Contacts of the strand formed by residues 199 - 206 (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 PHE 199 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142C  TYR*     3.4    21.1    -      -       -      -
    199C  PHE*     3.5    26.2    -      +       +      +
    200C  GLN*     4.6     3.1    -      -       -      +
    201C  GLY      3.4    30.5    -      -       -      -
    197E  PHE*     6.0     1.6    -      -       -      +
    199E  PHE*     3.4    54.3    +      +       +      +
    142F  TYR*     3.8     1.1    -      -       -      -
    144F  PHE*     3.6    31.9    -      +       +      -
    145F  PHE      3.5     9.6    -      -       -      -
    146F  GLN*     4.1    16.6    -      -       +      -
    181F  LEU*     3.8     6.7    -      -       -      +
    198F  GLY*     1.3    75.0    -      -       -      +
    200F  GLN*     1.3    73.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 200 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146E  GLN*     3.2    37.7    +      -       +      +
    147E  LEU      6.3     0.2    -      -       -      -
    148E  GLU*     5.8     1.8    -      -       -      +
    197E  PHE*     3.6    24.2    -      -       -      +
    198E  GLY      5.5     1.0    -      -       -      +
    199E  PHE*     4.6     5.1    -      -       -      +
    144F  PHE*     3.1     3.5    -      -       -      +
    145F  PHE*     2.8    41.2    +      -       +      +
    179F  LEU*     3.7    16.4    -      -       +      +
    180F  ALA      2.9    35.2    +      -       -      +
    181F  LEU*     4.0    13.6    -      -       +      +
    199F  PHE*     1.3    84.8    +      -       -      +
    201F  GLY*     1.3    62.4    +      -       -      +
    202F  ARG*     4.6     4.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 201 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144E  PHE*     4.1     2.1    -      -       -      -
    146E  GLN*     2.6    22.1    -      -       -      +
    199E  PHE*     3.2    16.6    -      -       -      -
    142F  TYR*     3.9    13.7    -      -       -      -
    143F  VAL      3.1    13.9    -      -       -      -
    144F  PHE*     3.7     8.1    -      -       -      -
    179F  LEU*     4.1     2.0    -      -       -      -
    199F  PHE*     3.9     5.5    -      -       -      -
    200F  GLN*     1.3    78.2    -      -       -      +
    202F  ARG*     1.3    59.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 202 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94E  GLN*     3.8    19.8    -      -       -      +
     96E  VAL*     5.2     1.8    -      -       -      +
    117E  GLY*     5.2     9.7    -      -       -      -
    144E  PHE*     3.9    13.7    -      -       +      -
    146E  GLN*     3.2    29.9    -      -       -      +
    231E  GLY      3.0    27.7    +      -       -      -
    232E  ALA*     4.3     5.9    -      -       -      +
    234E  VAL*     3.7    13.2    -      -       +      +
    142F  TYR*     3.9     9.5    -      -       -      -
    143F  VAL*     2.9    30.4    +      -       -      +
    178F  ALA      3.9    16.9    +      -       -      -
    179F  LEU*     3.4    23.5    -      -       +      +
    180F  ALA      5.9     0.2    -      -       -      +
    200F  GLN*     4.6     5.1    +      -       -      -
    201F  GLY*     1.3    74.1    -      -       -      +
    203F  LEU*     1.3    68.0    +      -       -      +
    204F  LEU*     3.6    10.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 203 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92E  PHE*     4.4    13.7    -      -       +      -
     93E  ALA      3.4    27.8    -      -       -      +
     94E  GLN*     2.8    49.3    +      -       +      +
    117E  GLY*     5.0     1.4    -      -       -      +
    119E  SER*     5.2     3.1    -      -       -      +
    144E  PHE*     3.9    12.6    -      -       +      -
    237E  LEU      4.2     9.0    -      -       -      +
    238E  PHE*     4.2     9.0    -      -       +      -
    140F  VAL*     4.0    14.4    -      -       +      -
    141F  TYR      3.2    11.7    -      -       -      +
    142F  TYR*     4.0    18.8    -      -       +      +
    202F  ARG*     1.3    71.5    -      -       -      +
    204F  LEU*     1.3    68.5    +      -       -      +
    240F  VAL*     4.0    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 204 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140F  VAL*     4.3     3.1    -      -       -      -
    141F  TYR      2.8    32.6    +      -       -      -
    143F  VAL*     3.7    28.5    -      -       +      -
    165F  LEU*     3.8    26.7    -      -       +      -
    167F  LEU*     5.0     3.1    -      -       +      -
    178F  ALA*     3.9    33.2    -      -       +      +
    179F  LEU*     5.1     2.2    -      -       +      -
    202F  ARG*     4.0    16.6    -      -       +      +
    203F  LEU*     1.3    81.9    -      -       -      +
    205F  HIS*     1.3    62.7    +      -       -      +
    206F  LEU*     3.3    25.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 205 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138F  ALA*     5.3     3.1    -      -       +      -
    139F  GLY*     3.4    19.4    +      -       -      -
    140F  VAL*     4.0    17.9    -      -       +      +
    167F  LEU*     5.3     5.0    -      -       -      +
    203F  LEU      4.3     0.8    +      -       -      -
    204F  LEU*     1.3    70.4    -      -       -      +
    206F  LEU*     1.3    80.2    +      -       -      +
    207F  SER*     4.2     8.6    +      -       -      -
    210F  GLN*     5.0     2.6    +      -       -      -
     39H  ASN*     4.4    12.6    +      -       -      -
     60H  ARG*     4.4    23.9    -      -       +      +
     61H  THR*     6.3     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 206 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135F  VAL*     3.9    26.7    -      -       +      -
    138F  ALA*     3.5     2.3    -      -       -      +
    139F  GLY      2.8    36.7    +      -       -      +
    141F  TYR*     3.5    33.2    -      -       +      -
    143F  VAL*     4.7     3.8    -      -       +      -
    167F  LEU*     4.2    26.9    -      -       +      -
    204F  LEU*     3.8    26.2    -      -       +      +
    205F  HIS*     1.3    87.1    +      -       -      +
    207F  SER*     1.3    68.0    +      -       -      +
    210F  GLN*     4.4    10.8    -      -       +      +
    237F  LEU*     4.5    11.9    -      -       +      -
----------------------------------------------------------
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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