Contacts of the strand formed by residues 68 - 75 (chain L) 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 VAL 68 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1993A    C      3.7    38.6    -      -       -      +
   2596A    A      4.6    17.9    -      -       -      +
   2597A    U      5.7     0.2    -      -       -      +
     32L  ILE*     4.5     3.4    -      -       +      -
     54L  THR*     3.9    21.3    -      -       +      -
     55L  VAL      3.2     9.9    -      -       -      +
     56L  SER*     4.4     4.7    -      -       -      -
     66L  ARG      3.7     3.6    +      -       -      +
     67L  GLN*     1.3    75.1    -      -       -      +
     69L  LEU*     1.3    68.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 69 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29L  LEU*     6.5     0.4    -      -       +      -
     54L  THR*     3.6     6.2    -      -       -      +
     55L  VAL*     2.7    42.5    +      -       +      +
     57L  VAL*     4.2    13.7    -      -       +      -
     64L  MET*     4.0    16.6    -      -       +      -
     67L  GLN*     3.6    30.7    +      -       +      +
     68L  VAL*     1.3    84.6    -      -       -      +
     70L  GLU*     1.3    59.2    +      -       -      +
     97L  ILE*     3.9    41.1    -      -       +      -
     98L  VAL      5.3     0.2    -      -       -      +
    105L  ARG*     4.5    12.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 70 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2597A    U      4.7     6.2    +      -       -      -
     35L  HIS*     5.2     5.0    +      -       -      +
     52L  LYS*     4.0    32.9    +      -       +      +
     53L  ILE      3.7    11.4    -      -       -      +
     54L  THR*     4.6    10.4    +      -       -      +
     69L  LEU*     1.3    76.7    -      -       -      +
     71L  ALA*     1.3    66.1    +      -       -      +
     97L  ILE*     3.4     7.1    -      -       -      +
     98L  VAL*     2.8    36.8    +      -       +      +
     99L  ASP      3.8    18.1    -      -       -      +
    100L  GLU*     4.7     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 71 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29L  LEU*     4.8     3.1    -      -       +      -
     52L  LYS*     3.3    10.0    -      -       -      +
     53L  ILE*     2.9    32.4    +      -       +      -
     55L  VAL*     4.1    21.3    -      -       +      -
     70L  GLU*     1.3    78.4    -      -       -      +
     72L  VAL*     1.3    64.9    +      -       -      +
     95L  ALA*     4.3    11.9    -      -       +      -
     96L  VAL      3.3    19.7    -      -       -      +
     97L  ILE*     3.9     7.6    -      -       +      +
     98L  VAL*     3.9     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 72 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50L  GLY      4.7     1.6    -      -       -      -
     51L  ASP      3.5     6.1    -      -       -      +
     52L  LYS*     4.5     8.1    -      -       +      -
     71L  ALA*     1.3    82.5    -      -       -      +
     73L  VAL*     1.3    74.6    +      -       -      +
     74L  VAL*     3.3     6.4    +      -       +      +
     95L  ALA*     3.0     6.3    -      -       -      -
     96L  VAL*     2.9    33.0    +      -       +      +
     98L  VAL*     4.6    18.2    -      -       +      -
    102L  GLU*     6.0     0.2    -      -       +      -
    117L  VAL*     4.1     9.2    -      -       +      -
    121L  PHE*     3.3    56.3    -      -       +      -
    124L  VAL*     5.1     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 73 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12L  LEU*     4.3    21.1    -      -       +      -
     18L  ILE*     5.1     0.2    -      -       +      -
     47L  ALA*     5.0     0.2    -      -       +      -
     48L  GLY*     3.3    36.3    -      -       -      +
     49L  LEU*     3.3     8.0    -      -       -      +
     50L  GLY*     3.0    24.3    +      -       -      -
     51L  ASP*     3.1    12.8    +      -       +      +
     53L  ILE*     3.9    32.5    -      -       +      -
     72L  VAL*     1.3    76.2    -      -       -      +
     74L  VAL*     1.3    62.2    +      -       -      +
     75L  ARG      4.0    14.1    -      -       -      +
     76L  GLN*     4.9     1.8    -      -       +      +
     94L  ALA      3.7    11.7    -      -       -      +
     95L  ALA*     4.1     3.1    -      -       +      -
    117L  VAL*     4.1     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 74 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21L  ALA*     5.6     2.7    -      -       +      -
     49L  LEU*     3.1    19.3    -      -       -      +
     72L  VAL*     3.3     9.6    +      -       +      +
     73L  VAL*     1.3    74.9    -      -       -      +
     75L  ARG*     1.3    63.5    +      -       +      +
     94L  ALA*     2.8    14.9    +      -       +      +
     96L  VAL*     3.7    28.9    -      -       +      -
    112L  PRO      3.7     5.4    -      -       -      +
    113L  ILE*     3.1    51.6    -      -       +      -
    114L  ALA*     3.6    11.6    +      -       -      +
    117L  VAL*     4.2    13.0    -      -       +      +
    124L  VAL*     4.7     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 75 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19L  THR*     4.8     4.2    -      -       -      +
     21L  ALA*     3.4    18.6    -      -       -      +
     49L  LEU*     3.9     3.3    -      -       -      +
     73L  VAL*     3.7     8.0    -      -       -      +
     74L  VAL*     1.3    87.3    -      -       +      +
     76L  GLN*     1.3    64.6    +      -       -      +
     90L  PHE*     3.3    33.4    -      -       +      -
     91L  GLU*     5.3     3.0    +      -       -      +
     92L  ASP*     3.2    36.9    +      -       -      +
     93L  ASN*     3.1     2.9    -      -       -      +
     94L  ALA*     2.7    55.9    +      -       -      +
    110L  LYS      3.6     7.2    +      -       -      -
    111L  GLY*     4.0     4.6    -      -       -      -
    112L  PRO*     3.3    46.1    +      -       -      +
     24V  LYS*     4.5     9.1    +      -       -      +
----------------------------------------------------------
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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