Contacts of the strand formed by residues 53 - 59 (chain B) in PDB entry 1JEQ


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 GLU 53 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  LYS*     4.1     8.9    +      -       +      +
      8B  ALA      2.9     7.1    +      -       -      +
      9B  ALA*     3.5     1.4    -      -       -      -
     10B  VAL*     2.8    26.5    +      -       -      +
     51B  LYS      3.5     8.3    +      -       -      +
     52B  ASP*     1.3    73.9    -      -       -      +
     54B  ILE*     1.3    63.3    +      -       -      +
     83B  LEU*     3.6    11.8    -      -       +      +
     84B  MET*     3.5    25.6    +      -       -      +
     85B  LEU*     4.2    14.2    -      -       +      +
    125B  LYS*     2.6    41.1    +      -       -      +
    127B  PHE*     3.5    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  VAL*     3.2    12.1    -      -       +      +
     12B  LEU*     4.0    24.0    -      -       +      -
     41B  PHE*     3.9    16.6    -      -       +      -
     42B  VAL*     4.9     5.2    -      -       +      -
     45B  GLN*     3.7    26.2    -      -       +      +
     52B  ASP      4.0     6.5    -      -       -      +
     53B  GLU*     1.3    80.1    -      -       -      +
     55B  ALA*     1.3    71.3    +      -       -      +
     56B  LEU*     5.7     0.4    -      -       +      -
     81B  ARG*     3.9     9.4    +      -       -      +
     82B  HIS      3.5     9.7    -      -       -      +
     83B  LEU*     3.9     3.4    -      -       -      -
     84B  MET      3.0    20.2    +      -       -      +
     86B  PRO*     3.5    36.7    -      -       +      +
     90B  LEU*     4.8    11.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 55 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  VAL      2.9     6.1    +      -       -      +
     11B  VAL*     3.3    10.0    -      -       +      -
     12B  LEU*     2.8    25.4    +      -       -      -
     54B  ILE*     1.3    81.0    -      -       -      +
     56B  LEU*     1.3    61.0    +      -       -      +
     57B  VAL*     4.2     0.9    -      -       +      -
     81B  ARG*     3.1    14.4    -      -       -      +
     82B  HIS      4.0     0.9    -      -       -      -
     83B  LEU*     3.7    22.6    -      -       +      +
    117B  VAL*     3.7    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 56 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  LEU*     2.9    40.6    -      -       +      +
     14B  MET*     4.2     8.7    -      -       +      -
     38B  ILE*     5.1     4.9    -      -       +      -
     55B  ALA*     1.3    74.1    -      -       -      +
     57B  VAL*     1.3    69.4    +      -       -      +
     58B  LEU*     3.7    13.5    -      -       +      -
     79B  VAL*     3.7     1.2    -      -       -      -
     80B  HIS*     3.0    35.1    +      -       +      -
     81B  ARG*     2.7    26.6    +      -       +      +
     90B  LEU*     4.4    10.8    -      -       +      -
     94B  ILE*     3.6    30.7    -      -       +      -
     98B  ILE*     3.7    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 57 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  VAL*     3.6    15.3    -      -       +      -
     12B  LEU      3.0     7.2    +      -       -      +
     13B  CYS*     4.1    11.0    -      -       -      -
     14B  MET      2.8    23.9    +      -       -      -
     55B  ALA      5.4     0.2    -      -       -      -
     56B  LEU*     1.3    75.7    -      -       -      +
     58B  LEU*     1.3    73.9    +      -       -      +
     77B  ILE*     3.8    24.2    -      -       +      -
     78B  THR      3.4    11.4    -      -       -      +
     79B  VAL*     4.3    14.1    -      -       +      +
    110B  ALA*     4.6     2.2    -      -       +      +
    113B  VAL*     4.5     5.8    -      -       +      -
    114B  SER*     3.4    34.8    -      -       -      +
    117B  VAL*     4.5     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 58 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  MET*     3.4    22.0    -      -       +      +
     16B  VAL*     4.2    12.1    -      -       +      -
     56B  LEU*     3.7    23.1    -      -       +      -
     57B  VAL*     1.3    87.2    -      -       -      +
     59B  PHE*     1.3    61.0    -      -       -      +
     61B  THR*     3.7    24.9    -      -       +      +
     76B  ASN      3.9     0.2    -      -       -      +
     77B  ILE*     3.2     3.6    -      -       -      +
     78B  THR*     2.5    47.9    +      -       +      +
     80B  HIS*     3.7    28.0    -      -       +      +
     98B  ILE*     3.9    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 59 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  CYS*     3.4    27.4    -      -       -      -
     14B  MET      3.3    10.1    +      -       -      -
     15B  ASP*     3.2    51.8    -      -       +      +
     16B  VAL*     3.0    23.6    +      -       -      -
     17B  GLY*     3.6     1.9    +      -       -      -
     58B  LEU*     1.3    76.9    -      -       -      +
     60B  GLY*     1.3    60.3    +      -       -      +
     61B  THR      3.5     0.4    -      -       -      -
     76B  ASN      3.3     3.8    -      -       -      -
     77B  ILE*     3.9     5.4    -      -       +      -
    105B  ALA*     3.4    24.7    -      -       +      -
    107B  PHE*     4.1    23.1    -      -       +      -
    110B  ALA*     3.3    27.8    -      -       +      -
    134B  ILE*     4.1     8.3    -      -       +      -
    135B  PHE      4.1     0.7    -      -       -      -
    136B  THR*     3.9    13.7    -      -       +      -
----------------------------------------------------------
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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