Contacts of the strand formed by residues 141 - 148 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138A  THR*     2.6    43.7    +      -       -      +
    139A  GLU      3.2     3.2    +      -       -      -
    140A  ASP*     1.3    80.4    -      -       -      +
    142A  ASN*     1.3    67.6    +      -       -      -
    340A  PRO*     4.9     1.0    -      -       -      +
    378A  PRO*     4.6     1.8    -      -       -      -
    381A  ALA*     3.7     7.9    -      -       -      +
     31B  ALA      3.3    13.7    -      -       -      -
     32B  GLY      3.5     9.0    +      -       -      -
     33B  ASN*     3.6     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  LYS*     4.1    19.4    -      -       +      +
    136A  PHE      3.4     5.4    -      -       -      +
    137A  TYR*     3.3    34.0    -      -       -      +
    138A  THR      5.1     0.3    -      -       -      +
    141A  GLY*     1.3    72.8    -      -       -      -
    143A  TRP*     1.3    60.2    +      -       -      +
    144A  ASP*     4.1     2.5    -      -       -      +
    338A  ASN*     3.5    28.1    +      -       -      +
    339A  MET      4.1     0.2    +      -       -      -
    340A  PRO*     5.0     0.4    -      -       -      -
    371A  LEU*     5.8     1.0    -      -       -      +
    376A  ASN      3.2    25.3    +      -       -      -
    377A  CYS      3.9     2.4    +      -       -      -
    378A  PRO*     3.4    24.8    -      -       -      +
     31B  ALA*     3.0    16.0    +      -       +      +
     33B  ASN*     3.3    16.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  VAL*     4.2    11.0    -      -       +      -
    100A  PHE*     3.8    32.8    -      +       -      -
    135A  LYS*     3.5     0.9    -      -       -      -
    136A  PHE*     2.8    87.8    +      +       +      +
    138A  THR*     4.5     4.3    -      -       +      -
    141A  GLY      3.8     0.2    +      -       -      -
    142A  ASN*     1.3    73.8    -      -       -      +
    144A  ASP*     1.3    73.7    +      -       -      +
    145A  LEU*     4.3    17.7    -      -       +      +
    220A  PHE*     6.1     2.2    -      -       -      -
    234A  PHE*     3.8    30.0    -      +       -      -
    279A  PHE*     4.2    11.9    -      +       -      -
    338A  ASN      3.4    12.3    -      -       -      -
    339A  MET*     4.2     6.2    -      -       +      +
    340A  PRO*     3.7    24.2    -      -       +      -
    343A  ILE*     3.7    28.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  VAL      3.4     2.2    -      -       -      +
    135A  LYS*     2.8    49.0    +      -       -      +
    142A  ASN*     5.1     1.3    -      -       -      -
    143A  TRP*     1.3    80.9    +      -       -      +
    145A  LEU*     1.3    60.1    +      -       -      +
    146A  VAL*     3.6     3.3    +      -       +      -
    220A  PHE*     6.1     0.7    -      -       -      -
    333A  ALA      3.9     0.3    -      -       -      +
    334A  PHE*     3.7    12.4    -      -       +      -
    335A  ASP      2.7    41.9    +      -       -      +
    336A  PRO*     4.0    16.6    -      -       -      +
    338A  ASN*     2.9    28.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  PHE      3.8     1.6    -      -       -      +
    133A  ALA*     3.5     0.3    -      -       -      -
    134A  VAL*     2.7    39.0    +      -       +      +
    136A  PHE*     4.0    17.5    -      -       +      -
    143A  TRP*     3.9    16.0    +      -       +      +
    144A  ASP*     1.3    71.8    -      -       -      +
    146A  VAL*     1.3    56.2    +      -       -      +
    147A  GLY      3.2     5.0    +      -       -      -
    216A  GLY*     4.2    16.2    -      -       -      -
    220A  PHE*     4.2    16.2    -      -       +      -
    234A  PHE*     3.8    28.9    -      -       +      -
    236A  TYR*     3.8    32.2    +      -       +      +
    279A  PHE*     3.8    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  ALA*     4.0    11.2    -      -       +      -
    144A  ASP*     3.6     6.7    +      -       +      +
    145A  LEU*     1.3    71.0    -      -       -      +
    147A  GLY*     1.3    58.6    +      -       -      +
    216A  GLY      4.8     1.5    -      -       -      +
    334A  PHE*     3.6    25.1    -      -       +      -
    336A  PRO*     3.6    31.1    -      -       +      +
    354A  ARG*     2.9    38.2    +      -       -      +
    358A  TYR*     4.0    10.1    -      -       +      -
   2000A  HEM      3.3    42.5    -      -       +      +
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Residues in contact with GLY 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  PHE      2.7    46.3    +      -       -      -
    145A  LEU      3.2     4.0    +      -       -      -
    146A  VAL*     1.3    74.9    -      -       -      +
    148A  ASN*     1.3    57.3    +      -       -      -
    215A  TYR      3.1    16.8    -      -       -      -
    216A  GLY*     4.5     3.1    -      -       -      -
    236A  TYR*     3.6     3.6    -      -       -      -
   2000A  HEM      3.3    18.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  HIS*     3.6    14.6    +      -       -      -
    116A  VAL*     5.7     0.2    -      -       -      +
    129A  PRO*     4.8     9.4    -      -       -      +
    130A  ARG      2.9    19.2    -      -       -      +
    131A  GLY*     3.4     8.1    -      -       -      -
    132A  PHE*     4.2     5.4    -      -       -      +
    147A  GLY*     1.3    76.5    -      -       -      +
    149A  ASN*     1.3    59.0    +      -       -      +
    150A  THR*     3.0    30.0    +      -       +      +
    152A  ILE      5.3     0.2    +      -       -      -
    153A  PHE*     4.0    22.2    -      -       -      -
    214A  GLY*     3.5     2.6    -      -       -      -
    215A  TYR*     2.9    29.8    +      -       -      +
    217A  SER*     4.5     0.4    -      -       -      +
   2000A  HEM      3.3    34.0    -      -       +      +
----------------------------------------------------------
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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