Contacts of the strand formed by residues 52 - 61 (chain C) in PDB entry 1PU5


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 52 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50C  PRO      4.1     1.2    -      -       -      -
     51C  LEU*     1.3    74.1    -      -       -      +
     53C  VAL*     1.3    62.1    +      -       -      +
     54C  ASP*     3.7    34.7    +      -       -      +
     78C  THR*     3.9    11.8    -      -       +      +
     79C  PHE      3.4    10.1    -      -       -      +
     80C  GLU*     4.1    20.1    -      -       +      +
    144C  VAL      3.4     1.6    -      -       -      +
    145C  LEU*     3.3     6.8    -      -       -      +
    146C  SER*     2.8    53.2    +      -       -      +
    147C  SER*     5.7     0.4    -      -       -      -
    149C  GLY*     6.0     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 53 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51C  LEU      4.0     0.2    +      -       -      -
     52C  LYS*     1.3    74.8    -      -       -      +
     54C  ASP*     1.3    62.5    +      -       -      +
     55C  LEU*     3.7    31.2    -      -       +      -
     77C  CYS      3.8     0.3    -      -       -      +
     78C  THR*     3.2     3.6    -      -       -      +
     79C  PHE*     2.8    47.2    +      -       +      +
     82C  PHE*     3.7    41.7    -      -       +      -
    143C  SER*     4.0     8.5    -      -       -      +
    144C  VAL      3.4     3.8    -      -       -      +
    145C  LEU*     3.8    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 54 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52C  LYS*     3.7    24.3    +      -       -      +
     53C  VAL*     1.3    72.5    -      -       -      +
     55C  LEU*     1.3    61.8    +      -       -      +
     56C  VAL*     5.6     2.5    -      -       +      +
     77C  CYS      4.0     2.0    -      -       -      -
     78C  THR*     2.8    37.7    +      -       -      +
    142C  GLU      3.4     2.1    -      -       -      +
    143C  SER*     3.4     2.9    -      -       -      -
    144C  VAL*     2.9    54.3    +      -       +      +
    146C  SER*     4.5     4.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 55 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53C  VAL*     3.7    16.4    -      -       +      -
     54C  ASP*     1.3    74.4    -      -       -      +
     56C  VAL*     1.3    65.9    +      -       -      +
     67C  LYS*     5.1     0.2    -      -       -      -
     75C  GLY      4.2    13.5    -      -       -      +
     76C  SER*     3.1    25.6    -      -       -      +
     77C  CYS*     2.9    26.4    +      -       +      +
     78C  THR*     4.7     1.3    +      -       -      -
     79C  PHE*     4.1    18.6    -      -       +      -
    141C  ILE*     4.4    21.8    -      -       +      -
    142C  GLU      3.3     2.7    -      -       -      +
    143C  SER*     3.1    36.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 56 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54C  ASP*     5.6     2.7    -      -       +      +
     55C  LEU*     1.3    78.3    -      -       -      +
     57C  LEU*     1.3    59.0    +      -       -      +
     58C  GLU*     4.1    28.9    -      -       +      +
     67C  LYS*     4.0    32.5    -      -       +      +
     76C  SER*     3.6     3.4    -      -       -      -
    140C  ARG      3.8     1.0    -      -       -      +
    141C  ILE*     3.2     6.2    -      -       -      -
    142C  GLU*     2.9    53.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 57 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55C  LEU      4.0     0.2    -      -       -      -
     56C  VAL*     1.3    74.8    -      -       -      +
     58C  GLU*     1.3    61.3    +      -       -      +
     67C  LYS*     3.5     2.8    -      -       -      -
     68C  ILE*     2.7    40.8    +      -       +      -
     74C  ILE*     5.8     0.4    -      -       +      -
     75C  GLY*     4.0    28.0    -      -       -      +
     76C  SER*     2.8    16.2    +      -       -      +
    133C  TRP*     3.5    33.4    -      -       +      -
    139C  TYR*     4.4    17.0    -      -       +      -
    140C  ARG      3.6    13.9    -      -       -      +
    141C  ILE*     4.1    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 58 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56C  VAL*     4.1    22.0    -      -       +      +
     57C  LEU*     1.3    79.0    -      -       -      +
     59C  LYS*     1.3    61.1    +      -       -      +
     65C  TRP*     3.9    26.7    -      -       +      +
     66C  ILE      3.2     6.7    -      -       -      +
     67C  LYS*     3.8    19.3    +      -       +      +
     68C  ILE*     4.5     1.6    -      -       -      -
    139C  TYR*     3.3    10.1    -      -       -      +
    140C  ARG*     2.5    80.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 59 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58C  GLU*     1.3    75.3    -      -       -      +
     60C  GLU*     1.3    74.8    +      -       -      +
     61C  VAL*     3.4    12.2    +      -       +      +
     65C  TRP*     3.7     3.4    -      -       -      -
     66C  ILE*     2.9    33.9    +      -       +      +
     68C  ILE*     4.1    17.4    -      -       +      +
    133C  TRP*     3.0    26.1    +      -       +      +
    135C  THR*     2.8    28.5    +      -       -      +
    136C  THR      4.2     9.0    -      -       -      -
    137C  GLY*     4.9     3.1    -      -       -      -
    138C  ASN      3.6     7.6    -      -       -      +
    139C  TYR*     3.6    32.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 60 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59C  LYS*     1.3    80.7    -      -       -      +
     61C  VAL*     1.3    65.7    +      -       -      +
     62C  ALA      5.2     0.5    +      -       -      -
     63C  GLY*     3.8    27.6    +      -       -      +
     64C  LEU      3.3     9.6    -      -       -      +
     65C  TRP*     3.6    27.3    -      -       +      -
    137C  GLY*     5.8     0.9    -      -       -      -
    138C  ASN*     2.8    55.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 61 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59C  LYS*     3.4    17.9    +      -       +      +
     60C  GLU*     1.3    79.0    -      -       -      +
     62C  ALA*     1.3    78.6    +      -       +      +
     63C  GLY      3.2     0.4    -      -       -      -
     64C  LEU*     2.7    28.3    +      -       -      +
     66C  ILE*     3.8    30.2    -      -       +      +
----------------------------------------------------------
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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