Contacts of the strand formed by residues 92 - 99 (chain C) in PDB entry 2ZOT


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 92 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90C  PHE*     3.4    12.4    -      -       -      -
     91C  ARG*     1.3    78.4    -      -       -      +
     93C  PHE*     1.3    60.9    +      -       -      +
    134C  GLU*     3.1    20.0    -      -       -      -
    163C  ILE      3.6     0.3    -      -       -      -
    164C  VAL*     2.7    46.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 93 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82C  LEU*     3.7    22.4    -      -       +      -
     90C  PHE*     3.9    18.4    -      +       +      -
     92C  GLY*     1.3    75.6    -      -       -      +
     94C  THR*     1.3    76.9    +      -       -      +
     95C  LEU*     4.1     5.4    -      -       +      -
    121C  GLU      4.6     0.2    -      -       -      -
    122C  THR*     3.9     6.7    -      -       +      -
    132C  VAL*     3.2    30.1    -      -       +      -
    133C  THR*     2.9    39.2    +      -       -      -
    134C  GLU*     2.8    33.3    +      -       +      +
    143C  ILE*     3.4    41.5    -      -       +      -
    162C  SER*     3.2    16.8    -      -       -      +
    163C  ILE*     4.2     1.8    -      -       +      +
    164C  VAL*     4.2     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 94 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48C  LEU*     3.5    33.0    -      -       +      +
     93C  PHE*     1.3    84.7    -      -       -      +
     95C  LEU*     1.3    64.9    +      -       -      +
     96C  ILE*     6.0     1.4    -      -       -      +
    125C  MET*     3.7    28.7    -      -       +      -
    131C  ALA*     5.4     3.1    -      -       -      -
    132C  VAL      3.3     7.9    -      -       -      -
    133C  THR*     4.3     0.2    -      -       -      +
    160C  LYS      4.4     0.6    +      -       -      -
    161C  ALA*     3.2     8.1    -      -       -      +
    162C  SER*     3.1    49.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 95 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63C  LEU*     3.7    32.3    -      -       +      -
     80C  VAL*     4.2    12.1    -      -       +      +
     82C  LEU*     5.6     1.3    -      -       +      +
     93C  PHE*     4.1     9.6    -      -       +      -
     94C  THR*     1.3    77.7    -      -       -      +
     96C  ILE*     1.3    68.7    +      -       -      +
    114C  PHE*     4.0    18.2    -      -       +      -
    131C  ALA*     3.3     6.9    -      -       -      -
    132C  VAL*     2.7    46.9    +      -       +      +
    143C  ILE*     4.8     6.7    -      -       +      -
    145C  VAL*     3.6    31.6    -      -       +      -
    159C  LEU*     4.7     2.9    -      -       +      -
    160C  LYS      3.3    16.8    -      -       -      +
    161C  ALA*     4.2     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 96 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46C  ARG*     3.6    40.6    -      -       +      +
     48C  LEU*     5.6    12.8    -      -       +      -
     94C  THR*     6.0     0.7    -      -       -      +
     95C  LEU*     1.3    80.7    -      -       -      +
     97C  ALA*     1.3    59.8    +      -       -      +
     98C  LEU*     3.6    27.6    -      -       +      -
    110C  HIS*     4.5    13.9    -      -       +      +
    114C  PHE*     3.7    12.3    -      -       -      -
    128C  CYS*     5.4     2.5    -      -       -      -
    130C  VAL*     4.3     6.3    -      -       +      +
    131C  ALA*     3.5    22.7    -      -       +      -
    159C  LEU*     3.4     4.3    -      -       -      +
    160C  LYS*     2.9    42.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 97 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96C  ILE*     1.3    75.3    -      -       -      +
     98C  LEU*     1.3    61.2    +      -       -      +
    110C  HIS*     3.0    32.8    +      -       +      +
    111C  ALA      3.3    24.5    -      -       -      +
    114C  PHE*     3.5    15.8    -      -       +      -
    130C  VAL      5.0     1.0    +      -       -      -
    147C  TRP*     3.5    17.5    -      -       -      +
    157C  VAL*     4.3     3.1    -      -       +      -
    158C  ILE      3.6     3.4    -      -       -      -
    159C  LEU*     3.8    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 98 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46C  ARG*     4.5     5.2    -      -       -      +
     96C  ILE*     3.6    27.8    -      -       +      -
     97C  ALA*     1.3    72.9    -      -       -      +
     99C  ARG*     1.3    63.6    +      -       -      +
    102C  ARG      4.6     3.6    -      -       -      +
    103C  GLU      3.8    18.8    -      -       -      +
    104C  GLY*     3.8    11.4    -      -       -      +
    109C  ASP*     3.7    27.8    -      -       -      +
    110C  HIS*     3.7    23.1    -      -       +      +
    111C  ALA      4.5     1.3    -      -       -      -
    157C  VAL*     3.3     6.8    -      -       -      +
    158C  ILE*     2.5    48.7    +      -       +      +
    160C  LYS*     3.6    28.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 99 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98C  LEU*     1.3    76.0    -      -       -      +
    100C  GLU*     1.3    67.0    +      -       -      +
    102C  ARG*     3.3    60.1    +      -       +      +
    108C  GLU*     4.2     6.1    +      -       -      +
    109C  ASP*     3.0    42.2    +      -       -      +
    110C  HIS      5.6     1.2    -      -       -      -
    111C  ALA*     4.4     8.5    -      -       +      +
    154C  THR*     3.3    42.0    -      -       +      +
    156C  CYS      3.4    15.9    -      -       -      +
    157C  VAL*     4.5     1.1    -      -       -      +
    158C  ILE*     4.2     1.5    -      -       -      +
----------------------------------------------------------
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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