Contacts of the strand formed by residues 161 - 168 (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 161 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  ASN      4.5     5.4    -      -       -      +
    160A  GLU*     1.3    88.8    -      -       +      +
    162A  ILE*     1.3    61.2    +      -       -      +
    163A  PRO*     3.0    17.5    -      -       -      +
    180A  SER*     5.6     3.4    -      -       -      -
    181A  PHE      3.6    11.2    -      -       -      +
    182A  GLN*     4.2    16.6    -      -       +      +
    210A  LYS*     4.5    28.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  VAL*     5.2     6.1    -      -       +      -
    148A  VAL*     5.1    11.0    -      -       +      -
    160A  GLU*     3.1    41.4    -      -       +      +
    161A  LEU*     1.3    65.8    -      -       -      +
    163A  PRO*     1.3    66.2    -      -       -      +
    164A  LEU*     3.7    26.4    -      -       -      +
    165A  VAL*     3.9    20.0    -      -       +      -
    178A  TRP      4.8     1.2    -      -       -      +
    179A  GLN      4.4     0.5    -      -       -      -
    180A  SER      3.8     0.3    +      -       -      -
    181A  PHE*     3.1    30.8    +      -       +      +
    183A  LEU*     4.5    20.0    -      -       +      -
    207A  VAL*     4.1    15.3    -      -       +      -
    208A  GLN      4.0     5.2    -      -       -      +
    209A  LYS*     4.3    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161A  LEU      3.0    11.8    -      -       -      +
    162A  ILE*     1.3    82.9    -      -       -      +
    164A  LEU*     1.4    57.3    +      -       +      +
    179A  GLN*     3.4    12.3    +      -       -      +
    180A  SER*     2.7    37.7    +      -       -      +
    208A  GLN*     3.3    28.0    -      -       -      +
    209A  LYS      3.6    11.2    -      -       -      +
    210A  LYS*     3.6    23.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  ILE*     3.3     5.0    -      -       -      +
    163A  PRO*     1.4    85.2    -      -       +      +
    165A  VAL*     1.3    58.2    +      -       -      +
    166A  TYR*     3.7    28.3    -      -       +      -
    174A  ARG*     4.4    12.3    -      -       -      +
    177A  GLN*     3.4    44.6    -      -       +      +
    178A  TRP      3.8     2.7    -      -       -      +
    179A  GLN*     4.1    16.4    -      -       +      +
    206A  VAL      4.3     0.5    -      -       -      +
    208A  GLN*     2.9    50.2    +      -       +      +
    214A  ARG*     5.9     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146A  PHE*     4.3     9.6    -      -       +      -
    148A  VAL*     5.5     3.8    -      -       +      -
    162A  ILE*     3.9    16.6    -      -       +      +
    164A  LEU*     1.3    72.4    -      -       -      +
    166A  TYR*     1.3    63.6    +      -       -      +
    177A  GLN*     3.4     3.6    -      -       -      +
    178A  TRP*     3.0    64.0    +      -       +      +
    181A  PHE*     5.6     2.2    -      -       +      -
    190A  PHE*     4.9    12.3    -      -       +      -
    205A  VAL*     4.1    16.4    -      -       +      -
    206A  VAL      3.2    11.4    -      -       -      +
    207A  VAL*     3.6    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  LEU*     3.7    23.6    -      -       +      -
    165A  VAL*     1.3    76.3    -      -       -      +
    167A  ILE*     1.3    66.8    +      -       -      +
    168A  GLN*     3.6    33.7    +      -       +      -
    174A  ARG*     3.4    49.7    +      -       +      -
    176A  ALA      3.3    12.8    -      -       -      +
    177A  GLN*     3.9     9.9    -      -       +      +
    178A  TRP*     4.5     1.8    -      -       -      -
    204A  LYS      3.8     0.3    -      -       -      +
    205A  VAL*     3.6     1.1    -      -       -      -
    206A  VAL*     2.8    76.2    +      -       +      +
    208A  GLN*     5.4     0.4    -      -       +      -
    214A  ARG*     3.5    26.5    +      -       -      -
    216A  GLU*     4.3     3.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  VAL*     4.3     7.6    -      -       +      -
    146A  PHE*     4.0    12.1    -      -       +      -
    166A  TYR*     1.3    76.6    -      -       -      +
    168A  GLN*     1.3    60.3    +      -       -      +
    174A  ARG*     3.6     1.4    -      -       -      -
    175A  ILE*     2.8    52.5    +      -       +      +
    176A  ALA*     3.0    11.2    +      -       +      +
    178A  TRP*     3.5    28.3    -      -       +      -
    192A  PHE*     3.7    29.6    -      -       +      -
    203A  TYR*     4.6     4.5    -      -       +      -
    204A  LYS      3.5     5.4    -      -       -      +
    205A  VAL*     3.9    19.1    -      -       +      -
    219A  PHE*     3.9    26.2    -      -       +      -
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Residues in contact with GLN 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  TYR*     3.6    33.0    +      -       +      -
    167A  ILE*     1.3    74.1    -      -       -      +
    169A  ASP*     1.3    66.4    +      -       -      +
    172A  GLY*     3.3    37.1    -      -       -      +
    173A  ASN      3.9     3.6    -      -       -      -
    174A  ARG*     4.0    15.8    +      -       -      +
    203A  TYR*     3.4     2.9    -      -       -      +
    204A  LYS*     2.7    66.2    +      -       +      +
    206A  VAL*     4.4     0.8    -      -       +      +
    216A  GLU*     4.6     2.4    +      -       -      -
----------------------------------------------------------
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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