Contacts of the strand formed by residues 146 - 150 (chain g) in PDB entry 3J7Y


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 146 (chain g).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1879A    G      5.3     3.8    -      -       -      +
    109g  VAL*     4.9     5.8    -      -       +      -
    110g  ILE      3.2     8.7    -      -       -      -
    111g  ARG*     3.6    30.3    -      -       +      +
    113g  VAL*     4.8     1.3    -      -       -      -
    117g  ILE*     4.1     7.8    -      -       -      +
    139g  GLN*     4.9     0.9    +      -       -      -
    140g  VAL*     3.8     1.4    -      -       -      -
    141g  ASN*     3.4    32.4    +      -       -      +
    144g  THR*     2.5    37.2    +      -       -      +
    145g  GLY*     1.3    76.5    -      -       -      -
    147g  LEU*     1.3    69.5    +      -       -      +
    148g  ARG*     5.3     5.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 147 (chain g). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108g  THR      3.4     3.3    -      -       -      +
    109g  VAL*     3.5     2.3    -      -       -      +
    110g  ILE*     2.8    38.5    +      -       +      +
    113g  VAL*     5.1     1.8    -      -       +      -
    117g  ILE*     4.5     6.7    -      -       +      +
    120g  LEU*     3.4    31.6    -      -       +      -
    121g  GLN*     3.7    23.6    -      -       +      +
    124g  VAL*     4.8     4.3    -      -       +      -
    138g  THR*     3.8    25.4    -      -       +      -
    139g  GLN      3.7     4.0    -      -       -      +
    140g  VAL*     3.8    13.9    -      -       +      -
    146g  THR*     1.3    80.9    -      -       -      +
    148g  ARG*     1.3    63.0    +      -       -      +
    149g  ILE*     3.2    33.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 148 (chain g). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1881A    A      5.4     4.6    -      -       -      +
     99g  ASP*     2.7    31.1    +      -       -      +
    107g  MET*     3.5    33.4    -      -       +      +
    108g  THR      3.6     5.6    -      -       -      -
    109g  VAL*     3.2    38.2    -      -       +      +
    138g  THR*     3.5     0.3    -      -       -      -
    139g  GLN*     2.8    64.4    +      -       +      +
    146g  THR*     5.5     4.7    -      -       -      +
    147g  LEU*     1.3    70.0    -      -       -      +
    149g  ILE*     1.3    61.1    +      -       -      +
     82o  PHE*     3.3    13.0    -      -       +      -
     83o  PRO*     5.5     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 149 (chain g). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107g  MET*     3.3     4.3    -      -       -      +
    108g  THR*     2.8    41.7    +      -       +      +
    110g  ILE*     3.8    17.3    -      -       +      -
    124g  VAL*     3.6    23.6    -      -       +      -
    128g  LEU*     4.2     9.2    -      -       +      -
    136g  PRO*     4.3    13.5    -      -       +      -
    137g  VAL      3.9     4.5    -      -       -      +
    138g  THR*     4.1     6.7    -      -       +      +
    147g  LEU*     3.6    23.8    -      -       +      +
    148g  ARG*     1.3    72.8    -      -       -      +
    150g  LYS*     1.3    71.0    -      -       -      +
    151g  GLY      3.6     0.2    -      -       -      +
    153g  PHE*     4.0    18.8    -      -       +      -
    157g  LEU*     3.7    25.6    -      -       +      -
     82o  PHE*     4.3     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 150 (chain g). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2052A    A      3.1    34.0    +      -       -      -
   2053A    U      2.7    30.4    +      -       -      +
    105g  ARG*     5.1     4.5    -      -       +      +
    106g  GLN      4.5     4.5    -      -       -      +
    107g  MET*     4.3     5.2    -      -       +      -
    132g  LEU*     5.3     0.9    -      -       -      +
    136g  PRO      3.9     9.0    -      -       -      +
    137g  VAL*     3.3    26.6    +      -       +      +
    149g  ILE*     1.3    70.1    -      -       -      +
    151g  GLY*     1.3    69.8    +      -       -      +
    153g  PHE*     3.3    18.4    -      -       -      -
     79o  THR*     2.8    36.6    +      -       -      +
     81o  LYS      4.9     1.1    -      -       -      -
     82o  PHE*     3.6    28.3    -      -       +      -
----------------------------------------------------------
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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