Contacts of the strand formed by residues 189 - 198 (chain A) in PDB entry 5MWF


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 HIS 189 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  ALA      3.9     0.2    -      -       -      +
     37A  LEU*     3.2     7.4    -      -       -      +
     38A  ARG*     3.1    56.4    +      -       +      -
    183A  PHE      3.4     5.8    -      -       -      +
    184A  SER*     2.7    35.2    +      -       -      -
    185A  GLY      5.7     2.1    +      -       -      -
    187A  VAL      5.3     3.1    -      -       -      -
    188A  ALA*     1.3    77.2    -      -       -      +
    190A  LEU*     1.3    64.6    +      -       -      +
    191A  GLU*     6.2     1.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 190 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  LEU*     4.1    16.6    -      -       +      -
     36A  ALA      3.5     3.8    -      -       -      +
     37A  LEU*     4.1    24.0    -      -       +      -
     71A  VAL*     5.3     2.7    -      -       +      -
    146A  VAL*     3.9    28.7    -      -       +      +
    148A  ALA*     5.5     5.6    -      -       +      +
    164A  GLU*     4.6    13.5    -      -       +      -
    166A  VAL*     4.3    15.7    -      -       +      -
    181A  LEU      4.2     0.2    -      -       -      +
    182A  HIS*     3.8     0.2    -      -       -      -
    183A  PHE*     2.9    47.3    +      -       +      +
    188A  ALA*     4.1    18.6    -      -       +      +
    189A  HIS*     1.3    82.1    -      -       -      +
    191A  GLU*     1.3    73.2    +      -       -      +
    192A  LEU*     4.4     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 191 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  LEU*     3.7     3.6    -      -       -      +
     35A  SER*     3.1    30.1    +      -       -      +
     36A  ALA*     3.0    33.0    +      -       +      -
    180A  SER*     5.8     0.5    -      -       -      -
    181A  LEU      3.8     3.7    -      -       -      +
    182A  HIS*     2.6    43.8    +      -       -      +
    183A  PHE      5.1     0.3    +      -       -      +
    189A  HIS*     5.8     1.7    -      -       +      +
    190A  LEU*     1.3    81.3    -      -       -      +
    192A  LEU*     1.3    64.3    +      -       -      +
    193A  GLN*     4.5     3.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  LEU*     4.1    14.1    -      -       +      -
     33A  GLN      3.1    17.3    -      -       -      +
     34A  LEU*     4.2    18.6    -      -       +      -
    144A  LEU*     4.5     1.3    -      -       +      -
    146A  VAL*     4.1    25.1    -      -       +      -
    180A  SER*     3.7     2.3    -      -       -      -
    181A  LEU*     2.9    57.2    +      -       +      +
    183A  PHE*     3.7    28.7    -      -       +      -
    190A  LEU*     4.4     5.2    -      -       +      -
    191A  GLU*     1.3    73.9    -      -       -      +
    193A  GLN*     1.3    69.3    +      -       -      +
    194A  ILE*     4.0    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  LEU*     3.4     2.6    -      -       -      +
     33A  GLN*     2.7    44.1    +      -       -      +
     35A  SER*     3.4    23.3    +      -       -      -
    107A  PRO*     3.6     9.0    -      -       -      +
    108A  ALA*     2.7    38.8    +      -       +      +
    178A  TRP*     3.5    28.2    -      -       +      -
    179A  LYS      3.2     8.7    -      -       -      +
    180A  SER*     3.8    24.2    +      -       -      +
    191A  GLU*     4.5     3.0    +      -       -      +
    192A  LEU*     1.3    89.5    +      -       -      +
    194A  ILE*     1.3    63.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  PHE*     4.0    19.1    -      -       +      -
     31A  GLU      3.2    10.3    -      -       -      +
     32A  LEU*     3.8    29.2    -      -       +      -
    142A  PHE*     3.9    28.7    -      -       +      -
    144A  LEU*     4.1     2.9    -      -       +      -
    172A  ILE*     4.3    12.8    -      -       +      +
    177A  ARG      4.3     0.2    -      -       -      +
    178A  TRP*     3.6     4.4    -      -       -      -
    179A  LYS*     2.9    46.0    +      -       +      +
    181A  LEU*     3.8    19.3    -      -       +      -
    192A  LEU*     4.0    12.1    -      -       +      -
    193A  GLN*     1.3    78.6    -      -       -      +
    195A  ARG*     1.3    64.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  PHE*     3.8     1.2    -      -       -      -
     31A  GLU*     2.5    61.1    +      -       -      +
    113A  ASP*     2.7    31.3    +      -       -      -
    172A  ILE*     3.9    10.1    -      -       -      -
    175A  GLU      3.9    13.7    -      -       -      +
    176A  ASP*     3.1    28.8    +      -       -      +
    177A  ARG      3.6    15.3    -      -       -      +
    178A  TRP*     3.3    38.4    -      -       +      +
    194A  ILE*     1.3    79.2    -      -       -      +
    196A  VAL*     1.3    69.9    +      -       -      +
    197A  ARG*     3.4    21.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  TYR      3.3    12.6    -      -       -      +
     30A  PHE*     3.8    15.7    -      -       +      -
    134A  PHE*     3.9    22.0    -      -       +      -
    138A  TRP*     3.8    32.8    -      -       +      +
    172A  ILE*     3.9    17.8    -      -       +      +
    173A  ASN      4.5     3.9    +      -       -      +
    174A  PRO*     3.2    22.9    -      -       +      +
    175A  GLU      2.9    32.1    +      -       -      +
    195A  ARG*     1.3    80.4    -      -       -      +
    197A  ARG*     1.3    66.9    +      -       -      +
    207A  CYS*     4.9     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  GLY*     3.3     1.7    -      -       -      -
     29A  TYR*     2.9    68.9    +      -       -      +
     31A  GLU*     2.7    40.7    +      -       -      +
    131A  VAL*     5.5     2.4    -      -       -      +
    174A  PRO*     4.8     1.8    -      -       -      -
    175A  GLU      4.1     3.4    -      -       -      +
    176A  ASP*     3.5    24.2    -      -       -      +
    195A  ARG*     3.4    26.8    -      -       -      +
    196A  VAL*     1.3    79.4    -      -       -      +
    198A  CYS*     1.3    69.5    +      -       -      +
    207A  CYS*     4.1     4.4    -      -       -      -
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Residues in contact with CYS 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  MET      3.8     1.3    -      -       -      +
     28A  GLY*     4.2     0.2    -      -       -      -
     29A  TYR*     4.8     1.9    -      -       -      -
    174A  PRO*     3.9    10.2    -      -       -      +
    197A  ARG*     1.3    89.1    +      -       -      +
    199A  ASP*     1.3    65.9    +      -       -      +
    202A  TYR      3.4    25.6    -      -       -      +
    203A  TYR*     4.5     2.5    -      -       -      -
    204A  SER      3.9    11.9    -      -       -      -
    207A  CYS*     2.0    55.4    -      -       +      -
----------------------------------------------------------
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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