Contacts of the strand formed by residues 140 - 145 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  ASP*     1.3    76.6    -      -       -      +
    141A  ALA*     1.3    61.1    +      -       -      +
    156A  SER*     6.0     2.2    -      -       -      +
    157A  GLY      3.6     6.5    -      -       -      +
    158A  ILE*     3.7    25.1    -      -       +      -
    159A  VAL*     5.1     0.2    -      -       -      +
    193A  ASN*     4.0    18.2    -      -       -      +
    194A  LEU*     3.8    34.7    +      -       +      +
    199A  ILE*     4.9     3.5    -      -       -      +
     13C  PRO*     3.2    35.6    +      -       +      -
     14C  SER*     3.7    17.0    -      -       -      -
     15C  LEU*     3.9    24.0    -      -       +      -
    156C  SER*     5.2     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 141 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  ASP      3.8     0.2    +      -       -      -
    140A  PHE*     1.3    75.1    -      -       -      +
    142A  VAL*     1.4    62.0    +      -       -      +
    143A  ALA      4.2     0.4    +      -       -      -
    155A  THR      4.2     0.2    -      -       -      +
    156A  SER*     3.6     5.2    +      -       -      -
    157A  GLY      2.7    39.5    +      -       -      +
    158A  ILE      4.5     1.1    -      -       -      -
    159A  VAL*     4.4    10.3    -      -       +      -
    178A  THR*     4.3    11.0    -      -       -      +
    180A  ALA*     4.5     1.1    -      -       -      +
    191A  LEU*     3.9    25.8    -      -       +      -
    192A  LEU      3.2     9.6    -      -       -      +
    199A  ILE*     4.2    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  LEU*     3.6    28.5    -      -       +      -
     18A  MET*     3.8    22.0    -      -       +      -
     19A  LEU*     3.9    25.4    -      -       +      -
    140A  PHE*     6.4     0.2    -      -       +      -
    141A  ALA*     1.4    77.2    -      -       -      +
    143A  ALA*     1.3    59.7    +      -       -      +
    144A  VAL*     4.0    11.4    -      -       +      -
    154A  ALA*     4.3     9.6    -      -       +      -
    155A  THR      3.3    13.5    -      -       -      +
    156A  SER*     4.3     2.0    -      -       -      +
    190A  ALA      3.5     1.9    -      -       -      +
    191A  LEU*     3.5     3.1    -      -       -      -
    192A  LEU*     2.7    44.5    +      -       +      +
    193A  ASN      4.8     1.8    -      -       -      +
    194A  LEU*     5.0     7.0    -      -       +      -
    158B  ILE*     4.9     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  ALA      4.2     1.0    -      -       -      -
    142A  VAL*     1.3    71.0    -      -       -      +
    144A  VAL*     1.3    59.4    +      -       -      +
    145A  GLY      4.3     0.2    -      -       -      -
    153A  THR      3.6     1.4    -      -       -      +
    154A  ALA*     3.4     4.2    -      -       -      -
    155A  THR*     2.8    52.9    +      -       -      +
    180A  ALA*     3.9    15.9    -      -       +      +
    181A  SER      4.4     0.4    -      -       -      +
    182A  ILE*     4.0    14.8    -      -       +      -
    186A  ASN*     5.0     4.3    -      -       -      +
    190A  ALA      3.3     5.6    -      -       -      -
    191A  LEU*     4.1     8.0    -      -       +      +
    202A  ASN*     3.8    13.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  LEU*     4.4     0.4    -      -       +      -
     23A  LEU*     3.8    22.7    -      -       +      -
     26A  VAL*     3.6    27.1    -      -       +      +
    142A  VAL*     4.0    14.4    -      -       +      +
    143A  ALA*     1.3    78.8    -      -       -      +
    145A  GLY*     1.3    60.6    +      -       -      +
    152A  GLN*     3.8    26.0    -      -       +      -
    153A  THR      3.4     5.8    -      -       -      +
    154A  ALA*     4.5     2.7    -      -       +      -
    186A  ASN*     4.3     2.9    -      -       -      +
    189A  GLY*     3.4     4.9    -      -       -      -
    190A  ALA      2.7    36.9    +      -       -      +
    192A  LEU*     3.8    27.6    -      -       +      -
    202A  ASN*     4.2     2.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  VAL*     4.8     3.1    -      -       -      -
     27A  VAL      5.7     0.2    -      -       -      -
     66A  SER*     3.2    15.0    -      -       -      -
    144A  VAL*     1.3    77.4    -      -       -      +
    146A  ASN*     1.3    60.5    +      -       -      -
    147A  PRO*     3.4     8.5    -      -       -      +
    151A  GLY      3.5     1.4    -      -       -      +
    152A  GLN*     3.6     3.9    -      -       -      -
    153A  THR      2.9    33.7    +      -       -      +
    186A  ASN*     3.7    13.2    +      -       -      -
----------------------------------------------------------
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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