Contacts of the strand formed by residues 117 - 125 (chain J) 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 LYS 117 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94J  ARG*     4.0     2.7    -      -       -      -
     95J  GLU      3.1    13.8    +      -       -      +
     97J  LYS*     3.5    49.9    -      -       +      +
    116J  GLY*     1.3    73.9    -      -       -      -
    118J  PRO*     1.4    79.8    -      -       +      +
    119J  VAL*     3.2    11.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 118 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14J  TYR*     5.0     7.0    -      -       +      +
     20J  ILE*     4.0    17.3    -      -       +      -
     21J  SER      3.7    17.5    -      -       -      +
     22J  GLY*     3.8    24.2    -      -       -      +
     23J  ILE*     4.6     1.1    -      -       -      -
     24J  PRO*     4.5     8.0    -      -       +      +
     92J  VAL*     4.2    15.9    -      -       +      -
     93J  ILE      3.7     8.5    -      -       -      +
     94J  ARG*     4.4     3.4    -      -       +      -
    115J  PHE*     6.4     0.7    -      -       +      -
    116J  GLY      4.4     3.1    -      -       -      +
    117J  LYS*     1.4    91.6    -      -       +      +
    119J  VAL*     1.3    63.0    +      -       -      +
    120J  GLY      3.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 119 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6J  TYR*     3.6    27.6    -      -       +      +
     24J  PRO*     3.6    15.0    -      -       -      +
     58J  HIS*     5.3     1.7    -      -       -      -
     93J  ILE*     2.9    19.1    +      -       +      +
     94J  ARG      3.8     6.3    -      -       -      -
     95J  GLU*     3.8    18.4    -      -       +      +
     97J  LYS*     3.9    25.8    -      -       +      +
    117J  LYS*     3.2    17.9    -      -       +      +
    118J  PRO*     1.3    75.8    -      -       -      +
    120J  GLY*     1.3    59.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 120 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24J  PRO*     3.9    15.7    -      -       -      +
     58J  HIS*     4.5     8.5    -      -       -      -
     92J  VAL*     3.6     5.4    -      -       -      +
     93J  ILE*     2.7    43.5    +      -       -      +
    118J  PRO      3.8     0.8    -      -       -      -
    119J  VAL*     1.3    81.8    -      -       -      +
    121J  THR*     1.3    65.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 121 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17J  ARG*     4.2     9.6    -      -       -      +
     23J  ILE*     3.6    26.7    -      -       +      -
     24J  PRO*     4.4     8.9    +      -       -      +
     26J  LYS*     4.9     3.8    -      -       -      +
     57J  ARG*     3.5     3.1    -      -       -      +
     58J  HIS*     3.1    45.1    +      -       -      +
     89J  PRO*     3.5    28.9    -      -       -      +
     91J  HIS      3.3     9.9    -      -       -      +
     92J  VAL*     4.5     4.9    -      -       +      -
     93J  ILE*     3.7     6.6    -      -       -      +
    120J  GLY*     1.3    79.9    -      -       -      +
    122J  ALA*     1.3    64.0    +      -       -      +
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Residues in contact with ALA 122 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6J  TYR      5.6     0.4    -      -       -      +
     55J  GLN*     4.3    13.9    -      -       +      +
     56J  ILE      3.2    25.1    -      -       -      +
     57J  ARG*     3.7     6.5    -      -       +      +
     89J  PRO*     3.1    12.4    -      -       -      +
     91J  HIS*     2.9    38.6    +      -       +      +
     93J  ILE*     3.9    17.3    -      -       +      -
    121J  THR*     1.3    77.3    -      -       -      +
    123J  ALA*     1.3    59.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 123 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55J  GLN*     3.4     1.7    -      -       -      -
     56J  ILE*     2.7    44.6    +      -       +      +
     61J  LEU*     4.3    11.0    -      -       +      -
     87J  LYS*     4.3    19.3    -      -       +      -
     88J  PHE      3.6    22.4    -      -       -      +
     89J  PRO*     3.7     7.6    -      -       +      +
     90J  PHE      4.5     0.4    -      -       -      +
    122J  ALA*     1.3    74.7    -      -       -      +
    124J  ARG*     1.3    63.7    +      -       -      +
    125J  VAL*     3.6     6.8    +      -       +      +
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Residues in contact with ARG 124 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1004A    C      4.3    14.0    +      -       -      -
   1005A    A      5.8     2.7    +      -       -      -
      9J  SER*     3.6    27.7    +      -       -      +
     11J  LYS*     2.5    38.0    +      -       -      +
     13J  ALA*     3.8    24.0    -      -       -      +
     54J  VAL      3.5     4.5    -      -       -      +
     55J  GLN*     2.7    30.8    -      -       +      +
     87J  LYS*     4.7     3.6    -      -       -      +
     91J  HIS*     3.3    32.7    +      -       +      +
    122J  ALA      4.1     0.8    +      -       -      -
    123J  ALA*     1.3    72.2    -      -       -      +
    125J  VAL*     1.3    63.0    +      -       -      +
    126J  HIS*     4.3    13.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 125 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50J  VAL*     3.8    33.7    -      -       +      -
     52J  LYS      3.9     0.9    -      -       -      +
     53J  PRO*     3.0     2.9    -      -       -      +
     54J  VAL*     2.9    34.9    +      -       +      +
     56J  ILE*     4.0    20.6    -      -       +      -
     61J  LEU*     6.3     0.2    -      -       +      -
     87J  LYS*     4.1    27.4    -      -       +      +
    123J  ALA*     3.9    12.6    -      -       +      +
    124J  ARG*     1.3    79.9    -      -       -      +
    126J  HIS*     1.3    68.9    +      -       -      +
    129J  ASN*     3.9    17.9    -      -       +      +
    131J  ILE*     5.0     6.5    -      -       +      -
----------------------------------------------------------
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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