Contacts of the strand formed by residues 161 - 167 (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 VAL 161 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2670A    G      3.9     7.6    -      -       -      +
   2671A    U      3.3    36.3    +      -       -      +
     23D  THR*     4.4     3.4    +      -       -      +
     25D  ARG*     3.2    16.8    +      -       -      -
    109D  LEU*     4.7     5.6    -      -       +      -
    112D  THR*     4.3    17.9    -      -       +      +
    113D  LEU*     4.3    16.4    -      -       +      -
    143D  ILE*     3.8    22.4    -      -       +      -
    144D  THR      3.2    10.8    -      -       -      +
    145D  HIS*     3.9    13.9    -      -       +      -
    159D  PRO      3.9     9.1    +      -       -      +
    160D  ASP*     1.3    76.2    -      -       -      +
    162D  MET*     1.3    65.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 162 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2671A    U      3.9     2.5    -      -       -      -
   2672A    C      3.8     0.2    -      -       -      -
     23D  THR*     3.3    12.1    -      -       +      -
     25D  ARG*     3.6    15.5    -      -       -      +
     42D  ALA*     4.1    14.8    -      -       +      -
     79D  MET*     5.0     9.6    -      -       +      +
    143D  ILE*     4.8     0.9    -      -       -      -
    144D  THR*     2.6    51.0    +      -       -      +
    146D  THR*     5.0     1.3    -      -       -      -
    160D  ASP      4.4     8.5    -      -       -      +
    161D  VAL*     1.3    79.0    -      -       -      +
    163D  GLU*     1.3    56.4    +      -       -      +
    164D  THR*     4.3     3.8    -      -       -      +
    308D  LEU*     3.2    34.3    -      -       +      -
    310D  ARG*     3.1    55.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 163 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2671A    U      2.7    27.1    +      -       -      +
   2672A    C      2.8    31.8    +      -       -      +
     29D  TRP*     3.6    11.8    -      -       -      -
     85D  ARG*     2.7    24.7    +      -       -      -
     87D  TYR*     2.4    28.0    +      -       -      -
    141D  ARG*     2.9    38.5    +      -       +      +
    142D  LEU      3.4     6.1    -      -       -      +
    143D  ILE*     3.7    11.1    -      -       +      +
    162D  MET*     1.3    72.9    -      -       -      +
    164D  THR*     1.3    61.3    +      -       -      +
    310D  ARG*     3.4    13.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 164 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29D  TRP*     3.6     9.4    -      -       +      -
     38D  VAL*     3.5    20.1    -      -       +      +
     39D  GLN      3.6     6.3    -      -       -      -
     40D  GLY*     3.5    38.0    +      -       -      +
     79D  MET*     5.5     3.1    -      -       -      +
    141D  ARG*     3.8     3.4    -      -       -      -
    142D  LEU*     2.7    41.8    +      -       -      +
    144D  THR*     4.2    11.6    +      -       -      +
    162D  MET*     4.3     4.9    +      -       -      +
    163D  GLU*     1.3    73.2    -      -       -      +
    165D  ARG*     1.3    63.1    +      -       -      +
    166D  VAL*     4.2     0.5    -      -       -      +
    310D  ARG*     3.3    17.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 165 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29D  TRP*     3.6    49.4    -      -       +      +
     30D  PRO      3.9     9.7    +      -       -      -
     32D  ASP*     2.8    43.8    +      -       -      -
     38D  VAL      3.8     0.5    -      -       -      -
     39D  GLN*     2.8    53.0    +      -       -      +
    139D  ASP*     3.1    41.1    +      -       -      +
    140D  LEU      3.9     3.8    -      -       -      +
    141D  ARG*     3.6    13.0    -      -       +      +
    164D  THR*     1.3    78.8    -      -       -      +
    166D  VAL*     1.3    66.7    +      -       -      +
    167D  GLY*     3.8     2.2    -      -       -      -
    174D  ARG*     3.9    10.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 166 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  GLY      3.5    25.6    -      -       -      +
     38D  VAL*     4.4     6.3    -      -       +      +
    140D  LEU*     2.7    28.5    +      -       +      +
    141D  ARG*     4.4     0.4    -      -       -      -
    142D  LEU*     3.5    41.7    -      -       +      +
    164D  THR      4.2     2.2    -      -       -      +
    165D  ARG*     1.3    83.3    +      -       -      +
    167D  GLY*     1.3    60.1    +      -       -      +
    174D  ARG*     3.1    38.0    +      -       +      +
    177D  HIS*     4.4    12.6    -      -       +      -
    178D  ALA*     5.0     7.6    -      -       +      -
    181D  ILE*     6.0     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 167 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32D  ASP*     3.1    24.0    -      -       -      -
     33D  ASP      5.9     0.2    -      -       -      -
     35D  GLN      3.7     3.3    -      -       -      +
     36D  PRO*     3.4     0.5    -      -       -      +
     37D  GLY*     2.8    28.7    +      -       -      +
     39D  GLN*     3.7    18.6    +      -       -      +
    165D  ARG*     3.8     5.8    -      -       -      -
    166D  VAL*     1.3    74.7    -      -       -      +
    168D  GLY*     1.3    57.4    +      -       -      -
    174D  ARG*     3.8     1.6    -      -       -      -
----------------------------------------------------------
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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