Contacts of the strand formed by residues 135 - 145 (chain C) in PDB entry 1G13


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 135 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57C  LYS*     5.0     4.5    -      -       -      -
     58C  GLU      5.9     1.3    -      -       -      -
    133C  THR      3.3     1.9    +      -       -      -
    134C  THR*     1.3    80.7    -      -       -      +
    136C  ASN*     1.3    66.8    +      -       -      -
    137C  TYR*     3.5    10.1    -      -       -      -
    158C  SER*     3.4     2.9    -      -       -      -
    159C  LEU      2.9    32.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 136 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1C  SER*     5.3     8.2    +      -       -      +
     57C  LYS*     3.6     4.7    -      -       -      +
     58C  GLU*     2.8    75.2    +      -       +      +
     63C  TRP*     4.1     7.0    -      -       +      -
    135C  GLY*     1.3    76.0    -      -       -      -
    137C  TYR*     1.3    62.3    +      -       -      +
    157C  ALA      3.9     3.4    -      -       -      +
    158C  SER*     3.0    22.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 137 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55C  LEU*     4.5    15.3    -      -       +      -
     56C  GLU      3.3    16.8    -      -       -      +
     57C  LYS*     3.3    31.2    -      -       +      -
     63C  TRP*     3.8     5.9    -      -       -      -
    131C  TRP*     3.1    31.2    +      +       -      -
    132C  LEU*     3.6     2.7    -      -       +      -
    133C  THR      2.5    44.7    +      -       -      -
    135C  GLY      3.5    19.7    -      -       -      -
    136C  ASN*     1.3    75.9    -      -       -      +
    138C  ARG*     1.3    64.0    +      -       -      +
    156C  ALA*     3.4     3.3    -      -       -      +
    157C  ALA*     2.9    37.0    +      -       +      +
    159C  LEU*     3.4    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 138 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54C  VAL      3.9     0.5    -      -       -      +
     55C  LEU*     3.5     3.4    -      -       -      +
     56C  GLU*     2.6    66.5    +      -       +      +
     63C  TRP*     3.5    58.9    -      -       +      +
    137C  TYR*     1.3    78.4    -      -       -      +
    139C  ILE*     1.3    65.0    +      -       -      +
    155C  ILE      3.1    12.3    -      -       -      +
    156C  ALA*     4.3     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 139 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53C  LEU*     4.4    27.4    -      -       +      -
     54C  VAL      3.3    17.0    -      -       -      +
     55C  LEU*     4.0    23.8    -      -       +      -
     73C  GLY      5.4     1.1    -      -       -      +
    138C  ARG*     1.3    77.6    -      -       -      +
    140C  GLU*     1.3    70.1    +      -       -      +
    141C  SER*     4.2     3.8    -      -       -      +
    153C  ILE*     3.8     1.0    -      -       +      +
    154C  LYS*     3.3     4.2    -      -       -      +
    155C  ILE*     2.7    63.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 140 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8C  CYS*     5.2     0.2    -      -       -      +
     52C  ASP      3.4     2.3    -      -       -      +
     53C  LEU*     3.4     4.0    -      -       -      -
     54C  VAL*     3.0    52.8    +      -       +      +
    139C  ILE*     1.3    76.3    -      -       -      +
    141C  SER*     1.3    63.7    +      -       -      +
    142C  VAL*     4.0    18.1    -      -       +      +
    152C  CYS*     4.1    15.8    -      -       -      -
    153C  ILE      3.3     9.4    -      -       -      +
    154C  LYS*     3.7    28.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 141 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51C  VAL*     4.0     9.9    -      -       -      +
     52C  ASP      3.3     3.8    -      -       -      -
     53C  LEU*     3.2    23.7    -      -       -      +
    139C  ILE*     4.2     5.5    -      -       -      +
    140C  GLU*     1.3    73.4    -      -       -      +
    142C  VAL*     1.3    64.3    +      -       -      +
    143C  LEU*     4.1     1.2    +      -       -      +
    151C  GLY      4.1     0.3    -      -       -      +
    152C  CYS*     3.2     3.6    -      -       -      -
    153C  ILE*     2.8    54.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 142 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50C  LYS      3.4     1.6    -      -       -      +
     51C  VAL*     3.4     5.0    -      -       -      +
     52C  ASP*     2.8    55.9    +      -       +      +
    140C  GLU*     4.0    18.8    -      -       +      +
    141C  SER*     1.3    78.2    +      -       -      +
    143C  LEU*     1.3    65.8    +      -       -      +
    144C  SER*     4.9     2.7    -      -       -      -
    149C  ARG*     3.3    46.9    -      -       -      +
    151C  GLY      3.5     2.7    -      -       -      -
    152C  CYS*     3.6    21.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 143 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15C  ALA*     4.7     9.0    -      -       +      -
     45C  LEU*     4.1    33.9    -      -       +      -
     49C  LEU*     3.6    32.5    -      -       +      -
     50C  LYS      3.3    12.8    -      -       -      +
     51C  VAL*     3.8    18.4    -      -       +      -
     80C  PHE*     5.7     0.9    -      -       +      -
    141C  SER*     4.1     1.3    +      -       -      +
    142C  VAL*     1.3    73.9    -      -       -      +
    144C  SER*     1.3    63.6    +      -       -      +
    149C  ARG*     3.8     3.3    -      -       -      -
    150C  LEU*     2.7    29.3    +      -       +      -
    151C  GLY*     2.8    20.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 144 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49C  LEU*     3.6     5.0    -      -       -      +
     50C  LYS*     2.8    57.0    +      -       -      +
     52C  ASP*     4.4     4.2    +      -       -      -
    142C  VAL*     4.9     6.7    -      -       -      -
    143C  LEU*     1.3    77.8    -      -       -      +
    145C  SER*     1.3    62.1    +      -       -      +
    147C  GLY*     4.8     7.2    +      -       -      -
    148C  LYS      3.2    22.4    -      -       -      -
    149C  ARG*     4.2     7.0    -      -       -      -
    150C  LEU*     3.8     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 145 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46C  SER      3.4    12.5    +      -       -      -
     47C  SER      4.5     0.5    +      -       -      -
     48C  PRO*     2.6    28.9    +      -       -      +
     49C  LEU*     4.5     0.2    -      -       -      -
     50C  LYS*     5.7     0.7    -      -       -      -
    144C  SER*     1.3    74.8    -      -       -      +
    146C  SER*     1.3    63.9    +      -       -      +
    147C  GLY      3.1     0.9    -      -       -      -
    148C  LYS*     2.7    38.8    +      -       -      +
    150C  LEU*     3.7    21.5    -      -       -      +
----------------------------------------------------------
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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