Contacts of the strand formed by residues 154 - 159 (chain D) in PDB entry 2J3T


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 LYS 154 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  TYR      3.4     1.7    -      -       -      +
      8D  VAL*     3.3     6.2    -      -       -      +
      9D  VAL*     2.9    52.5    +      -       +      +
     10D  ASN      5.3     3.0    +      -       -      +
     11D  LYS*     6.2     0.4    -      -       -      +
    115D  PHE*     3.8    19.3    -      -       +      -
    116D  HIS*     4.1    27.8    +      -       -      +
    119D  PHE*     3.4    39.1    -      -       +      +
    146D  CYS*     3.3    30.1    -      -       -      -
    147D  TYR      3.5     2.0    -      -       -      -
    148D  GLN*     3.6    24.5    -      -       +      +
    152D  GLY      4.5     4.4    +      -       -      +
    153D  ILE*     1.3    76.3    -      -       -      +
    155D  PHE*     1.3    64.3    +      -       -      +
    156D  VAL*     3.8     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 155 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6D  VAL*     5.9     1.1    -      -       +      -
      7D  TYR      3.6     2.7    -      -       -      -
      8D  VAL*     3.9    16.4    -      -       +      -
    146D  CYS*     3.5     1.2    -      -       -      -
    147D  TYR*     3.1    48.7    +      +       +      +
    149D  THR*     3.5    23.3    -      -       -      -
    153D  ILE*     4.0    14.8    -      -       +      -
    154D  LYS*     1.3    73.4    -      -       -      +
    156D  VAL*     1.3    60.5    +      -       -      +
    157D  VAL*     5.0     0.4    -      -       -      -
    170D  LEU*     3.5    24.5    -      -       +      +
    173D  ILE*     3.7    27.4    -      -       +      -
    174D  TYR*     3.6    28.0    -      +       +      -
    177D  TYR*     3.7    47.6    -      +       +      -
    198D  PHE*     5.7     0.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 156 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48C  PHE*     6.1     0.2    -      -       +      -
      5D  SER      4.0     0.3    -      -       -      +
      6D  VAL*     3.3     5.8    -      -       -      +
      7D  TYR*     2.6    58.3    +      -       +      +
      9D  VAL*     4.5     8.1    -      -       +      -
    115D  PHE*     3.8    30.5    -      -       +      -
    144D  LEU*     3.6    38.6    -      -       +      -
    145D  HIS      3.4     2.5    -      -       -      -
    146D  CYS*     4.1     8.5    -      -       -      -
    154D  LYS*     4.4     8.1    -      -       +      -
    155D  PHE*     1.3    74.8    -      -       -      +
    157D  VAL*     1.3    66.0    +      -       -      +
    158D  LEU*     4.5     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 157 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3D  ILE*     4.0    15.0    -      -       +      -
      5D  SER      3.5     7.9    -      -       -      +
      6D  VAL*     4.2     6.3    -      -       +      -
    143D  LYS      3.6     1.2    -      -       -      +
    144D  LEU*     3.5     0.7    -      -       -      -
    145D  HIS*     2.8    46.9    +      -       +      +
    155D  PHE      4.9     0.4    -      -       -      +
    156D  VAL*     1.3    78.5    -      -       -      +
    158D  LEU*     1.3    69.1    +      -       -      +
    159D  ALA*     4.8     0.2    -      -       +      -
    166D  ILE*     4.4    14.1    -      -       +      -
    169D  LEU*     3.6    32.1    -      -       +      -
    170D  LEU*     3.5    24.9    -      -       +      -
    173D  ILE*     4.1    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 158 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52C  MET*     3.3    44.0    -      -       +      +
     54C  PRO*     5.8     0.4    -      -       +      -
      3D  ILE*     3.7     3.3    -      -       -      +
      4D  PHE*     2.8    31.6    +      -       +      -
      5D  SER*     2.9    36.5    +      -       -      +
      7D  TYR*     4.5     5.8    -      -       +      -
    142D  PHE*     3.8    17.5    -      -       +      -
    143D  LYS      3.4     1.8    -      -       -      +
    144D  LEU*     3.3    48.2    -      -       +      -
    156D  VAL*     4.5     6.3    -      -       +      -
    157D  VAL*     1.3    72.6    -      -       -      +
    159D  ALA*     1.3    62.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 159 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2D  ALA      3.2    16.2    -      -       -      +
      3D  ILE*     4.0     6.3    -      -       +      -
      4D  PHE*     3.5    11.8    -      -       -      +
    142D  PHE*     3.3     4.4    -      -       -      +
    143D  LYS*     2.7    41.0    +      -       -      +
    145D  HIS*     4.9     5.2    -      -       +      +
    157D  VAL*     4.8     1.1    -      -       +      -
    158D  LEU*     1.3    76.9    -      -       -      +
    160D  ASP*     1.3    65.1    +      -       -      +
    163D  GLN*     3.9    17.7    -      -       +      -
    166D  ILE*     4.3    14.1    -      -       +      -
----------------------------------------------------------
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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