Contacts of the strand formed by residues 189 - 193 (chain A) in PDB entry 1MPU


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 CYS 189 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  TRP*     3.4    29.8    -      -       +      -
    121A  TYR*     5.6     0.4    -      -       -      -
    154A  TRP*     3.6    20.9    -      -       +      -
    157A  LEU      3.5     7.6    -      -       -      -
    158A  VAL*     4.0     5.8    -      -       -      -
    166A  TRP*     3.6     9.7    -      -       -      -
    187A  GLY      3.5     0.2    -      -       -      -
    188A  ASP*     1.3    80.4    -      -       -      +
    190A  ALA*     1.3    65.3    +      -       -      +
    200A  ILE*     3.6     0.9    -      -       -      +
    201A  GLU      3.1    24.7    +      -       -      +
    203A  CYS*     2.0    46.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 190 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  TRP*     4.8     0.2    -      -       -      -
    154A  TRP*     3.4    10.2    -      -       -      -
    155A  MET*     3.3    35.7    +      -       +      +
    157A  LEU*     3.2    34.3    +      -       +      +
    166A  TRP*     4.2     8.7    -      -       +      -
    181A  ILE*     6.2     1.3    -      -       +      -
    189A  CYS*     1.3    79.0    -      -       -      +
    191A  LEU*     1.3    60.7    +      -       -      +
    198A  GLY*     4.8     1.1    -      -       -      -
    199A  TYR      3.2    17.5    -      -       -      +
    200A  ILE*     4.7     1.8    -      -       +      -
    201A  GLU      4.4     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 191 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  TYR*     3.9    33.2    -      -       +      -
    153A  HIS      3.0    21.1    -      -       -      +
    154A  TRP*     3.5    29.4    -      -       +      -
    155A  MET*     3.5     6.4    -      -       -      +
    190A  ALA*     1.3    73.6    -      -       -      +
    192A  TYR*     1.3    63.1    +      -       -      +
    193A  ALA      3.8     0.2    +      -       -      -
    198A  GLY*     3.5     0.9    -      -       -      -
    199A  TYR*     2.9    36.1    +      -       +      +
    201A  GLU*     3.4    34.5    -      -       +      +
    207A  ASN*     3.5    31.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  LEU*     4.0    21.3    -      -       +      -
    137A  VAL*     4.4    10.1    -      -       +      -
    146A  LEU*     2.8    46.4    +      -       +      +
    147A  LYS      4.1     0.2    +      -       -      -
    149A  VAL*     4.1    21.8    -      -       +      -
    151A  SER      3.8     1.7    -      -       -      +
    152A  TYR*     3.6     6.5    -      -       -      -
    153A  HIS*     2.5    36.1    +      +       +      +
    155A  MET*     3.6    30.4    -      -       +      +
    179A  LEU*     4.5     3.4    -      -       +      -
    191A  LEU*     1.3    72.8    -      -       -      +
    193A  ALA*     1.3    81.5    +      -       -      +
    194A  SER*     3.8     2.7    -      -       -      -
    195A  SER      3.2    16.1    +      -       -      -
    196A  PHE*     3.2    26.1    +      +       -      -
    197A  LYS      3.9     6.1    -      -       -      -
    210A  ILE*     5.1     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  SER      4.1     6.1    -      -       -      +
    152A  TYR*     4.3     7.0    -      -       +      -
    192A  TYR*     1.3    94.2    -      -       -      +
    194A  SER*     1.3    65.0    +      -       -      +
    195A  SER      3.2     0.7    +      -       -      -
    197A  LYS*     3.0    25.4    +      -       -      +
    199A  TYR*     2.9    42.0    -      -       +      +
----------------------------------------------------------
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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