Contacts of the strand formed by residues 130 - 141 (chain C) in PDB entry 5UH8


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 ALA 130 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115C  VAL*     3.3     8.9    -      -       -      +
    116C  LYS*     3.2    33.2    +      -       +      +
    117C  ALA      5.9     0.2    -      -       -      +
    122C  CYS*     5.2     0.2    -      -       -      -
    128C  THR*     3.1    17.9    +      -       +      +
    129C  TYR*     1.3    78.3    -      -       -      +
    131C  ALA*     1.3    60.4    +      -       -      +
    132C  PRO*     4.6     0.2    -      -       -      -
    156C  ASP*     4.1    13.9    -      -       +      +
    157C  PHE      3.2    30.1    -      -       -      +
    158C  PRO*     3.7     2.9    -      -       +      -
    159C  MET*     4.0     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 131 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112C  PHE*     3.9    13.2    -      -       +      -
    113C  ASP      3.6    21.5    -      -       -      +
    115C  VAL*     4.1    14.1    -      -       +      +
    130C  ALA*     1.3    75.1    -      -       -      +
    132C  PRO*     1.3    68.3    -      -       +      +
    156C  ASP*     4.5     0.4    -      -       -      -
    157C  PHE*     2.9    32.4    +      -       -      +
    159C  MET*     3.8    20.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 132 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112C  PHE*     3.6     3.3    -      -       -      -
    113C  ASP*     3.1    46.6    +      -       +      +
    114C  ASP      3.4    16.8    -      -       -      +
    116C  LYS*     3.8    20.0    -      -       +      -
    131C  ALA*     1.3    83.5    -      -       +      +
    133C  LEU*     1.3    62.6    +      -       -      +
    134C  PHE*     4.9     6.2    -      -       +      -
    153C  PHE*     3.6    13.9    -      -       +      -
    155C  GLY      3.6     6.7    -      -       -      +
    156C  ASP*     3.6    17.2    -      -       -      +
    391F  GLY      4.1     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 133 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86C  LEU*     4.3    15.7    -      -       +      -
    110C  PRO*     4.3    10.3    -      -       +      -
    111C  ARG      3.7    15.9    -      -       -      +
    112C  PHE*     3.8    28.9    -      -       +      -
    131C  ALA      3.5     0.8    +      -       -      -
    132C  PRO*     1.3    71.9    -      -       -      +
    134C  PHE*     1.3    84.6    +      -       -      +
    135C  VAL*     4.9     3.6    -      -       +      -
    153C  PHE*     3.3     1.7    -      -       -      -
    154C  MET*     3.1    47.9    +      -       +      +
    155C  GLY      3.0    14.3    +      -       -      +
    157C  PHE*     4.3    24.0    -      -       +      -
    423C  VAL*     6.5     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 134 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110C  PRO*     3.2     0.5    -      -       -      +
    111C  ARG*     2.7    63.4    +      -       +      +
    112C  PHE      5.4     0.4    -      -       -      -
    113C  ASP*     3.4    37.2    -      -       +      -
    132C  PRO*     4.9     7.4    -      -       +      -
    133C  LEU*     1.3    83.2    -      -       -      +
    135C  VAL*     1.3    70.3    +      -       -      +
    151C  THR*     4.2    17.3    -      -       +      -
    152C  VAL      3.8     4.5    -      -       -      -
    153C  PHE*     3.3    39.7    -      +       +      -
    391F  GLY*     4.5    16.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 135 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90C  LEU*     4.2    19.5    -      -       +      -
    107C  PHE*     4.7    17.5    -      -       +      -
    108C  SER      4.3     3.4    -      -       -      +
    109C  ASP      3.8     6.1    -      -       -      -
    110C  PRO*     3.8    20.4    -      -       +      -
    111C  ARG*     4.2     2.9    -      -       -      -
    133C  LEU*     4.9     5.4    -      -       +      -
    134C  PHE*     1.3    79.0    -      -       -      +
    136C  THR*     1.3    60.3    +      -       -      +
    151C  THR*     3.2     5.4    -      -       -      +
    152C  VAL*     2.8    47.1    +      -       +      +
    154C  MET*     3.6    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 136 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106C  SER      3.9     0.9    -      -       -      +
    107C  PHE*     3.5     3.3    -      -       -      +
    108C  SER*     3.0    46.6    +      -       -      +
    109C  ASP*     3.8     5.5    +      -       -      +
    111C  ARG*     2.9    29.1    +      -       -      -
    135C  VAL*     1.3    72.1    -      -       -      +
    137C  ALA*     1.3    61.9    +      -       -      +
    138C  GLU*     5.9     0.3    -      -       -      +
    149C  SER*     3.9    18.4    -      -       -      +
    150C  GLN*     3.6    13.9    -      -       -      +
    151C  THR*     4.2     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 137 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105C  LEU*     4.3     2.5    -      -       +      -
    106C  SER      3.6     5.2    -      -       -      +
    107C  PHE*     3.6    29.8    -      -       +      -
    135C  VAL*     4.0     1.3    +      -       +      +
    136C  THR*     1.3    75.6    -      -       -      +
    138C  GLU*     1.3    57.2    +      -       -      +
    149C  SER*     3.5     2.0    -      -       -      -
    150C  GLN      2.7    41.3    +      -       -      +
    152C  VAL*     3.8    22.4    -      -       +      -
    414C  PRO*     3.6    18.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 138 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104C  SER      3.6     0.5    -      -       -      +
    105C  LEU*     3.3    16.5    -      -       -      +
    106C  SER*     3.3    35.2    +      -       -      +
    136C  THR*     6.1     0.2    -      -       +      -
    137C  ALA*     1.3    75.0    -      -       -      +
    139C  PHE*     1.3    60.5    +      -       -      +
    140C  ILE*     3.6    18.8    +      -       +      +
    147C  ILE*     4.0    22.1    -      -       +      +
    148C  LYS      3.3     4.5    -      -       -      +
    149C  SER*     3.5    26.8    +      -       -      +
    414C  PRO*     4.8     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 139 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103C  MET*     3.7    40.4    -      -       +      -
    104C  SER      3.7    11.0    -      -       -      -
    105C  LEU*     4.3     5.2    -      -       +      -
    138C  GLU*     1.3    70.8    -      -       -      +
    140C  ILE*     1.3    64.0    +      -       -      +
    141C  ASN*     3.7    18.2    +      -       +      -
    146C  GLU*     3.8     3.7    -      -       +      +
    147C  ILE*     3.7     6.0    -      -       -      -
    148C  LYS*     2.9    37.2    +      -       +      +
    404C  MET*     4.8     1.8    -      -       -      -
    409C  VAL*     4.0    13.7    -      -       +      -
    412C  ILE*     3.5    53.6    -      -       +      +
    414C  PRO*     4.1    17.0    -      -       +      +
    417C  LEU*     3.8    15.0    -      -       +      -
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Residues in contact with ILE 140 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95C  PRO*     5.9     0.9    -      -       +      -
    103C  MET*     3.4     1.4    -      -       -      -
    104C  SER*     2.5    64.2    +      -       -      +
    106C  SER*     4.0    12.1    -      -       -      +
    138C  GLU*     3.7    29.8    -      -       +      +
    139C  PHE*     1.3    75.2    -      -       -      +
    141C  ASN*     1.3    64.6    +      -       -      +
    142C  ASN*     4.2    16.2    -      -       -      +
    145C  GLY      6.4     0.2    -      -       -      -
    147C  ILE*     4.1    27.6    -      -       +      -
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Residues in contact with ASN 141 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102C  SER*     2.3    48.9    +      -       -      -
    103C  MET*     3.9     7.3    -      -       -      +
    139C  PHE*     4.2    15.0    -      -       +      -
    140C  ILE*     1.3    79.3    -      -       -      +
    142C  ASN*     1.3    61.9    +      -       -      +
    143C  ASN*     3.6     4.1    -      -       -      +
    144C  THR*     2.5    45.9    +      -       -      +
    145C  GLY*     2.9    29.5    +      -       -      -
    146C  GLU*     3.5    12.1    +      -       +      +
    409C  VAL*     3.5    15.1    -      -       +      +
----------------------------------------------------------
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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