Contacts of the strand formed by residues 129 - 136 (chain D) in PDB entry 4JDA


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 129 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36D  ILE*     4.8     6.5    -      -       +      -
     40D  HIS*     3.9    38.1    -      -       +      +
     66D  TRP*     3.4     6.5    -      -       -      -
    122D  VAL*     3.7    19.7    -      -       +      +
    124D  ASP*     2.9    35.7    +      -       +      -
    127D  LYS*     3.7    27.1    -      -       +      +
    128D  ARG*     1.3    76.6    -      -       -      +
    130D  LEU*     1.3    67.4    +      -       -      +
    147D  VAL*     4.2    14.1    -      -       +      -
    148D  THR      3.3     9.2    -      -       -      +
    149D  SER*     3.3    26.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 130 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66D  TRP*     3.8     5.2    -      -       +      -
     69D  VAL*     3.2    43.1    -      -       +      +
     70D  ARG*     3.8    17.3    -      -       -      +
     72D  PHE*     4.6    14.4    -      -       +      -
    103D  ARG*     5.9     0.7    -      -       -      +
    120D  LEU*     4.0    12.3    -      -       +      -
    122D  VAL      3.2     9.2    -      -       -      +
    123D  LEU*     4.0    13.5    -      -       +      -
    129D  ILE*     1.3    75.6    -      -       -      +
    131D  SER*     1.3    84.7    +      -       -      +
    132D  PHE*     4.3    17.5    -      -       +      -
    147D  VAL*     3.4     1.4    -      -       -      -
    148D  THR*     2.9    35.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 131 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120D  LEU*     3.6     2.4    -      -       -      +
    121D  GLU*     2.7    38.3    +      -       -      +
    122D  VAL*     2.9    36.6    +      -       -      +
    130D  LEU*     1.3    81.8    -      -       -      +
    132D  PHE*     1.3    54.0    +      -       -      +
    145D  ARG*     5.0     7.3    -      -       -      -
    146D  SER      2.8    20.4    +      -       -      -
    147D  VAL*     3.4    17.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 132 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72D  PHE*     4.0    17.3    -      +       +      -
     79D  LYS*     3.8    11.2    -      -       -      -
    103D  ARG*     3.8    22.9    -      -       -      -
    118D  GLU*     3.5    26.5    -      -       +      -
    119D  ILE      3.2    14.1    -      -       -      +
    120D  LEU*     4.3     0.2    -      -       -      -
    121D  GLU*     4.2     2.2    -      -       -      +
    130D  LEU*     4.3    13.9    -      -       +      -
    131D  SER*     1.3    74.6    -      -       -      +
    133D  ARG*     1.3    63.6    +      -       -      +
    134D  VAL*     4.2    17.5    -      -       +      -
    144D  TYR*     4.0    20.0    -      +       -      -
    145D  ARG*     3.5     4.2    -      -       -      +
    146D  SER*     3.0    43.8    +      -       -      +
    170D  GLU*     5.2     1.1    -      -       -      -
    301D  A9S      3.8    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 133 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118D  GLU*     3.3     2.6    -      -       -      -
    119D  ILE*     2.9    34.8    +      -       +      +
    121D  GLU*     3.3    35.8    +      -       -      +
    132D  PHE*     1.3    78.3    -      -       -      +
    134D  VAL*     1.3    71.4    +      -       -      +
    135D  LEU*     3.8    20.9    -      -       -      -
    143D  ASN*     4.4    21.8    +      -       -      +
    144D  TYR      3.6     6.3    -      -       -      +
    145D  ARG*     3.9    28.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 134 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116D  SER*     3.7    17.3    -      -       -      +
    117D  VAL      3.8     4.7    -      -       -      +
    118D  GLU*     5.0     2.0    -      -       +      -
    132D  PHE*     4.2    17.3    -      -       +      -
    133D  ARG*     1.3    83.7    +      -       -      +
    135D  LEU*     1.3    62.4    +      -       -      +
    136D  GLY*     3.5    24.7    -      -       -      +
    139D  HIS*     3.9    18.6    -      -       +      +
    141D  LEU      4.2     4.9    -      -       -      +
    142D  ASN*     5.4     0.9    -      -       -      -
    143D  ASN*     4.1    20.9    +      -       -      +
    144D  TYR*     2.8    40.0    +      -       +      +
    301D  A9S      4.8     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 135 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102D  ILE*     4.9     4.9    -      -       +      -
    117D  VAL*     2.9    28.0    +      -       +      +
    118D  GLU      4.8     0.2    -      -       -      -
    119D  ILE*     3.4    43.5    -      -       +      +
    133D  ARG*     3.7    28.5    +      -       -      -
    134D  VAL*     1.3    74.1    -      -       -      +
    136D  GLY*     1.3    57.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 136 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117D  VAL*     3.1    27.2    +      -       -      +
    134D  VAL*     3.5     7.7    -      -       -      +
    135D  LEU*     1.3    79.6    -      -       -      +
    137D  GLY*     1.3    60.8    +      -       -      -
    139D  HIS*     3.5    16.4    -      -       -      -
----------------------------------------------------------
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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