Contacts of the strand formed by residues 140 - 145 (chain C) in PDB entry 3STJ


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 PHE 140 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  PRO*     3.2    30.7    +      -       +      -
     14B  SER*     3.6    24.0    -      -       -      -
     15B  LEU*     3.8    26.5    -      -       +      -
    156B  SER*     5.1     3.8    -      -       -      -
    139C  ASP*     1.3    77.6    -      -       -      +
    141C  ALA*     1.3    59.4    +      -       -      +
    142C  VAL*     6.3     0.2    -      -       +      -
    156C  SER*     5.6     4.0    -      -       -      +
    157C  GLY      3.6     7.2    -      -       -      +
    158C  ILE*     3.7    24.0    -      -       +      -
    159C  VAL*     5.2     0.4    -      -       -      +
    193C  ASN*     3.9    19.3    -      -       -      +
    194C  LEU*     3.8    34.1    +      -       +      +
    199C  ILE*     4.8     2.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 141 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139C  ASP      3.8     0.4    +      -       -      -
    140C  PHE*     1.3    75.0    -      -       -      +
    142C  VAL*     1.3    65.5    +      -       -      +
    155C  THR      4.2     0.2    -      -       -      +
    156C  SER*     3.6     3.3    +      -       -      -
    157C  GLY      2.9    35.0    +      -       -      +
    158C  ILE      4.5     1.6    -      -       -      -
    159C  VAL*     4.5     9.2    -      -       +      -
    178C  THR*     4.2    13.0    -      -       -      +
    180C  ALA*     4.5     1.5    -      -       -      +
    191C  LEU*     3.9    22.4    -      -       +      -
    192C  LEU      3.2     8.7    -      -       -      +
    199C  ILE*     4.1    13.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 142 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158A  ILE*     4.8     2.9    -      -       +      -
     15C  LEU*     3.8    27.1    -      -       +      -
     18C  MET*     4.0    21.3    -      -       +      -
     19C  LEU*     4.0    24.0    -      -       +      -
    140C  PHE*     6.3     0.2    -      -       +      -
    141C  ALA*     1.3    77.9    -      -       -      +
    143C  ALA*     1.4    64.3    +      -       -      +
    144C  VAL*     4.2     2.9    -      -       +      -
    154C  ALA*     4.2    11.2    -      -       +      -
    155C  THR      3.3    14.6    -      -       -      +
    156C  SER*     4.4     3.6    -      -       -      +
    190C  ALA      3.6     1.7    -      -       -      +
    191C  LEU*     3.5     3.9    -      -       -      -
    192C  LEU*     2.8    47.0    +      -       +      +
    193C  ASN      4.9     0.2    -      -       -      +
    194C  LEU*     4.9     6.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 143 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141C  ALA      4.2     0.6    -      -       -      -
    142C  VAL*     1.4    71.8    -      -       -      +
    144C  VAL*     1.3    60.4    +      -       -      +
    145C  GLY      4.1     0.4    -      -       -      -
    153C  THR      3.6     1.2    -      -       -      +
    154C  ALA*     3.2     4.3    -      -       -      -
    155C  THR*     2.8    53.5    +      -       -      +
    180C  ALA*     4.1     8.9    -      -       +      +
    181C  SER      4.4     0.4    -      -       -      +
    182C  ILE*     4.0    19.1    -      -       +      -
    186C  ASN*     4.5     4.6    -      -       -      +
    190C  ALA      3.2     5.2    -      -       -      -
    191C  LEU*     4.2     7.9    -      -       +      +
    202C  ASN*     3.6    15.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 144 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19C  LEU*     4.3     1.1    -      -       +      -
     22C  VAL*     5.7     0.2    -      -       +      -
     23C  LEU*     3.6    33.0    -      -       +      -
     26C  VAL*     3.5    25.5    -      -       +      +
    142C  VAL*     4.2    10.8    -      -       +      -
    143C  ALA*     1.3    76.0    -      -       -      +
    145C  GLY*     1.3    60.4    +      -       -      +
    152C  GLN*     3.7    25.8    -      -       +      +
    153C  THR      3.4     4.5    -      -       -      +
    154C  ALA*     4.3     3.4    -      -       +      -
    186C  ASN*     4.5     1.8    -      -       -      -
    189C  GLY*     3.7     2.1    -      -       -      -
    190C  ALA*     2.7    36.5    +      -       +      +
    192C  LEU*     3.8    27.6    -      -       +      -
    202C  ASN*     4.3     0.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 145 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26C  VAL*     4.8     2.9    -      -       -      -
     66C  SER*     3.4    16.6    -      -       -      -
    144C  VAL*     1.3    75.5    -      -       -      +
    146C  ASN*     1.3    58.4    +      -       -      -
    147C  PRO*     3.4     8.0    -      -       -      +
    152C  GLN*     3.5     6.2    -      -       -      -
    153C  THR      2.8    33.5    +      -       -      +
    186C  ASN*     3.8    15.9    +      -       -      -
----------------------------------------------------------
 Back to top of page


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