Contacts of the strand formed by residues 137 - 145 (chain B) in PDB entry 1JJ2


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 LEU 137 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86B  ALA*     4.1    12.6    -      -       +      -
     87B  TYR      3.3    18.6    -      -       -      +
     88B  GLU*     4.5     0.7    -      -       -      +
     89B  ASP*     3.8     7.1    -      -       -      +
     97B  LEU*     5.0     1.8    -      -       +      -
    128B  ILE*     4.2    17.5    -      -       +      +
    131B  ALA*     3.9     9.1    +      -       +      -
    132B  HIS*     3.6    44.9    -      -       +      +
    135B  GLY      3.5     2.7    -      -       -      +
    136B  ASP*     1.3    77.5    -      -       -      +
    138B  GLY*     1.3    69.1    +      -       -      +
    140B  LEU*     3.8    29.6    -      -       +      -
    171B  VAL*     5.1    14.3    -      -       +      +
    175B  LEU*     4.3     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 138 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  TYR      2.5    25.5    +      -       -      +
     88B  GLU      4.6     0.2    -      -       -      -
     89B  ASP*     3.7    22.7    -      -       -      -
     94B  GLN*     4.0     5.4    -      -       -      -
    136B  ASP      3.3     3.4    +      -       -      -
    137B  LEU*     1.3    86.0    -      -       -      +
    139B  ASP*     1.3    73.9    +      -       -      +
    140B  LEU*     4.3     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 139 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  TRP*     5.0     0.3    -      -       -      -
     87B  TYR*     3.5    26.9    +      -       -      +
     94B  GLN*     3.2    31.2    +      -       -      +
    138B  GLY*     1.3    84.4    -      -       -      +
    140B  LEU*     1.3    60.8    +      -       -      +
    141B  ARG*     2.8    29.9    +      -       -      +
    165B  ARG*     3.2    44.1    +      -       -      +
    174B  ARG*     5.0     7.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 140 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  LEU*     4.2    17.0    -      -       +      -
     85B  ARG      4.0     2.5    -      -       -      +
     86B  ALA*     4.1    16.2    -      -       +      -
    128B  ILE*     4.8     4.7    -      -       +      -
    137B  LEU*     3.8    33.2    -      -       +      -
    138B  GLY      4.3     0.7    -      -       -      +
    139B  ASP*     1.3    84.9    -      -       -      +
    141B  ARG*     1.3    56.6    +      -       -      +
    165B  ARG*     3.9     0.7    -      -       -      +
    166B  VAL*     2.6    48.7    +      -       +      +
    171B  VAL*     4.0     8.7    -      -       +      +
    174B  ARG*     4.2    15.0    -      -       +      +
    175B  LEU*     3.5    43.3    -      -       +      +
    178B  ALA*     5.4     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 141 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   26720    C      3.2    13.1    +      -       -      -
   26730    U      3.0    36.4    +      -       -      -
   26740    G      5.6     0.8    +      -       -      -
     29B  TRP*     4.2    22.0    -      -       -      +
     84B  LEU*     3.3     5.4    -      -       -      +
     85B  ARG      2.7    39.5    +      -       -      +
     87B  TYR*     3.6    16.4    -      -       +      -
     94B  GLN*     3.6    21.6    +      -       -      -
    139B  ASP*     2.8    20.5    +      -       -      +
    140B  LEU*     1.3    78.0    -      -       -      +
    142B  LEU*     1.3    60.3    +      -       -      +
    163B  GLU*     2.9    36.3    +      -       +      +
    164B  THR      3.4    10.5    -      -       -      +
    165B  ARG*     3.4    20.9    -      -       -      +
    166B  VAL*     4.0     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 142 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  VAL*     3.6    31.4    -      -       +      -
     81B  ALA*     3.6    26.7    -      -       +      -
     83B  ALA      3.2    13.0    -      -       -      +
     84B  LEU*     3.8    22.2    -      -       +      -
    141B  ARG*     1.3    72.7    -      -       -      +
    143B  ILE*     1.3    64.1    +      -       -      +
    144B  THR*     3.3     7.7    +      -       -      +
    163B  GLU*     3.4     3.2    -      -       -      -
    164B  THR*     2.8    37.1    +      -       -      +
    166B  VAL*     3.5    13.0    -      -       +      -
    178B  ALA*     4.0    11.4    -      -       +      +
    181B  ILE*     4.5    13.7    -      -       +      -
    182B  VAL*     3.7    19.1    -      -       +      -
    188B  HIS*     6.1     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 143 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   26700    G      5.7     0.4    -      -       -      +
   26710    U      3.3    29.4    -      -       +      +
     81B  ALA*     3.4     3.5    -      -       -      -
     82B  VAL*     2.9    29.6    +      -       +      +
     83B  ALA*     2.8    33.3    +      -       +      +
     85B  ARG*     4.1    20.4    -      -       +      +
     99B  GLU*     4.6    10.3    -      -       -      +
    101B  TRP*     4.4    19.5    -      -       +      -
    113B  LEU*     6.0     0.9    -      -       +      -
    142B  LEU*     1.3    69.6    -      -       -      +
    144B  THR*     1.3    60.8    +      -       -      +
    161B  VAL*     3.9    24.2    -      -       +      -
    162B  MET      4.0     2.2    -      -       -      +
    163B  GLU*     3.6    20.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 144 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  VAL*     5.4     1.9    -      -       -      +
     79B  MET*     3.4    39.9    -      -       +      +
     80B  ARG      3.6     8.7    -      -       -      +
     81B  ALA*     4.1     8.0    -      -       -      +
     82B  VAL*     5.9     0.4    -      -       -      -
    142B  LEU*     3.4    15.1    +      -       -      +
    143B  ILE*     1.3    76.3    +      -       -      +
    145B  HIS*     1.3    71.1    +      -       -      +
    161B  VAL*     3.3     7.0    -      -       -      +
    162B  MET*     2.7    52.0    +      -       -      -
    164B  THR*     4.2    12.8    +      -       -      -
    188B  HIS*     4.0     7.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 145 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79B  MET*     3.4     5.4    -      -       -      +
     80B  ARG*     3.1    42.1    +      -       +      -
     82B  VAL*     3.4    33.1    -      -       +      +
    106B  HIS*     3.9    27.1    -      -       +      +
    109B  LEU*     4.0    19.5    -      -       +      +
    144B  THR*     1.3    79.1    -      -       -      +
    146B  THR*     1.3    91.2    +      -       -      +
    147B  VAL*     4.3     7.5    -      -       -      +
    159B  PRO*     3.4    15.7    -      -       +      +
    160B  ASP      3.1    14.6    -      -       -      +
    161B  VAL*     3.9    17.7    -      -       +      -
    162B  MET*     5.4     0.4    -      -       -      -
----------------------------------------------------------
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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