Contacts of the strand formed by residues 139 - 143 (chain A) in PDB entry 3LJK


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 ASP 139 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  ILE*     3.4     6.2    -      -       -      +
    138A  THR*     1.3   101.8    +      -       -      +
    140A  ILE*     1.3    65.5    +      -       -      +
    168A  LYS*     3.3    23.4    -      -       -      +
    170A  HIS*     2.8    25.2    +      -       +      +
    186A  VAL      4.5     5.4    -      -       -      +
    187A  VAL*     3.7    27.6    -      -       +      +
    188A  ASP      5.2     0.2    +      -       -      -
    191A  THR*     3.3     3.6    +      -       -      +
    192A  THR*     3.3    14.2    +      -       +      +
    193A  LEU      3.0    24.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 140 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  VAL*     4.3     0.7    -      -       +      -
    137A  ILE*     4.0    10.1    -      -       +      -
    139A  ASP*     1.3    81.0    -      -       -      +
    141A  VAL*     1.3    65.7    +      -       -      +
    167A  LEU*     3.9    24.9    -      -       +      -
    168A  LYS      2.8     8.5    +      -       -      +
    169A  VAL*     3.4    17.6    -      -       +      -
    170A  HIS*     2.9    30.3    +      -       -      +
    193A  LEU*     3.2    26.2    -      -       +      +
    195A  ILE*     3.6    31.0    -      -       +      -
    271A  SER*     5.0     0.4    -      -       -      -
    274A  PHE*     3.9    36.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 141 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140A  ILE*     1.3    79.5    -      -       -      +
    142A  ASN*     1.3    64.9    +      -       -      +
    143A  ILE*     3.7     6.1    +      -       +      +
    170A  HIS*     3.5    21.1    -      -       +      +
    172A  VAL*     3.6    31.0    -      -       +      -
    180A  LEU*     5.7     1.6    -      -       +      -
    183A  ALA*     4.2    12.3    -      -       +      -
    184A  LEU*     5.8     1.6    -      -       +      -
    187A  VAL*     4.4     9.4    -      -       +      -
    192A  THR*     3.6    22.4    -      -       +      -
    193A  LEU      3.0     8.5    +      -       -      -
    194A  LEU*     3.3    24.6    -      -       +      +
    195A  ILE      2.8    26.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140A  ILE*     4.1     2.0    -      -       -      +
    141A  VAL*     1.3    72.7    -      -       -      +
    143A  ILE*     1.3    62.0    +      -       -      +
    144A  GLY      4.2     4.8    +      -       -      +
    148A  SER      3.0    27.1    +      -       -      -
    149A  ASP*     4.4     2.8    +      -       -      +
    152A  PRO*     5.2     2.6    -      -       -      +
    170A  HIS      2.8    16.1    +      -       -      +
    171A  PHE*     3.8    25.1    -      -       +      -
    172A  VAL*     2.8    31.8    +      -       -      +
    195A  ILE*     3.6    30.6    -      -       +      +
    197A  ALA*     4.5     5.3    -      -       -      +
    234A  ILE*     5.1     0.3    -      -       -      +
    268A  ILE      4.8     6.5    +      -       -      +
    270A  MSE      5.5     0.2    -      -       -      +
    271A  SER*     4.0    21.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  VAL*     4.2    14.6    -      -       +      +
    142A  ASN*     1.3    77.6    -      -       -      +
    144A  GLY*     1.3    59.8    +      -       -      +
    172A  VAL*     3.4    13.5    -      -       +      +
    180A  LEU*     5.3     1.8    -      -       +      -
    194A  LEU*     4.1    14.4    -      -       +      -
    195A  ILE      2.8    19.4    +      -       -      +
    196A  ILE*     3.8    11.6    -      -       +      -
    197A  ALA*     2.9    30.1    +      -       -      +
    206A  THR*     3.8    19.9    -      -       +      +
    209A  ASN*     3.5    35.0    -      -       +      +
    210A  SER*     4.3     8.1    -      -       -      +
    213A  ALA*     3.9    27.8    -      -       +      -
    231A  PHE*     4.7     0.9    -      -       +      -
----------------------------------------------------------
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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