Contacts of the strand formed by residues 132 - 137 (chain A) in PDB entry 4CY1


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 132 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  SER*     4.1     5.4    +      -       -      -
    105A  ALA*     3.4    38.5    -      -       +      +
    106A  SER      3.0    15.9    +      -       -      +
    107A  ASP*     5.0     0.2    -      -       -      +
    109A  LYS      3.5    33.0    -      -       -      +
    110A  THR      3.7     9.6    -      -       -      +
    111A  LEU*     3.7    22.2    -      -       +      -
    128A  HIS*     3.6    25.1    -      -       +      -
    131A  TYR*     1.3    75.6    -      -       -      +
    133A  PHE*     1.3    61.2    +      -       -      +
    134A  CYS      4.1     0.9    -      -       -      +
    146A  SER*     4.1     4.3    -      -       -      -
    147A  GLY      3.5    12.1    -      -       -      +
    148A  SER*     4.3     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  SER*     3.5     9.4    -      -       -      -
     92A  ASP*     3.4     8.1    -      -       -      +
    105A  ALA*     4.1     3.8    -      -       -      -
    131A  TYR      3.7     0.4    +      -       -      -
    132A  VAL*     1.3    73.7    -      -       -      +
    134A  CYS*     1.3    59.2    +      -       -      +
    147A  GLY      2.9     8.8    +      -       -      +
    148A  SER*     4.8     1.1    -      -       -      -
    149A  PHE*     3.7    32.1    -      +       +      -
    174A  VAL      3.8    13.9    -      -       -      +
    175A  SER*     3.3    35.0    -      -       -      -
    191A  TYR*     4.1     5.8    -      -       -      -
    261A  CYS*     3.6    33.7    -      -       +      -
    591D  ALA*     3.7    17.0    -      -       +      -
    592D  ARG*     3.0    69.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  ASP*     3.3    12.1    -      -       -      +
    105A  ALA*     4.0     1.5    -      -       -      +
    132A  VAL*     3.8     2.8    -      -       -      +
    133A  PHE*     1.3    78.1    -      -       -      +
    135A  CYS*     1.3    67.1    +      -       -      +
    146A  SER*     3.3     4.2    -      -       -      -
    147A  GLY*     3.1    46.7    +      -       -      +
    174A  VAL      3.5     9.4    -      -       -      -
    175A  SER      3.7    11.9    -      -       -      +
    176A  ALA*     3.5    39.3    -      -       +      -
    177A  VAL*     3.7     6.1    -      -       -      +
    592D  ARG*     4.0     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  LYS*     4.5     0.9    +      -       -      -
     92A  ASP*     3.0    28.8    +      -       -      +
     93A  VAL*     4.3     2.2    -      -       -      -
     94A  ALA*     3.6     8.9    -      -       -      +
    103A  VAL*     3.6    34.1    -      -       +      -
    104A  SER      4.0     1.1    -      -       -      -
    105A  ALA*     3.9    22.0    -      -       -      -
    111A  LEU*     3.6    20.2    -      -       +      -
    134A  CYS*     1.3    78.6    -      -       -      +
    136A  ASN*     1.3    76.4    +      -       -      +
    144A  ILE*     4.8     0.2    -      -       +      -
    145A  VAL      3.2    10.1    -      -       -      +
    177A  VAL*     4.1     3.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  LYS*     4.4     9.1    +      -       -      +
     92A  ASP*     5.5     0.4    +      -       -      -
     94A  ALA*     3.7    16.6    -      -       -      +
     95A  TRP      5.6     0.5    -      -       -      +
    103A  VAL*     4.5     1.1    -      -       -      +
    135A  CYS*     1.3    80.5    +      -       -      +
    137A  PHE*     1.3    69.5    +      -       -      +
    144A  ILE*     3.3     6.3    -      -       -      -
    145A  VAL*     2.8    42.2    +      -       +      +
    177A  VAL      2.9    26.8    +      -       -      +
    178A  HIS*     3.5    29.1    -      -       +      +
    179A  PHE*     4.8     0.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ALA*     3.5    21.7    -      -       -      +
     95A  TRP      3.4    25.3    +      -       -      +
     96A  SER*     3.6    15.5    -      -       -      -
     97A  SER      5.2     0.2    -      -       -      +
    101A  LEU*     4.0    21.5    -      -       +      -
    102A  LEU      3.9     4.0    -      -       -      -
    103A  VAL*     3.5    20.6    -      -       +      -
    113A  ILE*     4.6     2.5    -      -       +      -
    136A  ASN*     1.3    82.5    +      -       -      +
    138A  ASN*     1.3    68.9    +      -       -      +
    139A  PRO*     4.7     0.3    -      -       -      +
    141A  SER*     3.8    21.8    -      -       -      +
    143A  LEU      3.4    11.7    -      -       -      -
    144A  ILE*     3.7    31.2    -      -       +      +
    158A  VAL*     3.7    18.2    -      -       +      -
    179A  PHE*     3.4    11.5    +      -       -      +
----------------------------------------------------------
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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