Contacts of the strand formed by residues 141 - 148 (chain C) in PDB entry 1DGH


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 141 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138C  THR*     2.6    39.8    +      -       -      +
    139C  GLU      3.2     6.3    +      -       -      -
    140C  ASP*     1.3    80.4    -      -       -      +
    142C  ASN*     1.3    67.4    +      -       -      -
    143C  TRP*     4.8     0.2    -      -       -      -
    340C  PRO*     4.9     1.0    -      -       -      +
    378C  PRO*     4.6     0.9    -      -       -      -
    381C  ALA*     3.6     9.3    -      -       -      +
     31D  ALA      3.3    13.9    -      -       -      -
     32D  GLY      3.3    10.8    +      -       -      -
     33D  ASN*     3.6     1.1    +      -       -      -
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Residues in contact with ASN 142 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135C  LYS*     4.2    11.1    -      -       +      +
    136C  PHE      3.4     4.3    -      -       -      +
    137C  TYR*     3.4    37.4    -      -       -      -
    138C  THR      5.0     0.3    -      -       -      +
    141C  GLY*     1.3    72.4    -      -       -      -
    143C  TRP*     1.3    59.1    +      -       -      +
    144C  ASP*     4.1    10.1    -      -       -      +
    338C  ASN*     3.5    20.9    +      -       -      +
    340C  PRO*     4.5     0.3    -      -       -      +
    371C  LEU*     5.8     0.4    -      -       -      +
    376C  ASN      3.3    24.5    +      -       -      -
    377C  CYS      3.8     3.0    +      -       -      -
    378C  PRO*     3.5    25.7    -      -       -      +
     31D  ALA*     3.0    20.5    +      -       +      +
     33D  ASN*     3.2    17.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 143 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99C  VAL*     4.1    16.6    -      -       +      -
    100C  PHE*     3.7    33.0    -      +       -      -
    136C  PHE*     2.7    90.7    +      +       +      +
    138C  THR*     4.3     4.0    -      -       +      -
    141C  GLY      3.7     0.2    +      -       -      -
    142C  ASN*     1.3    73.4    -      -       -      +
    144C  ASP*     1.3    73.8    +      -       -      +
    145C  LEU*     4.4    16.6    -      -       +      +
    220C  PHE*     6.3     1.2    -      -       -      -
    234C  PHE*     3.8    31.8    -      +       -      -
    279C  PHE*     4.3     8.7    -      +       -      -
    338C  ASN      3.3    13.5    -      -       -      -
    339C  MET*     4.3     6.2    -      -       +      +
    340C  PRO*     3.7    25.1    -      -       +      -
    343C  ILE*     3.7    20.5    -      -       +      +
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Residues in contact with ASP 144 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134C  VAL      3.4     2.9    -      -       -      +
    135C  LYS*     2.8    49.5    +      -       -      +
    142C  ASN*     4.7     1.2    -      -       -      +
    143C  TRP*     1.3    81.9    +      -       -      +
    145C  LEU*     1.3    59.7    +      -       -      +
    146C  VAL*     3.6     3.3    +      -       +      -
    333C  ALA      3.8     0.3    -      -       -      +
    334C  PHE*     3.8    11.7    -      -       +      -
    335C  ASP      2.8    41.8    +      -       -      +
    336C  PRO*     3.9    16.3    -      -       -      +
    338C  ASN*     3.0    26.7    +      -       -      +
    339C  MET*     5.7     0.2    -      -       -      +
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Residues in contact with LEU 145 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132C  PHE      3.9     1.4    -      -       -      +
    133C  ALA*     3.6     0.2    -      -       -      -
    134C  VAL*     2.8    37.1    +      -       +      +
    136C  PHE*     3.9    17.7    -      -       +      -
    143C  TRP*     3.9    14.7    +      -       +      +
    144C  ASP*     1.3    71.2    -      -       -      +
    146C  VAL*     1.3    59.7    +      -       -      +
    147C  GLY      3.3     4.9    +      -       -      -
    216C  GLY*     4.0    16.4    -      -       -      -
    220C  PHE*     4.4    13.0    -      -       +      -
    234C  PHE*     3.7    32.5    -      -       +      -
    236C  TYR*     3.6    34.0    +      -       +      +
    279C  PHE*     3.8    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 146 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133C  ALA*     4.1    10.3    -      -       +      +
    144C  ASP*     3.6     7.3    +      -       +      +
    145C  LEU*     1.3    73.6    -      -       -      +
    147C  GLY*     1.3    58.1    +      -       -      +
    216C  GLY      4.7     1.8    -      -       -      +
    220C  PHE*     6.2     0.4    -      -       -      -
    334C  PHE*     3.5    26.5    -      -       +      +
    336C  PRO*     3.7    29.7    -      -       +      +
    354C  ARG*     3.0    37.2    +      -       -      +
    358C  TYR*     4.1     7.2    -      -       +      -
   2002C  HEM      3.2    46.3    -      -       +      +
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Residues in contact with GLY 147 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132C  PHE*     2.7    45.5    +      -       -      -
    145C  LEU      3.3     3.4    +      -       -      -
    146C  VAL*     1.3    76.7    -      -       -      +
    148C  ASN*     1.3    56.6    +      -       -      -
    215C  TYR      3.0    19.7    -      -       -      -
    216C  GLY*     4.5     2.0    -      -       -      -
    236C  TYR*     3.7     4.2    +      -       -      -
   2002C  HEM      3.3    17.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 148 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75C  HIS*     3.5    24.6    -      -       -      -
    116C  VAL*     5.7     0.2    -      -       -      +
    129C  PRO*     4.9     8.6    -      -       -      +
    130C  ARG      3.1    16.3    -      -       -      +
    131C  GLY*     3.5     3.1    -      -       -      -
    132C  PHE*     4.5     4.5    -      -       -      -
    147C  GLY*     1.3    73.1    -      -       -      +
    149C  ASN*     1.3    59.6    +      -       -      +
    150C  THR*     3.0    28.0    +      -       +      +
    152C  ILE      5.1     0.6    +      -       -      -
    153C  PHE*     3.8    25.5    -      -       -      -
    214C  GLY*     3.6     1.6    -      -       -      -
    215C  TYR      2.9    29.5    +      -       -      +
    217C  SER*     4.4     0.7    -      -       -      +
   2002C  HEM      3.2    35.1    -      -       +      +
----------------------------------------------------------
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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