Contacts of the strand formed by residues 156 - 161 (chain A) in PDB entry 2C1E


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 LYS 156 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  PHE*     3.5     9.4    -      -       +      -
    143A  PHE*     3.1    36.7    +      -       +      +
    145A  GLY*     5.0     5.4    -      -       -      +
    151A  LEU*     2.9    42.0    +      -       +      -
    152A  THR*     4.4     2.2    -      -       -      +
    153A  GLY      4.3     3.6    -      -       -      +
    154A  LYS      2.8    24.4    +      -       -      +
    155A  PRO*     1.3    75.4    -      -       -      +
    157A  LEU*     1.3    62.8    +      -       -      +
    158A  PHE*     3.9    11.1    -      -       +      -
    191B  ALA      3.9     4.1    +      -       -      -
    192B  ASP*     2.9    23.5    +      -       -      +
    193B  PHE*     3.3    38.1    -      -       +      -
    194B  LEU      2.9    25.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  PHE*     5.9     1.6    -      -       +      -
     83A  TYR*     4.9     2.2    -      -       -      +
    113A  SER*     5.6     2.0    -      -       -      +
    114A  PHE*     2.8    17.9    +      -       -      +
    115A  VAL*     3.4    25.4    -      -       +      +
    116A  CYS*     2.8    27.2    +      -       -      +
    155A  PRO*     4.1    11.0    -      -       +      +
    156A  LYS*     1.3    76.2    -      -       -      +
    158A  PHE*     1.3    66.4    +      -       -      +
    159A  ILE*     4.1     7.0    -      -       +      -
    194B  LEU*     3.5    34.1    -      -       +      +
    232B  PHE*     3.8    22.9    -      -       +      -
    269B  LEU*     4.6     1.3    -      -       +      -
    273B  LEU*     3.9    27.8    -      -       +      -
    275B  PHE*     4.4    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  PHE*     4.0    10.3    -      +       -      -
    116A  CYS*     3.3    33.0    -      -       +      +
    118A  LEU*     5.2     6.5    -      -       +      -
    139A  ILE*     4.1    18.6    -      -       +      -
    140A  THR*     4.1    24.5    -      -       +      -
    143A  PHE*     3.8    26.7    -      +       -      -
    156A  LYS*     3.9    18.8    -      -       +      -
    157A  LEU*     1.3    76.1    -      -       -      +
    159A  ILE*     1.3    58.4    +      -       -      +
    160A  ILE*     3.9    12.3    +      -       +      +
    193B  PHE*     3.7    30.1    -      +       -      -
    194B  LEU      2.8    12.1    +      -       -      +
    195B  TYR*     3.3    19.0    -      +       +      +
    196B  ALA*     2.8    29.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  PHE*     3.8    29.4    -      -       +      -
    115A  VAL*     4.2     8.1    -      -       +      -
    116A  CYS      2.9    12.1    +      -       -      +
    117A  VAL*     3.3    20.7    -      -       +      +
    118A  LEU*     2.8    27.5    +      -       -      +
    157A  LEU*     5.0     6.3    -      -       +      -
    158A  PHE*     1.3    75.7    -      -       -      +
    160A  ILE*     1.3    62.0    +      -       -      +
    194B  LEU*     5.9     0.2    -      -       +      -
    196B  ALA*     3.5    15.9    -      -       +      +
    215B  PHE*     3.7    17.7    -      -       +      -
    216B  ILE*     4.1    11.9    -      -       +      -
    219B  LEU*     3.6    31.6    -      -       +      -
    223B  LEU*     5.8     0.2    -      -       +      -
    232B  PHE*     5.3    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  LEU*     3.7    17.9    -      -       +      +
    126A  ILE      6.0     0.9    -      -       -      +
    127A  ILE*     4.5     9.4    -      -       +      -
    136A  LEU*     3.8    27.4    -      -       +      -
    158A  PHE*     4.2    13.0    -      -       +      +
    159A  ILE*     1.3    77.6    -      -       -      +
    161A  GLN*     1.3    62.0    +      -       -      +
    162A  ALA*     3.7    22.0    +      -       +      +
    164A  ARG*     6.4     0.7    -      -       +      -
    195B  TYR*     4.5    14.1    -      -       +      -
    196B  ALA      3.0    10.5    +      -       -      +
    197B  TYR*     3.7    40.0    -      -       +      +
    198B  SER*     3.1    29.4    +      -       -      -
    215B  PHE*     4.2     3.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ARG*     3.9    14.6    -      -       -      +
     70A  ASP*     4.5     0.9    -      -       -      +
    118A  LEU      2.9     9.7    +      -       -      +
    119A  LEU*     3.7    22.0    -      -       +      -
    120A  SER      3.0    21.1    +      -       -      +
    159A  ILE      4.1     0.8    +      -       -      -
    160A  ILE*     1.3    69.6    -      -       -      +
    162A  ALA*     1.3    63.9    +      -       -      +
    198B  SER*     3.1    22.3    -      -       -      -
    205B  SER*     2.9    24.7    +      -       -      -
    206B  TRP      4.0     6.1    +      -       -      +
    213B  SER*     3.3    37.3    +      -       -      +
    215B  PHE*     3.5     7.1    +      -       -      +
    216B  ILE*     4.1    11.2    -      -       +      +
      5C  AA1      3.1    19.8    +      -       -      -
----------------------------------------------------------
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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