Contacts of the strand formed by residues 130 - 139 (chain D) in PDB entry 4ZHF


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 ARG 130 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3D  SER*     5.6     3.4    +      -       -      -
      4D  THR      5.1     0.4    -      -       -      -
      5D  SER*     3.0    50.4    +      -       -      +
      7D  LEU*     3.6    28.4    -      -       +      +
    126D  VAL*     3.3     4.3    -      -       -      -
    127D  SER      2.9    31.2    +      -       -      +
    128D  GLN*     3.0    18.7    +      -       -      +
    129D  ASN*     1.3    80.4    -      -       -      +
    131D  GLU*     1.3    60.3    +      -       -      +
    132D  TYR*     2.8    37.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 131 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  LEU*     3.8    10.8    -      -       -      +
      8D  ILE      4.7     0.9    -      -       -      +
     10D  ALA*     3.7    28.8    +      -       +      +
     39D  ASN*     3.0    18.5    +      -       -      -
    124D  LYS*     3.1    36.7    +      -       +      +
    125D  LYS      3.6     3.8    -      -       -      +
    126D  VAL*     4.1    17.9    -      -       +      +
    129D  ASN      4.0     2.1    +      -       -      +
    130D  ARG*     1.3    72.2    -      -       -      +
    132D  TYR*     1.3    60.5    +      -       -      +
    133D  PHE*     5.0     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 132 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  LEU*     3.9    20.0    -      -       +      -
     39D  ASN*     3.4     7.0    -      -       -      +
     40D  ALA*     3.9    20.2    -      -       +      -
    124D  LYS*     3.4     5.6    -      -       -      +
    125D  LYS*     2.8    47.1    +      -       +      +
    127D  SER*     4.1    15.4    +      -       -      -
    130D  ARG*     2.8    53.5    +      -       +      -
    131D  GLU*     1.3    75.1    -      -       -      +
    133D  PHE*     1.3    61.9    +      -       -      +
    202D  4OL      3.8    54.3    -      +       +      +
----------------------------------------------------------
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Residues in contact with PHE 133 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8D  ILE*     3.7     2.9    -      -       +      -
      9D  PRO      3.4    20.9    -      -       -      -
     10D  ALA*     3.6    16.6    -      -       +      -
     11D  PRO*     3.8    17.7    -      -       +      -
     38D  GLY*     3.2     2.1    -      -       -      -
     39D  ASN*     3.0    60.9    +      -       +      +
    122D  PHE*     3.9    22.0    -      +       +      -
    123D  PHE      3.2    12.8    -      -       -      +
    124D  LYS*     4.4     3.1    -      -       +      -
    132D  TYR*     1.3    76.3    -      -       -      +
    134D  LYS*     1.3    63.3    +      -       -      +
    135D  ILE*     4.4     5.6    -      -       +      -
    159D  LEU*     3.8    24.7    -      -       +      -
    161D  LEU*     3.7    38.8    -      -       +      -
    202D  4OL      4.0     7.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 134 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36D  LEU*     4.0    17.7    -      -       +      +
     37D  ALA      3.0    15.7    -      -       -      +
     38D  GLY*     3.9     2.5    -      -       -      -
     41D  ILE*     5.1     1.3    -      -       +      -
     52D  TYR*     4.3     2.6    +      -       -      -
    122D  PHE*     3.6     4.6    -      -       -      -
    123D  PHE*     2.9    64.3    +      -       +      +
    133D  PHE*     1.3    76.4    -      -       -      +
    135D  ILE*     1.3    66.6    +      -       -      +
    136D  THR*     3.8     2.7    -      -       -      +
    202D  4OL      2.9    73.1    +      -       +      +
    203D  SO4      3.1    28.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 135 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36D  LEU*     3.6     2.8    -      -       -      +
     37D  ALA      2.7    34.2    +      -       -      +
    111D  VAL*     5.5     0.2    -      -       +      -
    120D  MET*     4.6     4.7    -      -       +      -
    121D  VAL      3.3    15.5    -      -       -      +
    122D  PHE*     4.2     7.2    -      -       +      -
    133D  PHE*     4.4     5.8    -      -       +      -
    134D  LYS*     1.3    80.8    -      -       -      +
    136D  THR*     1.3    67.5    +      -       -      +
    152D  PHE*     3.6    26.2    -      -       +      -
    155D  PHE*     4.0    22.2    -      -       +      -
    156D  SER*     4.0    12.3    -      -       -      +
    159D  LEU*     3.8    29.4    -      -       +      -
    161D  LEU*     3.6    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 136 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33D  VAL*     3.9    20.0    -      -       +      -
     35D  GLY      3.6     2.9    -      -       -      -
     36D  LEU*     3.9     5.8    -      -       -      +
    119D  ALA      3.7     0.3    -      -       -      +
    120D  MET*     3.2     8.1    -      -       -      +
    121D  VAL*     2.9    31.3    +      -       -      +
    123D  PHE*     3.6    21.2    -      -       -      -
    134D  LYS*     3.8     7.6    -      -       -      -
    135D  ILE*     1.3    75.6    -      -       -      +
    137D  LEU*     1.3    61.7    +      -       -      +
    138D  TYR*     3.0    40.3    +      -       +      -
    152D  PHE*     4.1     2.7    -      -       -      -
    203D  SO4      3.5    17.1    +      -       -      +
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Residues in contact with LEU 137 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32D  TYR      3.6     0.3    -      -       -      +
     33D  VAL*     3.7     2.1    -      -       -      -
     34D  VAL*     2.8    39.7    +      -       +      -
     35D  GLY*     2.8    22.5    +      -       -      +
    118D  HIS*     5.1     3.6    -      -       +      -
    119D  ALA      3.5    16.2    -      -       -      +
    120D  MET*     3.9    16.6    -      -       +      -
    136D  THR*     1.3    72.9    -      -       -      +
    138D  TYR*     1.3    56.6    +      -       -      +
    144D  LEU*     3.8    29.2    -      -       +      -
    148D  LEU*     4.5     7.4    -      -       +      +
    149D  LYS*     4.1    23.3    -      -       +      +
    152D  PHE*     3.8    38.3    -      -       +      -
    168D  PHE*     4.7     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 138 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27D  PHE*     4.1     4.0    -      +       -      -
     31D  TRP*     3.4    35.7    -      +       +      -
     32D  TYR      3.3    10.3    -      -       -      -
     33D  VAL*     3.9    10.8    -      -       +      -
     54D  THR*     4.2     3.8    -      -       -      +
     56D  TYR*     2.7    39.6    +      +       -      -
    118D  HIS*     3.2     9.2    -      -       -      +
    119D  ALA*     2.7    43.9    +      -       +      +
    121D  VAL*     3.5    30.1    -      -       +      -
    123D  PHE*     3.9     2.9    -      -       -      -
    136D  THR*     3.0    31.2    -      -       +      -
    137D  LEU*     1.3    73.9    -      -       -      +
    139D  GLY*     1.3    58.5    +      -       -      +
    144D  LEU*     3.9     6.2    -      -       -      +
    203D  SO4      2.2    30.0    +      -       -      -
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Residues in contact with GLY 139 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31D  TRP*     3.6     6.0    -      -       -      -
     32D  TYR*     2.7    38.7    +      -       -      +
     34D  VAL*     4.0     8.1    -      -       -      +
    117D  GLN      3.3     7.0    -      -       -      -
    138D  TYR*     1.3    73.1    -      -       -      +
    140D  ARG*     1.3    64.5    +      -       -      -
    141D  THR      3.1    16.4    +      -       -      +
    144D  LEU*     4.3     9.6    -      -       -      -
----------------------------------------------------------
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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