Contacts of the strand formed by residues 127 - 131 (chain B) in PDB entry 1J3R


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 127 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  GLY*     4.6     8.3    -      -       -      -
      9A  VAL      3.7     7.2    -      -       -      +
     10A  LYS*     2.7    26.1    +      -       -      +
    100B  TYR      3.8     0.9    -      -       -      +
    101B  PHE*     3.5     2.3    -      -       -      -
    102B  ALA*     2.9    30.3    +      -       -      +
    122B  GLU      3.8    20.0    +      -       -      +
    123B  MET*     3.9     4.1    -      -       +      -
    124B  GLU*     2.8    30.2    +      -       -      +
    126B  GLY*     1.3    75.5    -      -       -      +
    128B  ILE*     1.3    65.6    +      -       -      +
    129B  VAL*     3.9    20.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 128 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  PHE      3.7     1.0    -      -       -      +
      8A  GLY*     3.2     2.9    -      -       -      -
      9A  VAL*     2.8    46.0    +      -       +      +
     11A  LEU*     3.9    29.2    -      -       +      -
     18A  ILE*     4.1     7.9    -      -       +      -
     69A  PHE*     3.7    45.3    -      -       +      -
    150A  LEU*     4.3     9.6    -      -       +      -
     99B  VAL*     3.9    17.3    -      -       +      -
    100B  TYR      3.3     9.0    -      -       -      +
    101B  PHE*     3.5    25.4    -      -       +      -
    126B  GLY      4.1     2.9    -      -       -      +
    127B  THR*     1.3    71.6    -      -       -      +
    129B  VAL*     1.3    64.7    +      -       -      +
    130B  TYR      4.1     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 129 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  PHE      3.4     7.6    -      -       -      +
      8A  GLY*     4.6     0.2    -      -       -      -
     99B  VAL*     3.4     5.9    -      -       -      +
    100B  TYR*     2.8    44.5    +      -       +      +
    109B  MET*     4.0    24.2    -      -       +      -
    111B  LEU*     5.2     0.9    -      -       +      -
    121B  ILE*     4.1    27.4    -      -       +      -
    123B  MET*     3.7    36.3    -      -       +      -
    127B  THR*     3.9    11.2    -      -       +      +
    128B  ILE*     1.3    78.8    -      -       -      +
    130B  TYR*     1.3    71.8    +      -       -      +
    131B  VAL*     3.7     2.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 130 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  LYS*     2.9    25.1    +      -       +      -
      5A  GLU      4.3     2.5    -      -       -      -
      6A  PRO*     3.3    15.1    -      -       -      +
      7A  PHE*     2.8    57.1    +      +       +      +
     60A  GLN*     3.7    23.8    -      -       -      -
     66A  ASP*     2.7    30.0    +      -       -      -
     67A  LEU      3.9    10.8    -      -       -      -
     69A  PHE*     4.6     9.4    -      +       +      -
     97B  ALA*     4.3     3.6    -      -       +      -
     98B  GLU      4.0     1.3    -      -       -      -
     99B  VAL*     4.4    16.6    -      -       +      -
    128B  ILE      4.1     1.4    +      -       -      -
    129B  VAL*     1.3    73.0    -      -       -      +
    131B  VAL*     1.3    65.5    +      -       -      +
    132B  PRO*     3.3    38.5    -      -       +      +
    133B  PRO*     3.5     5.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 131 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  HIS*     5.5     2.0    -      -       -      +
     96B  ARG      5.7     0.2    -      -       -      +
     97B  ALA*     3.2     4.8    -      -       -      +
     98B  GLU*     2.8    50.1    +      -       +      +
    100B  TYR*     4.3     9.9    -      -       +      -
    109B  MET*     3.4    37.2    -      -       +      -
    111B  LEU*     3.8    14.1    -      -       +      -
    129B  VAL*     3.7     3.8    +      -       +      +
    130B  TYR*     1.3    75.1    -      -       -      +
    132B  PRO*     1.3    74.1    -      -       +      +
    135B  TRP      3.9    11.2    -      -       -      +
    137B  HIS*     3.9    23.8    -      -       +      +
----------------------------------------------------------
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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