Contacts of the strand formed by residues 5 - 12 (chain G) in PDB entry 1ZMC


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 ILE 5 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3G  GLN      4.3     3.6    -      -       -      +
      4G  PRO*     1.3    83.4    -      -       -      +
      6G  ASP*     1.3    72.0    +      -       -      +
     31G  LYS*     5.0     9.2    -      -       -      +
     33G  VAL*     4.2    22.0    -      -       +      -
    113G  VAL*     5.3    12.6    -      -       +      -
    115G  VAL*     5.8     2.2    -      -       +      -
    137G  GLN*     3.5    30.1    -      -       +      +
    138G  VAL      3.0     3.8    +      -       -      -
    139G  ILE*     3.1    14.6    -      -       +      -
    140G  ASP*     2.7    28.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 6 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5G  ILE*     1.3    79.8    -      -       -      +
      7G  ALA*     1.3    63.9    +      -       -      +
     31G  LYS*     3.3    37.3    +      -       -      +
    139G  ILE*     4.9     0.2    -      -       -      -
    140G  ASP*     3.0    16.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 7 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6G  ASP*     1.3    79.1    -      -       -      +
      8G  ASP*     1.3    66.8    +      -       -      +
      9G  VAL      3.9    13.2    -      -       -      +
     10G  THR*     3.9    14.8    -      -       -      +
     31G  LYS*     3.4    19.1    -      -       +      +
     33G  VAL*     3.9    18.2    -      -       +      -
    139G  ILE*     4.4     2.0    -      -       +      +
    140G  ASP      2.9     6.8    +      -       -      +
    141G  THR*     3.1    19.8    -      -       -      +
    142G  LYS*     3.1     6.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 8 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7G  ALA*     1.3    75.1    -      -       -      +
      9G  VAL*     1.3    59.4    +      -       -      +
     29G  GLY      4.4     2.4    -      -       -      +
     30G  PHE*     3.6    30.1    -      -       +      -
     31G  LYS*     2.8    34.6    +      -       -      +
    141G  THR*     3.5     1.3    -      -       -      -
    142G  LYS*     3.0    34.7    +      -       +      +
    143G  ASN*     2.7    40.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 9 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7G  ALA*     3.9     1.3    -      -       -      +
      8G  ASP*     1.3    82.9    -      -       -      +
     10G  THR*     1.3    68.5    +      -       -      +
     11G  VAL*     3.9    22.2    -      -       +      -
     25G  ALA*     4.4     9.4    -      -       +      -
     30G  PHE*     3.7    31.4    -      -       +      -
     31G  LYS      3.1     4.1    +      -       -      +
     32G  THR*     3.3    16.7    -      -       +      +
     33G  VAL      2.8    26.2    +      -       -      +
    143G  ASN*     3.7     7.4    -      -       +      +
    145G  LEU*     4.7     2.9    -      -       +      -
    339G  VAL*     5.1     2.5    -      -       +      -
    342G  MET*     3.9    34.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 10 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7G  ALA*     3.9     2.9    -      -       -      +
      9G  VAL*     1.3    76.5    +      -       -      +
     11G  VAL*     1.3    64.5    +      -       -      +
     12G  ILE*     3.9     1.5    +      -       +      -
     33G  VAL*     3.2    24.1    -      -       +      +
     35G  ILE*     4.0    22.2    -      -       +      -
    127G  VAL*     4.3    13.5    -      -       +      -
    139G  ILE*     3.2    18.2    -      -       +      +
    141G  THR*     3.1    33.5    -      -       -      -
    143G  ASN      3.1     7.0    +      -       -      -
    144G  ILE*     3.5     4.5    -      -       -      +
    145G  LEU      2.8    26.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 11 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9G  VAL*     3.9    19.1    -      -       +      -
     10G  THR*     1.3    75.0    -      -       -      +
     12G  ILE*     1.3    64.8    +      -       -      +
     13G  GLY      3.6    13.3    +      -       -      +
     18G  GLY*     3.5    28.3    -      -       -      +
     21G  ALA*     4.6     0.2    -      -       +      -
     22G  ALA*     4.1    26.5    -      -       +      +
     32G  THR*     4.3     0.7    -      -       +      -
     33G  VAL      2.6    16.8    +      -       -      +
     34G  CYS*     3.3     5.4    -      -       -      -
     35G  ILE*     2.8    28.8    +      -       -      +
    145G  LEU*     3.4    24.2    -      -       +      +
    147G  ALA*     4.1     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 12 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10G  THR*     4.7     2.0    -      -       +      +
     11G  VAL*     1.3    74.1    -      -       -      +
     13G  GLY*     1.3    58.4    +      -       -      +
     35G  ILE*     3.9     8.7    -      -       +      -
    119G  GLY*     4.4     8.1    -      -       -      -
    121G  ILE*     3.9    17.0    -      -       +      -
    127G  VAL*     3.9    30.1    -      -       +      -
    144G  ILE*     3.9    24.5    -      -       +      -
    145G  LEU      2.9    12.7    +      -       -      +
    146G  ILE*     4.8     4.5    -      -       +      -
    147G  ALA*     3.0    28.2    +      -       -      -
    148G  THR*     3.5     6.5    +      -       +      +
    287G  LEU*     4.0    17.0    -      -       +      -
    480G  FAD      3.5    39.0    -      -       +      +
----------------------------------------------------------
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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