Contacts of the strand formed by residues 143 - 152 (chain F) in PDB entry 6D6Q


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 GLN 143 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68F  GLY      3.8     3.1    -      -       -      +
     70F  ARG*     3.5    39.6    +      -       +      +
     72F  ALA*     3.7    24.1    -      -       +      +
     95F  ARG*     3.3    32.2    +      -       +      -
     97F  LEU*     3.8    30.5    -      -       +      +
    142F  ALA*     1.3    74.0    -      -       -      +
    144F  LEU*     1.3    64.3    +      -       -      +
    145F  GLU*     3.7    17.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 144 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66F  VAL*     5.0     5.2    -      -       +      -
     67F  SER      3.9     2.5    -      -       -      +
     68F  GLY*     3.7     5.2    -      -       -      -
     69F  PRO*     3.4    44.2    -      -       +      -
     95F  ARG      2.9    17.4    +      -       -      +
     96F  LEU*     3.2    13.2    -      -       +      +
     97F  LEU*     2.9    26.3    +      -       -      +
    134F  VAL*     4.9     7.2    -      -       +      -
    136F  LEU*     4.7    15.3    -      -       +      -
    139F  TYR*     5.2    13.5    -      -       +      -
    142F  ALA*     5.7     1.8    -      -       +      -
    143F  GLN*     1.3    71.9    -      -       -      +
    145F  GLU*     1.3    61.2    +      -       -      +
    146F  VAL*     3.4     7.9    +      -       +      +
    169F  LEU*     4.7     9.0    -      -       +      -
    174F  VAL*     4.1    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 145 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87C  PRO*     4.9    12.3    -      -       +      +
     93C  PHE      5.0     3.5    -      -       -      +
     94C  ARG*     5.5     4.4    -      -       -      +
     95C  SER*     5.3    12.1    +      -       -      +
     65F  ALA      3.9     0.9    -      -       -      +
     66F  VAL*     3.6     1.6    -      -       -      -
     67F  SER*     2.9    56.9    +      -       -      +
     68F  GLY      5.8     0.2    -      -       -      +
     70F  ARG*     3.5    31.9    +      -       +      -
     97F  LEU*     3.5    28.2    -      -       +      +
    143F  GLN*     3.7    18.1    +      -       +      +
    144F  LEU*     1.3    70.6    -      -       -      +
    146F  VAL*     1.3    61.8    +      -       -      +
    147F  SER*     3.9     2.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 146 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64F  CYS*     3.6    24.5    -      -       -      -
     65F  ALA      3.6     4.3    -      -       -      +
     66F  VAL*     4.6     3.8    -      -       +      -
     96F  LEU*     4.7    14.8    -      -       +      -
     97F  LEU      2.9    10.9    +      -       -      +
     98F  CYS*     3.3    15.3    -      -       +      -
     99F  ASP*     2.9    26.2    +      -       -      +
    126F  LEU*     5.8     2.0    -      -       +      -
    130F  LEU*     4.9     3.4    -      -       +      -
    144F  LEU*     3.4     9.4    +      -       +      +
    145F  GLU*     1.3    73.6    -      -       -      +
    147F  SER*     1.3    65.3    +      -       -      +
    148F  ALA*     4.1     2.9    -      -       +      +
    165F  ALA*     4.1    15.5    -      -       +      +
    169F  LEU*     4.0    31.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 147 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86C  PRO*     5.0     1.0    -      -       -      +
     87C  PRO*     4.0    24.6    -      -       -      +
     88C  LEU*     3.5    36.1    -      -       -      +
     95C  SER*     5.9     0.2    -      -       -      -
     64F  CYS*     3.4     3.9    -      -       -      -
     65F  ALA      2.9    38.3    +      -       -      -
     99F  ASP*     3.6    11.4    +      -       -      +
    145F  GLU*     3.9     2.7    +      -       -      -
    146F  VAL*     1.3    74.7    -      -       -      +
    148F  ALA*     1.3    63.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 148 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88C  LEU*     4.8     0.2    -      -       -      +
     62F  VAL*     5.1     1.6    -      -       +      -
     63F  LEU      3.5     9.4    -      -       -      +
     64F  CYS*     4.2    12.3    -      -       +      -
     99F  ASP      3.0    18.7    +      -       -      +
    100F  PHE*     3.9    26.2    -      -       +      -
    101F  ARG*     3.6    16.2    +      -       -      +
    126F  LEU*     4.5    11.7    -      -       +      -
    146F  VAL*     4.1     1.9    -      -       +      +
    147F  SER*     1.3    79.3    +      -       -      +
    149F  LEU*     1.3    64.9    +      -       -      +
    161F  ALA*     4.8    10.5    -      -       +      +
    165F  ALA*     5.9     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 149 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84C  ASP*     5.9     1.6    -      -       -      +
     86C  PRO*     5.2     6.3    -      -       +      -
     88C  LEU*     4.0    17.0    -      -       +      -
    140C  ILE*     4.0    17.9    -      -       +      -
    142C  LEU*     3.9    24.5    -      -       +      -
     62F  VAL*     3.2     6.8    -      -       -      +
     63F  LEU*     2.9    41.7    +      -       +      +
    100F  PHE*     5.5     0.9    -      -       -      -
    101F  ARG*     3.2    33.7    -      -       +      +
    103F  ALA*     4.3    14.4    -      -       +      +
    148F  ALA*     1.3    77.9    -      -       -      +
    150F  LEU*     1.3    60.2    +      -       -      +
    151F  LEU*     3.8    28.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 150 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60F  THR*     5.5     3.6    -      -       +      -
     61F  LYS      4.0     4.5    -      -       -      +
     62F  VAL*     4.5     9.0    -      -       +      -
    100F  PHE*     4.0    23.1    -      -       +      -
    101F  ARG      2.9     9.4    +      -       -      +
    102F  ARG*     3.9    26.0    -      -       +      +
    103F  ALA*     2.8    28.5    +      -       -      -
    106F  ALA*     4.0     8.7    -      -       +      +
    149F  LEU*     1.3    72.0    -      -       -      +
    151F  LEU*     1.3    61.2    +      -       -      +
    152F  GLU      3.5    31.4    -      -       -      +
    153F  ASP*     3.7    13.0    -      -       +      +
    157F  ALA*     3.5    35.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 151 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42C  ILE*     4.5     7.0    -      -       +      +
     59C  ILE*     4.5    17.0    -      -       +      -
    140C  ILE*     5.0     0.4    -      -       +      -
    142C  LEU*     5.2     2.0    -      -       +      -
     54F  TYR*     4.4     7.4    -      -       +      -
     61F  LYS*     2.9    22.5    +      -       +      +
     63F  LEU*     4.2    25.4    -      -       +      -
    103F  ALA*     4.2     2.2    -      -       +      -
    105F  PHE*     3.1    48.2    -      -       +      +
    106F  ALA*     3.4    10.2    -      -       -      +
    149F  LEU*     3.8    31.4    -      -       +      +
    150F  LEU*     1.3    72.5    -      -       -      +
    152F  GLU*     1.3    61.6    +      -       +      +
    637J  LEU*     4.0    26.2    -      -       +      -
    638J  PHE*     4.8     2.0    -      -       +      -
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Residues in contact with GLU 152 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42C  ILE*     3.7    11.5    -      -       +      -
     43C  SER*     2.6    42.9    +      -       -      -
     44C  THR*     3.7    19.0    -      -       +      +
     59F  GLY*     3.0    27.7    -      -       -      +
     60F  THR*     3.5     4.2    -      -       -      +
     61F  LYS*     2.5    63.5    +      -       +      +
    106F  ALA*     3.8     5.2    -      -       -      -
    150F  LEU*     3.4    11.7    -      -       -      +
    151F  LEU*     1.3    81.1    -      -       -      +
    153F  ASP*     1.3    62.5    +      -       -      +
----------------------------------------------------------
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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