Contacts of the strand formed by residues 101 - 107 (chain B) in PDB entry 2ZJR


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 LYS 101 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99B  GLY      3.9    12.3    -      -       -      +
    100B  GLU*     1.3    77.8    -      -       -      +
    102B  ILE*     1.3    65.5    +      -       -      +
    169B  ASN*     4.0    37.2    +      -       -      +
    170B  LEU      3.3     5.4    -      -       -      -
    171B  GLU*     3.9    28.9    +      -       +      +
    200B  SER*     4.8     0.9    -      -       -      -
    201B  ALA*     3.8    21.3    +      -       +      +
    204B  ALA*     4.8     4.7    -      -       +      -
   2710X    C      5.1     7.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 102 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  PHE*     4.0    23.8    -      -       +      -
    100B  GLU*     4.3     6.1    -      -       +      +
    101B  LYS*     1.3    79.4    -      -       -      +
    103B  ASP*     1.3    74.6    +      -       -      +
    104B  ALA      5.0     0.9    -      -       -      +
    168B  GLN      3.7     0.5    -      -       -      -
    169B  ASN      3.1     1.6    +      -       -      -
    170B  LEU*     2.7    54.2    +      -       +      +
    172B  VAL*     3.8    18.6    -      -       +      -
    182B  ILE*     4.8     5.6    -      -       +      -
    184B  VAL*     3.6    17.9    -      -       +      -
    198B  LEU*     3.4    36.1    -      -       +      -
    199B  ARG      3.1    17.9    -      -       -      +
    200B  SER*     4.8     1.6    -      -       -      -
    201B  ALA      4.4     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 103 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102B  ILE*     1.3    96.0    -      -       -      +
    104B  ALA*     1.3    62.7    +      -       -      +
    105B  THR*     3.7     4.7    +      -       -      +
    166B  THR*     4.2    13.2    -      -       +      -
    167B  VAL      3.5     8.3    -      -       -      +
    168B  GLN*     3.6    16.8    +      -       -      +
    169B  ASN*     2.7    19.8    +      -       -      +
    197B  VAL      3.4     5.2    -      -       -      +
    198B  LEU*     3.9     0.8    -      -       -      -
    199B  ARG*     3.1    32.1    +      -       +      +
    200B  SER      4.3     5.2    -      -       -      +
    201B  ALA*     3.3     5.8    -      -       -      +
    202B  ALA*     2.6    42.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 104 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102B  ILE*     4.1     2.5    +      -       +      +
    103B  ASP*     1.3    71.6    -      -       -      +
    105B  THR*     1.3    60.3    +      -       -      +
    106B  GLY      4.3     0.2    -      -       -      -
    166B  THR*     4.5     0.2    -      -       -      -
    167B  VAL*     3.1    29.4    +      -       +      +
    170B  LEU*     4.4    10.7    -      -       +      +
    188B  ILE*     3.3    44.9    -      -       +      -
    189B  PRO*     4.0     7.4    -      -       +      +
    196B  VAL*     5.6     0.7    -      -       +      -
    197B  VAL      3.5     5.6    -      -       -      +
    198B  LEU*     4.1    13.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 105 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  ASP      4.1     2.5    -      -       -      +
    104B  ALA*     1.3    75.7    -      -       -      +
    106B  GLY*     1.3    58.1    +      -       -      +
    164B  ARG*     3.7    23.1    +      -       -      +
    165B  VAL      3.0    11.0    +      -       -      -
    166B  THR*     3.1    22.7    +      -       +      -
    188B  ILE*     5.2     0.2    -      -       -      +
    196B  VAL*     3.8     2.3    -      -       -      +
    197B  VAL*     2.8    52.4    +      -       +      +
    199B  ARG*     3.0    31.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 106 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104B  ALA      4.3     0.2    -      -       -      -
    105B  THR*     1.3    74.1    +      -       -      +
    107B  THR*     1.3    62.8    +      -       -      -
    108B  SER      4.0     0.2    -      -       -      -
    163B  GLU      3.7     0.3    -      -       -      +
    164B  ARG*     3.7     4.8    -      -       -      +
    165B  VAL*     3.1    28.3    +      -       -      +
    188B  ILE*     5.0     0.6    -      -       -      +
    189B  PRO*     4.0    23.2    -      -       -      +
    195B  LEU      3.9    17.0    -      -       -      -
    196B  VAL*     4.3     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 107 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106B  GLY*     1.3    73.8    -      -       -      -
    108B  SER*     1.3    77.6    +      -       -      +
    162B  MET*     3.7    27.8    -      -       +      +
    163B  GLU      3.0    11.7    +      -       -      +
    164B  ARG*     4.9     2.3    -      -       -      +
    189B  PRO*     4.7     1.2    +      -       -      +
    190B  GLY*     3.1    18.5    -      -       -      -
    195B  LEU      4.4     4.8    +      -       -      -
      2M  GLN*     4.8    14.8    +      -       -      +
----------------------------------------------------------
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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