Contacts of the strand formed by residues 238 - 242 (chain D) in PDB entry 3NJ4


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 238 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238A  ARG*     5.3    10.6    -      -       +      +
    239A  VAL      6.0     0.2    -      -       -      -
    256A  GLY*     3.6    21.0    -      -       -      +
    257A  TYR      4.5     0.6    +      -       -      -
    258A  GLU*     3.3    65.5    +      -       -      +
    402B  LEU      5.7     1.6    +      -       -      -
    403B  ASN      5.9     0.8    +      -       -      -
    213D  GLY      5.4     1.1    -      -       -      +
    214D  LYS      3.0     9.2    +      -       -      +
    215D  VAL*     3.2    34.4    -      -       +      +
    216D  ALA      2.8    25.6    +      -       -      +
    237D  ALA*     1.3    69.5    -      -       -      +
    239D  VAL*     1.3    65.4    +      -       -      +
    240D  ILE*     4.3     8.6    -      -       +      +
    258D  GLU*     4.0    17.4    +      -       -      -
    268D  GLU*     3.9    19.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 239 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216D  ALA*     3.2    10.3    -      -       +      +
    218D  VAL*     3.9    12.1    -      -       +      -
    229D  ALA*     3.7    19.1    -      -       +      +
    232D  LEU*     3.6    32.8    -      -       +      -
    233D  ARG*     3.8     4.0    -      -       -      +
    237D  ALA      3.4    10.2    +      -       -      +
    238D  ARG*     1.3    80.6    -      -       -      +
    240D  ILE*     1.3    69.4    +      -       -      +
    241D  ILE*     3.6    27.1    -      -       +      -
    257D  TYR*     3.8    26.1    -      -       +      -
    258D  GLU*     3.9     9.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 240 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215D  VAL*     4.0    24.0    -      -       +      -
    216D  ALA      2.8     9.9    +      -       -      +
    217D  VAL*     3.5    11.3    -      -       +      +
    218D  VAL      2.8    25.8    +      -       -      -
    238D  ARG*     4.3    10.1    -      -       +      +
    239D  VAL*     1.3    78.6    -      -       -      +
    241D  ILE*     1.3    71.8    +      -       -      +
    242D  THR*     5.5     0.2    -      -       +      -
    258D  GLU*     3.4    39.9    -      -       +      +
    260D  THR*     3.8    22.4    -      -       -      +
    265D  ALA*     4.3    13.0    -      -       +      -
    268D  GLU*     3.9    25.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 241 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218D  VAL*     3.4    28.3    -      -       +      +
    220D  GLY      4.6     0.9    -      -       -      +
    221D  TYR*     3.9    27.8    -      -       +      -
    229D  ALA*     4.0    12.8    -      -       +      -
    239D  VAL*     3.6    13.2    -      -       +      -
    240D  ILE*     1.3    84.2    -      -       -      +
    242D  THR*     1.3    79.5    +      -       -      +
    243D  GLU*     4.4     2.5    -      -       +      -
    252D  ALA*     4.1    12.1    -      -       +      -
    257D  TYR*     3.9    25.1    -      -       +      -
    258D  GLU      2.6    14.0    +      -       -      +
    259D  VAL*     3.1    16.6    -      -       +      -
    260D  THR      2.9    27.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 242 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407C  THR*     4.3     6.7    -      -       -      -
    217D  VAL*     4.4    16.6    -      -       +      -
    218D  VAL      3.1     6.8    +      -       -      +
    219D  ALA*     3.0    22.8    -      -       -      +
    220D  GLY*     2.8    27.7    +      -       -      -
    240D  ILE*     5.5     0.4    -      -       +      -
    241D  ILE*     1.3    77.5    -      -       -      +
    243D  GLU*     1.3    64.5    +      -       -      +
    259D  VAL*     4.7     0.7    -      -       -      -
    260D  THR      3.2    21.8    -      -       -      +
    261D  THR      4.1     2.2    -      -       -      +
    262D  MET*     4.0    26.8    -      -       +      +
    265D  ALA*     4.8     2.2    -      -       +      -
    504D  NAD      3.4    11.9    +      -       -      -
----------------------------------------------------------
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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