Contacts of the strand formed by residues 69 - 77 (chain W) 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 LYS 69 (chain W).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   28560    A      5.2     7.6    -      -       -      +
   28570    C      3.0    33.0    +      -       -      +
   28580    U      5.7     1.4    +      -       -      -
   28950    C      5.3     9.0    -      -       -      -
     11W  THR*     4.1    18.8    -      -       +      -
     12W  ILE      3.3    12.1    -      -       -      +
     13W  PRO*     4.8     5.6    -      -       +      -
     14W  LEU*     4.1     3.1    -      -       -      -
     67W  PRO*     3.2    21.6    -      -       -      +
     68W  SER*     1.3    91.7    +      -       -      +
     70W  ILE*     1.3    67.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 70 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11W  THR*     4.6     1.1    -      -       -      -
     12W  ILE*     3.0    45.9    +      -       +      +
     14W  LEU*     4.1    14.6    -      -       +      -
     33W  ILE*     4.2    15.7    -      -       +      -
     54W  ILE*     4.3    24.7    -      -       +      +
     57W  ALA*     3.7    31.2    -      -       +      -
     58W  ALA*     4.8     4.7    -      -       +      +
     67W  PRO*     5.3     3.8    -      -       +      -
     69W  LYS*     1.3    81.7    -      -       -      +
     71W  ARG*     1.3    73.0    +      -       -      +
     72W  VAL*     3.5     6.8    +      -       +      -
     87W  ALA*     5.8     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 71 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9W  VAL*     5.3     4.9    -      -       +      -
     10W  VAL      3.5     5.2    -      -       -      +
     11W  THR*     3.9    23.3    +      -       +      +
     70W  ILE*     1.3    80.5    -      -       -      +
     72W  VAL*     1.3    61.1    +      -       -      +
     87W  ALA*     4.2     1.6    -      -       -      -
     88W  GLU*     2.9    40.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 72 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8W  ARG      3.9     0.2    -      -       -      +
      9W  VAL*     3.6     0.3    -      -       -      -
     10W  VAL*     2.7    44.5    +      -       +      +
     12W  ILE*     4.0    17.0    -      -       +      -
     33W  ILE*     5.2     5.4    -      -       +      -
     37W  LEU*     3.6    22.2    -      -       +      -
     54W  ILE*     3.3    24.5    -      -       +      -
     70W  ILE*     3.5     6.0    +      -       +      +
     71W  ARG*     1.3    75.0    -      -       -      +
     73W  ARG*     1.3    58.7    +      -       -      +
     74W  ALA*     3.9     1.7    +      -       +      +
     85W  VAL*     3.2    28.0    -      -       +      -
     86W  GLU      3.1    18.8    -      -       -      +
     87W  ALA*     4.5     0.4    -      -       -      +
     88W  GLU*     2.7     5.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 73 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7W  GLU*     3.3    30.5    -      -       +      +
      8W  ARG      3.6     8.7    -      -       -      +
      9W  VAL*     4.0    17.7    -      -       +      +
     72W  VAL*     1.3    71.0    -      -       -      +
     74W  ALA*     1.3    60.9    +      -       -      +
     84W  ILE      3.9     0.7    -      -       -      +
     85W  VAL*     3.2     2.2    -      -       -      -
     86W  GLU*     2.8    57.7    +      -       +      +
     87W  ALA      3.6    16.5    +      -       -      +
     88W  GLU*     2.7    38.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 74 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7W  GLU*     3.1     6.1    -      -       -      +
      8W  ARG      3.0    32.4    +      -       -      +
     37W  LEU*     4.0     8.1    -      -       +      -
     41W  PHE*     3.7    28.1    -      -       +      -
     72W  VAL*     3.9     2.3    +      -       +      +
     73W  ARG*     1.3    74.1    -      -       -      +
     75W  ALA*     1.3    61.1    +      -       -      +
     83W  ALA*     5.0     1.3    -      -       +      -
     84W  ILE      3.3     4.7    -      -       -      -
     85W  VAL*     3.1    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 75 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7W  GLU*     3.9    24.5    -      -       +      +
     41W  PHE*     5.0     1.6    -      -       -      -
     74W  ALA*     1.3    73.9    -      -       -      +
     76W  ARG*     1.3    61.2    +      -       -      +
     77W  PHE*     4.3    19.8    -      -       +      -
     82W  GLU      3.6     0.2    -      -       -      +
     83W  ALA*     2.8    26.8    -      -       -      -
     84W  ILE*     2.9    18.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 76 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7W  GLU      4.3    10.8    +      -       -      +
      8W  ARG*     6.2     0.7    -      -       -      +
     41W  PHE*     3.3    44.7    +      -       +      +
     42W  SER*     3.6    13.1    +      -       -      -
     43W  VAL*     2.9    24.7    -      -       -      +
     75W  ALA*     1.3    75.0    -      -       -      +
     77W  PHE*     1.3    73.9    +      -       -      +
     81W  GLY*     3.9    10.5    -      -       -      -
     82W  GLU      3.1    20.1    -      -       -      +
     83W  ALA*     5.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 77 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75W  ALA*     4.3    22.7    -      -       +      -
     76W  ARG*     1.3    89.7    -      -       -      +
     78W  GLU*     1.3    98.6    +      -       +      +
     81W  GLY*     3.4     6.8    -      -       -      -
     82W  GLU*     3.0    54.3    +      -       +      +
     84W  ILE*     4.3    19.3    -      -       +      -
----------------------------------------------------------
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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