Contacts of the strand formed by residues 153 - 161 (chain A) in PDB entry 1TFZ


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 VAL 153 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  ILE      3.7     0.3    -      -       -      +
    148A  VAL*     3.4     2.6    -      -       -      -
    149A  LEU*     2.7    41.5    +      -       +      +
    152A  ALA*     1.3    88.2    -      -       +      +
    154A  THR*     1.3    67.8    +      -       -      +
    155A  ILE*     5.5     0.4    -      -       +      -
    169A  VAL*     3.9    23.3    -      -       +      -
    170A  SER      3.3    11.2    -      -       -      +
    171A  TYR*     3.6    25.4    -      -       +      -
    172A  LYS*     5.6     0.4    -      -       -      -
    181A  PHE      5.5     1.1    -      -       -      +
    182A  LEU*     3.9    17.3    -      -       +      -
    183A  PRO*     3.6    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 154 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  ASP*     5.5     1.1    -      -       -      +
    128A  ALA*     3.4    18.6    -      -       +      +
    129A  GLU*     3.9    16.4    -      -       +      +
    146A  PRO*     4.3    16.6    -      -       +      -
    147A  ILE      3.4    11.0    -      -       -      +
    148A  VAL*     3.4    25.2    -      -       +      +
    153A  VAL*     1.3    76.7    -      -       -      +
    155A  ILE*     1.3    63.6    +      -       -      +
    169A  VAL*     3.3     5.2    -      -       -      -
    170A  SER*     2.9    43.7    +      -       -      -
    172A  LYS*     4.5    10.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  ILE*     4.5    14.1    -      -       +      -
    100A  PRO*     4.2    16.6    -      -       +      -
    101A  SER*     4.9     2.2    -      -       -      +
    145A  PRO      3.6     2.6    -      -       -      +
    146A  PRO*     3.3     3.0    -      -       -      +
    147A  ILE*     3.0    36.4    +      -       +      +
    149A  LEU*     3.7    23.3    -      -       +      -
    153A  VAL*     5.5     2.0    -      -       +      -
    154A  THR*     1.3    76.9    -      -       -      +
    156A  ALA*     1.3    63.5    +      -       -      +
    157A  GLU*     4.2     7.4    -      -       -      +
    167A  ARG*     3.4    44.0    -      -       +      +
    168A  TYR      3.2     4.3    -      -       -      +
    169A  VAL*     4.6     7.0    -      -       +      -
    182A  LEU*     4.6    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  ALA*     4.0     9.2    -      -       +      +
    132A  PHE*     3.7    33.7    -      -       +      -
    144A  SER*     3.7     6.5    -      -       -      +
    145A  PRO      4.2     1.3    -      -       -      -
    146A  PRO*     3.8    14.6    -      -       +      -
    155A  ILE*     1.3    77.7    -      -       -      +
    157A  GLU*     1.3    67.6    +      -       -      +
    167A  ARG*     3.3     0.7    -      -       -      +
    168A  TYR*     2.7    42.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  SER*     2.6    40.2    +      -       -      -
    119A  ARG*     4.7     8.7    +      -       -      -
    132A  PHE*     3.3     5.7    -      -       -      -
    143A  SER*     2.9    12.3    +      -       -      -
    144A  SER*     2.8    45.0    +      -       -      +
    155A  ILE*     4.2     4.3    -      -       +      +
    156A  ALA*     1.3    81.2    -      -       -      +
    158A  VAL*     1.3    63.7    +      -       -      +
    165A  VAL*     3.6    21.2    -      -       +      +
    166A  LEU      3.4     5.2    -      -       -      +
    167A  ARG*     2.7    43.4    +      -       +      -
    168A  TYR*     5.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  PHE*     3.8    22.0    -      -       +      -
    135A  SER*     4.4     5.4    -      -       -      -
    136A  VAL*     4.4     4.5    -      -       +      -
    140A  ALA*     4.0    20.0    -      -       +      -
    141A  ILE      3.4    11.2    -      -       -      +
    143A  SER*     4.0     5.6    -      -       -      +
    157A  GLU*     1.3    78.8    -      -       -      +
    159A  LYS*     1.3    59.1    +      -       -      +
    165A  VAL*     3.2     4.3    -      -       -      +
    166A  LEU*     2.8    40.4    +      -       +      +
    168A  TYR*     3.9    18.4    -      -       +      +
    223A  PHE*     3.6    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  ILE*     2.8    51.9    +      -       +      +
    142A  PRO      4.1     8.3    -      -       -      -
    143A  SER*     4.3    16.2    -      -       -      +
    158A  VAL*     1.3    75.4    -      -       -      +
    160A  LEU*     1.3    61.3    +      -       -      +
    161A  TYR*     5.1     1.3    -      -       -      +
    162A  GLY      5.3    10.1    -      -       -      +
    164A  VAL      4.2     3.8    -      -       -      +
    165A  VAL*     4.4     5.4    -      -       +      +
    219A  TYR*     2.9    31.0    +      -       +      +
    223A  PHE*     3.8     9.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  VAL*     4.4    25.1    -      -       +      -
    158A  VAL      3.5     0.6    +      -       -      -
    159A  LYS*     1.3    73.7    -      -       -      +
    161A  TYR*     1.3   105.9    +      -       +      +
    164A  VAL*     2.9    21.6    +      -       +      +
    165A  VAL      4.6     2.0    -      -       -      +
    166A  LEU*     4.1    26.2    -      -       +      +
    216A  ALA*     6.0     0.7    -      -       -      +
    219A  TYR*     3.7    18.7    -      -       -      -
    220A  VAL*     3.8    41.0    -      -       +      +
    223A  PHE*     4.6     2.0    -      -       +      -
    258A  LEU*     4.5    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  LYS*     5.1     1.1    -      -       -      +
    160A  LEU*     1.3   110.5    -      -       +      +
    162A  GLY*     1.3    70.7    +      -       -      +
    163A  ASP      3.1     0.2    +      -       -      -
    164A  VAL*     2.9    41.9    +      -       +      +
    206A  ALA      4.3     4.2    +      -       -      -
    207A  VAL      3.9     0.3    -      -       -      -
    208A  GLY*     3.3    28.8    +      -       -      -
    210A  VAL*     3.9    23.1    -      -       +      -
    216A  ALA*     5.6     4.0    -      -       +      -
    220A  VAL*     5.1     0.2    -      -       +      -
    258A  LEU*     5.7     4.5    -      -       +      +
    259A  PRO      4.7     0.8    +      -       -      -
    260A  ILE*     4.2    29.4    -      -       +      -
    283A  ALA*     4.6     0.4    -      -       +      -
    284A  GLY*     4.0    14.8    -      -       -      -
    285A  LEU*     2.9    26.2    -      -       -      +
----------------------------------------------------------
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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