Contacts of the strand formed by residues 187 - 193 (chain A) in PDB entry 6TAV


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 LEU 187 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  ARG*     3.8    29.4    -      -       +      -
    148A  VAL      3.1    24.7    -      -       -      +
    149A  VAL*     4.0    11.9    -      -       +      -
    183A  LEU*     3.7     7.9    -      -       -      +
    184A  GLU*     3.6    13.3    +      -       -      +
    185A  GLY*     3.9    12.0    +      -       -      +
    186A  GLY*     1.4    78.3    -      -       -      +
    188A  LYS*     1.4    68.5    +      -       -      +
    189A  GLN*     4.9    11.4    -      -       +      +
    594A  VAL*     4.4    23.1    -      -       +      -
    596A  ALA*     4.4    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 188 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  VAL*     3.0    32.8    +      -       -      +
    181A  PHE*     3.7    35.9    -      -       +      -
    182A  GLN*     2.7    32.2    +      -       -      +
    183A  LEU*     3.5    13.1    -      -       +      +
    184A  GLU*     4.4    17.4    +      -       +      +
    187A  LEU*     1.4    77.9    -      -       -      +
    189A  GLN*     1.4    65.3    +      -       -      +
    190A  PHE*     3.4    23.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 189 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146A  PHE      3.5     7.0    -      -       -      +
    147A  ARG*     3.3    48.7    +      -       +      +
    187A  LEU*     4.9    13.4    -      -       +      +
    188A  LYS*     1.4    76.5    -      -       -      +
    190A  PHE*     1.3    70.9    +      -       -      +
    596A  ALA*     5.1     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 190 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  LYS*     3.5     6.8    -      -       -      +
    146A  PHE*     2.7    68.9    +      +       +      +
    148A  VAL*     3.7    16.2    -      -       +      -
    165A  VAL*     4.9     7.4    -      -       +      -
    178A  TRP*     3.4    46.4    -      +       +      -
    181A  PHE*     4.1    37.2    -      +       +      -
    188A  LYS*     3.4    33.4    -      -       +      -
    189A  GLN*     1.3    76.2    -      -       -      +
    191A  SER*     1.3    63.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 191 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  THR*     4.6    11.4    -      -       -      +
    144A  VAL      3.3    10.7    +      -       -      -
    145A  LYS*     4.7    11.5    -      -       -      +
    146A  PHE*     4.6     0.6    -      -       -      -
    178A  TRP*     4.0    14.1    +      -       -      +
    190A  PHE*     1.3    79.8    -      -       -      +
    192A  PHE*     1.3    64.9    +      -       -      +
    193A  PRO*     4.3     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  THR*     4.4     0.2    -      -       -      -
    144A  VAL*     2.8    57.9    +      -       +      +
    146A  PHE*     5.3     0.6    -      -       +      -
    167A  ILE*     3.7    31.6    -      -       +      -
    175A  ILE*     3.8    38.8    -      -       +      -
    176A  ALA*     3.8    18.8    -      -       +      -
    178A  TRP*     4.2     7.4    -      +       +      -
    191A  SER*     1.3    76.5    +      -       -      +
    193A  PRO*     1.4    91.7    -      -       +      +
    194A  LEU*     4.3    19.3    -      -       +      -
    195A  SER*     5.1     2.5    -      -       -      -
    203A  TYR*     5.9     2.2    -      +       -      -
    219A  PHE*     6.1     0.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with PRO 193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  GLY      5.5     1.6    -      -       -      +
    143A  THR*     3.6    25.5    -      -       +      -
    191A  SER*     4.3     6.7    -      -       -      +
    192A  PHE*     1.4   107.8    -      -       +      +
    194A  LEU*     1.3    66.1    +      -       -      +
    195A  SER*     3.9     0.3    +      -       -      -
----------------------------------------------------------
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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