Contacts of the strand formed by residues 255 - 259 (chain D) in PDB entry 3DC1


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 VAL 255 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217D  TYR*     4.0    11.4    -      -       +      -
    227D  ILE*     3.4    17.3    -      -       +      +
    229D  GLU*     4.1     8.7    -      -       +      +
    246D  PHE*     3.9    27.8    -      -       +      +
    247D  LEU*     3.8    31.5    -      -       +      +
    250D  ASP*     3.3    29.2    +      -       +      +
    253D  GLY      3.5     0.6    -      -       -      -
    254D  ARG*     1.3    82.7    -      -       -      +
    256D  ILE*     1.3    71.3    +      -       -      +
    257D  ARG      4.1     1.9    +      -       -      +
    275D  THR      4.1     0.2    -      -       -      +
    276D  GLY*     3.8     4.9    -      -       -      -
    277D  PRO*     3.4    18.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 256 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124D  VAL*     3.9    31.0    -      -       +      -
    127D  MET*     4.2    16.8    -      -       +      -
    128D  ILE*     4.6     0.9    -      -       +      -
    226D  LEU*     4.0    20.9    -      -       +      -
    227D  ILE      2.8    12.0    +      -       -      +
    228D  ILE*     3.7    14.1    -      -       +      +
    229D  GLU      3.1    21.7    +      -       -      +
    254D  ARG      5.4     0.2    -      -       -      -
    255D  VAL*     1.3    77.9    -      -       -      +
    257D  ARG*     1.3    62.7    +      -       -      +
    258D  ALA      3.9     0.2    +      -       -      -
    274D  LEU*     3.9    18.8    -      -       +      -
    275D  THR      3.6     5.8    -      -       -      +
    276D  GLY*     5.0     0.2    -      -       -      -
    277D  PRO*     4.3     4.3    -      -       +      -
    280D  LEU*     3.6    34.5    -      -       +      -
    281D  ILE*     4.9     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 257 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91D  GLN*     3.8    14.8    -      -       -      +
     95D  HIS*     3.7    11.7    +      -       -      -
    229D  GLU*     3.1    28.2    +      -       -      +
    231D  ASP*     2.3    38.6    +      -       -      +
    234D  TYR*     4.0     8.5    -      -       -      -
    245D  THR*     2.9    36.1    +      -       -      +
    247D  LEU*     4.1    18.1    -      -       +      +
    255D  VAL*     4.0     2.8    -      -       -      +
    256D  ILE*     1.3    73.2    -      -       -      +
    258D  ALA*     1.3    67.1    +      -       -      +
    259D  ASP*     2.7    50.9    +      -       -      +
    274D  LEU*     2.9    22.7    -      -       -      +
    275D  THR*     2.6    36.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 258 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117D  SER*     4.1    23.3    -      -       -      +
    121D  LEU*     4.4    12.6    -      -       +      -
    228D  ILE*     6.2     0.2    -      -       +      -
    229D  GLU      3.0    14.1    +      -       -      +
    230D  ASP*     4.2    14.6    -      -       -      +
    231D  ASP*     3.2    28.6    +      -       -      +
    232D  PRO*     6.3     0.2    -      -       -      -
    256D  ILE      5.4     0.2    -      -       -      +
    257D  ARG*     1.3    76.5    -      -       -      +
    259D  ASP*     1.3    64.5    +      -       -      +
    273D  PHE      4.0     4.7    -      -       -      +
    274D  LEU*     4.1    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 259 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91D  GLN*     3.3    12.1    +      -       -      +
     95D  HIS*     4.6     0.3    +      -       -      -
    117D  SER*     3.5     8.1    -      -       -      -
    231D  ASP      3.6    11.6    -      -       -      +
    234D  TYR*     4.1     1.2    -      -       -      +
    235D  PHE*     4.0    18.4    -      -       -      -
    257D  ARG*     2.7    48.3    +      -       +      +
    258D  ALA*     1.3    72.8    -      -       -      +
    260D  SER*     1.3    60.6    +      -       -      +
    272D  GLY*     3.6     0.7    -      -       -      -
    273D  PHE*     2.9    69.4    +      -       +      +
----------------------------------------------------------
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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