Contacts of the strand formed by residues 162 - 170 (chain E) in PDB entry 5ZR1


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 ILE 162 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85E  LEU*     3.7    36.8    -      -       +      -
     89E  TYR*     5.2     1.3    -      -       +      -
    116E  PHE*     3.7    44.7    +      -       +      +
    119E  TYR*     3.7    30.7    -      -       +      -
    122E  LEU*     4.2    15.5    -      -       +      -
    126E  THR*     3.3    10.8    -      -       +      +
    128E  LEU*     4.4    22.0    -      -       +      +
    160E  SER*     3.3    15.0    +      -       -      +
    161E  LYS*     1.3    81.2    -      -       +      +
    163E  ASN*     1.3    65.8    +      -       -      +
    164E  ILE*     3.9     0.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 163 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26E  PRO*     3.4    29.6    -      -       +      +
    125E  LYS*     3.4    29.5    -      -       -      +
    126E  THR      3.0    12.3    +      -       -      +
    127E  CYS*     3.3     8.5    -      -       -      +
    128E  LEU      3.3    18.2    +      -       -      -
    157E  PRO      4.4     4.9    -      -       -      +
    158E  LYS      4.2    10.8    +      -       -      +
    160E  SER*     3.7    15.0    +      -       -      +
    161E  LYS      4.9     0.2    +      -       -      -
    162E  ILE*     1.3    77.0    -      -       -      +
    164E  ILE*     1.3    66.2    +      -       -      +
    165E  LYS*     3.6    11.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 164 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31E  SER*     5.0     4.7    -      -       -      +
     77E  ILE*     4.9     0.7    -      -       +      -
     81E  VAL*     4.2    18.4    -      -       +      -
    112E  LEU*     4.5    15.7    -      -       +      -
    116E  PHE*     4.3    13.8    -      -       +      -
    128E  LEU*     3.5    17.5    -      -       +      +
    130E  LEU*     3.7    37.5    -      -       +      -
    152E  LEU*     6.1     0.4    -      -       +      -
    153E  ASN*     5.5     8.5    -      -       -      +
    156E  LEU*     3.7    28.2    -      -       +      +
    162E  ILE*     3.9     4.2    +      -       -      +
    163E  ASN*     1.3    74.2    -      -       -      +
    165E  LYS*     1.3    69.4    +      -       -      +
    166E  PHE*     4.1    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 165 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26E  PRO*     3.6    17.8    +      -       -      +
     29E  THR*     3.3    29.2    +      -       +      -
     30E  PRO      3.6    17.7    -      -       -      +
     31E  SER*     3.9    18.6    -      -       -      +
    127E  CYS*     3.9    22.0    -      -       +      -
    128E  LEU      2.9     7.3    +      -       -      +
    129E  PHE*     3.4    29.2    -      -       +      +
    130E  LEU*     2.6    35.1    +      -       -      +
    163E  ASN*     3.6    21.8    -      -       -      +
    164E  ILE*     1.3    80.1    -      -       -      +
    166E  PHE*     1.3    59.9    +      -       -      +
    167E  ILE*     3.9     0.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 166 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30E  PRO      5.2     0.9    -      -       -      +
     31E  SER*     3.3    15.4    +      -       -      +
     32E  ASN*     3.5     9.1    +      -       -      +
     33E  LEU*     3.2    22.2    +      -       -      +
     77E  ILE*     4.9     2.0    -      -       +      -
    112E  LEU*     5.9     1.8    -      -       +      -
    130E  LEU*     3.5    37.9    -      -       +      -
    132E  LEU*     4.3    10.5    -      -       +      -
    149E  TYR*     4.1    26.7    -      +       -      -
    152E  LEU*     3.6    32.3    -      -       +      -
    153E  ASN*     5.1     7.0    -      -       +      -
    164E  ILE*     4.1    28.0    -      -       +      -
    165E  LYS*     1.3    76.0    -      -       -      +
    167E  ILE*     1.3    64.2    +      -       -      +
    168E  TYR*     3.3    36.1    -      +       +      +
----------------------------------------------------------
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Residues in contact with ILE 167 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22E  ILE*     3.8    26.0    -      -       +      -
     33E  LEU*     3.4    21.8    -      -       +      +
     35E  LEU*     4.4    20.6    -      -       +      -
     47E  LEU*     4.6    12.3    -      -       +      -
     51E  PHE*     4.1     9.6    -      -       +      -
    129E  PHE*     3.6    39.7    -      -       +      -
    130E  LEU      3.1     6.7    +      -       -      -
    131E  ILE*     3.5    16.2    -      -       +      +
    132E  LEU*     2.9    27.0    +      -       -      +
    166E  PHE*     1.3    76.8    -      -       -      +
    168E  TYR*     1.3    69.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 168 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32E  ASN*     3.1    28.8    +      -       +      -
     33E  LEU      2.7    25.2    +      -       -      +
     34E  ILE*     4.1     3.8    -      -       +      -
     35E  LEU*     2.7    33.9    +      -       -      +
    132E  LEU*     3.6    37.7    -      -       +      +
    135E  PHE*     4.4     8.1    -      +       +      -
    146E  PHE*     3.5    36.6    -      +       -      -
    149E  TYR*     3.1    38.8    +      -       +      +
    150E  ILE*     4.0     0.4    +      -       +      -
    166E  PHE*     3.3    18.7    -      -       +      +
    167E  ILE*     1.3    74.7    -      -       -      +
    169E  THR*     1.3    59.9    +      -       -      +
    170E  MET*     3.9    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 169 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35E  LEU*     3.5     8.5    -      -       -      +
     43E  LYS*     3.6    34.0    +      -       +      -
     44E  THR*     4.7     3.8    -      -       +      -
     47E  LEU*     3.7    17.3    -      -       -      +
    131E  ILE*     5.1     0.5    -      -       -      +
    132E  LEU      3.1     5.3    +      -       -      -
    133E  ASP*     3.5    24.8    +      -       -      +
    134E  GLY*     3.1    21.6    +      -       -      +
    135E  PHE*     2.8    28.1    +      -       -      +
    167E  ILE      5.1     0.7    +      -       -      -
    168E  TYR*     1.3    76.9    +      -       -      +
    170E  MET*     1.3    64.0    +      -       -      +
   2001E  AGS      5.8     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 170 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34E  ILE*     3.7    19.3    -      -       +      -
     35E  LEU      3.3     4.3    +      -       -      +
     36E  GLN*     3.3    13.5    -      -       +      +
     37E  GLY      3.1    25.9    +      -       -      +
     43E  LYS*     3.8     2.6    -      -       -      -
    134E  GLY*     5.2     1.3    -      -       -      -
    135E  PHE*     4.6     6.7    -      -       +      -
    136E  ASP*     3.7    18.2    -      -       +      +
    146E  PHE*     3.8    26.9    -      -       +      -
    168E  TYR*     3.9    18.2    -      -       +      -
    169E  THR*     1.3    73.4    -      -       -      +
    171E  LEU*     1.3    65.0    +      -       -      +
    172E  GLU      5.6     0.4    -      -       -      +
    173E  THR      6.3     0.2    -      -       -      +
    175E  PHE*     3.6    35.4    -      -       +      -
    176E  LEU*     3.8    27.4    -      -       +      -
    179E  TYR*     6.1     0.2    -      -       -      -
----------------------------------------------------------
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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