Contacts of the strand formed by residues 139 - 146 (chain F) in PDB entry 6CU0


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 139 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138F  ALA*     1.3    79.7    -      -       -      +
    140F  VAL*     1.3    60.3    +      -       -      -
    141F  TYR*     3.7     8.6    -      -       -      -
    205F  HIS*     3.4     8.5    +      -       -      -
    206F  LEU*     2.8    34.7    +      -       -      +
    241F  THR*     4.4    13.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 140 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92E  PHE*     4.0    29.2    -      -       +      -
    119E  SER*     5.3     8.3    -      -       -      +
    139F  GLY*     1.3    73.9    -      -       -      -
    141F  TYR*     1.3    68.2    +      -       -      +
    203F  LEU*     4.0    32.1    -      -       +      -
    204F  LEU      3.5     7.0    -      -       -      +
    205F  HIS*     4.0    22.4    -      -       +      +
    239F  ARG*     3.8     1.6    -      -       -      +
    240F  VAL*     2.9    26.1    +      -       +      -
    241F  THR*     3.2    23.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 141 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91F  MET*     3.2    29.2    -      -       +      +
    124F  LEU*     5.0     0.7    -      -       +      -
    135F  VAL*     3.5    11.1    -      -       +      +
    137F  LYS*     2.6    29.9    +      -       -      +
    138F  ALA      4.2     1.8    +      -       -      -
    139F  GLY*     3.7    24.0    -      -       -      -
    140F  VAL*     1.3    77.0    -      -       -      +
    142F  TYR*     1.3    60.9    +      -       -      +
    143F  VAL*     3.5    18.9    +      -       +      +
    203F  LEU*     3.2     7.2    -      -       -      -
    204F  LEU*     2.8    34.4    +      -       -      +
    206F  LEU*     3.5    24.5    -      -       +      -
    237F  LEU*     4.1    20.2    -      -       +      -
    238F  PHE      3.3     9.9    -      -       -      +
    239F  ARG*     3.4    35.3    -      -       +      +
    240F  VAL      4.3     0.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 142 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142C  TYR*     3.3    32.2    +      +       -      -
    142E  TYR*     3.4    11.4    +      +       -      -
    144E  PHE*     4.1    22.0    -      +       -      -
    199E  PHE*     3.1    26.5    -      -       -      -
    238E  PHE*     4.1    15.0    -      +       +      -
    141F  TYR*     1.3    68.8    -      -       -      +
    143F  VAL*     1.3    59.4    +      -       -      +
    144F  PHE*     3.9    16.8    +      +       +      -
    199F  PHE*     3.8     5.7    -      -       -      -
    201F  GLY*     3.9    21.4    -      -       -      -
    202F  ARG      3.6    13.5    -      -       -      -
    203F  LEU*     4.0    11.9    -      -       +      +
    237F  LEU*     3.2     3.6    -      -       -      -
    238F  PHE*     3.0    67.3    +      +       +      -
    240F  VAL*     4.0     2.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 143 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141F  TYR*     3.9    18.6    -      -       +      +
    142F  TYR*     1.3    75.8    -      -       -      +
    144F  PHE*     1.3    64.1    +      -       -      +
    165F  LEU*     4.1    20.0    -      -       +      -
    179F  LEU*     3.8     8.5    -      -       +      +
    201F  GLY*     3.1     2.1    -      -       -      -
    202F  ARG      2.9    30.9    +      -       -      +
    204F  LEU*     3.7    27.6    -      -       +      -
    206F  LEU*     4.7     4.3    -      -       +      -
    235F  LEU*     4.0    19.1    -      -       +      -
    236F  GLY      3.5     9.9    -      -       -      +
    237F  LEU*     3.9    22.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 144 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142C  TYR*     4.0    13.0    -      +       -      -
    201C  GLY      3.9    13.2    -      -       -      -
    202C  ARG*     3.9    12.3    -      -       +      -
    203C  LEU*     4.1     6.5    -      -       +      -
     94F  GLN*     3.6    22.7    -      -       -      -
    142F  TYR*     3.9    22.2    -      +       +      -
    143F  VAL*     1.3    75.0    -      -       -      +
    145F  PHE*     1.3    65.6    +      -       -      +
    146F  GLN*     5.3     2.5    -      -       +      -
    179F  LEU*     4.1     2.7    -      -       -      -
    199F  PHE*     3.6    31.2    -      +       +      -
    200F  GLN      3.1    13.2    -      -       -      +
    201F  GLY*     3.8     4.0    -      -       -      -
    234F  VAL*     4.5     7.6    -      -       +      -
    235F  LEU*     3.6     1.9    -      -       -      +
    236F  GLY*     2.8    63.5    +      -       -      +
    237F  LEU*     3.8     5.4    -      -       -      -
    238F  PHE*     4.4     9.2    -      +       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 145 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109F  TRP*     5.9     0.4    -      +       +      -
    144F  PHE*     1.3    76.7    -      -       -      +
    146F  GLN*     1.3    61.8    +      -       -      +
    163F  LEU*     3.7    38.6    -      -       +      -
    165F  LEU*     3.8    24.7    -      -       +      -
    179F  LEU*     3.6    45.1    -      -       +      +
    180F  ALA*     3.9     7.4    -      -       -      -
    181F  LEU*     3.8    26.9    -      -       +      +
    199F  PHE*     3.5     5.5    -      -       -      -
    200F  GLN*     2.8    36.8    +      -       +      +
    214F  VAL*     4.1    12.8    -      -       +      -
    234F  VAL      3.2    13.9    -      -       -      +
    235F  LEU*     4.0    17.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 146 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200C  GLN*     3.1    38.6    +      -       -      +
    201C  GLY      3.0    26.3    +      -       -      +
    202C  ARG*     3.0    39.0    -      -       -      +
    144F  PHE*     5.3     2.0    -      -       +      -
    145F  PHE*     1.3    73.9    -      -       -      +
    147F  LEU*     1.3    65.5    +      -       -      +
    148F  GLU*     5.6     0.9    -      -       +      +
    163F  LEU*     4.2     3.7    -      -       -      +
    181F  LEU*     4.8     0.2    -      -       -      -
    198F  GLY      3.3     7.9    -      -       -      +
    199F  PHE*     4.1    10.9    -      -       +      +
    232F  ALA*     3.3    18.6    +      -       -      +
    233F  THR*     3.5     5.7    -      -       -      +
    234F  VAL*     2.9    35.8    +      -       +      +
----------------------------------------------------------
 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