Contacts of the strand formed by residues 17 - 25 (chain F) 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 ARG 17 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3030B    C      3.2    28.5    +      -       -      -
   3031B    C      4.8    11.7    +      -       -      -
     15F  GLU      4.7     1.8    -      -       -      +
     16F  PRO*     1.3    78.4    -      -       -      +
     18F  ILE*     1.3    70.4    +      -       -      +
     19F  GLU*     3.6    18.4    +      -       -      +
    134F  LEU*     3.7     7.9    -      -       -      +
    135F  VAL*     3.1    37.1    +      -       +      +
    136F  ARG      4.8     0.4    -      -       -      -
    137F  PRO*     3.7    25.7    +      -       +      +
    139F  TYR*     4.1    23.0    -      -       -      +
    140F  ARG*     5.0     2.0    -      -       -      +
    165F  PHE*     4.0    10.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 18 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17F  ARG*     1.3    80.0    +      -       -      +
     19F  GLU*     1.3    63.7    +      -       -      +
     20F  LYS      4.0     6.3    +      -       -      +
     21F  VAL*     3.9    24.0    -      -       +      -
     77F  ASP*     5.1     8.4    +      -       -      +
     80F  ALA*     4.3    10.8    -      -       +      +
     81F  GLU*     5.3    14.8    -      -       +      -
     84F  LEU*     3.2    30.7    -      -       +      -
    132F  VAL*     4.2     6.5    -      -       +      -
    134F  LEU*     3.4    21.5    -      -       +      -
    165F  PHE*     4.2    14.6    -      -       +      -
    166F  ILE*     6.1     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 19 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3044B    A      4.5    16.2    +      -       -      +
     17F  ARG*     3.6    18.5    +      -       -      +
     18F  ILE*     1.3    73.0    -      -       -      +
     20F  LYS*     1.3    85.4    +      -       -      +
     76F  ARG*     4.6    21.3    +      -       -      +
    133F  ASN*     2.9    41.1    +      -       -      +
    135F  VAL*     4.3    17.8    -      -       +      +
    139F  TYR*     3.1    41.6    -      -       -      -
    143F  LYS*     5.4     0.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 20 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2348A    C      2.8    20.6    +      -       -      -
   2349A    G      2.6    26.9    +      -       -      -
     18F  ILE*     3.9     4.5    +      -       -      +
     19F  GLU*     1.3    96.7    -      -       -      +
     21F  VAL*     1.3    65.2    +      -       -      +
     22F  VAL*     4.4    16.1    +      -       +      +
     74F  THR*     4.9     5.5    -      -       +      +
     75F  LEU      2.8    19.4    +      -       -      +
     76F  ARG*     3.6    53.0    -      -       -      +
    133F  ASN*     3.2    42.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 21 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18F  ILE*     3.9    12.6    -      -       +      -
     20F  LYS*     1.3    78.3    -      -       -      +
     22F  VAL*     1.3    60.8    +      -       -      +
     23F  VAL*     3.7     2.9    +      -       +      -
     73F  VAL      3.1     4.5    -      -       -      +
     75F  LEU*     2.9    35.2    +      -       +      +
     80F  ALA*     3.7    26.0    -      -       +      +
     83F  PHE*     4.4    13.5    -      -       +      -
     84F  LEU*     3.9    17.9    -      -       +      -
    130F  VAL*     3.7    25.6    -      -       +      -
    131F  THR      3.0    19.1    -      -       -      +
    132F  VAL*     4.1     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 22 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2347A    C      3.2    27.9    +      -       -      +
   2348A    C      3.6    27.6    -      -       -      -
     20F  LYS*     4.4    16.4    -      -       +      +
     21F  VAL*     1.3    73.1    -      -       -      +
     23F  VAL*     1.3    64.3    +      -       -      +
     24F  HIS      3.8     1.0    +      -       -      -
     72F  LYS*     4.1    23.3    -      -       +      -
     73F  VAL      3.2     7.9    -      -       -      +
     74F  THR*     3.8    20.0    -      -       +      -
    129F  ASP*     3.6     1.7    -      -       -      +
    130F  VAL*     3.5     1.7    -      -       -      -
    131F  THR*     2.9    40.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 23 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21F  VAL*     4.5     7.4    -      -       +      +
     22F  VAL*     1.3    72.5    -      -       -      +
     24F  HIS*     1.3    58.9    +      -       -      +
     41F  LEU*     3.5    21.1    -      -       +      +
     44F  ILE*     5.6     0.7    -      -       +      -
     45F  THR*     3.3    27.4    -      -       +      -
     72F  LYS*     3.2     2.4    -      -       -      -
     73F  VAL*     2.8    40.6    +      -       +      +
     75F  LEU*     4.7     1.6    -      -       +      -
     83F  PHE*     3.4    41.5    -      -       +      -
    128F  LEU*     5.6     1.6    -      -       +      -
    129F  ASP      3.2     7.9    -      -       -      +
    130F  VAL*     3.7    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 24 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2338A    G      3.5     9.2    -      -       -      -
   2346A    C      2.8    48.1    +      -       -      -
   2347A    C      3.3    33.8    +      -       -      +
     22F  VAL      3.8     1.6    +      -       -      -
     23F  VAL*     1.3    75.6    -      -       -      +
     25F  MET*     1.3    63.7    +      -       -      +
     26F  GLY*     3.0    28.3    +      -       -      -
     41F  LEU*     4.6     0.7    -      -       -      -
     52F  THR*     4.3     2.5    -      -       +      -
     71F  ALA      3.1    25.6    -      -       -      +
     72F  LYS*     3.4    14.4    -      -       +      -
    128F  LEU*     4.1     0.8    -      -       -      +
    129F  ASP*     3.1    41.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 25 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24F  HIS*     1.3    76.7    -      -       -      +
     26F  GLY*     1.3    60.4    +      -       -      +
     27F  ILE*     2.8    25.1    +      -       +      +
     37F  ALA*     2.9    50.3    -      -       +      +
     40F  ILE*     3.4    23.1    -      -       +      -
     41F  LEU*     3.2    30.7    -      -       +      +
     70F  GLY*     3.4    13.5    -      -       -      -
     71F  ALA*     3.0    10.4    +      -       +      +
    128F  LEU*     4.1    33.4    -      -       +      +
----------------------------------------------------------
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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