Contacts of the strand formed by residues 93 - 101 (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 GLY 93 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   26740    G      3.7    13.2    -      -       -      -
   26750    A      6.0     1.3    -      -       -      -
     89B  ASP*     4.9     1.1    -      -       -      -
     90B  THR*     2.9    39.2    +      -       -      +
     91B  PRO      3.5     1.4    -      -       -      -
     92B  TYR*     1.3    78.0    -      -       -      +
     94B  GLN*     1.3    65.2    +      -       -      -
    144I  THR*     3.7     7.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   26730    U      2.6    44.3    +      -       -      +
   26740    G      3.1    16.0    +      -       -      +
     87B  TYR*     4.1    13.8    -      -       +      -
     88B  GLU      3.6     7.6    -      -       -      +
     89B  ASP*     3.6    22.2    +      -       -      +
     93B  GLY*     1.3    75.0    -      -       -      -
     95B  ARG*     1.3    61.6    +      -       -      +
    138B  GLY*     4.0     1.0    -      -       -      -
    139B  ASP*     3.2    39.9    +      -       -      +
    141B  ARG*     3.6    16.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   26730    U      4.3     5.8    +      -       -      +
   28110    A      5.8     3.0    -      -       -      +
   28170    G      3.6    25.8    +      -       -      +
   28180    A      3.9    28.7    -      -       -      +
     87B  TYR*     3.3     3.9    -      -       -      -
     88B  GLU*     2.9    38.5    +      -       +      +
     90B  THR*     4.3    15.6    +      -       +      -
     92B  TYR*     3.6    41.4    +      -       -      +
     93B  GLY      4.3     7.0    -      -       -      +
     94B  GLN*     1.3    81.7    -      -       -      +
     96B  PRO*     1.3    76.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 96 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   26720    C      3.8    10.3    -      -       -      +
   26730    U      4.6     6.3    -      -       -      +
   28170    G      5.0     0.9    -      -       -      +
   28180    A      2.9    50.9    +      -       +      +
   28190    C      3.2    33.3    -      -       -      +
     85B  ARG*     3.9    17.9    -      -       +      +
     86B  ALA      3.6     6.5    -      -       -      +
     87B  TYR*     3.6    25.8    -      -       +      -
     88B  GLU*     5.4     1.8    -      -       -      +
     95B  ARG*     1.3    84.6    -      -       +      +
     97B  LEU*     1.3    59.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 97 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   28190    C      3.1    23.1    -      -       -      +
   28200    A      4.1     0.7    +      -       -      -
     86B  ALA*     2.5    26.9    +      -       +      +
     87B  TYR      5.0     2.9    -      -       -      +
     88B  GLU*     4.0    34.3    -      -       +      +
     95B  ARG      3.2     1.2    +      -       -      -
     96B  PRO*     1.3    71.6    -      -       -      +
     98B  THR*     1.3    74.5    +      -       -      +
    127B  GLN*     3.7    30.2    +      -       +      +
    128B  ILE*     4.6     8.1    -      -       -      -
    131B  ALA*     3.5    32.3    -      -       +      -
    137B  LEU*     5.0     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   28190    C      3.8     7.2    -      -       -      -
   28200    A      2.9    28.9    -      -       -      +
     84B  LEU      3.9     0.4    -      -       -      +
     85B  ARG*     4.2     1.0    -      -       -      +
     86B  ALA*     2.9    28.2    +      -       -      +
     96B  PRO      4.0     0.2    -      -       -      -
     97B  LEU*     1.3    80.6    -      -       -      +
     99B  GLU*     1.3    72.8    +      -       -      +
    119B  HIS*     6.1     0.2    -      -       +      -
    124B  ALA*     4.2    26.0    +      -       +      -
    127B  GLN*     2.8    38.8    +      -       -      +
    128B  ILE*     4.3     6.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   26700    G      4.8     1.6    +      -       -      -
   28190    C      2.5    21.6    +      -       -      +
   28200    A      3.1    25.1    -      -       -      +
     83B  ALA*     5.0     0.9    -      -       +      -
     84B  LEU      3.3     5.8    -      -       -      +
     85B  ARG*     2.6    49.4    +      -       +      +
     98B  THR*     1.3    85.7    -      -       -      +
    100B  VAL*     1.3    65.5    +      -       -      +
    101B  TRP*     3.0    36.7    +      -       +      +
    119B  HIS*     3.2    15.4    -      -       -      -
    124B  ALA*     3.2    15.5    -      -       -      +
    143B  ILE*     4.6     5.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  ALA*     3.1     4.7    -      -       -      -
     84B  LEU*     2.9    35.8    +      -       +      +
     99B  GLU*     1.3    76.3    -      -       -      +
    101B  TRP*     1.3    69.4    +      -       -      +
    119B  HIS*     3.8     2.2    -      -       -      -
    121B  PRO*     4.1    20.0    -      -       +      +
    124B  ALA*     3.7    16.8    -      -       +      -
    125B  GLU*     3.9    13.2    -      -       +      +
    128B  ILE*     4.1    15.5    -      -       +      -
    179B  LEU*     4.0    31.9    -      -       +      -
    182B  VAL*     3.7     7.0    -      -       +      +
    183B  GLU*     4.2    12.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   26700    G      6.2     1.1    -      -       -      -
   28200    A      3.2    26.4    +      -       -      -
     82B  VAL*     3.3    39.7    -      -       +      -
     83B  ALA*     3.4    15.6    -      -       +      +
     99B  GLU*     3.0    38.3    +      -       +      +
    100B  VAL*     1.3    81.3    -      -       -      +
    102B  THR*     1.3    71.4    +      -       -      +
    105B  PHE*     4.0    11.2    -      +       -      -
    109B  LEU*     5.0     0.4    -      -       +      -
    113B  LEU*     4.1    27.6    -      -       +      -
    116B  PRO*     4.1    23.1    -      -       +      -
    119B  HIS*     3.1    30.5    +      +       +      -
    121B  PRO*     3.9    18.9    -      -       -      +
    143B  ILE*     4.4    20.4    -      -       +      -
    182B  VAL*     4.5     0.4    -      -       -      -
    183B  GLU*     4.3     3.8    -      -       -      +
----------------------------------------------------------
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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