Contacts of the strand formed by residues 189 - 196 (chain B) 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 GLU 189 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121B  TYR*     3.8     9.2    -      -       -      -
    122B  LYS*     3.2    25.1    +      -       -      +
    186B  LYS*     3.6    38.4    +      -       -      +
    187B  LYS      3.3     7.9    -      -       -      +
    188B  GLU*     1.3    84.1    -      -       -      +
    190B  LEU*     1.3    69.2    +      -       -      +
    191B  PHE*     3.7     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 190 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119B  ASN*     3.8    22.4    -      -       +      +
    120B  VAL*     3.2    36.3    -      -       -      +
    121B  TYR*     3.7    18.5    -      -       +      +
    166B  ASN*     4.7     2.1    +      -       -      +
    189B  GLU*     1.3    79.5    -      -       -      +
    191B  PHE*     1.3    59.1    +      -       -      +
    192B  THR*     6.1     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 191 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119B  ASN*     3.3     4.3    -      -       -      +
    120B  VAL*     2.8    70.8    +      -       +      +
    122B  LYS*     4.3     9.6    -      -       +      -
    127B  LEU*     4.0    30.3    -      -       +      -
    150B  ILE*     5.0     4.0    -      -       +      -
    165B  ILE*     4.6     4.0    -      -       +      -
    166B  ASN*     3.4    23.1    -      -       -      +
    182B  LEU*     4.2     6.3    -      -       +      -
    185B  LEU*     3.6    31.4    -      -       +      -
    189B  GLU      4.3     6.3    -      -       -      -
    190B  LEU*     1.3    75.9    -      -       -      +
    192B  THR*     1.3    76.1    +      -       -      +
    193B  MET*     3.9    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 192 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117B  GLU*     4.9    14.6    -      -       -      +
    118B  VAL*     3.1     8.1    -      -       -      -
    119B  ASN*     2.9    25.8    -      -       -      +
    165B  ILE*     3.7     0.9    -      -       -      -
    166B  ASN*     3.1    40.1    +      -       -      +
    167B  GLY      4.5     3.3    +      -       -      -
    190B  LEU*     5.8     2.5    -      -       +      -
    191B  PHE*     1.3    81.8    -      -       -      +
    193B  MET*     1.3    71.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 193 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116B  LYS      3.7     0.5    -      -       -      +
    117B  GLU*     3.3     6.7    -      -       -      +
    118B  VAL*     2.8    49.2    +      -       +      +
    120B  VAL*     5.6     0.7    -      -       -      -
    129B  LEU*     5.5     6.3    -      -       +      -
    141B  ILE*     6.3     0.7    -      -       +      -
    150B  ILE*     5.9     2.9    -      -       -      -
    156B  ILE*     5.3     7.2    -      -       -      -
    162B  ILE*     3.7    35.2    -      -       +      -
    164B  SER*     3.4    15.0    -      -       -      +
    165B  ILE*     4.1     6.1    -      -       +      -
    182B  LEU*     3.7    32.3    -      -       +      -
    191B  PHE*     3.9    19.1    -      -       +      -
    192B  THR*     1.3    82.0    -      -       -      +
    194B  LYS*     1.3    66.8    +      -       -      +
    195B  LEU*     4.5    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 194 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115B  GLU*     3.8    25.4    +      -       +      +
    116B  LYS      3.2     8.3    -      -       -      +
    117B  GLU*     3.4    29.8    -      -       +      -
    162B  ILE*     3.9     0.3    -      -       -      -
    163B  GLU*     3.0    43.0    +      -       +      +
    164B  SER*     3.4    27.1    +      -       -      +
    193B  MET*     1.3    78.3    -      -       -      +
    195B  LEU*     1.3    65.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 195 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114B  ILE      3.9     0.3    -      -       -      +
    115B  GLU*     3.3     5.4    -      -       -      +
    116B  LYS*     2.8    50.4    +      -       -      +
    118B  VAL*     4.4    12.8    -      -       +      -
    141B  ILE*     5.0     4.5    -      -       +      -
    156B  ILE*     4.0    31.2    -      -       +      -
    160B  ASP*     3.8    28.7    -      -       +      +
    161B  HIS      3.2    14.6    -      -       -      +
    162B  ILE*     3.7    26.0    -      -       +      -
    163B  GLU      4.6     0.2    -      -       -      +
    193B  MET*     4.5    14.1    -      -       +      -
    194B  LYS*     1.3    79.4    -      -       -      +
    196B  ILE*     1.3    64.1    +      -       -      +
    197B  GLU      4.3     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 196 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113B  GLY*     4.6    17.9    -      -       -      +
    114B  ILE      3.6     5.4    -      -       -      +
    115B  GLU*     3.8    22.0    -      -       +      +
    138B  TYR*     3.7    25.1    -      -       +      +
    160B  ASP*     3.7     2.4    -      -       -      -
    161B  HIS*     2.9    37.6    +      -       +      +
    163B  GLU*     3.2    36.1    -      -       +      +
    195B  LEU*     1.3    80.7    -      -       -      +
    197B  GLU*     1.3    76.9    +      -       -      +
    198B  PRO      3.7     0.2    -      -       -      -
    169C  ASN*     5.1     0.2    -      -       -      +
    171C  VAL*     4.1    17.9    -      -       +      -
----------------------------------------------------------
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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