Contacts of the strand formed by residues 146 - 153 (chain A) in PDB entry 1X82


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 146 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  THR      3.7     1.9    -      -       -      +
     73A  LEU*     2.9    42.5    +      -       +      +
    101A  ALA*     4.5    11.4    -      -       +      -
    103A  LYS      3.4    16.2    -      -       -      -
    104A  GLY*     4.4     2.2    -      -       -      -
    105A  LYS      3.9     6.3    -      -       -      +
    106A  GLY*     3.7    26.9    -      -       -      -
    107A  GLY      3.8     4.7    -      -       -      -
    122A  MSE      3.7    39.3    -      -       +      -
    138A  THR*     4.3     9.0    -      -       -      -
    139A  VAL      3.6    23.8    -      -       -      -
    140A  ASN*     3.4    23.3    -      -       +      +
    145A  PRO*     1.3    71.2    -      -       -      +
    147A  ILE*     1.3    61.6    +      -       -      +
    148A  PHE*     3.6    31.3    -      +       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
     12A  PHE      4.7     2.2    -      -       -      +
     13A  GLU      3.5    26.0    -      -       -      +
     14A  THR*     3.7    16.6    -      -       -      +
     15A  GLY*     3.5    26.2    -      -       -      +
     70A  THR*     5.3     0.7    -      -       -      -
     71A  THR      3.3     8.7    -      -       -      +
     72A  VAL*     4.3    15.5    -      -       +      -
    101A  ALA*     3.9     0.7    -      -       -      -
    102A  LEU*     2.9    38.4    +      -       +      +
    103A  LYS*     2.9    31.4    +      -       +      +
    145A  PRO*     4.3    16.6    -      -       +      +
    146A  PHE*     1.3    81.2    -      -       -      +
    148A  PHE*     1.3    68.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  THR*     3.2     6.8    -      -       -      -
     71A  THR*     3.0    67.0    +      -       +      -
     73A  LEU*     4.6     3.6    -      -       +      -
     99A  TYR*     3.3    32.1    -      +       -      -
    100A  VAL      3.4    15.7    -      -       -      +
    101A  ALA*     4.0     9.0    -      -       +      -
    102A  LEU*     4.2     7.4    -      -       -      +
    122A  MSE      4.2     6.1    -      -       +      -
    138A  THR*     3.1    31.4    -      -       +      -
    146A  PHE*     3.6    39.5    -      +       +      -
    147A  ILE*     1.3    78.2    -      -       -      +
    149A  LEU*     1.3    62.5    +      -       -      +
    150A  ALA*     4.9     1.8    -      -       +      -
    301A  PA5      3.6     7.2    -      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
     10A  VAL*     5.4     9.0    -      -       +      -
     12A  PHE*     5.8     7.0    -      -       +      -
     17A  ILE*     5.1     0.9    -      -       +      -
     68A  PHE*     4.1    22.7    -      -       +      -
     69A  ALA      3.5    17.5    -      -       -      +
     70A  THR*     3.9    16.4    -      -       +      -
     98A  VAL      4.0     0.2    -      -       -      +
     99A  TYR*     3.2     4.9    -      -       -      +
    100A  VAL*     2.7    52.4    +      -       +      +
    102A  LEU*     4.2    16.4    -      -       +      +
    148A  PHE*     1.3    75.4    -      -       -      +
    150A  ALA*     1.3    62.1    +      -       -      +
    151A  ILE*     4.0    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  PHE*     3.1     7.4    -      -       -      +
     69A  ALA      2.8    36.4    +      -       -      +
     97A  GLU*     4.1     1.1    -      -       -      +
     98A  VAL      3.5     4.3    -      -       -      -
     99A  TYR*     3.6    26.2    -      -       +      -
    148A  PHE*     4.9     1.5    -      -       +      -
    149A  LEU*     1.3    74.1    -      -       -      +
    151A  ILE*     1.3    62.4    +      -       -      +
    152A  TYR*     3.9     2.2    -      -       +      -
    301A  PA5      3.3    31.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  LEU*     4.4    28.0    -      -       +      -
     67A  ASN      3.4    10.8    -      -       -      +
     68A  PHE*     3.9    13.0    -      -       +      -
     97A  GLU*     3.5     2.3    -      -       -      +
     98A  VAL*     2.8    51.0    +      -       +      +
    100A  VAL*     4.5    11.7    -      -       +      -
    149A  LEU*     4.0    24.7    -      -       +      -
    150A  ALA*     1.3    79.4    -      -       -      +
    152A  TYR*     1.3    65.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  ALA*     4.3     1.7    -      -       -      +
     58A  GLU*     2.8    25.8    +      -       -      +
     66A  LEU*     3.7     7.0    -      -       -      -
     67A  ASN*     2.8    61.3    +      -       +      +
     68A  PHE*     4.0     8.1    +      -       -      -
     69A  ALA*     3.9    16.9    -      -       +      +
     90A  HIS*     4.9     1.6    -      +       -      +
     96A  ALA      4.2     0.4    -      -       -      -
     97A  GLU*     3.3    30.5    -      -       +      +
    150A  ALA      3.9    14.6    -      -       -      -
    151A  ILE*     1.3    78.4    -      -       -      +
    153A  PRO*     1.3    82.1    -      -       +      +
    156A  ALA*     5.1     4.7    -      -       +      -
    158A  HIS*     5.0    16.3    -      +       -      -
    301A  PA5      3.3    25.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 153 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  GLY      6.2     1.3    -      -       -      +
     65A  ASP      3.5     9.9    -      -       -      +
     66A  LEU*     4.2     9.2    -      -       +      -
     67A  ASN*     4.3     0.9    +      -       -      -
     95A  ARG*     3.6    33.7    -      -       +      +
     96A  ALA*     2.9    31.4    -      -       +      +
     97A  GLU*     5.1     0.2    -      -       -      -
    152A  TYR*     1.3    90.3    -      -       +      +
    154A  ALA*     1.3    65.2    +      -       -      +
    155A  ASP*     3.1    10.0    +      -       -      +
    156A  ALA*     3.2    18.3    +      -       +      +
    157A  GLY      4.9     0.5    +      -       -      -
----------------------------------------------------------
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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