Contacts of the strand formed by residues 136 - 146 (chain G) in PDB entry 1ZMD


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 THR 136 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3G  GLN*     3.9    17.7    +      -       -      +
    128G  THR*     3.8    10.8    -      -       +      +
    129G  ALA      3.3     4.8    +      -       -      -
    130G  THR*     3.7    18.2    +      -       -      +
    131G  LYS*     5.7     2.5    -      -       -      -
    134G  GLY      3.7     4.1    +      -       -      -
    135G  GLY*     1.3    72.9    +      -       -      -
    137G  GLN*     1.3    64.4    +      -       -      +
    138G  VAL*     4.4    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 137 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3G  GLN*     2.9    46.3    +      -       -      +
      5G  ILE*     3.6    33.8    -      -       +      +
    115G  VAL*     4.2    25.1    -      -       +      -
    128G  THR*     3.4     1.6    -      -       -      -
    129G  ALA*     2.8    39.2    +      -       +      +
    131G  LYS*     4.9    11.5    -      -       -      +
    136G  THR*     1.3    74.7    +      -       -      +
    138G  VAL*     1.3    80.1    +      -       -      +
    139G  ILE*     3.8     4.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 138 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3G  GLN*     5.3     1.0    +      -       -      -
      4G  PRO*     3.4    18.4    -      -       +      +
      5G  ILE*     2.9    24.4    +      -       -      +
    126G  GLN*     3.5    35.7    -      -       +      +
    127G  VAL      3.6     3.4    -      -       -      -
    128G  THR*     3.8    20.6    -      -       +      +
    136G  THR*     4.4    11.2    -      -       +      +
    137G  GLN*     1.3    85.7    +      -       -      +
    139G  ILE*     1.3    62.8    +      -       -      +
    140G  ASP*     4.1     8.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 139 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5G  ILE*     3.1    39.3    -      -       +      +
      7G  ALA*     4.0    12.8    -      -       +      -
     10G  THR*     3.2    29.2    -      -       +      +
     33G  VAL*     4.1    13.0    -      -       +      -
     35G  ILE*     4.0    23.1    -      -       +      -
    115G  VAL*     4.6     7.0    -      -       +      -
    126G  GLN*     3.4     4.7    -      -       -      +
    127G  VAL*     2.8    43.2    +      -       +      +
    129G  ALA      4.7     1.3    -      -       -      +
    137G  GLN*     3.8    14.8    -      -       +      +
    138G  VAL*     1.3    77.2    -      -       -      +
    140G  ASP*     1.3    71.6    +      -       -      +
    141G  THR*     3.6     1.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 140 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4G  PRO*     3.8    24.4    -      -       -      +
      5G  ILE      2.7    11.3    +      -       -      +
      6G  ASP*     3.0    15.0    -      -       +      +
      7G  ALA      2.9    23.4    +      -       -      +
    125G  ASN      3.4     7.2    -      -       -      +
    126G  GLN*     3.1    27.4    -      -       -      +
    138G  VAL*     4.1     4.1    -      -       -      +
    139G  ILE*     1.3    71.5    -      -       -      +
    141G  THR*     1.3    60.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 141 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7G  ALA      3.2    12.4    +      -       -      -
      8G  ASP      3.6     2.8    +      -       -      -
      9G  VAL      3.8     0.3    +      -       -      -
     10G  THR*     3.1    31.8    +      -       -      +
    125G  ASN*     2.9    36.1    +      -       -      +
    126G  GLN      4.2     1.1    -      -       -      +
    127G  VAL*     4.4     2.7    -      -       +      -
    139G  ILE*     4.1     8.1    -      -       -      +
    140G  ASP*     1.3    76.6    -      -       -      +
    142G  LYS*     1.3    64.2    +      -       -      +
    143G  ASN      2.7    18.9    +      -       -      -
    144G  ILE*     3.7    29.4    -      -       +      -
    314G  ASN*     4.8     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 142 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7G  ALA      3.2    11.2    +      -       -      +
      8G  ASP*     3.2    32.7    +      -       +      +
    125G  ASN*     3.2     9.1    -      -       -      +
    141G  THR*     1.3    73.3    +      -       -      +
    143G  ASN*     1.3    70.6    +      -       -      +
    314G  ASN*     2.9    28.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 143 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8G  ASP*     2.9    24.9    +      -       -      +
      9G  VAL*     3.5     8.8    -      -       +      +
     10G  THR      3.0    14.0    +      -       -      -
     30G  PHE*     4.9     9.3    -      -       -      -
    141G  THR*     2.7    22.6    +      -       -      +
    142G  LYS*     1.3    93.5    -      -       -      +
    144G  ILE*     1.3    65.0    +      -       -      +
    314G  ASN*     3.3    19.7    -      -       -      +
    316G  TYR*     4.0    12.8    +      -       +      -
    342G  MET*     4.3    27.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 144 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10G  THR      3.5     6.5    -      -       -      +
     12G  ILE*     3.9    28.0    -      -       +      -
    121G  ILE*     3.7    34.3    -      -       +      -
    123G  GLY      3.9     3.6    -      -       -      +
    124G  LYS      3.7    20.9    -      -       -      +
    126G  GLN      4.2     5.4    -      -       -      +
    127G  VAL*     3.6    20.0    -      -       +      -
    141G  THR*     3.7    14.8    -      -       +      -
    143G  ASN*     1.3    77.9    -      -       -      +
    145G  LEU*     1.3    61.7    +      -       -      +
    146G  ILE*     4.4     0.9    -      -       +      -
    314G  ASN*     3.0     7.0    +      -       -      +
    315G  ILE*     3.4    16.9    -      -       +      -
    316G  TYR*     2.7    37.7    +      -       -      +
    342G  MET*     5.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 145 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9G  VAL*     4.6     2.5    -      -       +      -
     10G  THR      2.8    12.8    +      -       -      +
     11G  VAL*     3.4    19.0    -      -       +      +
     12G  ILE*     2.9    27.0    +      -       -      +
     21G  ALA*     3.4    33.7    -      -       +      -
    143G  ASN      4.3     0.2    -      -       -      -
    144G  ILE*     1.3    75.1    -      -       -      +
    146G  ILE*     1.3    64.8    +      -       -      +
    147G  ALA*     3.6     0.4    +      -       +      -
    316G  TYR*     3.7    24.9    -      -       +      +
    318G  ILE*     3.7    34.8    -      -       +      -
    335G  GLY      4.8     0.9    -      -       -      +
    338G  CYS*     4.2     5.2    -      -       -      -
    339G  VAL*     4.1    16.8    -      -       +      -
    342G  MET*     4.3    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 146 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12G  ILE*     4.3     7.6    -      -       +      -
    121G  ILE*     4.0    22.9    -      -       +      -
    144G  ILE*     4.4     3.1    -      -       +      -
    145G  LEU*     1.3    73.6    -      -       -      +
    147G  ALA*     1.3    61.5    +      -       -      +
    148G  THR*     3.6    22.9    -      -       +      +
    287G  LEU*     3.6    17.0    -      -       +      -
    289G  LEU*     4.1    13.2    -      -       +      -
    302G  ILE*     3.7    27.6    -      -       +      -
    310G  THR*     4.6     6.7    -      -       +      -
    315G  ILE*     3.7    21.8    -      -       +      -
    316G  TYR      2.6    21.5    +      -       -      +
    317G  ALA*     3.2     4.0    -      -       +      +
    318G  ILE      3.0    26.2    +      -       -      +
    321G  VAL*     4.3     3.6    -      -       +      -
----------------------------------------------------------
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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