Contacts of the strand formed by residues 2 - 9 (chain C) in PDB entry 3ZO7


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 LEU 2 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  TRP*     3.7    19.7    -      -       +      +
      1C  MET*     1.3    77.3    -      -       -      +
      3C  TYR*     1.3    65.7    +      -       -      +
     41C  ARG*     3.7    26.7    -      -       -      +
     55C  VAL*     4.1     9.9    -      -       +      -
     56C  PHE      3.2     4.3    -      -       -      +
     57C  ASP*     3.8    22.2    -      -       +      +
     83C  PRO*     3.9     2.3    -      -       -      +
     84C  LEU*     2.9    48.4    +      -       +      +
     85C  SER      6.6     0.2    -      -       -      -
     94C  ASP*     3.5    36.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 3 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1C  MET*     3.2    41.7    -      -       +      +
      2C  LEU*     1.3    78.5    -      -       -      +
      4C  LEU*     1.3    59.8    +      -       -      +
      5C  VAL*     3.6    10.1    +      -       +      +
     55C  VAL*     3.2     5.4    -      -       -      -
     56C  PHE*     2.9    38.5    +      -       +      +
     58C  VAL*     3.6    25.1    -      -       +      -
     60C  SER      3.5     9.2    -      -       -      -
     61C  HIS*     2.8    38.5    +      +       +      -
     64C  LEU*     3.4    31.4    -      -       +      -
     81C  VAL*     4.0    13.0    -      -       +      -
     82C  GLU      3.4     7.6    -      -       -      +
     83C  PRO*     4.4    17.0    -      -       +      -
     84C  LEU*     4.0     4.5    -      -       -      +
     47E  THR*     5.7     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 4 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  LEU*     4.7    16.4    -      -       +      -
      6B  ARG*     4.1     7.4    -      -       -      +
     44B  TRP*     5.0     5.8    -      -       +      -
     53B  ILE*     4.0    24.7    -      -       +      -
      3C  TYR*     1.3    71.2    -      -       -      +
      5C  VAL*     1.3    60.4    +      -       -      +
      6C  ARG*     4.1     2.4    +      -       +      +
     44C  TRP*     5.4     0.7    -      -       +      -
     53C  ILE*     3.7    25.8    -      -       +      -
     54C  SER      3.4    12.3    -      -       -      +
     55C  VAL*     4.1    14.1    -      -       +      -
     80C  ASP      3.5     4.0    -      -       -      +
     82C  GLU*     2.8    59.4    +      -       +      +
     84C  LEU*     3.8    19.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 5 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3C  TYR*     4.1    15.9    -      -       +      +
      4C  LEU*     1.3    79.5    -      -       -      +
      6C  ARG*     1.3    61.5    +      -       -      +
      7C  MET*     3.9    24.2    +      -       +      -
     52C  ASN*     3.9     1.9    -      -       -      +
     53C  ILE*     3.7     1.2    -      -       -      -
     54C  SER*     2.8    40.1    +      -       -      +
     56C  PHE*     3.8    27.8    -      -       +      -
     64C  LEU*     4.6     7.9    -      -       +      -
     68C  LEU*     4.3     6.1    -      -       +      -
     79C  ILE*     3.8    27.1    -      -       +      -
     80C  ASP      3.3     2.9    -      -       -      +
     81C  VAL*     4.2    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 6 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  LEU*     4.1     7.3    -      -       -      +
      6B  ARG*     5.5     5.7    -      -       -      +
     82B  GLU*     2.8    42.8    +      -       -      -
      4C  LEU*     4.1     2.9    +      -       +      +
      5C  VAL*     1.3    72.8    -      -       -      +
      7C  MET*     1.3    66.6    +      -       -      +
      8C  THR*     4.5    14.4    -      -       -      +
     46C  THR*     4.2     7.5    -      -       +      +
     49C  LYS*     6.1     2.6    -      -       -      +
     52C  ASN      3.5     5.8    -      -       -      +
     53C  ILE*     3.5    28.1    -      -       +      +
     78C  THR      3.5     1.3    -      -       -      +
     79C  ILE*     3.4     7.1    -      -       -      +
     80C  ASP*     3.0    54.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 7 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  VAL*     3.9    15.9    -      -       +      -
      6C  ARG*     1.3    79.1    -      -       -      +
      8C  THR*     1.3    63.9    +      -       -      +
      9C  VAL*     6.0     0.2    -      -       +      -
     40C  TRP*     4.0    12.8    -      -       +      -
     46C  THR*     5.1     0.9    +      -       -      +
     51C  GLY*     3.0     5.1    -      -       -      -
     52C  ASN*     2.9    63.4    +      -       -      +
     54C  SER*     4.3     0.4    -      -       -      +
     56C  PHE*     3.6    32.3    -      -       +      -
     68C  LEU*     3.9     4.0    -      -       +      -
     71C  LEU*     3.9    29.6    -      -       +      -
     77C  LEU*     4.0    23.1    -      -       +      -
     78C  THR      3.5     4.5    -      -       -      -
     79C  ILE*     4.4     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 8 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  ARG*     4.5    14.6    -      -       -      +
      7C  MET*     1.3    75.6    +      -       -      +
      9C  VAL*     1.3    67.9    +      -       -      +
     10C  ASN*     3.5    20.9    -      -       -      +
     49C  LYS*     6.2     4.9    -      -       +      -
     50C  TYR      3.8     8.3    -      -       -      +
     51C  GLY*     4.3     0.4    -      -       -      -
     77C  LEU*     3.3     5.5    -      -       -      -
     78C  THR*     2.9    44.0    +      -       -      +
     80C  ASP*     5.7     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 9 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8C  THR*     1.3    74.5    -      -       -      +
     10C  ASN*     1.3    71.6    +      -       -      +
     11C  LEU*     3.7    33.1    +      -       +      -
     50C  TYR*     2.8    59.1    +      -       +      +
     51C  GLY*     4.5     5.2    -      -       -      -
     52C  ASN*     6.3     0.4    -      -       -      +
     73C  PHE*     4.0    23.1    -      -       +      -
     76C  TYR*     3.6     5.6    -      -       +      +
     77C  LEU*     3.6    19.5    -      -       +      -
----------------------------------------------------------
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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