Contacts of the strand formed by residues 359 - 366 (chain A) in PDB entry 5A63


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 359 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274A  ARG*     4.6     4.7    +      -       -      -
    275A  VAL*     3.3     7.0    -      -       -      -
    277A  VAL*     3.3    27.1    -      -       +      -
    347A  MET*     4.5    13.0    -      -       +      -
    354A  VAL*     4.3    14.4    -      -       +      -
    355A  GLN      4.7     0.4    -      -       -      +
    356A  LEU*     3.5    13.3    +      -       +      +
    357A  GLU      3.4     8.2    -      -       -      +
    358A  ASN*     1.3    77.0    -      -       -      +
    360A  ASP*     1.3    60.6    +      -       -      +
    361A  SER      3.7    26.9    -      -       -      +
    362A  PHE*     4.2     8.1    -      -       +      +
    430A  PHE*     4.7     7.9    -      -       +      -
    434A  ARG*     6.0     0.3    -      -       -      -
    436A  ILE*     4.2    27.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 360 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274A  ARG*     2.9    44.1    +      -       +      +
    275A  VAL      2.7    15.8    +      -       -      +
    323A  ARG*     4.2    26.3    +      -       -      -
    358A  ASN      3.0     0.8    +      -       -      -
    359A  VAL*     1.3    74.0    -      -       -      +
    361A  SER*     1.3    62.7    +      -       -      +
    393A  GLN*     4.4    10.8    -      -       -      +
    436A  ILE*     5.8     0.9    -      -       -      -
    437A  SER*     3.7    19.4    +      -       -      -
    501A  LEU*     6.1     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 361 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    275A  VAL      3.8     0.6    +      -       -      -
    276A  VAL*     3.3    18.1    -      -       -      +
    277A  VAL      2.8    31.9    +      -       -      -
    359A  VAL*     3.6     6.9    -      -       -      +
    360A  ASP*     1.3    82.3    -      -       -      +
    362A  PHE*     1.3    54.0    +      -       -      +
    397A  LEU*     4.3     5.8    -      -       -      -
    437A  SER*     3.7    13.2    -      -       -      +
    501A  LEU*     2.6    46.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 362 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    277A  VAL*     3.3    31.6    -      -       +      -
    279A  ALA*     3.7    20.2    -      -       +      -
    330A  PHE*     4.2     2.5    -      +       -      -
    359A  VAL*     4.2     9.6    -      -       +      +
    361A  SER*     1.3    73.7    -      -       -      +
    363A  VAL*     1.3    70.6    +      -       -      +
    364A  GLU*     3.8    20.6    -      -       +      -
    397A  LEU*     4.2     0.5    -      -       -      +
    427A  LEU*     3.5    39.7    -      -       +      -
    430A  PHE*     3.5    51.6    -      +       +      -
    436A  ILE*     4.8     5.8    -      -       +      -
    437A  SER      3.5     6.5    +      -       -      +
    438A  GLY*     3.3    11.5    -      -       -      -
    439A  VAL*     2.8    27.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 363 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276A  VAL*     4.9     0.4    -      -       +      -
    277A  VAL      2.7    14.5    +      -       -      +
    278A  ALA*     3.0     9.0    -      -       +      +
    279A  ALA      2.7    31.2    +      -       -      -
    305A  GLN*     4.6     0.5    +      -       -      -
    362A  PHE*     1.3    81.9    -      -       -      +
    364A  GLU*     1.3    58.2    +      -       -      +
    365A  LEU*     4.3     1.4    +      -       -      +
    397A  LEU*     4.7     8.7    -      -       +      -
    401A  LEU*     5.4     4.7    -      -       +      -
    439A  VAL*     3.4     9.6    -      -       +      +
    441A  LEU*     3.7    33.0    -      -       +      -
    494A  LEU*     4.0    15.9    -      -       +      -
    497A  ALA*     6.1     4.3    -      -       +      -
    498A  LEU*     4.3    11.2    -      -       +      -
    501A  LEU*     4.2    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 364 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279A  ALA*     2.2    34.7    -      -       +      +
    280A  THR*     3.4    15.6    -      -       -      +
    281A  ARG*     3.4    10.4    +      -       -      +
    333A  GLU*     5.0     0.5    -      -       -      +
    362A  PHE*     3.8    21.2    -      -       +      -
    363A  VAL*     1.3    73.4    -      -       -      +
    365A  LEU*     1.3    64.0    +      -       -      +
    425A  SER*     2.9    16.3    -      -       -      -
    426A  SER*     2.4    47.5    +      -       -      +
    427A  LEU*     3.1     2.0    +      -       +      -
    439A  VAL      3.0     7.1    +      -       -      -
    440A  VAL*     2.9    24.0    -      -       +      +
    441A  LEU      2.9    20.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 365 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279A  ALA      3.8     1.1    +      -       -      +
    280A  THR*     3.0    55.0    -      -       +      +
    281A  ARG*     5.3     1.4    +      -       -      -
    301A  SER*     3.5     6.9    +      -       -      +
    304A  THR*     2.6    32.5    -      -       -      +
    305A  GLN*     3.3    23.1    -      -       +      +
    363A  VAL      4.8     1.3    -      -       -      +
    364A  GLU*     1.3    79.3    -      -       -      +
    366A  GLY*     1.3    58.0    +      -       -      +
    367A  GLN      4.2     0.2    -      -       -      -
    368A  VAL*     3.7    13.9    -      -       +      -
    441A  LEU*     3.1    17.0    -      -       +      +
    490A  VAL*     5.2     4.5    -      -       +      -
    491A  ALA*     6.1     0.2    -      -       -      -
    494A  LEU*     3.4    34.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 366 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281A  ARG*     5.8     5.2    -      -       -      -
    301A  SER*     4.3     0.9    -      -       -      -
    364A  GLU*     3.7     3.8    +      -       -      -
    365A  LEU*     1.3    73.4    -      -       -      +
    367A  GLN*     1.3    75.6    +      -       -      +
    368A  VAL      3.4     2.8    +      -       -      -
    425A  SER*     6.4     1.1    -      -       -      -
    440A  VAL*     4.0    10.1    -      -       -      +
    441A  LEU      2.8     9.0    +      -       -      +
    442A  ALA*     3.1    25.8    -      -       -      +
    443A  ASP      3.4     0.2    +      -       -      -
    444A  HIS*     4.7     2.0    -      -       -      -
----------------------------------------------------------
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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