Contacts of the strand formed by residues 138 - 148 (chain S) 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 SER 138 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2053A    G      2.5    25.3    +      -       -      -
     22S  GLN*     4.1    18.5    +      -       -      -
    121S  GLU*     3.1     6.1    -      -       -      -
    122S  GLN*     2.7    55.9    +      -       -      +
    136S  TRP      5.1     0.9    +      -       -      -
    137S  ASN*     1.3    74.5    -      -       -      +
    139S  PRO*     1.3    72.5    -      -       -      +
    140S  GLN*     4.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 139 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1370A    G      3.4    29.6    -      -       +      +
   2053A    G      4.4     9.0    -      -       -      +
   2054A    A      5.6     2.0    -      -       -      +
     21S  ARG      3.4     1.0    -      -       -      +
     22S  GLN*     3.4    23.4    -      -       -      +
     23S  MET      3.6    20.5    +      -       -      +
     25S  PHE*     4.4    14.4    -      -       +      +
    118S  LYS*     4.1    24.5    -      -       -      +
    120S  GLY      3.7     6.3    -      -       -      +
    121S  GLU*     4.5     3.1    -      -       +      +
    137S  ASN      4.2     3.8    -      -       -      +
    138S  SER*     1.3    88.0    -      -       -      +
    140S  GLN*     1.3    60.6    +      -       -      +
    141S  VAL*     4.1     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 140 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20S  GLU*     3.9    39.8    +      -       +      +
     21S  ARG      3.3     3.6    -      -       -      -
     22S  GLN*     4.5    15.8    -      -       +      +
    118S  LYS*     3.5     5.2    -      -       -      -
    119S  VAL*     2.8    29.4    +      -       +      +
    120S  GLY*     2.7    22.6    +      -       -      +
    121S  GLU      3.6    16.3    +      -       -      +
    122S  GLN*     3.9    31.1    +      -       -      +
    138S  SER      4.1     0.7    -      -       -      +
    139S  PRO*     1.3    77.5    -      -       -      +
    141S  VAL*     1.3    62.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 141 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18S  LEU      4.2     0.7    -      -       -      +
     19S  ARG*     3.5     1.7    -      -       -      -
     20S  GLU      3.0     4.9    +      -       -      -
     21S  ARG*     2.6    44.2    +      -       -      +
     23S  MET*     3.8    42.2    -      -       +      +
     25S  PHE*     3.7    37.2    -      -       +      -
     28S  SER*     4.2     1.6    -      -       -      +
    116S  ALA*     4.0    17.9    -      -       +      -
    117S  HIS      3.6     6.1    -      -       -      +
    139S  PRO*     4.8     0.2    -      -       +      -
    140S  GLN*     1.3    81.9    -      -       -      +
    142S  ASP*     1.3    80.2    +      -       -      +
    143S  VAL*     4.8     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 142 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1S  GLY*     3.3     7.0    -      -       -      -
      2S  ILE*     3.0    43.4    +      -       +      -
     18S  LEU      3.2     8.7    -      -       -      +
     19S  ARG*     3.0    19.7    +      -       -      -
     20S  GLU*     2.7    35.0    +      -       -      +
    117S  HIS      2.9    30.8    +      -       -      +
    119S  VAL*     3.1    22.0    -      -       +      +
    141S  VAL*     1.3    78.8    -      -       -      +
    143S  VAL*     1.3    62.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 143 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2S  ILE*     4.2     5.3    -      -       -      +
     17S  MET*     3.2     8.1    -      -       -      +
     18S  LEU*     3.0    71.7    +      -       +      -
     23S  MET*     4.9     7.4    -      -       +      -
     88S  PHE*     4.2    20.0    -      -       +      -
     91S  LEU*     3.7    16.0    -      -       +      +
    114S  VAL*     4.4     0.9    -      -       +      -
    115S  ALA      3.1    24.5    -      -       -      +
    116S  ALA*     4.1     6.1    -      -       +      +
    141S  VAL*     4.8     1.6    -      -       +      -
    142S  ASP*     1.3    78.4    -      -       -      +
    144S  GLU*     1.3    68.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 144 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2S  ILE*     3.8    19.3    -      -       +      -
      3S  SER      4.4     1.0    -      -       -      +
      4S  TYR*     3.3    25.2    -      -       +      +
      5S  SER*     2.5    45.2    +      -       -      -
      6S  VAL      4.4     0.3    +      -       -      -
     16S  ALA      3.6     4.5    -      -       -      -
     17S  MET*     4.0     2.7    -      -       +      -
    113S  HIS*     3.1    27.3    +      -       +      +
    114S  VAL*     3.2     4.8    -      -       -      +
    115S  ALA*     3.0    33.3    +      -       -      +
    117S  HIS*     3.1    19.2    -      -       +      -
    143S  VAL*     1.3    79.6    -      -       -      +
    145S  LEU*     1.3    61.7    +      -       -      +
    146S  ILE*     5.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 145 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4S  TYR*     4.0     0.9    -      -       -      -
     14S  ALA      3.9     0.2    -      -       -      +
     15S  LYS*     3.4     5.7    -      -       -      +
     16S  ALA*     3.0    37.6    +      -       +      +
     35S  ILE*     5.7     1.8    -      -       +      -
     91S  LEU*     4.0    25.6    -      -       +      -
     92S  LEU*     3.5    35.0    -      -       +      -
     95S  ALA*     4.1    20.4    -      -       +      -
    111S  ILE*     3.4    29.2    -      -       +      -
    113S  HIS      3.0    17.9    -      -       -      +
    114S  VAL*     3.8     9.4    -      -       +      -
    144S  GLU*     1.3    77.2    -      -       -      +
    146S  ILE*     1.3    72.0    +      -       -      +
    147S  LEU*     4.2     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 146 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4S  TYR*     4.2    22.0    -      -       +      -
      6S  VAL*     4.0    33.4    -      -       +      +
      7S  GLU      4.9     0.2    -      -       -      +
      8S  ALA*     4.1    18.6    -      -       +      -
     13S  THR*     3.7    22.4    -      -       +      +
     14S  ALA      3.4     5.8    -      -       -      +
     15S  LYS*     4.5     3.6    -      -       +      -
    111S  ILE*     3.7     2.3    -      -       -      -
    112S  LYS*     2.9    41.4    +      -       +      +
    113S  HIS*     2.7    37.8    +      -       +      +
    145S  LEU*     1.3    80.0    -      -       -      +
    147S  LEU*     1.3    63.8    +      -       -      +
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Residues in contact with LEU 147 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13S  THR*     3.2    10.6    +      -       -      -
     14S  ALA*     2.7    39.0    +      -       +      +
     40S  ALA*     4.1    15.3    -      -       +      -
     92S  LEU*     5.1     1.1    -      -       +      -
     95S  ALA*     3.6    44.4    -      -       +      +
     96S  VAL*     3.9    13.7    -      -       +      +
     99S  ALA*     4.4     5.4    -      -       +      -
    106S  GLY      4.7     0.7    -      -       -      +
    109S  MET*     3.8    21.8    -      -       +      -
    110S  THR      3.2    13.5    -      -       -      +
    111S  ILE*     4.1    20.9    -      -       +      -
    145S  LEU*     4.7     9.6    -      -       +      -
    146S  ILE*     1.3    74.5    -      -       -      +
    148S  GLU*     1.3    60.4    +      -       -      +
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Residues in contact with GLU 148 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12S  THR*     3.4    20.8    +      -       -      +
     13S  THR*     4.3     5.5    +      -       -      +
    109S  MET*     3.5     5.9    -      -       -      +
    110S  THR*     2.8    41.6    +      -       -      +
    112S  LYS*     3.8    44.5    +      -       +      +
    147S  LEU*     1.3    78.2    -      -       -      +
    149S  GLU*     1.3    77.8    +      -       -      +
    150S  PRO      3.4     0.3    -      -       -      -
----------------------------------------------------------
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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