Contacts of the strand formed by residues 163 - 176 (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 GLU 163 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  PHE*     3.1     6.8    -      -       -      -
    160A  ILE*     2.9    36.9    +      -       +      +
    161A  ASP      3.2     3.0    +      -       -      +
    162A  GLY*     1.3    78.4    -      -       -      +
    164A  MET*     1.3    63.1    +      -       -      +
    165A  ILE*     3.3    18.6    +      -       +      +
    193A  PHE*     3.6    43.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  LEU*     3.6    38.6    -      -       +      -
    159A  PHE*     3.5    31.8    -      -       +      -
    162A  GLY      3.8     1.2    +      -       -      -
    163A  GLU*     1.3    71.1    -      -       -      +
    165A  ILE*     1.3    62.9    +      -       -      +
    167A  GLY*     3.8    11.9    -      -       -      +
    191A  TYR*     3.6    23.1    -      -       +      +
    192A  HIS*     3.5    30.3    -      -       -      +
    193A  PHE*     2.8    32.0    +      -       -      +
    311A  PRO*     3.7    35.5    +      -       +      +
    312A  ARG*     4.2     3.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158A  LYS*     2.8    39.6    +      -       +      +
    159A  PHE*     4.2     0.4    -      -       -      -
    160A  ILE*     3.9    35.2    -      -       +      -
    163A  GLU*     3.7    32.3    -      -       +      +
    164A  MET*     1.3    79.9    -      -       -      +
    166A  GLU*     1.3    60.0    +      -       +      +
    192A  HIS*     3.1    21.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  GLU*     5.5     0.7    -      -       -      +
    156A  TYR      4.0     0.5    -      -       -      +
    157A  GLY*     3.3     5.8    -      -       -      -
    158A  LYS*     3.0    44.7    +      -       +      +
    165A  ILE*     1.3    80.5    -      -       +      +
    167A  GLY*     1.3    58.0    +      -       -      +
    168A  LYS*     3.0    33.4    +      -       +      +
    190A  VAL*     3.9    26.3    -      -       +      +
    191A  TYR      3.6     3.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  LEU*     4.2     3.6    -      -       -      -
    156A  TYR      3.7    14.6    -      -       -      -
    157A  GLY      4.4     0.4    -      -       -      -
    159A  PHE*     5.0     1.1    -      -       -      -
    164A  MET*     3.8    18.6    -      -       -      +
    166A  GLU*     1.3    74.0    -      -       -      +
    168A  LYS*     1.3    62.5    +      -       -      -
    190A  VAL*     3.8     1.3    -      -       -      -
    191A  TYR*     2.9    45.4    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  LEU*     3.4     3.3    -      -       -      -
    156A  TYR*     2.8    37.2    +      -       -      +
    166A  GLU*     3.0    31.9    +      -       +      +
    167A  GLY*     1.3    76.2    -      -       -      -
    169A  LEU*     1.3    65.6    +      -       -      +
    170A  ALA*     3.3     0.5    +      -       -      +
    184A  LEU*     3.5    36.0    -      -       +      +
    189A  SER      4.4     7.2    -      -       -      +
    190A  VAL*     4.5    12.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  THR*     3.9    16.8    -      -       +      -
    154A  ALA      3.6    10.3    -      -       -      +
    155A  LEU*     4.3     4.5    -      -       +      -
    167A  GLY      4.2     0.8    +      -       -      -
    168A  LYS*     1.3    72.0    -      -       -      +
    170A  ALA*     1.3    66.6    +      -       -      +
    184A  LEU*     3.6     5.5    -      -       -      +
    185A  MET*     2.9    46.2    +      -       +      +
    186A  PRO      5.2     5.6    -      -       -      +
    189A  SER*     4.4     5.5    +      -       -      +
    191A  TYR*     4.4    16.0    -      -       +      +
    210A  PRO*     3.7    36.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  THR*     3.9     4.3    -      -       -      +
    154A  ALA*     2.8    32.9    +      -       +      +
    156A  TYR*     3.9    25.6    -      -       +      -
    168A  LYS      3.9     0.2    -      -       -      +
    169A  LEU*     1.3    80.7    -      -       -      +
    171A  THR*     1.3    66.3    +      -       -      +
    182A  PHE*     4.3    14.4    -      -       +      -
    183A  GLU      3.2    17.3    -      -       -      +
    184A  LEU*     4.4     4.3    -      -       +      -
    185A  MET*     3.7     6.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  ARG*     3.2    42.5    +      -       +      +
    153A  THR*     5.7     0.5    -      -       -      -
    170A  ALA*     1.3    73.8    +      -       -      +
    172A  LEU*     1.3    71.7    +      -       -      +
    173A  MET*     3.3     5.9    +      -       +      -
    182A  PHE*     3.3     6.6    -      -       -      -
    183A  GLU*     2.9    53.3    +      -       +      +
    185A  MET*     3.0    24.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 172 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  TRP*     4.0    22.9    -      -       +      -
    147A  VAL*     4.2    19.1    -      -       +      -
    151A  GLU*     3.8    23.8    -      -       +      +
    152A  ARG*     2.7    25.5    +      -       -      +
    154A  ALA*     4.6     0.2    -      -       -      +
    171A  THR*     1.3    77.1    -      -       -      +
    173A  MET*     1.3    62.0    +      -       -      +
    174A  SER*     3.6    17.5    -      -       -      +
    175A  THR*     4.3     5.2    -      -       -      +
    180A  PRO*     3.6    29.8    -      -       +      -
    181A  HIS      3.8     4.0    -      -       -      +
    182A  PHE*     3.7    20.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 173 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171A  THR*     3.9    14.4    -      -       +      +
    172A  LEU*     1.3    76.5    -      -       -      +
    174A  SER*     1.3    64.9    +      -       -      +
    181A  HIS*     2.8    20.5    +      -       +      +
    182A  PHE      3.9     8.7    -      -       -      +
    183A  GLU*     3.7    47.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 174 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172A  LEU*     3.6     6.1    -      -       -      +
    173A  MET*     1.3    81.7    -      -       -      +
    175A  THR*     1.3    69.1    +      -       -      +
    176A  GLU*     5.5     2.1    -      -       -      +
    180A  PRO*     3.5     0.5    -      -       -      +
    181A  HIS*     2.8    45.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 175 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  TRP*     3.7    25.0    -      -       +      -
    172A  LEU*     4.3     4.7    -      -       -      +
    174A  SER*     1.3    80.5    +      -       -      +
    176A  GLU*     1.3    71.9    +      -       -      +
    177A  GLU      4.1     1.0    +      -       -      +
    178A  GLY*     3.4    33.0    -      -       -      +
    179A  ARG      3.1    13.7    -      -       -      +
    180A  PRO*     4.0     2.4    -      -       -      +
    181A  HIS*     4.1     0.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 176 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174A  SER*     5.5     2.2    -      -       -      +
    175A  THR*     1.3    77.2    -      -       -      +
    177A  GLU*     1.3    83.5    +      -       -      +
    178A  GLY      3.2     0.4    -      -       -      -
    179A  ARG*     2.6    30.0    +      -       +      +
    181A  HIS*     3.2    23.3    +      -       +      +
----------------------------------------------------------
 Back to top of page


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