Contacts of the strand formed by residues 153 - 164 (chain D) 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 THR 153 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143D  ALA      3.6     1.2    -      -       -      +
    144D  VAL*     3.4     6.2    -      -       -      +
    145D  GLY      2.8    31.6    +      -       -      -
    147D  PRO*     3.7    30.0    -      -       +      +
    150D  LEU*     4.7     1.4    -      -       -      +
    151D  GLY      3.0     4.7    +      -       -      -
    152D  GLN*     1.3    71.3    -      -       -      +
    154D  ALA*     1.3    60.8    -      -       -      +
    155D  THR*     4.1    17.0    -      -       +      +
    186D  ASN*     4.8     2.4    -      -       -      +
    160E  SER*     3.7    13.2    -      -       -      -
    164E  ARG*     2.8    24.8    +      -       -      -
    177E  GLN*     3.3    25.5    +      -       -      +
    215E  ILE*     4.5     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 154 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19D  LEU*     4.6     4.5    -      -       +      -
     23D  LEU*     4.6     7.2    -      -       +      -
    142D  VAL*     4.3    11.2    -      -       +      -
    143D  ALA      3.2     7.0    -      -       -      +
    144D  VAL*     4.4     9.0    -      -       +      +
    153D  THR*     1.3    73.1    -      -       -      +
    155D  THR*     1.3    58.3    +      -       -      +
    137E  VAL*     3.9    24.9    -      -       +      -
    158E  ILE*     3.3    13.8    -      -       +      +
    160E  SER*     2.8    39.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 155 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142D  VAL*     3.3     5.4    -      -       -      +
    143D  ALA*     2.7    45.8    +      -       -      +
    153D  THR*     4.1    14.6    -      -       +      -
    154D  ALA*     1.3    78.7    -      -       -      +
    156D  SER*     1.3    59.9    +      -       -      +
    180D  ALA*     4.1     1.5    -      -       -      +
    181D  SER*     2.6    43.9    +      -       -      +
    186D  ASN*     5.2     1.4    +      -       -      -
    158E  ILE*     4.0     4.0    -      -       -      -
    160E  SER*     4.0     3.8    -      -       -      +
    179E  ASP*     3.5    27.4    -      -       +      -
    214E  GLY      4.4     4.5    -      -       -      +
    215E  ILE*     5.4     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 156 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15D  LEU*     3.9    16.3    -      -       -      +
    140D  PHE*     5.6     5.0    -      -       -      +
    141D  ALA      3.6     7.5    +      -       -      -
    142D  VAL*     4.4     2.3    -      -       -      +
    155D  THR*     1.3    74.8    -      -       -      +
    157D  GLY*     1.3    62.3    +      -       -      +
    179D  ASP      4.6     1.4    -      -       -      +
    180D  ALA*     3.7    12.5    -      -       -      -
    181D  SER      4.7     0.5    +      -       -      -
    194D  LEU*     6.1     0.3    -      -       -      +
    140E  PHE*     5.2     3.7    -      -       -      -
    157E  GLY*     6.0     0.9    -      -       -      -
    158E  ILE*     4.0    29.0    -      -       -      +
    179E  ASP*     3.0    15.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 157 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140D  PHE*     3.6    11.1    -      -       -      +
    141D  ALA*     2.9    30.0    +      -       -      +
    156D  SER*     1.3    78.1    +      -       -      +
    158D  ILE*     1.3    65.3    +      -       -      +
    178D  THR*     4.6     0.7    -      -       -      -
    179D  ASP*     3.3    13.5    -      -       -      -
    180D  ALA*     3.8     8.9    -      -       -      +
    156F  SER*     6.1     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 158 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138D  GLY*     3.9    14.4    -      -       -      +
    139D  ASP      3.3     6.5    -      -       -      +
    140D  PHE*     3.7    29.2    -      -       +      -
    141D  ALA*     4.6     2.2    -      -       -      -
    157D  GLY*     1.3    76.3    -      -       -      -
    159D  VAL*     1.3    72.3    +      -       -      +
    160D  SER      3.4     0.7    +      -       -      -
    178D  THR*     2.8    27.2    +      -       -      -
    179D  ASP*     2.7    23.8    +      -       -      +
     15F  LEU*     3.9    18.4    -      -       +      -
     19F  LEU*     5.0     0.4    -      -       +      -
    142F  VAL*     4.7     2.5    -      -       +      -
    154F  ALA*     3.3    40.8    -      -       +      +
    155F  THR*     3.9    10.1    -      -       -      -
    156F  SER*     3.9    11.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 159 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135D  LEU*     4.5     7.2    -      -       +      -
    136D  ARG      3.7    20.4    -      -       -      +
    137D  VAL*     3.4     7.3    -      -       -      +
    138D  GLY*     2.9    24.8    +      -       -      -
    139D  ASP*     2.8    28.8    +      -       +      +
    140D  PHE      5.1     0.2    -      -       -      +
    141D  ALA*     4.5     5.4    -      -       +      -
    158D  ILE*     1.3    73.6    -      -       -      +
    160D  SER*     1.3    58.0    +      -       -      +
    161D  ALA      3.7    20.0    -      -       -      +
    162D  LEU*     3.8    24.2    -      -       +      -
    176D  ILE*     4.0    11.0    -      -       +      -
    177D  GLN      3.7     3.1    -      -       -      -
    178D  THR*     4.8     0.7    -      -       -      +
    191D  LEU*     5.6     0.4    -      -       +      -
    199D  ILE*     4.3    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 160 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137D  VAL*     3.5    12.3    -      -       -      +
    158D  ILE      3.4     2.0    +      -       -      -
    159D  VAL*     1.3    73.0    -      -       -      +
    161D  ALA*     1.4    59.9    +      -       -      +
    177D  GLN*     2.7    28.3    +      -       -      -
    178D  THR*     3.8     1.2    -      -       -      -
    179D  ASP*     3.5    20.4    +      -       -      +
    214D  GLY      4.9     0.2    +      -       -      -
    152F  GLN      4.2     1.4    -      -       -      +
    153F  THR*     3.7    18.3    -      -       -      -
    154F  ALA      2.6    43.4    +      -       -      -
    155F  THR*     3.9     7.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 161 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137D  VAL*     3.8    10.0    -      -       -      +
    159D  VAL*     3.6     4.6    -      -       -      +
    160D  SER*     1.4    79.2    -      -       -      +
    162D  LEU*     1.3    66.5    +      -       -      +
    164D  ARG*     3.4    42.8    -      -       +      +
    175D  PHE      4.8     0.4    -      -       -      -
    176D  ILE*     3.7     0.9    -      -       -      -
    177D  GLN*     2.9    38.8    +      -       +      +
    152F  GLN      3.9     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 162 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132D  SER      4.9     3.6    -      -       -      +
    135D  LEU*     3.4    43.1    -      -       +      +
    136D  ARG*     3.8    11.9    -      -       -      -
    137D  VAL*     4.0    14.4    -      -       +      +
    159D  VAL*     3.8    18.4    -      -       +      -
    161D  ALA*     1.3    78.8    -      -       -      +
    163D  GLY*     1.3    66.9    +      -       -      +
    164D  ARG*     3.3    10.2    +      -       -      +
    175D  PHE      3.9     3.6    -      -       -      -
    176D  ILE*     3.9    22.9    -      -       +      -
    293D  LYS*     6.4     0.2    -      -       -      +
    296D  ASN*     3.5    12.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 163 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162D  LEU*     1.3    75.4    -      -       -      +
    164D  ARG*     1.4    60.7    +      -       -      +
    165D  SER*     3.6     7.8    +      -       -      -
    174D  ASN*     3.1    32.1    +      -       -      +
    175D  PHE      3.2     6.9    +      -       -      -
    176D  ILE*     5.9     0.2    -      -       -      +
    296D  ASN*     3.1    29.4    -      -       -      +
    297D  SER*     4.8     0.5    +      -       -      -
    300D  GLU*     4.8     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 164 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161D  ALA*     3.4    25.0    -      -       +      +
    162D  LEU      4.5     6.1    +      -       -      +
    163D  GLY*     1.4    73.6    -      -       -      +
    165D  SER*     1.3    63.4    +      -       -      +
    167D  LEU*     4.4    11.4    -      -       +      -
    173D  GLU*     3.8     0.2    -      -       -      +
    174D  ASN      3.7     1.7    +      -       -      -
    175D  PHE*     2.9    53.1    +      -       +      +
    177D  GLN*     2.8    27.0    +      -       +      +
    217D  PHE*     4.4    10.3    -      -       +      -
    150F  LEU*     3.4    32.3    +      -       -      +
    151F  GLY*     3.5    14.3    +      -       -      -
    152F  GLN      2.8    18.4    +      -       -      +
    153F  THR*     2.8    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