Contacts of the strand formed by residues 113 - 121 (chain C) in PDB entry 3GGE


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 113 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  GOL      3.3    20.7    +      -       -      -
     -1C  SER*     2.9    35.9    +      -       -      -
    112C  LYS*     1.3    80.9    -      -       -      +
    114C  ILE*     1.3    62.8    +      -       -      -
    115C  GLU      4.3     0.5    +      -       -      -
    196C  ILE*     4.3     1.3    -      -       -      -
    197C  GLU      3.3    13.0    -      -       -      -
    199C  LYS*     3.9     4.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 114 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     -1C  SER      3.8    11.0    -      -       -      +
    113C  GLY*     1.3    73.8    -      -       -      +
    115C  GLU*     1.3    72.5    +      -       -      +
    116C  LYS*     3.7     7.2    +      -       +      +
    196C  ILE*     3.4     3.3    -      -       -      -
    197C  GLU*     2.8    47.6    +      -       +      +
    199C  LYS*     3.3    47.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 115 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167B  GLY      5.4     3.5    -      -       -      +
    169B  ASN*     4.6    11.5    +      -       +      +
     -1C  SER      5.7     0.6    -      -       -      +
    113C  GLY      4.3     1.2    +      -       -      -
    114C  ILE*     1.3    80.8    -      -       -      +
    116C  LYS*     1.3    65.2    +      -       -      +
    163C  GLU*     3.1    29.7    -      -       -      +
    194C  LYS*     3.1    29.3    -      -       +      +
    195C  LEU      3.3    11.9    -      -       -      +
    196C  ILE*     4.4     5.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 116 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114C  ILE*     4.1    12.1    -      -       +      +
    115C  GLU*     1.3    81.0    -      -       -      +
    117C  GLU*     1.3    65.5    +      -       -      +
    118C  VAL*     4.8     4.0    -      -       +      -
    155C  THR*     2.6    35.9    +      -       -      +
    157C  CYS*     3.8     6.3    -      -       -      -
    160C  ASP*     2.6    30.9    +      -       -      -
    193C  MET      3.9     0.2    -      -       -      +
    194C  LYS*     3.4     5.8    -      -       -      +
    195C  LEU*     2.8    46.0    +      -       +      +
    197C  GLU*     2.6    37.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 117 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116C  LYS*     1.3    74.5    -      -       -      +
    118C  VAL*     1.3    73.3    +      -       -      +
    119C  ASN*     4.2    17.7    +      -       -      +
    155C  THR*     5.1     0.5    +      -       -      -
    192C  THR*     4.9     8.5    -      -       -      +
    193C  MET      3.5    14.8    -      -       -      +
    194C  LYS*     4.5    17.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 118 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116C  LYS*     4.8     4.3    -      -       +      -
    117C  GLU*     1.3    85.0    -      -       -      +
    119C  ASN*     1.3    62.9    +      -       -      +
    120C  VAL*     4.2     8.9    +      -       +      +
    153C  VAL*     4.8     3.4    -      -       +      -
    155C  THR*     3.3    30.1    -      -       -      +
    156C  ILE*     4.0    32.8    -      -       +      -
    191C  PHE      4.0     0.2    -      -       -      +
    192C  THR*     3.3     5.5    -      -       -      -
    193C  MET*     3.0    46.3    +      -       +      +
    195C  LEU*     4.2    14.4    -      -       +      -
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Residues in contact with ASN 119 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117C  GLU*     4.2    10.6    +      -       -      +
    118C  VAL*     1.3    72.8    -      -       -      +
    120C  VAL*     1.3    66.2    +      -       -      +
    153C  VAL*     4.7    10.9    -      -       -      +
    190C  LEU*     3.8    27.3    -      -       +      +
    191C  PHE      3.5     3.1    -      -       -      -
    192C  THR*     3.1    27.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 120 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118C  VAL*     4.3    10.8    -      -       +      -
    119C  ASN*     1.3    80.3    -      -       -      +
    121C  TYR*     1.3    62.3    +      -       -      +
    127C  LEU*     4.5     1.1    -      -       +      -
    149C  VAL*     3.6    27.6    -      -       +      -
    150C  ILE*     4.4     9.0    -      -       +      -
    153C  VAL*     4.4    12.6    -      -       +      -
    156C  ILE*     3.9    27.1    -      -       +      -
    190C  LEU*     3.4     4.8    -      -       -      +
    191C  PHE*     2.9    69.3    +      -       +      +
    193C  MET*     5.7     1.3    -      -       -      +
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Residues in contact with TYR 121 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120C  VAL*     1.3    75.2    -      -       -      +
    122C  LYS*     1.3    57.4    +      -       -      +
    123C  SER*     3.0    28.7    +      -       -      -
    149C  VAL*     3.5    18.2    -      -       -      +
    188C  GLU*     3.5    58.4    +      -       -      +
    189C  GLU*     3.8     4.3    -      -       -      -
    190C  LEU*     3.8    25.9    -      -       +      +
----------------------------------------------------------
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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