Contacts of the strand formed by residues 136 - 145 (chain B) in PDB entry 2O6E


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 GLY 136 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  LYS*     4.3     9.2    -      -       -      -
    134B  GLY      3.7     1.4    +      -       -      -
    135B  LEU*     1.3    76.4    -      -       -      +
    137B  THR*     1.3    63.8    +      -       -      -
    138B  TYR*     3.6     8.1    -      -       -      -
    179B  GLU*     3.7     1.1    -      -       -      -
    180B  TRP      2.9    35.9    +      -       -      +
    181B  LYS*     4.9    11.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  LYS*     3.5     5.0    -      -       -      +
    104B  HIS*     2.8    66.7    +      -       +      +
    136B  GLY*     1.3    73.4    -      -       -      -
    138B  TYR*     1.3    56.9    +      -       -      +
    177B  ASP*     3.7    26.5    -      -       +      +
    178B  PHE      3.3     7.0    -      -       -      +
    179B  GLU*     3.6    22.4    +      -       +      +
    181B  LYS*     4.9     3.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 138 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  LEU*     4.1    15.3    -      -       +      -
    102B  GLN      3.5    11.2    -      -       -      -
    103B  LYS*     3.5    35.0    -      -       +      -
    104B  HIS*     3.8     6.1    -      -       -      -
    110B  GLN*     5.6     2.5    -      -       +      -
    131B  PHE*     3.6    29.2    -      +       +      +
    133B  GLU*     3.4    13.6    +      -       +      +
    134B  GLY      2.7    43.0    +      -       -      -
    136B  GLY      3.6    20.9    -      -       -      -
    137B  THR*     1.3    76.2    -      -       -      +
    139B  LYS*     1.3    63.5    +      -       -      +
    140B  VAL*     3.8     4.2    +      -       +      -
    176B  ASP      3.5     4.3    -      -       -      +
    178B  PHE*     2.6    54.3    +      +       +      +
    180B  TRP*     4.1    11.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 139 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100B  PHE      3.6     1.7    -      -       -      +
    101B  LEU*     3.5     4.5    -      -       -      -
    102B  GLN*     2.9    52.8    +      -       +      +
    104B  HIS*     3.5    26.2    +      -       +      +
    138B  TYR*     1.3    73.4    -      -       -      +
    140B  VAL*     1.3    59.0    +      -       -      +
    141B  ARG*     4.2     0.7    -      -       -      -
    174B  GLU*     4.8    12.6    -      -       -      +
    175B  TRP      3.5     6.1    -      -       -      +
    176B  ASP*     3.5    34.1    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 140 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  ILE*     4.2    19.1    -      -       +      -
     71B  ILE*     5.7     2.5    -      -       +      -
    100B  PHE      3.5     3.1    -      -       -      -
    101B  LEU*     3.9    24.7    -      -       +      -
    138B  TYR*     4.3     3.4    -      -       +      +
    139B  LYS*     1.3    75.1    -      -       -      +
    141B  ARG*     1.3    62.0    +      -       -      +
    142B  PHE*     3.9    25.6    -      -       +      -
    174B  GLU*     3.4     4.1    -      -       -      +
    175B  TRP*     2.6    50.4    +      -       +      +
    178B  PHE*     3.6    41.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 141 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98B  VAL      3.6     1.6    -      -       -      +
     99B  ALA*     3.1     3.5    -      -       -      -
    100B  PHE*     2.7    57.7    +      -       +      +
    139B  LYS      5.6     0.7    -      -       -      -
    140B  VAL*     1.3    73.1    -      -       -      +
    142B  PHE*     1.3    63.2    +      -       -      +
    143B  GLU*     2.8    35.1    +      -       +      +
    172B  VAL*     3.6    28.7    -      -       +      +
    174B  GLU*     3.2    46.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 142 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  ILE*     3.9    22.9    -      -       +      -
     44B  VAL*     4.1     9.2    -      -       +      -
     45B  GLY      4.3     0.9    -      -       -      -
     46B  GLY*     4.1     5.2    -      -       -      -
     71B  ILE*     4.1     3.6    -      -       +      -
     72B  GLU      4.4     1.6    -      -       -      -
     73B  ALA*     3.5    32.1    -      -       +      -
     97B  VAL*     4.7     4.7    -      -       +      -
     98B  VAL      3.4     4.3    -      -       -      +
     99B  ALA*     3.8    14.8    -      -       +      -
    114B  PHE*     3.7    31.9    -      +       -      -
    140B  VAL*     3.9    16.4    -      -       +      -
    141B  ARG*     1.3    77.2    -      -       -      +
    143B  GLU*     1.3    62.1    +      -       -      +
    144B  ILE*     4.4    10.9    -      -       +      +
    171B  LEU      3.5     1.2    -      -       -      +
    172B  VAL*     3.4     7.3    -      -       -      +
    173B  ALA*     2.8    38.2    +      -       +      +
    175B  TRP*     3.7    29.4    -      +       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 143 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  ARG      3.6     2.0    -      -       -      +
     97B  VAL*     3.4     4.2    -      -       -      +
     98B  VAL*     2.7    39.2    +      -       +      +
    100B  PHE*     3.6    29.5    -      -       +      -
    141B  ARG*     2.8    40.4    +      -       +      +
    142B  PHE*     1.3    75.4    -      -       -      +
    144B  ILE*     1.3    61.2    +      -       -      +
    145B  ALA      4.1     0.7    -      -       -      -
    170B  PRO*     4.2    19.9    -      -       +      +
    171B  LEU      3.5     3.4    -      -       -      -
    172B  VAL*     4.1    10.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 144 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  VAL*     6.2     0.9    -      -       +      -
     42B  LEU*     3.8    24.7    -      -       +      -
     44B  VAL*     3.8    34.8    -      -       +      -
     75B  ILE*     4.1    13.7    -      -       +      -
     95B  LEU*     3.8    23.1    -      -       +      -
     96B  ARG      3.7     2.5    -      -       -      -
     97B  VAL*     4.0    19.1    -      -       +      -
    142B  PHE*     4.4    11.7    -      -       +      +
    143B  GLU*     1.3    77.6    -      -       -      +
    145B  ALA*     1.3    61.2    +      -       -      +
    167B  TRP*     3.0    12.1    +      -       +      -
    170B  PRO*     3.9     1.8    -      -       -      -
    171B  LEU*     2.8    47.8    +      -       +      +
    172B  VAL      5.3     0.4    -      -       -      -
    173B  ALA*     4.6     5.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 145 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95B  LEU*     3.6     8.3    -      -       -      +
     96B  ARG*     2.9    53.8    +      -       +      +
    143B  GLU      4.1     0.8    -      -       -      -
    144B  ILE*     1.3    74.3    -      -       -      +
    146B  ALA*     1.3    69.4    +      -       -      +
    167B  TRP*     3.8     3.8    -      -       -      +
    168B  SER      5.9     1.3    -      -       -      +
    170B  PRO*     4.0    21.7    -      -       +      +
----------------------------------------------------------
 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