Contacts of the strand formed by residues 136 - 146 (chain D) 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 THR 136 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1D  ALA      3.3    12.5    -      -       -      +
      2D  ASP*     3.3    28.0    +      -       -      +
    128D  THR*     4.6    11.7    -      -       +      -
    129D  ALA      3.2     6.7    -      -       -      -
    130D  THR*     3.5    18.6    -      -       +      +
    131D  LYS*     4.3     4.1    +      -       -      +
    134D  GLY      3.5    10.3    -      -       -      +
    135D  GLY*     1.3    80.0    -      -       -      +
    137D  GLN*     1.3    61.8    +      -       -      +
    138D  VAL*     5.4     5.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 137 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1D  ALA*     3.6    27.9    +      -       -      +
      2D  ASP*     5.6     0.4    -      -       -      +
      3D  GLN*     3.2    28.0    +      -       -      +
      4D  PRO*     3.9     0.4    -      -       -      +
      5D  ILE*     3.6    11.0    -      -       -      +
    115D  VAL*     4.1    31.0    -      -       +      -
    127D  VAL      3.9     0.5    -      -       -      +
    128D  THR*     3.5     1.7    -      -       -      -
    129D  ALA*     2.7    41.4    +      -       -      +
    131D  LYS*     3.8    17.0    -      -       -      +
    136D  THR*     1.3    75.9    -      -       -      +
    138D  VAL*     1.3    95.2    +      -       -      +
    139D  ILE*     4.4     5.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 138 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3D  GLN      5.6     0.2    -      -       -      -
      4D  PRO*     4.4    17.5    -      -       +      -
      5D  ILE*     3.0    15.5    +      -       -      +
    126D  GLN*     3.2    37.9    -      -       +      +
    127D  VAL      3.7     2.9    -      -       -      +
    128D  THR*     4.4    14.1    -      -       +      +
    136D  THR*     5.4     5.2    -      -       -      +
    137D  GLN*     1.3   102.1    +      -       -      +
    139D  ILE*     1.3    65.8    +      -       -      +
    140D  ASP*     4.4     8.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 139 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5D  ILE*     3.3    26.7    -      -       +      +
      7D  ALA*     4.1    15.3    -      -       +      -
     10D  THR*     3.5    25.8    -      -       +      +
     33D  VAL*     4.1    13.7    -      -       +      -
     35D  ILE*     3.3    39.3    -      -       +      -
    115D  VAL*     4.5     6.3    -      -       +      -
    126D  GLN*     3.3     4.0    -      -       -      -
    127D  VAL*     2.8    49.3    +      -       +      +
    129D  ALA*     4.6     4.7    -      -       +      -
    137D  GLN*     4.4    10.8    -      -       +      +
    138D  VAL*     1.3    78.7    -      -       -      +
    140D  ASP*     1.3    61.4    +      -       -      +
    141D  THR*     3.6     1.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 140 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  PRO*     3.9    20.6    -      -       -      +
      5D  ILE      2.8    10.9    +      -       -      +
      6D  ASP*     3.2    15.9    -      -       -      +
      7D  ALA*     2.8    24.1    +      -       -      +
    125D  ASN      3.4     7.0    -      -       -      +
    126D  GLN*     3.3    31.5    -      -       -      +
    138D  VAL*     4.1     2.6    -      -       -      +
    139D  ILE*     1.3    73.7    -      -       -      +
    141D  THR*     1.3    58.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 141 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  ALA*     2.9    14.0    +      -       -      -
      8D  ASP      3.3     9.7    +      -       -      -
      9D  VAL      3.5     0.3    +      -       -      -
     10D  THR*     3.0    27.0    +      -       -      +
    124D  LYS      4.9     0.3    -      -       -      +
    125D  ASN*     3.0    35.2    +      -       -      +
    127D  VAL*     4.4     2.9    -      -       +      -
    139D  ILE*     4.4     7.0    -      -       -      +
    140D  ASP*     1.3    75.9    -      -       -      +
    142D  LYS*     1.3    62.2    +      -       -      +
    143D  ASN      2.8    27.9    +      -       -      +
    144D  ILE*     3.7    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 142 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  ALA      3.1     7.8    +      -       -      +
      8D  ASP*     2.5    39.5    +      -       +      +
    125D  ASN*     3.2    10.1    +      -       -      +
    141D  THR*     1.3    73.0    +      -       -      +
    143D  ASN*     1.3    73.6    +      -       -      +
    314D  ASN*     3.0    24.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 143 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8D  ASP*     2.8    25.2    +      -       -      +
      9D  VAL*     4.2    16.4    -      -       +      +
     10D  THR      3.1    12.0    +      -       -      -
     30D  PHE*     5.2     5.3    -      -       -      -
    141D  THR*     2.8    26.0    +      -       -      +
    142D  LYS*     1.3    93.5    -      -       -      +
    144D  ILE*     1.3    66.4    +      -       -      +
    314D  ASN*     3.5    21.1    -      -       -      +
    316D  TYR*     4.0    14.7    +      -       +      -
    342D  MET*     4.4    18.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 144 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10D  THR      3.5     4.9    -      -       -      +
     12D  ILE*     4.0    19.5    -      -       +      -
    121D  ILE*     4.0    40.2    -      -       +      -
    123D  GLY      4.0     3.4    -      -       -      +
    124D  LYS      3.8    21.5    -      -       -      +
    126D  GLN      4.1     4.5    -      -       -      +
    127D  VAL*     3.6    27.4    -      -       +      -
    141D  THR*     3.7     6.5    -      -       +      -
    143D  ASN*     1.3    82.8    -      -       -      +
    145D  LEU*     1.3    61.5    +      -       -      +
    146D  ILE*     4.4     4.7    -      -       +      -
    314D  ASN      3.1     6.2    +      -       -      +
    315D  ILE*     3.3    16.4    -      -       +      -
    316D  TYR*     2.7    35.0    +      -       -      -
    342D  MET*     5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 145 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9D  VAL*     4.7     3.1    -      -       +      -
     10D  THR      2.8    13.7    +      -       -      +
     11D  VAL*     3.3    20.6    -      -       +      +
     12D  ILE*     2.8    32.0    +      -       -      -
     21D  ALA*     3.6    31.6    -      -       +      -
    144D  ILE*     1.3    74.6    -      -       -      +
    146D  ILE*     1.3    62.9    +      -       -      +
    147D  ALA*     3.5     1.0    +      -       +      -
    316D  TYR*     3.5    24.5    -      -       +      +
    318D  ILE*     3.9    32.3    -      -       +      -
    335D  GLY      5.0     0.9    -      -       -      +
    338D  CYS*     4.0     5.8    -      -       -      -
    339D  VAL*     4.2    15.7    -      -       +      -
    342D  MET*     4.5     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 146 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12D  ILE*     4.3     6.1    -      -       +      -
    121D  ILE*     4.1     5.2    -      -       +      -
    144D  ILE*     4.4     8.3    -      -       +      -
    145D  LEU*     1.3    72.5    -      -       -      +
    147D  ALA*     1.3    60.7    +      -       -      +
    148D  THR*     3.4    25.4    -      -       +      +
    287D  LEU*     3.4    27.8    -      -       +      -
    289D  LEU*     4.0    15.0    -      -       +      -
    294D  ILE*     5.3     0.2    -      -       +      -
    302D  ILE*     3.7    28.3    -      -       +      -
    310D  THR*     4.8     3.8    -      -       +      -
    315D  ILE*     4.0    22.7    -      -       +      -
    316D  TYR      2.7    18.7    +      -       -      +
    317D  ALA*     3.1     6.5    -      -       +      +
    318D  ILE      3.0    28.1    +      -       -      +
    321D  VAL*     4.3     2.7    -      -       +      -
----------------------------------------------------------
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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