Contacts of the strand formed by residues 231 - 240 (chain A) in PDB entry 2A3K


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 TYR 231 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228A  CYS*     2.8    53.8    +      -       +      +
    229A  PRO*     3.4    10.3    -      -       +      -
    230A  GLU*     1.3    80.6    -      -       +      +
    232A  THR*     1.3    60.1    +      -       -      +
    233A  VAL*     3.5    25.6    -      -       +      -
    250A  ILE*     3.7    19.3    -      -       +      -
    251A  LEU      3.0    21.5    -      -       -      +
    252A  PHE*     3.8    12.8    -      +       +      +
    253A  SER*     4.8     1.1    -      -       -      -
    266A  PRO*     4.5     4.5    -      -       +      -
    269A  ARG*     3.8    21.6    +      -       +      +
    270A  LEU*     4.1    28.9    -      -       +      -
    273A  GLU*     2.5    33.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 232 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  MET*     3.9    24.2    -      -       +      -
    226A  LYS      3.6    10.8    -      -       -      +
    227A  GLU*     3.9    24.5    -      -       +      +
    228A  CYS      5.2     0.7    +      -       -      -
    231A  TYR*     1.3    76.0    +      -       -      +
    233A  VAL*     1.3    63.0    +      -       -      +
    234A  ARG*     3.7    27.7    +      -       -      +
    249A  HIS      3.6     2.1    -      -       -      +
    250A  ILE*     3.5     2.4    -      -       -      -
    251A  LEU*     2.9    39.1    +      -       -      +
    253A  SER*     5.7     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 233 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224A  ASP      3.6     1.7    -      -       -      +
    225A  MET*     3.5     3.5    -      -       -      -
    226A  LYS*     2.9    47.3    +      -       +      +
    228A  CYS*     4.9     4.9    -      -       -      -
    231A  TYR*     3.5    31.6    -      -       +      -
    232A  THR*     1.3    70.2    -      -       -      +
    234A  ARG*     1.3    63.3    +      -       -      +
    235A  GLN*     4.0    11.8    +      -       +      +
    248A  LYS*     4.0    26.7    -      -       +      -
    249A  HIS      3.6     6.3    -      -       -      +
    250A  ILE*     4.5     3.4    -      -       +      +
    273A  GLU*     4.3    16.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 234 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208A  TRP*     3.3    42.9    -      -       -      +
    209A  PRO      5.2     0.6    +      -       -      -
    222A  ILE*     3.8    19.1    -      -       +      +
    224A  ASP      3.4     2.0    -      -       -      +
    225A  MET*     3.6    39.3    -      -       +      -
    232A  THR*     3.7    24.9    +      -       -      +
    233A  VAL*     1.3    71.7    -      -       -      +
    235A  GLN*     1.3    62.7    +      -       -      +
    236A  LEU*     3.8     8.7    +      -       +      +
    247A  VAL      3.8     0.2    -      -       -      +
    248A  LYS*     3.7     0.3    -      -       -      -
    249A  HIS*     2.7    60.5    +      -       +      +
    251A  LEU*     4.2    23.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222A  ILE*     3.5     3.1    -      -       -      +
    223A  GLN*     2.5    39.1    +      -       +      -
    224A  ASP*     2.7    39.6    +      -       +      +
    233A  VAL*     4.0    11.0    +      -       +      +
    234A  ARG*     1.3    72.4    -      -       -      +
    236A  LEU*     1.3    56.2    +      -       -      +
    246A  SER*     5.2     8.3    -      -       -      -
    247A  VAL      3.5    19.2    +      -       -      +
    248A  LYS*     3.7    30.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  TRP*     4.5    18.2    -      -       +      -
    191A  ILE*     6.1     0.2    -      -       +      -
    208A  TRP*     5.2     9.2    -      -       +      -
    209A  PRO*     6.1     0.2    -      -       +      -
    220A  ILE*     4.2    21.3    -      -       +      -
    221A  ARG      3.2    14.8    -      -       -      +
    222A  ILE*     4.0     9.0    -      -       +      -
    223A  GLN*     3.9     3.5    -      -       -      +
    234A  ARG*     4.3     9.2    -      -       +      +
    235A  GLN*     1.3    76.6    +      -       -      +
    237A  THR*     1.3    77.9    +      -       -      +
    238A  ILE*     4.5     0.7    -      -       +      +
    246A  SER*     3.4     6.8    -      -       -      -
    247A  VAL*     2.8    62.1    +      -       +      +
    249A  HIS*     4.0    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219A  GLN      4.5     0.2    -      -       -      -
    220A  ILE*     3.5     4.9    -      -       -      -
    221A  ARG*     2.9    45.8    +      -       -      +
    223A  GLN*     3.6    31.8    +      -       +      +
    236A  LEU*     1.3    87.2    -      -       -      +
    238A  ILE*     1.3    60.9    +      -       -      +
    239A  GLN*     6.1     0.3    -      -       -      +
    244A  ARG*     3.9    34.0    +      -       -      +
    245A  ARG      3.1    10.8    -      -       -      +
    246A  SER*     4.5     9.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  TRP*     4.0    26.5    -      -       +      +
    183A  VAL*     4.8     7.0    -      -       +      -
    184A  TRP*     3.7    23.3    -      -       +      -
    188A  VAL      5.8     0.4    -      -       -      +
    218A  PHE*     4.0    32.5    -      -       +      -
    219A  GLN      3.4     8.7    -      -       -      +
    220A  ILE*     4.0    16.4    -      -       +      -
    236A  LEU*     4.9     0.9    -      -       +      -
    237A  THR*     1.3    75.8    -      -       -      +
    239A  GLN*     1.3    65.2    +      -       -      +
    244A  ARG*     3.3     5.0    -      -       -      -
    245A  ARG*     2.7    56.0    +      -       +      +
    247A  VAL*     3.9    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217A  PRO      3.7     1.4    -      -       -      +
    218A  PHE*     3.2     8.7    -      -       -      -
    219A  GLN*     3.0    55.6    +      -       +      +
    221A  ARG*     5.9     2.2    -      -       +      -
    238A  ILE*     1.3    77.9    -      -       -      +
    240A  TYR*     1.3    61.2    +      -       -      +
    241A  GLN      3.2    22.8    +      -       -      +
    242A  GLU*     4.4    12.7    +      -       -      +
    243A  GLU      3.0    20.9    -      -       -      +
    244A  ARG*     4.5    12.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184A  TRP*     3.7    37.4    -      +       +      -
    217A  PRO*     3.8    33.0    -      -       +      -
    218A  PHE*     3.5    32.5    -      +       +      -
    239A  GLN*     1.3    74.1    -      -       -      +
    241A  GLN*     1.3   102.7    +      -       +      +
    242A  GLU      3.0     4.0    +      -       -      -
    243A  GLU*     3.0    21.5    +      -       -      +
----------------------------------------------------------
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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