Contacts of the strand formed by residues 69 - 77 (chain Y) in PDB entry 1NJI


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 Y).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2856A    A      5.2     7.2    -      -       -      -
   2857A    C      3.1    31.8    +      -       -      +
   2858A    U      5.8     1.2    +      -       -      -
   2895A    C      5.3     8.5    +      -       -      -
     11Y  THR*     4.0    19.5    -      -       +      -
     12Y  ILE      3.2    12.3    -      -       -      +
     13Y  PRO*     4.8     5.6    -      -       +      -
     14Y  LEU*     4.1     2.9    -      -       -      -
     67Y  PRO*     3.6    21.2    -      -       -      +
     68Y  SER*     1.3    89.8    +      -       -      +
     70Y  ILE*     1.3    67.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 70 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11Y  THR*     4.6     1.1    -      -       -      -
     12Y  ILE*     3.0    48.5    +      -       +      +
     14Y  LEU*     4.0    14.4    -      -       +      -
     33Y  ILE*     4.1    14.4    -      -       +      -
     54Y  ILE*     4.3    25.4    -      -       +      +
     57Y  ALA*     3.8    29.4    -      -       +      -
     58Y  ALA*     4.9     4.5    -      -       +      +
     67Y  PRO*     5.3     4.0    -      -       +      -
     69Y  LYS*     1.3    82.3    -      -       -      +
     71Y  ARG*     1.3    73.7    +      -       -      +
     72Y  VAL*     5.1     3.8    -      -       +      -
     87Y  ALA*     5.9     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 71 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9Y  VAL*     5.1     5.2    -      -       +      -
     10Y  VAL      3.5     4.3    -      -       -      +
     11Y  THR*     4.1    21.1    +      -       +      +
     70Y  ILE*     1.3    81.7    -      -       -      +
     72Y  VAL*     1.3    59.8    +      -       -      +
     87Y  ALA*     4.2     1.9    -      -       -      +
     88Y  GLU*     2.8    40.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 72 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8Y  ARG      4.0     0.2    -      -       -      +
      9Y  VAL*     3.7     0.2    -      -       -      -
     10Y  VAL*     2.7    42.5    +      -       +      +
     12Y  ILE*     3.9    17.9    -      -       +      -
     33Y  ILE*     5.1     4.7    -      -       +      -
     37Y  LEU*     3.7    21.3    -      -       +      -
     54Y  ILE*     3.3    25.4    -      -       +      -
     70Y  ILE*     4.4     5.4    -      -       +      +
     71Y  ARG*     1.3    74.8    -      -       -      +
     73Y  ARG*     1.3    59.3    +      -       -      +
     74Y  ALA*     3.8     1.7    +      -       +      +
     85Y  VAL*     3.2    26.5    -      -       +      -
     86Y  GLU      3.1    18.4    -      -       -      +
     87Y  ALA*     4.5     0.4    -      -       -      +
     88Y  GLU*     2.8     5.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 73 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7Y  GLU*     3.4    29.8    -      -       +      +
      8Y  ARG      3.6     9.6    -      -       -      +
      9Y  VAL*     3.9    20.8    -      -       +      +
     72Y  VAL*     1.3    71.2    -      -       -      +
     74Y  ALA*     1.3    60.1    +      -       -      +
     84Y  ILE      3.9     0.3    -      -       -      +
     85Y  VAL*     3.2     2.6    -      -       -      -
     86Y  GLU*     2.9    56.8    +      -       +      +
     87Y  ALA      3.6    16.3    +      -       -      +
     88Y  GLU*     2.8    33.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 74 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7Y  GLU*     3.1     6.3    -      -       -      +
      8Y  ARG      3.0    32.5    +      -       -      +
     37Y  LEU*     4.0     8.5    -      -       +      -
     41Y  PHE*     3.6    28.7    -      -       +      -
     72Y  VAL*     3.8     2.5    +      -       +      +
     73Y  ARG*     1.3    73.0    -      -       -      +
     75Y  ALA*     1.3    59.9    +      -       -      +
     83Y  ALA*     5.0     1.6    -      -       +      -
     84Y  ILE      3.3     4.9    -      -       -      -
     85Y  VAL*     3.2    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 75 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7Y  GLU*     3.8    25.1    -      -       +      +
     41Y  PHE*     4.9     1.6    -      -       -      -
     74Y  ALA*     1.3    75.6    -      -       -      +
     76Y  ARG*     1.3    61.8    +      -       -      +
     77Y  PHE*     4.3    18.8    -      -       +      -
     82Y  GLU      3.6     0.2    -      -       -      +
     83Y  ALA*     2.9    26.5    -      -       -      +
     84Y  ILE*     2.9    18.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 76 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7Y  GLU      4.2    11.6    +      -       -      +
      8Y  ARG*     6.2     0.9    -      -       -      +
     41Y  PHE*     3.3    44.9    +      -       +      +
     42Y  SER*     3.6    13.3    +      -       -      -
     43Y  VAL*     2.9    24.1    -      -       +      +
     75Y  ALA*     1.3    75.7    -      -       -      +
     77Y  PHE*     1.3    73.7    +      -       -      +
     81Y  GLY*     3.9    10.3    -      -       -      -
     82Y  GLU      3.1    19.4    -      -       -      +
     83Y  ALA*     5.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 77 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75Y  ALA*     4.3    22.7    -      -       +      -
     76Y  ARG*     1.3    89.8    -      -       -      +
     78Y  GLU*     1.3    97.6    +      -       +      +
     81Y  GLY*     3.4     6.0    -      -       -      -
     82Y  GLU*     3.0    56.1    +      -       -      +
     84Y  ILE*     4.4    18.4    -      -       +      -
----------------------------------------------------------
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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