Contacts of the strand formed by residues 180 - 190 (chain D) in PDB entry 3DGG


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 LEU 180 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120D  ALA*     4.2     7.4    -      -       +      -
    121D  LYS      5.5     0.2    -      -       -      +
    123D  THR*     3.9    22.2    -      -       +      +
    150D  GLY*     3.8    29.8    -      -       -      +
    151D  TYR      3.7     3.6    -      -       -      +
    152D  PHE*     3.7    23.3    -      -       +      -
    176D  LEU*     3.5     7.0    -      -       -      +
    177D  GLN*     2.7    36.0    +      -       -      +
    178D  SER*     3.2    11.6    -      -       -      +
    179D  ASP*     1.3    89.0    -      -       +      +
    181D  TYR*     1.3    61.4    +      -       -      +
    182D  THR*     4.9     0.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 181 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116D  THR*     4.7    13.9    -      -       +      +
    150D  GLY      2.9    22.2    +      -       -      -
    151D  TYR*     2.8    51.8    +      -       +      +
    152D  PHE*     3.9    23.7    -      +       -      -
    154D  GLU*     3.5    52.6    -      -       +      +
    174D  ALA*     3.9    10.5    -      -       +      -
    175D  VAL      3.5     8.3    -      -       -      -
    176D  LEU*     3.6    38.5    -      -       +      +
    180D  LEU*     1.3    70.8    -      -       -      +
    182D  THR*     1.3    62.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 182 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163C  LEU*     6.3     1.8    -      -       -      -
    181C  THR*     5.8     5.6    -      -       +      -
    147D  LEU*     3.7    24.9    -      -       +      -
    148D  VAL      3.3    11.4    -      -       -      +
    149D  LYS*     3.6    18.5    +      -       +      +
    150D  GLY*     3.6     9.5    +      -       -      -
    151D  TYR*     4.2     1.3    -      -       -      -
    173D  PRO      4.5     0.5    -      -       -      +
    174D  ALA*     3.4     2.0    -      -       -      -
    175D  VAL*     3.0    36.0    +      -       -      +
    177D  GLN*     4.3    16.6    +      -       -      +
    180D  LEU      4.9     1.9    +      -       -      -
    181D  TYR*     1.3    77.4    +      -       -      +
    183D  LEU*     1.3    64.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 183 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147D  LEU*     3.7     2.6    -      -       -      +
    148D  VAL*     2.8    56.9    +      -       +      +
    151D  TYR*     3.6    19.9    -      -       -      +
    156D  VAL*     3.6    19.3    -      -       +      +
    158D  VAL*     4.1    11.9    -      -       +      -
    171D  THR*     4.3    11.4    -      -       +      -
    172D  PHE*     3.5    23.8    -      -       -      +
    173D  PRO*     4.4     2.5    -      -       +      -
    174D  ALA*     3.9    12.6    -      -       +      +
    182D  THR*     1.3    77.9    -      -       -      +
    184D  SER*     1.3    78.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 184 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136C  VAL*     4.1    12.3    -      -       -      +
    138C  PHE*     3.8    22.7    -      -       -      -
    179C  SER*     4.0    10.8    +      -       -      -
    181C  THR*     4.6     3.5    +      -       -      -
    130D  LEU*     4.8     0.3    -      -       -      +
    146D  CYS      3.3    10.2    +      -       -      -
    147D  LEU*     3.4    24.3    -      -       -      +
    171D  THR*     3.7     0.2    -      -       -      -
    172D  PHE*     2.9    35.1    +      -       -      +
    183D  LEU*     1.3    79.1    -      -       -      +
    185D  SER*     1.3    63.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 185 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138C  PHE*     3.7     5.1    -      -       -      -
    145D  GLY*     3.3     3.8    -      -       -      -
    146D  CYS*     2.9    35.0    +      -       -      -
    148D  VAL*     6.0     0.4    -      -       -      -
    158D  VAL*     3.8    18.8    -      -       -      +
    160D  TRP*     3.0    28.2    +      -       -      -
    169D  VAL*     4.1     0.2    -      -       -      +
    170D  HIS      3.2     7.9    +      -       -      -
    171D  THR*     2.8    25.6    +      -       -      -
    172D  PHE*     4.5     0.2    -      -       -      -
    183D  LEU*     5.1     0.2    -      -       -      -
    184D  SER*     1.3    77.0    -      -       -      +
    186D  SER*     1.3    60.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 186 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138C  PHE*     3.5    31.9    -      -       -      -
    140C  ASN*     3.1    24.8    +      -       -      -
    143D  THR*     4.1     4.5    -      -       -      -
    144D  LEU      3.3     6.7    -      -       -      -
    160D  TRP*     4.3     2.0    -      -       -      -
    168D  GLY      4.3     0.7    +      -       -      -
    169D  VAL*     3.3     7.4    -      -       -      +
    170D  HIS*     2.8    45.5    +      -       -      +
    172D  PHE*     4.2     1.1    -      -       -      -
    185D  SER*     1.3    76.4    +      -       -      +
    187D  VAL*     1.3    61.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 187 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142D  VAL      3.9     0.7    -      -       -      +
    143D  THR*     3.3     4.5    -      -       -      -
    144D  LEU*     2.8    50.6    +      -       +      +
    160D  TRP*     3.4    43.3    -      -       +      -
    165D  LEU*     4.0    20.2    -      -       +      +
    168D  GLY      3.3     4.9    -      -       -      +
    169D  VAL*     3.9    17.7    -      -       +      -
    186D  SER*     1.3    75.6    -      -       -      +
    188D  THR*     1.3    64.0    +      -       -      +
    189D  VAL*     4.0    18.8    +      -       +      -
    199D  VAL*     4.2     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 188 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140C  ASN*     6.0     2.7    -      -       -      -
    141D  MET*     3.3    26.1    -      -       +      +
    142D  VAL      3.5     4.4    +      -       -      -
    143D  THR*     3.7    18.6    +      -       -      +
    168D  GLY*     2.9    38.5    +      -       -      +
    170D  HIS*     6.3     1.1    -      -       +      -
    187D  VAL*     1.3    72.4    -      -       -      +
    189D  VAL*     1.3    66.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 189 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141D  MET*     3.4     6.6    -      -       -      +
    142D  VAL*     2.6    47.2    +      -       +      +
    144D  LEU*     4.8     9.4    -      -       +      -
    165D  LEU*     3.9    36.6    -      -       +      -
    187D  VAL*     4.0    12.8    -      -       +      -
    188D  THR*     1.3    80.1    -      -       -      +
    190D  PRO*     1.3    67.6    -      -       +      +
    193D  THR*     3.2    21.1    -      -       -      +
    194D  TRP*     4.0    19.5    -      -       +      -
    199D  VAL*     4.8     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 190 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140D  SER      4.1     2.7    -      -       -      +
    141D  MET*     3.8    22.6    -      -       -      -
    142D  VAL*     4.7     0.3    -      -       -      +
    189D  VAL*     1.3    90.9    -      -       +      +
    191D  SER*     1.3    60.3    +      -       -      +
    192D  SER*     3.8    11.2    -      -       -      +
    193D  THR*     2.5    54.8    +      -       +      +
    194D  TRP      3.5     2.9    +      -       -      -
----------------------------------------------------------
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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