Contacts of the strand formed by residues 153 - 160 (chain A) in PDB entry 1O9S


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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  VAL*     3.5     2.9    -      -       -      +
    148A  TYR*     2.8    50.6    +      -       +      -
    150A  ASP*     2.8    24.8    +      -       -      -
    152A  ARG*     1.3    77.5    -      -       -      +
    154A  ALA*     1.3    61.9    +      -       -      +
    169A  LEU*     3.9    24.0    -      -       +      -
    170A  ALA      3.9     4.0    -      -       -      +
    171A  THR*     5.0     0.7    -      -       -      +
    210A  PRO*     4.9     1.6    -      -       +      -
    211A  TYR*     4.4    14.8    -      -       +      +
    214A  GLU*     4.1    15.0    +      -       -      +
    215A  ARG*     3.9     5.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 154 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  ALA*     4.7     0.2    -      -       +      -
    146A  TYR      3.1    12.1    -      -       -      +
    147A  VAL*     4.1     6.3    -      -       +      -
    148A  TYR*     4.7     0.4    -      -       -      -
    152A  ARG      4.3     4.0    -      -       -      +
    153A  THR*     1.3    76.4    -      -       -      +
    155A  LEU*     1.3    73.3    -      -       -      +
    156A  TYR      3.9     0.2    -      -       -      -
    169A  LEU*     3.6     2.6    -      -       -      +
    170A  ALA*     2.8    38.6    +      -       +      +
    172A  LEU      4.6     0.2    -      -       -      +
    182A  PHE*     3.5    36.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  ALA*     3.2     3.7    -      -       -      -
    146A  TYR*     2.8    34.9    +      -       +      +
    148A  TYR*     3.8    32.8    -      -       +      +
    154A  ALA*     1.3    82.2    -      -       -      +
    156A  TYR*     1.3    59.4    +      -       -      +
    159A  PHE*     3.7     7.4    -      -       -      -
    164A  MET*     3.6    35.7    -      -       +      -
    167A  GLY*     4.2     7.0    -      -       -      -
    168A  LYS      3.4     4.7    -      -       -      -
    169A  LEU*     4.3     5.4    -      -       +      -
    191A  TYR*     3.8    33.9    -      -       +      -
    210A  PRO*     4.3     9.0    -      -       +      -
    310A  HIS*     5.5     1.3    -      -       +      -
    311A  PRO*     3.9    18.4    -      -       +      -
    312A  ARG*     5.8     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  GLU      5.0     2.2    -      -       -      -
    143A  LYS*     3.3    55.2    -      -       +      +
    144A  ILE      3.5    11.0    -      -       -      -
    145A  ALA*     3.9     5.6    -      -       +      -
    155A  LEU*     1.3    72.8    -      -       -      +
    157A  GLY*     1.3    60.0    +      -       -      +
    166A  GLU      4.0     0.2    -      -       -      +
    167A  GLY*     4.0     1.1    -      -       -      -
    168A  LYS*     2.8    42.2    +      -       -      +
    170A  ALA*     3.9    19.3    -      -       +      -
    182A  PHE*     3.4    45.8    -      +       +      -
    184A  LEU*     4.5    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  GLU      3.1    20.9    -      -       -      +
    144A  ILE      2.9    36.3    +      -       -      +
    155A  LEU      4.2     0.6    +      -       -      -
    156A  TYR*     1.3    79.4    -      -       -      +
    158A  LYS*     1.3    63.1    +      -       -      -
    159A  PHE*     3.6     3.6    +      -       -      -
    166A  GLU*     3.3     8.3    +      -       -      -
    168A  LYS*     5.8     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140A  THR*     6.1     1.4    -      -       -      +
    141A  GLY*     3.5    10.1    +      -       -      +
    142A  GLU*     3.2    37.2    +      -       -      +
    157A  GLY*     1.3    70.7    -      -       -      -
    159A  PHE*     1.3    68.5    +      -       -      +
    160A  ILE*     4.5    23.5    -      -       -      +
    165A  ILE*     2.8    44.2    +      -       +      -
    166A  GLU*     3.0    31.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  LEU*     4.4    16.8    -      -       +      -
    139A  MET      3.8     8.5    -      -       -      +
    140A  THR*     3.4     0.9    -      -       -      +
    141A  GLY      3.1    29.1    +      -       -      +
    144A  ILE*     3.3    50.5    -      -       +      -
    145A  ALA      4.0     0.7    -      -       -      -
    146A  TYR*     3.7    21.5    -      -       +      -
    155A  LEU      3.7    10.5    -      -       -      -
    156A  TYR      4.9     0.2    -      -       -      -
    157A  GLY      3.6     7.4    -      -       -      -
    158A  LYS*     1.3    83.3    +      -       -      +
    160A  ILE*     1.3    68.9    +      -       -      +
    162A  GLY*     3.7    15.0    -      -       -      -
    163A  GLU      3.1    22.2    -      -       -      +
    164A  MET*     3.5    32.3    -      -       +      -
    165A  ILE*     4.2     0.4    -      -       -      +
    167A  GLY*     5.0     0.9    -      -       -      -
    311A  PRO*     5.2     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140A  THR*     4.0    18.2    -      -       +      +
    158A  LYS*     4.5    21.1    -      -       -      +
    159A  PHE*     1.3    79.0    -      -       -      +
    161A  ASP*     1.3    77.4    +      -       +      +
    162A  GLY      3.2     0.2    -      -       -      -
    163A  GLU*     2.9    27.0    +      -       +      +
    165A  ILE*     3.9    27.1    -      -       +      +
----------------------------------------------------------
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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