Contacts of the strand formed by residues 110 - 122 (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 THR 110 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37S  GLY*     4.0    21.1    -      -       -      +
     38S  LYS      3.6     3.8    -      -       -      -
     39S  THR*     4.5     4.8    +      -       -      +
    108S  ALA      3.8     1.1    +      -       -      -
    109S  MET*     1.3    72.5    -      -       -      +
    111S  ILE*     1.3    74.0    +      -       -      +
    112S  LYS*     2.9     9.8    +      -       +      +
    147S  LEU*     3.2     4.8    -      -       -      -
    148S  GLU*     2.8    47.5    +      -       -      +
    149S  GLU      5.5     0.4    -      -       -      -
    150S  PRO*     4.4    15.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 111 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35S  ILE*     3.5    28.9    -      -       +      +
     36S  LYS*     3.9     5.9    -      -       -      +
     37S  GLY*     3.0    23.0    +      -       -      +
     38S  LYS      2.8    20.4    +      -       -      +
     40S  ALA*     4.3     5.2    -      -       -      +
     43S  ALA*     3.7    27.4    -      -       +      -
     92S  LEU*     4.1    10.1    -      -       +      -
    110S  THR*     1.3    72.0    -      -       -      +
    112S  LYS*     1.3    62.6    +      -       -      +
    113S  HIS      4.0     1.3    -      -       -      +
    114S  VAL*     3.9    22.9    -      -       +      -
    145S  LEU*     3.4    24.0    -      -       +      -
    146S  ILE      3.8     3.8    -      -       -      -
    147S  LEU*     4.1    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 112 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6S  VAL*     4.6    10.8    -      -       +      +
      7S  GLU      3.4    23.9    +      -       -      +
      8S  ALA*     4.7     4.6    -      -       -      +
      9S  ASP      5.4     1.2    -      -       -      +
     13S  THR*     5.0     2.1    +      -       -      +
     36S  LYS*     3.5    19.6    +      -       -      -
    110S  THR*     2.9     9.7    +      -       -      -
    111S  ILE*     1.3    73.5    -      -       -      +
    113S  HIS*     1.3    65.0    +      -       +      +
    146S  ILE*     2.9    30.0    +      -       +      +
    148S  GLU*     3.8    47.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 113 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    525A    G      3.4    26.0    +      -       -      +
      5S  SER*     3.5     8.7    +      -       -      -
      6S  VAL*     3.5    27.8    -      -       +      +
     36S  LYS*     4.9    10.1    -      -       +      +
    111S  ILE*     3.3     1.1    -      -       -      -
    112S  LYS*     1.3    86.2    -      -       +      +
    114S  VAL*     1.3    67.3    +      -       -      +
    115S  ALA*     4.0    13.8    -      -       +      +
    144S  GLU*     3.1    46.8    +      -       +      +
    145S  LEU*     3.0     9.2    -      -       -      +
    146S  ILE*     2.7    52.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 114 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    525A    G      4.7     8.7    -      -       -      +
     32S  ALA*     3.7    34.7    -      -       +      +
     35S  ILE*     4.4     8.5    -      -       +      -
     36S  LYS*     3.5    39.9    -      -       +      +
     88S  PHE*     4.1    16.4    -      -       +      -
     91S  LEU*     5.2     1.1    -      -       +      -
    111S  ILE*     3.9     4.3    -      -       +      -
    113S  HIS*     1.3    81.7    -      -       -      +
    115S  ALA*     1.3    68.6    +      -       -      +
    143S  VAL*     4.4     2.5    -      -       +      -
    144S  GLU      3.2    12.6    -      -       -      +
    145S  LEU*     3.8    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 115 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    524A    A      3.5    17.0    -      -       -      +
    525A    G      3.8    15.7    -      -       -      +
     32S  ALA*     4.3     6.3    -      -       -      -
    113S  HIS*     4.0    16.2    -      -       +      +
    114S  VAL*     1.3    79.2    -      -       -      +
    116S  ALA*     1.3    59.4    +      -       -      +
    117S  HIS*     3.7    15.1    +      -       +      -
    143S  VAL*     3.1     7.5    -      -       -      +
    144S  GLU*     3.0    34.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 116 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    524A    A      2.8    32.8    +      -       -      +
     25S  PHE*     3.6    10.4    -      -       +      -
     28S  SER*     3.6    39.9    -      -       -      +
     29S  LYS*     4.3     3.5    -      -       -      +
     32S  ALA*     4.5     3.0    -      -       -      +
     88S  PHE*     4.9     1.6    -      -       +      -
    115S  ALA*     1.3    72.2    -      -       -      +
    117S  HIS*     1.3    63.9    +      -       -      +
    141S  VAL*     4.0     9.4    -      -       +      -
    142S  ASP      3.5     4.7    -      -       -      -
    143S  VAL*     4.1     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 117 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A    G      3.2    35.1    +      -       -      +
     21A    G      4.6     6.7    -      -       -      +
    523A    C      5.7     1.3    -      -       -      +
    524A    A      3.2    29.3    +      -       -      -
      2S  ILE*     3.8    35.2    -      -       +      +
      5S  SER*     4.8     1.2    +      -       -      -
     25S  PHE*     3.6     6.3    -      -       -      -
    115S  ALA*     3.7    25.2    +      -       +      -
    116S  ALA*     1.3    75.1    -      -       -      +
    118S  LYS*     1.3    63.5    +      -       -      +
    119S  VAL*     3.2     2.3    +      -       +      +
    141S  VAL*     3.6     1.4    -      -       -      -
    142S  ASP      2.9    32.6    +      -       -      +
    144S  GLU*     3.1    29.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 118 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A    G      4.0    16.4    +      -       -      +
     22A    U      4.2     8.3    +      -       -      +
    523A    C      5.1     3.7    +      -       -      +
   1366A    C      4.7    17.4    +      -       -      +
     25S  PHE*     3.3    37.0    -      -       +      -
    117S  HIS*     1.3    68.2    -      -       -      +
    119S  VAL*     1.3    61.8    +      -       -      +
    120S  GLY*     4.0    13.9    -      -       -      +
    121S  GLU*     3.5    39.3    +      -       -      -
    139S  PRO*     4.1    14.4    -      -       -      +
    140S  GLN      3.5     8.3    -      -       -      +
   8506S   CL      3.3    29.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 119 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A    G      4.3     9.6    -      -       -      +
     22A    U      3.4    41.7    -      -       -      +
     23A    G      5.0     1.6    +      -       -      -
      1S  GLY*     4.2    11.2    -      -       -      +
      2S  ILE*     4.4     3.4    -      -       +      -
     20S  GLU*     4.7    16.6    -      -       +      +
    117S  HIS      3.6     4.7    -      -       -      +
    118S  LYS*     1.3    73.4    -      -       -      +
    120S  GLY*     1.3    56.1    +      -       -      +
    140S  GLN*     2.8    17.0    +      -       +      +
    142S  ASP*     3.1    47.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 120 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A    U      5.1     6.1    -      -       -      -
     23A    G      5.5     2.7    -      -       -      -
    118S  LYS*     3.4    10.4    +      -       -      +
    119S  VAL*     1.3    82.0    -      -       -      +
    121S  GLU*     1.3    65.6    +      -       -      +
    139S  PRO*     3.6     1.0    -      -       -      +
    140S  GLN*     2.7    41.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 121 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1366A    C      6.0     1.6    -      -       -      -
   2054A    A      4.9     5.2    +      -       -      -
    118S  LYS*     3.5    28.2    +      -       -      -
    120S  GLY*     1.3    79.7    -      -       -      +
    122S  GLN*     1.3    59.8    +      -       -      +
    123S  GLN*     3.0    21.1    +      -       +      +
    137S  ASN*     3.2    40.4    +      -       +      +
    138S  SER      3.1    10.9    -      -       -      +
    139S  PRO*     4.6     2.5    -      -       +      +
    140S  GLN*     3.6     7.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 122 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1427A    A      4.1     1.4    +      -       -      +
   1428A    C      2.9    39.1    +      -       -      +
   1429A    U      3.7    24.2    +      -       -      +
     22S  GLN*     3.0    25.7    +      -       -      +
    121S  GLU*     1.3    69.0    -      -       -      +
    123S  GLN*     1.3    67.5    +      -       -      +
    136S  TRP      4.6     0.2    -      -       -      +
    137S  ASN*     3.5     1.7    -      -       -      -
    138S  SER*     2.7    47.6    +      -       -      +
    140S  GLN*     3.9    20.1    +      -       +      +
----------------------------------------------------------
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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