Contacts of the strand formed by residues 28 - 39 (chain C) 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 GLY 28 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27C  MET*     1.3    74.6    -      -       -      +
     29C  TYR*     1.3    67.4    +      -       -      +
    133C  PRO*     3.5     5.0    -      -       -      +
    134C  PHE*     3.1    40.9    +      -       -      +
    197C  ARG      3.2    14.4    -      -       -      -
    198C  CYS*     4.0     1.1    -      -       -      -
    199C  ASP*     3.3    15.6    +      -       -      +
    207C  CYS*     4.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 29 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28C  GLY*     1.3    78.8    -      -       -      +
     30C  PHE*     1.3    59.4    +      -       -      +
     31C  GLU*     3.4    41.9    +      -       +      +
    131C  VAL*     4.0    18.6    -      -       +      -
    132C  ILE      3.6     5.8    -      -       -      -
    133C  PRO*     3.7    14.4    -      -       +      -
    134C  PHE*     3.4     8.4    -      -       -      -
    195C  ARG*     4.6     3.3    +      -       -      -
    196C  VAL*     3.8     1.6    -      -       -      -
    197C  ARG*     2.9    67.3    +      -       +      +
    198C  CYS      4.4     6.7    -      -       -      -
    199C  ASP*     3.9    15.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 30 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  TYR*     1.3    72.7    -      -       -      +
     31C  GLU*     1.3    70.2    +      -       -      +
     32C  LEU*     4.3    16.2    -      -       +      -
     73C  VAL*     5.1     2.9    -      -       +      -
     75C  LEU*     3.6    41.1    -      -       +      -
    130C  VAL      3.8     0.7    -      -       -      +
    131C  VAL*     3.4     2.6    -      -       -      -
    132C  ILE*     2.7    54.4    +      -       +      +
    134C  PHE*     3.8     8.5    -      -       +      -
    138C  TRP*     3.7    15.5    -      +       -      -
    142C  PHE*     4.4    12.1    -      +       -      -
    144C  LEU*     4.7     7.6    -      -       +      -
    172C  ILE*     4.8     1.6    -      -       +      -
    194C  ILE*     3.9    30.5    -      -       +      -
    195C  ARG      3.9     7.0    -      -       -      -
    196C  VAL*     3.6    25.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 31 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  TYR*     3.4    35.5    +      -       +      +
     30C  PHE*     1.3    78.0    -      -       -      +
     32C  LEU*     1.3    61.6    +      -       -      +
    129C  LEU*     4.4    13.1    -      -       +      +
    130C  VAL      3.5     2.7    -      -       -      -
    131C  VAL*     3.9    23.0    -      -       +      +
    178C  TRP*     4.0    17.7    -      -       +      -
    194C  ILE*     3.4     6.5    -      -       -      +
    195C  ARG*     2.8    76.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 32 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30C  PHE*     4.3     7.4    -      -       +      -
     31C  GLU*     1.3    77.2    -      -       -      +
     33C  GLN*     1.3    63.7    +      -       -      +
     34C  LEU*     4.3    15.0    -      -       +      +
     71C  VAL*     5.7     2.9    -      -       +      -
     73C  VAL*     4.0    32.3    -      -       +      -
    128C  GLY      3.7     1.9    -      -       -      +
    129C  LEU*     3.4     4.6    -      -       -      +
    130C  VAL*     2.9    45.5    +      -       +      +
    144C  LEU*     3.9    25.4    -      -       +      -
    146C  VAL*     4.3     6.7    -      -       +      -
    178C  TRP*     4.7     0.2    -      -       -      -
    192C  LEU*     4.1    17.7    -      -       +      -
    193C  GLN      3.3    11.4    -      -       -      +
    194C  ILE*     3.8    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 33 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32C  LEU*     1.3    73.2    -      -       -      +
     34C  LEU*     1.3    87.9    +      -       -      +
     35C  SER*     3.8     5.3    +      -       -      +
    105C  LEU*     4.6     5.3    -      -       -      +
    106C  PRO      5.5     4.0    +      -       -      -
    107C  PRO*     6.1     5.5    -      -       +      +
    126C  ASP*     4.5    11.1    -      -       -      +
    127C  PRO*     5.9     0.8    -      -       -      +
    128C  GLY*     3.6    15.0    +      -       -      +
    129C  LEU*     3.4    27.0    +      -       +      +
    178C  TRP*     4.1    21.7    -      -       +      -
    192C  LEU*     3.2     6.7    -      -       -      -
    193C  GLN*     2.8    48.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 34 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32C  LEU*     4.1     8.9    -      -       +      +
     33C  GLN*     1.3    96.1    +      -       -      +
     35C  SER*     1.3    60.3    +      -       -      +
     36C  ALA      3.3    29.2    -      -       -      +
     37C  LEU*     4.9     3.6    -      -       +      -
     71C  VAL*     3.7    33.7    -      -       +      -
     95C  THR*     6.2     0.4    -      -       +      -
     98C  LEU*     4.5    10.1    -      -       +      -
    103C  PHE*     4.0    23.8    -      -       +      -
    105C  LEU*     3.3    15.8    -      -       +      +
    128C  GLY*     2.9    15.8    +      -       -      +
    190C  LEU*     4.5    15.3    -      -       +      -
    191C  GLU      3.4    13.5    -      -       -      +
    192C  LEU*     4.0    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 35 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266B  TYR*     4.3    17.0    -      -       -      +
     33C  GLN*     3.8     6.9    +      -       -      +
     34C  LEU*     1.3    75.7    -      -       -      +
     36C  ALA*     1.3    63.1    +      -       -      +
    104C  TYR*     3.6     6.9    -      -       -      -
    105C  LEU*     3.0    40.9    +      -       -      +
    107C  PRO*     5.8     8.1    -      -       -      -
    191C  GLU*     2.9    32.2    +      -       -      +
    192C  LEU*     4.1     2.0    +      -       -      -
    193C  GLN*     5.8     6.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 36 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266B  TYR*     3.6    31.6    -      -       +      -
    291B  TRP*     3.7    16.8    -      -       +      -
     34C  LEU*     3.3    15.2    -      -       -      +
     35C  SER*     1.3    80.7    -      -       -      +
     37C  LEU*     1.3    61.2    +      -       -      +
    103C  PHE*     3.6     9.9    -      -       -      +
    104C  TYR*     4.3     4.9    -      -       +      -
    190C  LEU*     3.5     1.4    -      -       -      -
    191C  GLU*     3.1    30.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 37 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291B  TRP*     3.2     8.7    -      -       -      -
     34C  LEU*     4.9     5.8    -      -       +      -
     36C  ALA*     1.3    76.8    -      -       -      +
     38C  ARG*     1.3    69.1    +      -       -      +
     39C  ASN*     4.5     2.5    -      -       +      -
     69C  THR*     4.2    10.5    -      -       +      +
     71C  VAL*     5.1     3.6    -      -       +      -
    101C  ASN      3.8    17.3    -      -       -      +
    102C  SER*     3.3     1.0    -      -       -      -
    103C  PHE*     3.0    63.9    +      -       +      -
    148C  ALA*     4.1    20.6    -      -       +      -
    163C  ILE*     5.7     2.5    -      -       +      -
    188C  ALA*     4.3    11.7    -      -       +      -
    189C  HIS      3.3    12.6    -      -       -      +
    190C  LEU*     3.6    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 38 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279B  TYR*     3.2    42.5    -      -       -      +
    280B  PRO*     3.8    36.8    +      -       -      +
    291B  TRP*     3.6    16.5    -      -       +      -
     37C  LEU*     1.3    77.1    -      -       -      +
     39C  ASN*     1.3    59.9    +      -       -      +
     40C  VAL*     4.4    18.9    -      -       +      +
    101C  ASN      4.0     0.4    -      -       -      -
    102C  SER*     3.3     4.3    -      -       -      -
    187C  VAL      4.2     0.9    -      -       -      +
    188C  ALA*     3.1     7.6    -      -       -      +
    189C  HIS*     3.0    76.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 39 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37C  LEU*     4.5     3.1    -      -       +      -
     38C  ARG*     1.3    72.2    -      -       -      +
     40C  VAL*     1.3    69.0    +      -       -      +
     41C  ASN      4.2     1.6    +      -       -      -
     42C  GLY*     3.3     8.8    +      -       -      -
     43C  GLU*     3.1    42.4    +      -       -      +
     67C  CYS*     3.8    11.3    -      -       -      -
    101C  ASN*     3.2    32.8    +      -       -      +
    102C  SER*     2.9    12.5    +      -       -      -
    163C  ILE*     3.8    11.1    -      -       +      +
    187C  VAL*     3.3    27.4    -      -       -      +
    188C  ALA*     4.4     7.6    -      -       +      -
----------------------------------------------------------
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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