Contacts of the strand formed by residues 153 - 160 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147B  VAL*     3.6     2.6    -      -       -      +
    148B  TYR*     2.8    54.1    +      -       +      -
    150B  ASP*     2.7    31.0    +      -       -      -
    152B  ARG*     1.3    77.5    -      -       -      +
    154B  ALA*     1.3    57.4    +      -       -      +
    169B  LEU*     3.8    23.3    -      -       +      -
    170B  ALA      3.8     4.5    -      -       -      +
    171B  THR*     5.0     0.9    -      -       -      +
    210B  PRO*     5.1     0.4    -      -       +      -
    211B  TYR*     4.4    10.7    -      -       -      +
    214B  GLU*     3.5    24.7    +      -       -      +
    215B  ARG*     4.1     0.2    +      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
    145B  ALA*     4.5     3.6    -      -       +      -
    146B  TYR      3.1    13.2    -      -       -      +
    147B  VAL*     4.1     5.2    -      -       +      -
    148B  TYR*     4.4     2.0    -      -       -      -
    152B  ARG      4.4     2.0    -      -       -      +
    153B  THR*     1.3    76.6    -      -       -      +
    155B  LEU*     1.3    72.7    +      -       -      +
    156B  TYR      3.9     0.4    -      -       -      -
    169B  LEU*     3.5     2.9    -      -       -      +
    170B  ALA*     2.9    36.6    +      -       +      +
    182B  PHE*     3.6    37.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 155 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145B  ALA*     3.3     2.1    -      -       -      -
    146B  TYR*     2.8    36.6    +      -       +      +
    148B  TYR*     3.7    31.9    -      -       +      +
    154B  ALA*     1.3    82.6    -      -       -      +
    156B  TYR*     1.3    59.9    +      -       -      +
    159B  PHE*     3.6     8.0    -      -       -      -
    164B  MET*     3.6    38.8    -      -       +      -
    167B  GLY*     4.4     4.3    -      -       -      -
    168B  LYS      3.5     3.4    -      -       -      -
    169B  LEU*     4.2     7.6    -      -       +      -
    191B  TYR*     3.9    36.3    -      -       +      -
    210B  PRO*     4.3     6.5    -      -       +      -
    310B  HIS*     5.4     2.5    -      -       +      -
    311B  PRO*     3.9    13.9    -      -       +      -
    312B  ARG*     5.7     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 156 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142B  GLU      4.5     4.5    -      -       -      -
    143B  LYS*     3.1    57.6    -      -       +      +
    144B  ILE      3.5    10.1    -      -       -      -
    145B  ALA*     3.8     7.9    -      -       +      -
    155B  LEU*     1.3    73.8    -      -       -      +
    157B  GLY*     1.3    59.7    +      -       -      +
    166B  GLU      3.8     0.2    -      -       -      +
    167B  GLY*     3.6     2.6    -      -       -      -
    168B  LYS*     2.8    44.6    +      -       -      +
    170B  ALA*     4.0    15.7    -      -       +      -
    182B  PHE*     3.3    42.2    -      +       +      -
    184B  LEU*     4.4    18.6    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
    141B  GLY      3.5     1.4    -      -       -      +
    142B  GLU      3.2    20.7    -      -       -      +
    144B  ILE      2.8    36.0    +      -       -      +
    156B  TYR*     1.3    81.1    -      -       -      +
    158B  LYS*     1.3    62.7    +      -       -      -
    159B  PHE*     3.5     4.1    -      -       -      -
    166B  GLU*     3.3     7.4    -      -       -      -
    168B  LYS*     5.8     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 158 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141B  GLY      3.3    10.3    -      -       -      +
    142B  GLU*     3.3    34.4    +      -       -      +
    157B  GLY*     1.3    70.7    -      -       -      -
    159B  PHE*     1.3    68.3    +      -       -      +
    160B  ILE*     4.4    22.0    -      -       +      +
    165B  ILE*     2.9    44.2    +      -       +      +
    166B  GLU*     3.0    29.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 159 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129B  LEU*     5.0     6.7    -      -       +      -
    139B  MET      3.8     6.1    -      -       -      +
    140B  THR*     3.4     1.0    -      -       -      +
    141B  GLY      3.1    28.2    +      -       -      +
    144B  ILE*     3.4    52.3    -      -       +      -
    145B  ALA      4.1     0.7    -      -       -      -
    146B  TYR*     3.7    22.0    -      -       +      -
    155B  LEU      3.6    19.7    -      -       -      -
    156B  TYR      4.6     0.7    -      -       -      -
    157B  GLY*     3.5    12.6    -      -       -      -
    158B  LYS*     1.3    83.1    -      -       -      +
    160B  ILE*     1.3    69.8    +      -       -      +
    162B  GLY*     3.9    14.1    -      -       -      -
    163B  GLU      3.0     9.0    -      -       -      +
    164B  MET*     3.6    45.5    -      -       +      -
    165B  ILE*     4.3     0.4    -      -       -      -
    167B  GLY*     5.0     0.7    -      -       -      -
    311B  PRO*     5.0     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 160 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140B  THR*     4.0    16.8    -      -       +      +
    158B  LYS*     4.4    18.6    -      -       -      -
    159B  PHE*     1.3    79.3    -      -       -      +
    161B  ASP*     1.3    77.5    +      -       +      +
    162B  GLY      3.2     0.4    -      -       -      -
    163B  GLU*     2.8    27.0    +      -       -      +
    165B  ILE*     3.7    29.6    -      -       +      +
----------------------------------------------------------
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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