Contacts of the strand formed by residues 127 - 133 (chain D) 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 PHE 127 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90D  ILE*     3.9    24.9    -      -       +      -
    116D  LEU*     4.1    41.7    -      -       +      -
    119D  LEU*     3.9    12.1    -      -       +      -
    120D  GLN*     4.3    10.3    -      -       +      -
    123D  TYR      3.2    25.1    -      -       -      -
    124D  LYS*     3.8    14.2    -      -       +      +
    125D  GLU      3.4     0.8    -      -       -      -
    126D  GLN*     1.3    79.8    -      -       -      +
    128D  ILE*     1.3    64.8    +      -       -      +
    129D  THR*     4.3    13.7    -      -       +      -
    153D  GLN*     5.3     0.5    -      -       -      +
    157D  ILE*     3.8     8.2    -      -       -      +
    210D  ILE*     4.4     0.9    -      -       -      -
    211D  THR*     3.2    25.6    -      -       +      +
    213D  VAL*     3.7    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 128 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    410A  LEU*     4.9     1.8    -      -       +      -
    127D  PHE*     1.3    74.1    -      -       -      +
    129D  THR*     1.3    60.7    +      -       -      +
    130D  ILE*     4.5     4.5    -      -       +      -
    150D  LEU*     3.7    30.1    -      -       +      +
    153D  GLN*     3.7    39.7    -      -       +      +
    154D  LEU*     4.1    23.6    -      -       +      -
    157D  ILE*     3.7    23.6    -      -       +      -
    210D  ILE*     4.0     7.1    -      -       +      +
    211D  THR      3.3     2.9    +      -       -      +
    212D  VAL*     3.8    28.5    -      -       +      -
    213D  VAL*     3.2    27.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 129 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116D  LEU*     4.0    15.8    -      -       +      +
    127D  PHE*     4.3    13.0    -      -       +      -
    128D  ILE*     1.3    77.2    -      -       -      +
    130D  ILE*     1.3    69.1    +      -       -      +
    131D  ARG*     4.3    14.2    +      -       -      +
    149D  GLN*     4.5     2.8    -      -       -      +
    153D  GLN*     3.4    36.3    +      -       -      +
    213D  VAL*     3.5    18.8    +      -       -      +
    215D  ILE*     4.2     6.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 130 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128D  ILE*     4.5     6.5    -      -       +      -
    129D  THR*     1.3    82.4    +      -       -      +
    131D  ARG*     1.3    64.6    +      -       -      +
    132D  LEU*     4.7     3.1    -      -       +      -
    146D  ILE*     4.3    18.8    -      -       +      +
    149D  GLN*     3.3    46.0    -      -       +      +
    150D  LEU*     3.7    17.5    -      -       +      +
    153D  GLN*     4.7     0.2    -      -       +      -
    212D  VAL*     3.9    24.2    -      -       +      -
    213D  VAL      2.8     9.9    +      -       -      +
    214D  PHE*     3.7    32.3    -      -       +      -
    215D  ILE*     2.9    24.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 131 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109D  THR*     5.1     6.5    -      -       -      +
    113D  ASP*     3.0    30.7    +      -       -      -
    116D  LEU*     3.9    23.8    -      -       -      +
    129D  THR*     4.2    14.3    +      -       -      +
    130D  ILE*     1.3    75.9    -      -       -      +
    132D  LEU*     1.3    66.1    +      -       -      +
    149D  GLN*     3.0    34.3    +      -       -      +
    215D  ILE*     3.4    32.8    -      -       +      +
    217D  ASP*     5.9     3.8    -      -       -      +
    154E  GLU*     3.5    22.2    +      -       -      +
    155E  LEU*     3.6    18.1    -      -       +      +
    158E  LYS*     3.1    25.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 132 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130D  ILE*     4.7     5.4    -      -       +      -
    131D  ARG*     1.3    82.7    -      -       -      +
    133D  ASN*     1.3    64.7    +      -       -      +
    137D  HIS*     3.5    32.8    -      -       +      +
    142D  ALA*     3.7    22.0    -      -       +      +
    145D  GLY*     4.1    22.2    -      -       -      +
    146D  ILE*     3.7    26.5    -      -       +      +
    149D  GLN*     4.8     1.1    -      -       -      +
    215D  ILE      2.8    16.6    +      -       -      +
    216D  PHE*     3.5    37.6    -      -       +      -
    217D  ASP*     3.4    16.3    +      -       -      +
    222D  PHE*     4.4     5.8    -      -       +      -
    230D  LEU*     4.5     1.1    -      -       +      -
    155E  LEU*     4.8     2.2    -      -       -      +
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Residues in contact with ASN 133 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132D  LEU*     1.3    80.2    -      -       -      +
    134D  GLY*     1.3    61.8    +      -       -      +
    135D  PHE*     3.1    22.5    +      -       -      +
    136D  ILE*     3.4     6.1    +      -       +      +
    137D  HIS*     3.1    38.5    +      -       +      +
    217D  ASP*     3.0    36.8    +      -       +      +
    218D  GLU*     4.2     0.2    -      -       -      +
    222D  PHE*     4.4     2.2    -      -       -      -
    151E  LYS*     3.3    34.6    -      -       -      +
    154E  GLU*     4.6     0.8    +      -       -      -
    155E  LEU*     3.5    26.6    -      -       +      +
----------------------------------------------------------
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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