Contacts of the strand formed by residues 93 - 101 (chain D) 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 GLY 93 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2674A    G      3.7    14.1    -      -       -      -
   2675A    A      6.1     0.4    -      -       -      -
     89D  ASP*     5.0     1.1    -      -       -      -
     90D  THR*     2.9    38.7    +      -       -      -
     91D  PRO      3.5     0.8    -      -       -      -
     92D  TYR*     1.3    77.1    -      -       -      +
     94D  GLN*     1.3    66.0    +      -       -      -
     95D  ARG*     4.8     0.2    -      -       -      -
    144K  THR*     3.8     7.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 94 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2673A    U      2.5    41.2    +      -       -      +
   2674A    G      3.2    15.4    +      -       -      +
     87D  TYR*     4.1    14.0    -      -       +      -
     88D  GLU      3.5     6.7    -      -       -      +
     89D  ASP*     3.6    22.4    +      -       -      +
     93D  GLY*     1.3    76.0    -      -       -      -
     95D  ARG*     1.3    62.2    +      -       -      +
    138D  GLY*     4.0     1.2    -      -       -      -
    139D  ASP*     3.1    40.8    +      -       -      +
    141D  ARG*     3.6    15.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 95 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2673A    U      4.3     5.6    +      -       -      +
   2811A    A      5.7     3.6    -      -       -      +
   2817A    G      3.5    26.6    +      -       -      +
   2818A    A      3.9    29.3    -      -       -      +
     87D  TYR*     3.2     5.2    -      -       -      -
     88D  GLU*     2.8    36.5    +      -       +      +
     90D  THR*     4.3    20.9    +      -       +      -
     92D  TYR*     3.7    36.2    +      -       -      +
     93D  GLY      4.3     6.3    -      -       -      +
     94D  GLN*     1.3    83.4    -      -       -      +
     96D  PRO*     1.3    75.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 96 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2672A    C      3.8    10.1    -      -       -      +
   2673A    U      4.8     4.7    -      -       -      +
   2817A    G      5.0     0.9    -      -       -      +
   2818A    A      2.9    51.7    +      -       +      +
   2819A    C      3.1    34.0    -      -       -      +
     85D  ARG*     3.9    17.3    -      -       +      +
     86D  ALA      3.5     6.1    -      -       -      +
     87D  TYR*     3.6    24.7    -      -       +      -
     88D  GLU*     5.5     1.6    -      -       -      +
     94D  GLN      4.7     0.9    -      -       -      +
     95D  ARG*     1.3    83.5    -      -       +      +
     97D  LEU*     1.3    61.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 97 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2819A    C      3.1    23.5    -      -       -      +
   2820A    A      4.0     0.7    +      -       -      -
     86D  ALA*     2.5    27.3    +      -       +      +
     87D  TYR      4.5     6.3    -      -       -      +
     88D  GLU*     4.0    30.1    -      -       +      +
     95D  ARG      3.3     1.6    +      -       -      -
     96D  PRO*     1.3    72.3    -      -       -      +
     98D  THR*     1.3    75.9    +      -       -      +
    127D  GLN*     3.6    30.2    +      -       +      +
    128D  ILE*     4.5     7.2    -      -       -      -
    131D  ALA*     3.5    32.5    -      -       +      -
    137D  LEU*     5.0     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 98 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2819A    C      3.9     7.2    -      -       -      -
   2820A    A      3.0    28.0    -      -       -      +
     84D  LEU      4.0     0.3    -      -       -      +
     85D  ARG*     4.1     1.2    -      -       -      +
     86D  ALA*     2.9    26.9    +      -       -      +
     97D  LEU*     1.3    81.2    -      -       -      +
     99D  GLU*     1.3    74.2    +      -       -      +
    119D  HIS*     6.1     0.2    -      -       +      -
    124D  ALA*     4.2    25.8    -      -       +      -
    127D  GLN*     2.7    39.6    +      -       -      +
    128D  ILE*     4.4     6.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 99 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2670A    G      4.7     2.1    +      -       -      -
   2819A    C      2.4    22.6    +      -       -      +
   2820A    A      2.9    24.0    -      -       -      +
     83D  ALA*     4.9     0.9    -      -       +      -
     84D  LEU      3.3     5.8    -      -       -      +
     85D  ARG*     2.7    49.5    +      -       +      +
     98D  THR*     1.3    86.3    -      -       -      +
    100D  VAL*     1.3    65.8    +      -       -      +
    101D  TRP*     3.0    36.5    +      -       +      +
    119D  HIS*     3.2    22.5    +      -       -      -
    124D  ALA*     3.2     8.2    -      -       -      +
    143D  ILE*     4.6     6.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 100 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83D  ALA*     3.0     5.4    -      -       -      -
     84D  LEU*     2.9    36.2    +      -       +      +
     99D  GLU*     1.3    76.3    -      -       -      +
    101D  TRP*     1.3    69.2    +      -       -      +
    119D  HIS*     3.8     2.2    -      -       -      -
    121D  PRO*     4.2    19.1    -      -       +      +
    124D  ALA*     3.8    16.4    -      -       +      -
    125D  GLU*     4.0    13.5    -      -       +      +
    128D  ILE*     4.1    15.5    -      -       +      -
    179D  LEU*     3.9    32.1    -      -       +      -
    182D  VAL*     3.8     5.6    -      -       +      +
    183D  GLU*     4.3    12.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 101 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2670A    G      6.1     1.3    -      -       -      -
   2820A    A      3.2    25.9    +      -       -      -
     82D  VAL*     3.3    39.0    -      -       +      -
     83D  ALA*     3.5    14.3    -      -       +      +
     99D  GLU*     3.0    38.2    +      -       +      +
    100D  VAL*     1.3    85.0    -      -       -      +
    102D  THR*     1.3    70.6    +      -       -      +
    105D  PHE*     4.0     9.9    -      +       -      -
    109D  LEU*     5.1     0.7    -      -       +      -
    113D  LEU*     4.1    27.8    -      -       +      -
    116D  PRO*     4.0    24.7    -      -       +      -
    119D  HIS*     3.1    32.8    +      +       +      -
    121D  PRO*     4.0    17.0    -      -       -      +
    143D  ILE*     4.5    17.7    -      -       +      -
    182D  VAL*     4.4     0.2    -      -       -      -
    183D  GLU*     4.3     4.3    -      -       -      +
----------------------------------------------------------
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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