Contacts of the strand formed by residues 3 - 16 (chain B) in PDB entry 2ZJQ


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 3 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  LYS*     1.3    80.0    -      -       -      +
      4B  ILE*     1.3    62.3    +      -       -      +
     49B  ILE*     4.5     6.2    -      -       -      +
     81B  PHE*     4.2    18.9    -      -       -      -
     84B  PHE*     4.1    11.9    -      -       -      -
     90B  SER*     4.2    10.0    +      -       -      -
     95B  ILE*     5.0     5.2    -      -       -      +
     96B  PHE*     3.9     9.9    -      -       -      -
    198B  LEU      3.1    15.3    -      -       -      -
    199B  ARG*     4.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 4 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  GLY*     1.3    75.0    -      -       -      +
      5B  LEU*     1.3    68.7    +      -       -      +
     28B  ALA*     3.4    25.6    -      -       +      +
     29B  GLY      3.6    14.1    -      -       -      +
     31B  CYS*     3.7    11.0    -      -       +      -
     49B  ILE*     4.3     4.3    -      -       +      -
     81B  PHE*     4.3     3.2    -      -       -      -
     90B  SER*     2.9    33.7    -      -       -      +
     91B  VAL*     3.3    27.4    -      -       -      -
     92B  ASN*     3.5     7.4    -      -       +      +
     95B  ILE*     5.1     4.0    -      -       +      -
     96B  PHE*     4.1    19.7    -      -       +      -
    197B  VAL*     4.0     1.0    -      -       -      +
    198B  LEU*     3.1    29.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 5 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  ILE*     1.3    80.9    -      -       -      +
      6B  GLY*     1.3    59.7    +      -       -      +
     28B  ALA*     3.1    26.1    -      -       -      +
     29B  GLY      4.0     0.5    +      -       -      -
     31B  CYS*     3.6    14.6    -      -       -      -
     49B  ILE*     3.6    20.9    -      -       +      -
     50B  GLY      4.4     1.1    -      -       -      -
     51B  TYR*     3.8    28.8    -      -       +      -
     77B  ILE*     4.0    18.4    -      -       +      -
     79B  ARG*     4.1    16.6    -      -       +      +
     81B  PHE*     3.1    40.2    -      -       +      -
    195B  LEU*     4.1    11.9    -      -       +      -
    196B  VAL      4.0     4.0    -      -       -      +
    197B  VAL*     4.3     7.6    -      -       +      +
    198B  LEU*     5.2     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 6 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  LEU*     1.3    78.1    -      -       -      +
      7B  THR*     1.3    64.6    +      -       -      -
     26B  VAL*     4.6     1.3    -      -       -      -
     27B  LEU      2.9    13.9    -      -       -      -
     28B  ALA*     3.6     4.7    -      -       -      -
     51B  TYR*     4.0     6.7    -      -       -      -
    195B  LEU*     3.6    11.6    -      -       -      +
    196B  VAL*     3.0    37.8    +      -       -      +
    198B  LEU*     5.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 7 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  GLY*     1.3    72.5    +      -       -      -
      8B  LYS*     1.3    87.2    +      -       -      +
      9B  ILE*     3.8     3.7    -      -       +      +
     26B  VAL*     3.2     5.4    -      -       -      +
     27B  LEU*     2.6    39.2    +      -       -      -
     51B  TYR*     2.5    36.8    +      -       -      -
    193B  GLY*     3.9    18.8    -      -       -      -
    194B  GLY      3.3    10.1    -      -       -      +
    196B  VAL*     4.6     0.7    -      -       -      -
      3M  THR*     3.3    11.6    +      -       -      +
      5M  ILE*     4.0    14.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 8 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  THR*     1.3    94.0    -      -       -      +
      9B  ILE*     1.3    71.0    +      -       -      +
     10B  GLY*     4.1     5.8    -      -       -      +
     11B  MET*     5.3     4.6    -      -       -      +
     24B  THR*     4.3    23.3    +      -       +      -
     25B  VAL      4.3     2.5    -      -       -      -
     26B  VAL*     4.5     4.5    -      -       -      +
    187B  ALA*     5.8     0.2    -      -       -      +
    188B  ILE*     3.3    18.3    +      -       +      +
    189B  PRO      3.9     6.1    -      -       -      +
    190B  GLY      2.7    29.6    +      -       -      +
    191B  ALA      3.6    17.5    -      -       -      +
    192B  ASN*     3.2    23.6    -      -       -      +
    193B  GLY      3.7     6.8    +      -       -      -
    194B  GLY      3.0     9.7    +      -       -      +
    196B  VAL*     3.9    19.1    -      -       +      +
   2659X    C      3.2    11.9    +      -       -      -
   2660X    C      3.1    20.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 9 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  THR*     3.8    10.5    -      -       +      +
      8B  LYS*     1.3    86.4    -      -       -      +
     10B  GLY*     1.3    60.6    +      -       -      +
     25B  VAL*     3.0    20.6    +      -       +      +
     26B  VAL      4.9     0.4    -      -       -      -
     27B  LEU*     3.6    22.0    -      -       +      +
    181B  LEU*     4.4     4.7    -      -       +      -
    192B  ASN*     3.9    10.2    -      -       -      -
    193B  GLY      5.1     0.2    -      -       -      +
      7M  ILE*     5.2     3.8    -      -       +      -
      9M  ARG*     3.8    37.9    +      -       +      +
     12M  LEU*     3.2    34.1    -      -       +      -
     13M  LEU*     3.1    33.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 10 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  LYS*     4.1     2.7    -      -       -      +
      9B  ILE*     1.3    81.5    -      -       -      +
     11B  MET*     1.3    61.6    +      -       -      -
     24B  THR*     4.3     1.6    -      -       -      -
     25B  VAL*     2.6    41.4    +      -       -      +
    192B  ASN*     3.6    18.5    +      -       -      -
     13M  LEU*     4.6     8.3    -      -       -      -
   2661X    G      5.9     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 11 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  LYS*     5.3     5.2    -      -       -      -
     10B  GLY*     1.3    76.1    -      -       -      -
     12B  THR*     1.3    67.2    +      -       -      +
     22B  PRO*     4.3    12.8    -      -       +      -
     23B  VAL      2.8    11.7    -      -       -      +
     24B  THR*     3.0    23.3    -      -       +      +
     25B  VAL*     4.9     0.2    -      -       -      -
    186B  GLY      4.1    18.4    -      -       -      +
    187B  ALA*     4.3     6.1    -      -       +      -
     13M  LEU*     5.0     6.1    -      -       -      +
     63M  ARG*     5.2     0.3    -      -       -      -
   2659X    C      3.5    22.4    -      -       -      +
   2660X    C      4.0    12.8    -      -       -      +
   2661X    G      3.0    75.5    +      -       +      +
   2708X    U      5.6     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 12 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  MET*     1.3    79.8    -      -       -      +
     13B  GLN*     1.3    70.6    +      -       -      +
     14B  ILE*     4.4     2.0    -      -       +      -
     22B  PRO*     3.5     5.4    -      -       -      +
     23B  VAL*     3.1    42.9    +      -       +      +
     25B  VAL*     4.6    11.0    -      -       +      -
     13M  LEU*     5.4     7.0    -      -       +      +
     16M  ILE      3.7    22.4    -      -       -      +
     17M  GLU*     2.2    31.1    +      -       -      +
     63M  ARG*     3.7     9.9    +      -       -      -
   2661X    G      3.5    17.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 13 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  THR*     1.3    79.8    +      -       -      +
     14B  ILE*     1.3    72.8    +      -       -      +
     15B  TRP*     3.9    18.4    -      -       +      -
     20B  ALA*     4.2    19.3    -      -       +      +
     21B  ILE      4.1     4.7    -      -       -      +
     22B  PRO*     5.5     2.9    -      -       +      -
     86H  GLY*     5.2     9.3    +      -       -      -
     16M  ILE      5.0     0.2    -      -       -      +
     20M  HIS*     4.3     3.1    -      -       -      +
     62M  SER*     3.1    46.1    +      -       -      +
     63M  ARG*     3.8    12.8    -      -       +      +
     82M  PRO*     4.9     7.7    -      -       -      +
   2661X    G      3.3    27.6    +      -       +      +
   2662X    C      4.1    25.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 14 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  THR*     4.4     2.9    -      -       +      -
     13B  GLN*     1.3    87.2    -      -       -      +
     15B  TRP*     1.3    73.8    +      -       -      +
     16B  LYS*     4.7     2.2    -      -       +      +
     20B  ALA*     5.3     0.2    -      -       -      +
     21B  ILE*     2.6    49.1    +      -       +      +
     23B  VAL*     3.6    24.0    -      -       +      -
    173B  VAL*     4.9    10.5    -      -       +      -
    174B  GLU*     4.3     7.6    -      -       -      +
    183B  LEU*     3.3    34.5    -      -       +      -
     16M  ILE*     3.8    11.4    -      -       +      +
     20M  HIS*     3.3    31.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 15 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  GLN*     3.9    17.3    -      -       +      -
     14B  ILE*     1.3    84.1    -      -       -      +
     16B  LYS*     1.3    60.9    +      -       -      +
     17B  ASN      3.6     7.1    +      -       -      +
     18B  ASP      4.1     4.5    -      -       -      -
     19B  ARG      3.7     3.8    -      -       -      -
     20B  ALA*     3.0    42.8    -      -       +      +
     85H  ASP      3.2    11.1    +      -       -      -
     20M  HIS*     3.8    38.2    +      -       +      +
     62M  SER*     3.7    19.7    -      -       -      -
     82M  PRO*     4.1    13.5    -      -       +      -
     84M  ALA*     3.5    41.1    -      -       +      -
     85M  SER*     3.8     9.4    -      -       -      -
     86M  PRO*     3.1    37.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 16 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  ILE*     3.9     3.2    +      -       +      -
     15B  TRP*     1.3    71.2    -      -       -      +
     17B  ASN*     1.3    80.0    +      -       -      +
     18B  ASP      3.3     4.4    +      -       -      -
     19B  ARG*     3.3    26.7    +      -       +      +
     21B  ILE*     3.6    22.2    -      -       +      -
     98B  GLU*     4.6     7.6    +      -       -      +
     99B  GLY*     5.5     3.6    -      -       -      +
    171B  GLU*     3.3    25.1    +      -       -      +
    172B  VAL      4.8     0.8    +      -       -      -
    173B  VAL*     3.5    43.1    +      -       +      +
----------------------------------------------------------
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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