Contacts of the strand formed by residues 171 - 176 (chain C) in PDB entry 3DM6


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 171 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  ASP*     5.3     0.7    -      -       -      -
      6C  LEU      3.1    18.2    -      -       -      -
      7C  ARG*     4.0    11.0    -      -       -      +
     14C  TYR*     3.5     9.1    -      -       -      -
    155C  CYS*     2.9    35.4    +      -       -      +
    170C  VAL*     1.3    74.8    -      -       -      +
    172C  GLY*     1.3    59.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 172 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  ASP*     3.1    21.5    +      -       -      -
      6C  LEU*     3.0    31.8    +      -       -      +
    153C  GLN*     3.1    13.5    -      -       -      -
    155C  CYS*     3.8    13.5    -      -       -      -
    171C  GLY*     1.3    72.7    -      -       -      -
    173C  SER*     1.3    63.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 173 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2C  MET      4.1     1.1    -      -       -      -
      3C  VAL*     3.9     8.6    -      -       -      +
      4C  ASP*     2.9    25.7    +      -       -      +
      5C  ASN*     3.2     4.3    -      -       -      -
      6C  LEU*     3.6     7.3    -      -       -      +
    151C  SER      3.8     0.5    -      -       -      +
    152C  LEU*     3.6     2.4    -      -       -      -
    153C  GLN*     2.8    58.2    +      -       -      +
    172C  GLY*     1.3    74.4    -      -       -      -
    174C  MET*     1.3    59.7    +      -       -      +
    175C  ILE*     3.9     4.4    -      -       -      +
    183C  LEU*     3.7    21.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 174 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2C  MET*     3.9     3.3    -      -       -      +
      5C  ASN*     2.6    34.2    +      -       -      +
      6C  LEU*     3.8    14.3    -      -       +      +
     16C  VAL*     4.9     7.0    -      -       +      -
     31C  VAL*     4.0    33.0    -      -       -      -
     87C  ILE*     5.3     1.1    -      -       +      -
    119C  LEU*     4.1    12.6    -      -       +      -
    121C  LEU*     4.0    28.9    -      -       +      -
    136C  PHE*     6.2     0.9    -      -       +      -
    137C  PHE*     5.6     3.1    -      -       +      -
    150C  PHE*     5.1     7.6    -      -       +      -
    151C  SER      3.4     6.3    -      -       -      +
    152C  LEU*     3.8    14.8    -      -       +      -
    173C  SER*     1.3    72.3    -      -       -      +
    175C  ILE*     1.3    62.1    +      -       -      +
    176C  ILE*     3.5    40.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 175 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2C  MET*     4.1    20.9    -      -       +      -
      3C  VAL*     4.1    14.1    -      -       +      +
     47C  PHE*     3.8    29.8    -      -       +      +
    150C  PHE*     3.3     5.2    -      -       -      +
    151C  SER*     2.9    43.0    +      -       -      +
    173C  SER*     4.2     5.8    -      -       -      -
    174C  MET*     1.3    70.2    -      -       -      +
    176C  ILE*     1.3    62.1    +      -       -      +
    177C  GLY      3.6     0.3    +      -       -      -
    178C  GLY*     3.3    25.1    -      -       -      +
    179C  ILE      4.3     0.9    -      -       -      +
    180C  ASP*     3.9    11.2    -      -       +      +
    183C  LEU*     3.6    32.3    -      -       +      -
    342C  TYR*     3.7    11.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 176 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2C  MET*     3.5    21.6    -      -       -      +
      5C  ASN*     5.6     1.3    -      -       -      +
     16C  VAL*     6.1     0.7    -      -       +      -
     47C  PHE*     4.3     2.4    -      -       -      -
     87C  ILE*     3.6    33.2    -      -       +      -
     90C  GLY*     4.7     2.7    -      -       -      -
     91C  PRO*     3.8    26.1    -      -       +      +
    137C  PHE*     4.2     7.4    -      -       +      -
    140C  LEU*     3.7    27.6    -      -       +      -
    146C  VAL*     3.8    13.8    -      -       +      +
    150C  PHE*     4.2     5.4    -      -       +      -
    174C  MET*     3.5    43.3    -      -       +      +
    175C  ILE*     1.3    76.0    -      -       -      +
    177C  GLY*     1.3    64.2    +      -       -      +
    178C  GLY      3.7     0.2    +      -       -      -
----------------------------------------------------------
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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