Contacts of the strand formed by residues 143 - 150 (chain A) in PDB entry 1PT6


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 143 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  GLN*     1.3    90.1    -      -       -      +
    144A  ASP*     1.3    57.9    +      -       -      +
    145A  ILE*     4.1    10.8    -      -       +      -
    178A  GLN      3.9     2.2    +      -       -      -
    179A  THR*     3.4    11.3    +      -       +      +
    180A  GLN      2.9    27.7    +      -       -      +
    241A  ARG*     3.0     7.8    +      -       -      +
    244A  VAL*     3.8     0.2    -      -       -      -
    245A  LYS*     3.7    20.9    -      -       +      +
    247A  VAL*     4.1    18.8    -      -       +      -
    331A  ILE*     3.5    44.2    -      -       +      +
    332A  PHE*     3.7    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  LEU*     1.3    69.7    -      -       -      +
    145A  ILE*     1.3    60.6    +      -       -      +
    180A  GLN*     3.2    14.5    -      -       -      +
    196A  LEU*     3.9    15.0    -      -       +      -
    234A  PHE*     3.4    21.2    -      -       +      -
    240A  ALA*     3.3     7.4    -      -       -      +
    241A  ARG*     2.8    61.8    +      -       -      +
    244A  VAL*     3.5     6.4    -      -       -      +
    245A  LYS      2.9    14.7    +      -       -      +
    246A  LYS*     3.5     3.4    -      -       +      +
    247A  VAL*     2.9    25.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  LEU*     4.1    13.7    -      -       +      -
    144A  ASP*     1.3    77.7    -      -       -      +
    146A  VAL*     1.3    66.6    -      -       -      +
    147A  ILE*     4.4     9.4    -      -       +      -
    168A  LEU*     6.4     0.2    -      -       +      -
    172A  MET*     3.8    25.4    -      -       +      -
    179A  THR*     3.7    21.3    -      -       +      -
    180A  GLN      2.8    15.0    +      -       -      +
    181A  VAL*     3.1    12.0    -      -       +      +
    182A  GLY      3.1    23.9    +      -       -      +
    196A  LEU*     3.5     1.2    -      -       -      +
    247A  VAL*     3.2    19.1    -      -       +      +
    249A  VAL*     4.2    22.4    -      -       +      -
    331A  ILE*     3.8    21.5    -      -       +      -
    332A  PHE*     3.8     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  ILE*     1.3    77.1    -      -       -      +
    147A  ILE*     1.3    71.2    +      -       -      +
    148A  VAL*     4.1     1.6    -      -       +      -
    182A  GLY*     3.3    11.0    -      -       -      +
    184A  VAL*     4.1     8.5    -      -       +      -
    196A  LEU*     4.2    15.3    -      -       +      -
    229A  ALA*     3.9    24.7    -      -       +      -
    233A  ALA*     4.0    23.8    -      -       +      -
    234A  PHE*     3.5    35.0    -      -       +      -
    247A  VAL      2.9     9.7    +      -       -      -
    248A  MET*     3.3     7.8    -      -       +      +
    249A  VAL      3.0    22.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  ILE*     4.4    11.4    -      -       +      -
    146A  VAL*     1.3    74.9    -      -       -      +
    148A  VAL*     1.3    58.9    +      -       -      +
    149A  LEU*     3.8    27.6    -      -       +      -
    164A  PHE*     5.3     0.9    -      -       +      -
    165A  LEU*     3.8    25.4    -      -       +      -
    168A  LEU*     4.3    20.0    -      -       +      -
    169A  LEU*     4.3    20.2    -      -       +      -
    172A  MET*     5.9     0.2    -      -       +      -
    181A  VAL*     4.4     4.3    -      -       +      -
    182A  GLY      3.0     6.9    +      -       -      +
    183A  ILE*     3.4    17.2    -      -       +      +
    184A  VAL      2.9    31.4    +      -       -      +
    249A  VAL*     3.3    24.9    -      -       +      +
    251A  VAL*     4.6     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146A  VAL*     4.1     3.1    -      -       +      -
    147A  ILE*     1.3    72.8    -      -       -      +
    149A  LEU*     1.3    58.9    +      -       -      +
    184A  VAL*     3.4     8.7    -      -       +      +
    186A  TYR*     3.6    27.4    -      -       +      -
    225A  GLY*     3.7    22.2    -      -       -      +
    226A  THR*     3.9     7.6    -      -       -      +
    229A  ALA*     3.6    29.6    -      -       +      -
    248A  MET*     3.9    22.7    -      -       +      -
    249A  VAL      2.8    10.4    +      -       -      +
    250A  ILE*     3.4     8.9    -      -       +      -
    251A  VAL*     2.9    28.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  ILE*     4.0    15.3    -      -       +      -
    148A  VAL*     1.3    71.5    -      -       -      +
    150A  ASP*     1.3    65.4    +      -       -      +
    151A  GLY      3.4     0.5    +      -       -      -
    158A  TRP*     4.3    18.8    -      -       +      -
    161A  VAL*     4.0    24.9    -      -       +      -
    164A  PHE*     5.3     1.3    -      -       +      -
    165A  LEU*     3.8    32.1    -      -       +      -
    183A  ILE*     4.2    16.6    -      -       +      -
    184A  VAL      2.8    15.2    +      -       -      +
    185A  GLN*     3.3     9.8    -      -       +      +
    186A  TYR*     2.9    29.0    +      -       -      -
    212A  ILE*     4.8     7.4    -      -       +      -
    251A  VAL*     3.9    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  LEU*     1.3    73.4    -      -       -      +
    151A  GLY*     1.3    59.2    +      -       -      +
    152A  SER*     2.9    37.5    +      -       -      -
    155A  ILE*     3.1    21.2    -      -       +      +
    158A  TRP*     3.6    10.9    -      -       -      -
    161A  VAL*     5.7     0.5    -      -       -      +
    186A  TYR*     3.5    22.4    -      -       -      +
    187A  GLY*     5.1     0.7    -      -       -      -
    220A  THR*     3.3    16.3    -      -       -      +
    251A  VAL*     2.9    24.2    +      -       -      +
    252A  THR*     2.7    26.6    +      -       -      -
    253A  ASP*     3.2    14.9    +      -       -      +
----------------------------------------------------------
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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