residues 135 - 139 (chain t) in PDB entry 5GJQ


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 PHE 135 (chain t).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14t  ALA      3.1    14.6    -      -       -      +
     15t  ILE*     4.2    15.3    -      -       +      -
    121t  VAL*     4.8     2.0    -      -       -      -
    133t  ASP*     3.2    10.0    -      -       -      +
    134t  SER*     1.3    97.5    -      -       -      +
    136t  LYS*     1.3    68.2    -      -       -      +
    146t  GLN*     3.7    11.8    +      -       -      -
    149t  LEU*     3.4    52.9    -      -       +      -
    150t  ASP*     3.2    31.0    -      -       -      -
    153t  VAL*     3.7    22.9    -      -       +      -
    154t  GLY*     4.4     8.7    -      -       -      -
    156t  LYS*     4.8     7.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 136 (chain t). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177c  ARG*     4.4     3.6    -      -       -      +
     27s  ALA*     2.9    27.9    +      -       +      +
     28s  SER*     4.0     3.8    +      -       -      +
     13t  LEU*     4.1     3.8    -      -       -      +
     14t  ALA*     2.9    32.2    +      -       -      +
    109t  ILE*     3.4    19.2    -      -       +      +
    121t  VAL*     4.5     8.6    -      -       +      +
    123t  SER*     3.4    32.8    -      -       -      +
    131t  GLN*     3.7    20.2    -      -       -      +
    133t  ASP*     3.7    14.8    +      -       -      +
    135t  PHE*     1.3    79.0    +      -       -      +
    137t  ALA*     1.3    72.0    +      -       -      +
    138t  GLY*     5.4     0.2    -      -       -      -
    146t  GLN*     3.3    25.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 137 (chain t). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12t  ILE      3.1    10.8    -      -       -      +
     13t  LEU*     4.1     7.4    -      -       +      +
    109t  ILE*     3.9     3.1    -      -       -      -
    136t  LYS*     1.3    85.8    -      -       -      +
    138t  GLY*     1.3    54.5    +      -       -      +
    142t  SER*     2.7    30.2    +      -       -      +
    145t  LEU*     3.6    37.2    -      -       +      -
    146t  GLN*     3.1    15.7    -      -       -      +
    149t  LEU*     4.4     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 138 (chain t). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11t  THR*     3.7     4.3    -      -       -      +
     12t  ILE*     2.9    35.0    +      -       -      +
     55t  SER*     5.2     1.8    -      -       -      -
    107t  TYR*     5.0     9.9    -      -       -      -
    109t  ILE*     3.6    13.3    -      -       -      +
    136t  LYS*     5.4     0.4    -      -       -      -
    137t  ALA*     1.3    75.3    -      -       -      +
    139t  GLY*     1.3    62.8    +      -       -      -
    142t  SER*     3.7     7.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 139 (chain t). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7t  PHE*     5.0     6.3    -      -       -      -
     10t  GLY      3.3    10.3    -      -       -      -
     55t  SER*     3.9    12.3    -      -       -      -
    107t  TYR*     4.6    18.8    -      -       -      +
    138t  GLY*     1.3    75.0    -      -       -      -
    140t  SER*     1.3    65.1    +      -       -      +
    141t  ALA      3.4     2.2    -      -       -      -
    142t  SER*     3.1    16.6    +      -       -      -
----------------------------------------------------------
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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