Contacts of the strand formed by residues 180 - 188 (chain A) in PDB entry 5E63


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 GLY 180 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176A  VAL*     2.8    41.2    +      -       -      +
    177A  SER      5.3     0.7    -      -       -      +
    178A  GLY      4.5     0.9    -      -       -      +
    179A  ASP*     1.3    73.8    -      -       -      +
    181A  SER*     1.3    67.5    +      -       -      -
    182A  PHE*     5.6     0.7    -      -       -      -
    203A  GLN      3.3     9.4    -      -       -      -
    204A  ILE*     4.1     6.3    -      -       -      -
     16E    C      4.1    11.1    -      -       -      +
     17E    A      4.4     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176A  VAL*     4.9     2.4    -      -       -      +
    179A  ASP      4.9     1.0    +      -       -      -
    180A  GLY*     1.3    75.2    -      -       -      -
    182A  PHE*     1.3    65.8    +      -       -      +
    183A  LYS*     3.8    13.4    -      -       -      +
    201A  VAL      3.6     2.1    -      -       -      +
    202A  PHE*     3.4     6.8    -      -       -      -
    203A  GLN*     2.6    55.0    +      -       -      +
    205A  THR*     5.2     1.2    +      -       -      -
     16E    C      3.4    18.8    -      -       -      +
     17E    A      2.8    29.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176A  VAL*     4.1    11.2    -      -       +      -
    180A  GLY      5.7     0.4    -      -       -      -
    181A  SER*     1.3    73.8    -      -       -      +
    183A  LYS*     1.3    62.0    +      -       -      +
    201A  VAL      3.8     2.7    -      -       -      -
    202A  PHE*     3.4    34.3    -      +       -      -
    249A  ILE*     4.6     0.2    -      -       +      -
    253A  PHE*     4.3    10.3    -      +       -      -
    258A  ILE*     3.9    30.5    -      -       +      -
    262A  ALA*     4.8     8.7    -      -       +      -
    265A  ASP*     4.6     9.3    -      -       +      +
    266A  TYR*     3.8    38.1    -      +       +      -
    269A  TRP*     3.6    47.1    -      +       +      +
    297A  MET*     3.4    19.2    -      -       +      +
    298A  ASN*     5.9     0.3    +      -       -      -
     17E    A      4.6     3.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 183 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181A  SER*     4.4    14.8    -      -       -      +
    182A  PHE*     1.3    75.2    -      -       -      +
    184A  SER*     1.3    60.6    +      -       -      +
    185A  ILE*     3.7    16.2    -      -       +      +
    199A  ILE      3.8     0.2    -      -       -      +
    200A  LEU*     3.4     3.5    -      -       -      -
    201A  VAL*     2.7    52.0    +      -       +      +
    203A  GLN*     3.1    41.5    +      -       -      +
    269A  TRP*     2.9    19.0    +      -       -      +
     17E    A      3.7    26.7    +      -       +      +
     18E    G      3.2    43.5    +      -       +      +
     19E    G      5.5     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 184 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182A  PHE      4.0     1.8    +      -       -      -
    183A  LYS*     1.3    73.2    -      -       -      +
    185A  ILE*     1.3    64.9    +      -       -      +
    186A  LEU*     5.1     0.3    -      -       -      +
    198A  SER*     5.5     0.9    +      -       -      -
    199A  ILE      3.5     6.2    +      -       -      -
    200A  LEU*     4.4     4.3    -      -       -      -
    269A  TRP*     4.9     0.4    -      -       -      -
    272A  ILE*     3.7    32.0    -      -       -      +
    290A  ILE*     4.2     9.4    -      -       -      +
    294A  LYS*     2.9    44.2    +      -       -      +
    297A  MET*     4.6     9.0    -      -       -      +
     18E    G      4.3     8.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 185 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  LYS*     3.7    35.2    -      -       +      +
    184A  SER*     1.3    76.7    +      -       -      +
    186A  LEU*     1.3    71.4    +      -       -      +
    187A  LYS*     4.2     4.0    -      -       +      +
    197A  GLN      3.3     2.1    -      -       -      +
    198A  SER*     3.6     2.3    +      -       -      -
    199A  ILE*     2.7    51.3    +      -       +      +
    201A  VAL*     4.1    20.9    -      -       +      -
    294A  LYS*     3.8     1.8    -      -       -      +
     18E    G      4.6    10.1    -      -       +      +
     19E    G      4.0    38.1    -      -       +      +
     20E    T      3.7    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184A  SER*     5.1     0.9    -      -       -      +
    185A  ILE*     1.3    81.1    -      -       -      +
    187A  LYS*     1.3    60.6    +      -       -      +
    188A  LYS      4.0     1.4    +      -       -      -
    196A  PHE*     4.2    17.2    -      -       +      -
    197A  GLN      3.3     9.0    -      -       -      +
    198A  SER*     4.0    10.8    -      -       -      +
    287A  LEU*     4.2    17.7    -      -       +      -
    290A  ILE*     4.1    18.4    -      -       +      -
    291A  ARG*     3.5    42.8    -      -       +      +
    294A  LYS*     3.7    30.2    -      -       +      +
     19E    G      3.6    19.5    +      -       -      +
     20E    T      4.5     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 187 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  ILE*     4.3     4.7    -      -       +      -
    186A  LEU*     1.3    73.6    -      -       -      +
    188A  LYS*     1.3    81.3    +      -       -      +
    189A  SER*     3.1     4.5    +      -       -      +
    196A  PHE*     3.2     5.7    -      -       -      -
    197A  GLN*     2.9    54.5    +      -       +      +
    199A  ILE*     4.2     7.6    -      -       +      -
      3B    T      6.0     0.4    -      -       -      -
      4B    A      3.4     2.2    -      -       -      +
     20E    T      3.4    52.4    -      -       +      +
     21E    G      2.5    51.2    +      -       -      +
     22E    T      2.8    18.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 188 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186A  LEU      4.0     1.2    +      -       -      -
    187A  LYS*     1.3    88.7    -      -       -      +
    189A  SER*     1.3    58.3    +      -       -      +
    190A  GLU*     3.5    28.7    -      -       -      +
    195A  GLY*     3.0    35.6    +      -       -      +
    196A  PHE*     3.9    31.0    -      -       +      -
     20E    T      3.3    24.3    +      -       -      +
     22E    T      5.9     1.2    -      -       -      +
----------------------------------------------------------
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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