Contacts of the strand formed by residues 160 - 166 (chain D) in PDB entry 3J82


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 THR 160 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153D  MET*     5.7     2.5    -      -       +      -
    154D  ASP      3.3     7.6    -      -       -      +
    155D  SER*     2.7    34.9    +      -       -      +
    159D  VAL*     1.3    75.5    -      -       -      +
    161D  HIS*     1.3    74.7    +      -       -      +
    162D  THR*     5.3     4.7    -      -       +      -
    176D  LEU*     5.6     0.2    -      -       -      +
    177D  ARG*     3.6     0.7    -      -       -      -
    178D  LEU*     2.7    52.4    +      -       +      +
    180D  LEU*     2.9    16.6    +      -       -      +
    181D  ALA*     4.1     2.4    -      -       -      +
    261D  LEU*     5.9     0.7    -      -       -      +
    274D  ILE*     4.9    13.2    -      -       +      -
    277D  THR*     6.2     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 161 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109D  PRO*     4.2    24.3    -      -       +      +
    152D  VAL      4.7     0.2    -      -       -      -
    153D  MET*     3.6     1.2    -      -       -      -
    154D  ASP*     2.9    39.4    +      -       +      +
    159D  VAL*     3.7    27.0    -      -       +      +
    160D  THR*     1.3    76.2    -      -       -      +
    162D  THR*     1.3    68.6    +      -       -      +
    163D  VAL*     4.6     4.5    -      -       +      -
    175D  ILE*     3.7    29.8    -      -       +      +
    176D  LEU*     3.6    16.6    -      -       -      -
    177D  ARG*     2.8    40.6    -      -       +      +
    277D  THR*     5.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 162 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151D  ILE*     4.5    12.3    -      -       -      -
    152D  VAL      3.4     8.5    -      -       -      -
    153D  MET*     4.7     8.5    -      -       +      -
    160D  THR*     5.3     4.5    -      -       +      -
    161D  HIS*     1.3    78.9    -      -       -      +
    163D  VAL*     1.3    67.9    +      -       -      +
    164D  PRO*     3.8     0.7    -      -       -      +
    175D  ILE*     3.5    16.5    -      -       -      +
    176D  LEU*     3.7     7.3    +      -       -      +
    274D  ILE*     4.8     3.4    -      -       +      +
    277D  THR*     2.9    41.9    -      -       +      +
    278D  THR*     4.4     9.0    -      -       +      +
    281D  SER*     3.3    21.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 163 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142D  LEU*     5.9     1.1    -      -       +      -
    151D  ILE*     3.5     4.0    -      -       -      -
    152D  VAL*     3.0    44.4    +      -       +      -
    154D  ASP*     6.1     2.0    -      -       +      -
    161D  HIS*     4.6     7.0    -      -       +      -
    162D  THR*     1.3    71.8    -      -       -      +
    164D  PRO*     1.3    70.1    -      -       +      +
    165D  ILE*     3.6    17.6    +      -       +      +
    170D  ALA*     4.9     8.7    -      -       +      -
    171D  LEU      5.4     1.1    -      -       -      +
    175D  ILE*     3.0    46.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 164 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150D  GLY      3.6     5.6    -      -       -      +
    151D  ILE*     3.5     8.7    -      -       +      -
    162D  THR      3.8     0.9    -      -       -      +
    163D  VAL*     1.3    90.5    -      -       +      +
    165D  ILE*     1.3    68.2    +      -       -      +
    166D  TYR      4.2     0.2    -      -       -      -
    170D  ALA*     3.8     0.5    -      -       -      -
    171D  LEU*     3.7    19.5    +      -       +      +
    174D  ALA*     3.0    26.0    -      -       +      -
    175D  ILE      4.4     0.9    -      -       -      +
    281D  SER*     2.9    42.2    -      -       -      +
    285D  CYS*     4.1     9.4    -      -       -      -
    289D  ILE*     5.5     1.8    -      -       +      -
    293D  LEU*     3.5    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 165 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142D  LEU*     3.5    34.1    -      -       +      -
    147D  ARG      4.3     3.1    -      -       -      +
    148D  THR      2.7    28.3    -      -       -      +
    149D  THR*     2.8    25.2    -      -       -      -
    150D  GLY      2.6    22.1    +      -       -      +
    152D  VAL*     5.2     4.9    -      -       +      +
    163D  VAL*     3.6    22.0    -      -       +      +
    164D  PRO*     1.3    85.1    -      -       -      +
    166D  TYR*     1.3    59.3    +      -       -      +
    168D  GLY*     2.7    30.5    -      -       -      +
    169D  TYR      3.9     1.1    -      -       -      -
    170D  ALA*     3.6    24.2    -      -       +      -
    293D  LEU*     5.7     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 166 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148D  THR      3.7     0.4    -      -       -      -
    149D  THR*     3.5    11.9    -      -       +      -
    164D  PRO*     4.2     0.8    -      -       -      +
    165D  ILE*     1.3    74.6    -      -       -      +
    167D  GLU*     1.3   109.4    +      -       +      +
    169D  TYR*     3.1    23.9    +      -       +      +
    171D  LEU*     5.4     2.1    -      -       +      +
    289D  ILE*     3.9    47.5    -      -       +      +
    292D  ASP*     3.4    26.2    +      -       +      -
    293D  LEU*     5.6     2.2    -      -       +      -
----------------------------------------------------------
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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