Contacts of the strand formed by residues 41 - 53 (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 PHE 41 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  GLY*     1.3    74.8    -      -       -      +
     42B  ALA*     1.3    80.9    +      -       -      +
     76B  THR*     3.7    11.0    -      -       -      -
     77B  PRO      3.0    28.0    -      -       -      -
     78B  PRO*     4.0     0.2    -      -       +      -
     79B  MET*     3.2    44.6    -      -       +      -
    162B  MET*     6.0     0.2    -      -       -      -
    164B  THR*     5.2     1.0    +      -       -      -
    188B  HIS*     3.7    28.3    -      +       -      -
    189B  ALA*     3.7    10.3    -      -       -      -
    190B  MET*     3.2    56.8    -      -       +      -
    193B  ILE*     4.1     6.7    -      -       +      -
    194B  PHE*     4.1     2.7    -      -       +      -
    310B  ARG*     3.5     7.7    -      -       -      +
    311B  PHE*     2.7    34.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 42 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  PHE*     1.3   102.6    -      -       -      +
     43B  GLY*     1.3    59.2    +      -       -      +
     76B  THR*     4.0     3.5    -      -       -      +
     77B  PRO*     4.5     1.4    -      -       -      +
     79B  MET*     3.3    23.5    -      -       -      +
    146B  THR*     4.0     7.0    -      -       +      +
    162B  MET*     4.1    17.9    -      -       +      -
    308B  LEU*     3.7    17.0    -      -       +      -
    309B  VAL      3.4    12.6    -      -       -      +
    310B  ARG*     4.3     1.1    -      -       +      -
    311B  PHE*     4.2     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 43 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  ALA*     1.3    76.8    -      -       -      +
     44B  TYR*     1.3    69.9    +      -       -      -
     74B  ILE*     3.8    13.2    -      -       -      -
     75B  GLU      3.2    13.7    -      -       -      -
     76B  THR*     4.0     2.7    -      -       -      -
     77B  PRO*     5.1     1.3    -      -       -      -
    308B  LEU*     3.3     7.1    -      -       -      +
    309B  VAL*     2.9    31.1    +      -       -      -
    311B  PHE*     4.2     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 44 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43B  GLY*     1.3    75.9    -      -       -      -
     45B  LYS*     1.3    65.2    -      -       -      +
     46B  ALA      3.5     0.2    +      -       -      -
     74B  ILE*     3.7     3.3    -      -       -      +
     75B  GLU*     2.9    37.8    +      -       +      +
     77B  PRO*     5.4     2.2    -      -       +      -
    146B  THR*     2.6    33.4    +      -       +      -
    147B  VAL      5.3     0.7    -      -       -      -
    148B  PRO*     3.2    26.9    -      -       +      +
    151B  VAL*     4.3    19.3    -      -       +      -
    154B  VAL*     4.0    25.6    -      -       +      -
    156B  LYS*     4.2    13.9    -      -       +      -
    160B  ASP*     2.5    29.3    +      -       -      -
    287B  TYR*     4.2     4.1    +      -       -      +
    306B  LYS      3.3    22.4    -      -       -      +
    307B  ARG      3.6     1.1    -      -       -      -
    308B  LEU*     4.0    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 45 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   27170    C      2.8    13.9    +      -       -      -
   27180    C      2.8    26.6    +      -       -      -
     43B  GLY      4.2     0.4    -      -       -      -
     44B  TYR*     1.3    70.4    -      -       -      +
     46B  ALA*     1.3    61.6    +      -       -      +
     47B  GLY*     4.4     3.4    -      -       -      +
     48B  MET*     5.6     3.1    -      -       -      +
     72B  THR*     4.1    27.8    -      -       +      -
     73B  VAL      4.2     3.1    -      -       -      -
     74B  ILE*     4.2     9.4    -      -       +      -
    287B  TYR*     3.1    10.6    -      -       -      -
    301B  VAL*     3.2    18.0    +      -       +      +
    302B  PRO      4.6     3.4    -      -       -      +
    303B  GLY      2.7    30.3    +      -       -      +
    304B  PRO      3.6    19.3    -      -       -      +
    305B  ASP*     3.7    12.8    -      -       -      +
    306B  LYS*     2.8    24.9    +      -       -      +
    307B  ARG*     3.1    14.1    +      -       +      +
    309B  VAL*     4.3    10.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 46 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  TYR      4.5     2.5    -      -       -      +
     45B  LYS*     1.3    74.0    -      -       -      +
     47B  GLY*     1.3    61.3    +      -       -      +
     73B  VAL*     3.0    21.6    +      -       +      +
     75B  GLU*     4.6     2.2    -      -       +      -
    284B  PHE*     3.7     9.2    -      -       +      +
    285B  VAL      4.9     0.3    -      -       -      +
    287B  TYR*     3.3    46.6    -      -       +      +
    290B  VAL*     4.1    16.4    -      -       +      -
    305B  ASP*     3.1    20.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 47 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   27190    A      5.9     0.4    -      -       -      -
     45B  LYS*     4.4     3.2    -      -       -      +
     46B  ALA*     1.3    83.3    -      -       -      +
     48B  MET*     1.3    61.7    +      -       -      -
     72B  THR*     3.3     8.4    -      -       -      +
     73B  VAL      2.7    33.2    +      -       -      +
    284B  PHE*     3.7    15.4    -      -       -      -
    305B  ASP*     3.6    10.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 48 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   27170    C      3.6    23.6    -      -       -      +
   27180    C      3.8    14.4    -      -       -      +
   27190    A      2.8    58.4    +      -       +      +
   27640    C      5.9     0.4    -      -       -      +
     45B  LYS*     5.6     3.1    -      -       -      -
     47B  GLY*     1.3    75.7    -      -       -      -
     49B  THR*     1.3    63.8    +      -       -      +
     70B  PRO*     4.0    15.5    -      -       +      -
     71B  VAL      3.2    13.2    -      -       -      +
     72B  THR*     3.4    20.0    -      -       +      +
     73B  VAL*     4.6     0.9    -      -       -      +
    284B  PHE*     3.9     3.7    -      -       -      -
    299B  GLY      3.3    28.3    -      -       -      +
    300B  SER*     4.6     1.8    -      -       -      +
    335B  ASN*     3.0    24.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 49 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   27190    A      3.3    19.7    -      -       -      +
     48B  MET*     1.3    80.3    -      -       -      +
     50B  HIS*     1.3    64.9    +      -       -      +
     70B  PRO*     3.8     0.3    -      -       -      +
     71B  VAL*     2.9    32.3    +      -       -      +
     73B  VAL*     4.2    13.4    -      -       -      +
    278B  PRO      4.2     6.2    +      -       -      +
    280B  VAL*     3.0    37.5    -      -       +      -
    284B  PHE*     4.0     6.3    -      -       +      -
    296B  LEU*     5.6     1.4    -      -       -      +
    330B  VAL*     4.7     6.2    -      -       -      +
    331B  SER*     3.5    22.3    +      -       -      +
    333B  GLU      5.2     0.4    -      -       -      +
    335B  ASN*     4.4     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   27190    A      2.7    43.4    +      +       +      +
   27200    C      4.5     4.5    -      -       -      -
     49B  THR*     1.3    80.0    +      -       -      +
     51B  VAL*     1.3    66.2    +      -       -      +
     52B  VAL*     5.6     4.0    -      -       +      -
     68B  THR*     3.7    22.2    -      -       +      -
     69B  VAL      3.3    13.0    -      -       -      +
     71B  VAL*     4.4     1.3    -      -       -      +
    329B  TYR*     5.3     2.1    -      +       -      -
    330B  VAL*     3.9     1.0    -      -       -      +
    331B  SER*     3.1    52.5    +      -       -      -
    333B  GLU*     5.1     2.5    -      -       -      -
     14T  GLU*     4.5     2.7    -      -       +      -
     15T  PRO      2.8    28.6    +      -       -      -
     16T  GLY*     3.4    17.7    +      -       -      -
     17T  THR*     4.1     7.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  HIS*     1.3    76.7    -      -       -      +
     52B  VAL*     1.3    63.6    +      -       -      +
     53B  LEU*     3.3    19.7    +      -       +      -
     67B  GLU      3.5     0.3    -      -       -      +
     68B  THR*     3.6     2.6    -      -       -      -
     69B  VAL*     2.8    35.5    +      -       +      +
     71B  VAL*     3.5    28.9    -      -       +      -
    270B  ILE*     4.4     7.2    -      -       +      -
    296B  LEU*     5.4     5.2    -      -       +      -
    327B  VAL*     3.1    30.5    -      -       +      -
    329B  TYR*     2.7    22.4    -      -       -      +
    330B  VAL*     3.9     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  HIS*     5.6     2.7    -      -       +      -
     51B  VAL*     1.3    74.7    -      -       -      +
     53B  LEU*     1.3    67.7    +      -       -      +
     66B  GLU*     4.0    29.4    -      -       +      +
     67B  GLU      3.3    21.8    -      -       -      +
     68B  THR*     4.8    12.6    -      -       +      +
    328B  ARG*     2.9    29.4    +      -       +      -
    329B  TYR*     2.6    44.9    +      -       +      +
     15T  PRO*     4.9    13.5    -      -       +      -
     16T  GLY      5.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  VAL*     3.3    27.1    -      -       +      -
     52B  VAL*     1.3    87.3    -      -       -      +
     54B  VAL*     1.3    66.7    +      -       -      +
     65B  MET      3.4     0.5    -      -       -      +
     66B  GLU*     3.3     6.1    -      -       -      -
     67B  GLU*     2.7    43.7    +      -       +      +
     69B  VAL*     4.0    23.6    -      -       +      -
    268B  ARG*     5.2     6.1    -      -       -      +
    270B  ILE*     3.7    35.0    -      -       +      -
    325B  PRO*     4.8    10.8    -      -       +      -
    326B  GLU      3.5     9.2    -      -       -      +
    327B  VAL*     3.7    19.3    -      -       +      -
    328B  ARG*     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