Contacts of the strand formed by residues 153 - 164 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  LEU*     5.8     0.2    -      -       -      -
    143B  ALA      3.6     1.2    -      -       -      +
    144B  VAL*     3.4     6.5    -      -       -      +
    145B  GLY      2.9    29.3    +      -       -      -
    147B  PRO*     3.6    29.5    -      -       +      +
    150B  LEU*     4.6     1.7    -      -       -      +
    151B  GLY      3.2     3.5    +      -       -      -
    152B  GLN*     1.3    71.7    -      -       -      +
    154B  ALA*     1.3    61.6    +      -       -      +
    155B  THR*     4.0    17.2    +      -       +      +
    186B  ASN*     5.2     0.5    -      -       -      +
    160C  SER*     3.7    14.4    -      -       -      -
    164C  ARG*     2.8    24.8    +      -       -      -
    177C  GLN*     3.1    25.9    +      -       -      +
    215C  ILE*     4.5     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 154 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  LEU*     4.0    18.8    -      -       +      -
     23B  LEU*     4.5     4.7    -      -       +      +
    142B  VAL*     4.2     4.5    -      -       +      -
    143B  ALA      3.2     7.9    -      -       -      +
    144B  VAL*     4.3     8.3    -      -       +      -
    153B  THR*     1.3    72.6    -      -       -      +
    155B  THR*     1.3    57.7    +      -       -      +
    137C  VAL*     3.8    25.4    -      -       +      -
    158C  ILE*     3.4     9.7    -      -       +      +
    160C  SER*     2.7    39.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 155 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142B  VAL*     3.3     4.7    -      -       -      +
    143B  ALA*     2.7    47.1    +      -       -      +
    147B  PRO*     6.0     0.9    -      -       +      -
    153B  THR*     4.0    15.5    -      -       +      +
    154B  ALA*     1.3    78.6    -      -       -      +
    156B  SER*     1.3    59.9    +      -       -      +
    180B  ALA*     4.1     1.5    -      -       -      +
    181B  SER*     2.6    42.9    +      -       -      +
    186B  ASN*     5.3     1.1    +      -       -      +
    158C  ILE*     4.0     3.8    -      -       -      -
    160C  SER*     3.9     3.6    -      -       -      +
    179C  ASP*     3.5    27.1    -      -       +      -
    214C  GLY      4.3     4.5    -      -       -      +
    215C  ILE*     5.4     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 156 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  LEU*     3.9    15.7    -      -       -      +
    140B  PHE*     5.7     4.0    -      -       -      +
    141B  ALA      3.6     8.6    +      -       -      -
    142B  VAL*     4.4     2.2    -      -       -      +
    155B  THR*     1.3    73.9    -      -       -      +
    157B  GLY*     1.3    62.5    +      -       -      +
    179B  ASP      4.6     1.6    -      -       -      +
    180B  ALA*     3.7    12.1    -      -       -      -
    181B  SER      4.7     0.2    +      -       -      -
    140C  PHE*     5.1     3.7    -      -       -      -
    157C  GLY*     5.8     1.3    -      -       -      -
    158C  ILE*     3.9    31.3    -      -       -      +
    179C  ASP*     2.9    16.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 157 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  SER*     5.8     1.8    -      -       -      -
    140B  PHE*     3.6    11.2    -      -       -      +
    141B  ALA      2.9    29.0    +      -       -      +
    156B  SER*     1.3    77.8    +      -       -      +
    158B  ILE*     1.3    64.5    +      -       -      +
    178B  THR*     4.6     0.9    -      -       -      -
    179B  ASP*     3.3    13.5    -      -       -      -
    180B  ALA*     3.8     9.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 158 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  LEU*     4.1    10.5    -      -       +      -
     19A  LEU*     5.0     0.4    -      -       +      -
    142A  VAL*     4.9     2.5    -      -       +      -
    154A  ALA*     3.4    40.2    -      -       +      +
    155A  THR*     4.0     9.6    -      -       -      -
    156A  SER*     4.0    17.0    -      -       -      +
    138B  GLY*     3.8    18.8    -      -       -      +
    139B  ASP      3.3     7.6    -      -       -      +
    140B  PHE*     3.7    28.9    -      -       +      -
    141B  ALA*     4.3     2.7    -      -       -      +
    157B  GLY*     1.3    75.3    -      -       -      -
    159B  VAL*     1.4    70.1    +      -       -      +
    160B  SER*     3.4     1.1    +      -       -      +
    178B  THR*     2.9    28.6    +      -       -      -
    179B  ASP*     2.7    24.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 159 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135B  LEU*     4.5     6.1    -      -       +      -
    136B  ARG      3.6    20.0    -      -       -      +
    137B  VAL*     3.4     6.8    -      -       -      +
    138B  GLY*     2.9    24.4    +      -       -      -
    139B  ASP*     2.7    29.2    +      -       +      +
    140B  PHE      5.2     0.2    -      -       -      +
    141B  ALA*     4.5     5.4    -      -       +      -
    158B  ILE*     1.4    71.5    -      -       -      +
    160B  SER*     1.4    58.0    +      -       -      +
    161B  ALA      3.7    21.5    -      -       -      +
    162B  LEU*     3.7    23.6    -      -       +      -
    176B  ILE*     4.0    11.9    -      -       +      -
    177B  GLN      3.7     2.7    -      -       -      -
    178B  THR*     4.8     0.7    -      -       -      +
    191B  LEU*     5.4     0.4    -      -       +      -
    199B  ILE*     4.2    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 160 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  GLN      3.9     1.9    -      -       -      +
    153A  THR*     3.6    18.0    -      -       -      -
    154A  ALA      2.7    44.6    +      -       -      -
    155A  THR*     4.0     2.0    -      -       -      +
    137B  VAL*     3.6    12.0    -      -       -      +
    158B  ILE*     3.4     1.9    +      -       -      +
    159B  VAL*     1.4    71.9    -      -       -      +
    161B  ALA*     1.4    59.5    +      -       -      +
    177B  GLN*     2.7    26.5    +      -       -      -
    178B  THR      3.8     1.5    -      -       -      -
    179B  ASP*     3.5    26.3    +      -       -      +
    214B  GLY      5.0     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 161 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  GLN      3.7     4.3    -      -       -      +
    137B  VAL*     3.8    10.1    -      -       -      +
    159B  VAL*     3.6     4.8    -      -       -      +
    160B  SER*     1.4    79.5    -      -       -      +
    162B  LEU*     1.3    69.6    +      -       -      +
    164B  ARG*     3.4    42.2    -      -       +      +
    175B  PHE      4.8     0.2    -      -       -      -
    176B  ILE*     3.8     0.5    -      -       -      -
    177B  GLN*     2.9    37.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 162 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132B  SER      5.0     2.5    -      -       -      +
    135B  LEU*     3.4    39.0    -      -       +      +
    136B  ARG*     3.8    16.2    -      -       -      -
    137B  VAL*     3.9    14.3    -      -       +      +
    159B  VAL*     3.7    19.3    -      -       +      -
    161B  ALA*     1.3    79.6    -      -       -      +
    163B  GLY*     1.3    65.3    +      -       -      +
    164B  ARG*     3.3    10.4    +      -       -      +
    175B  PHE      3.9     3.6    -      -       -      -
    176B  ILE*     3.9    23.3    -      -       +      -
    293B  LYS*     6.2     1.3    -      -       -      +
    296B  ASN*     3.6    13.2    +      -       -      +
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Residues in contact with GLY 163 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162B  LEU*     1.3    75.8    -      -       -      +
    164B  ARG*     1.3    61.8    +      -       -      +
    165B  SER*     3.6     8.0    +      -       -      -
    174B  ASN*     3.1    31.0    +      -       -      -
    175B  PHE      3.2     7.7    +      -       -      -
    176B  ILE*     5.9     0.2    -      -       -      +
    296B  ASN*     3.1    29.0    -      -       -      +
    297B  SER*     4.8     0.9    +      -       -      -
    300B  GLU*     4.8     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 164 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  LEU*     3.5    32.4    +      -       -      +
    151A  GLY*     3.1    20.2    +      -       -      -
    152A  GLN      3.2    12.1    +      -       -      +
    153A  THR*     2.8    28.9    +      -       -      -
    161B  ALA*     3.4    25.0    -      -       +      +
    162B  LEU      4.4     5.5    +      -       -      +
    163B  GLY*     1.3    75.3    -      -       -      +
    165B  SER*     1.3    65.0    +      -       -      +
    167B  LEU*     4.4    18.2    -      -       +      -
    174B  ASN      3.7     2.9    +      -       -      -
    175B  PHE*     2.9    52.0    +      -       +      +
    177B  GLN*     2.9    26.9    +      -       +      +
    217B  PHE*     4.4     3.1    -      -       +      -
----------------------------------------------------------
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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