Contacts of the strand formed by residues 103 - 112 (chain C) in PDB entry 5UHA


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 MET 103 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96C  ILE      4.4     0.7    -      -       -      -
     97C  GLU*     3.3    25.3    -      -       -      +
     98C  ASP*     3.2    34.8    +      -       +      +
    101C  GLY      3.9     2.8    -      -       -      +
    102C  SER*     1.3    89.9    -      -       -      +
    104C  SER*     1.3    64.9    +      -       -      +
    139C  PHE*     3.5    22.7    -      -       +      -
    140C  ILE      3.6     4.0    -      -       -      -
    141C  ASN*     4.0     3.4    -      -       -      +
    404C  MET*     3.6    45.5    -      -       +      +
    405C  THR*     4.7     3.8    -      -       +      +
    409C  VAL*     5.0    12.8    -      -       +      -
    412C  ILE*     3.8    26.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 104 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95C  PRO*     3.5    24.1    -      -       -      +
     96C  ILE      3.5     6.3    -      -       -      -
     97C  GLU*     3.7    16.3    +      -       -      +
    103C  MET*     1.3    78.4    -      -       -      +
    105C  LEU*     1.3    58.3    +      -       -      +
    139C  PHE*     3.6     3.6    -      -       -      -
    140C  ILE*     2.7    67.1    +      -       -      +
    142C  ASN*     4.9     6.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 105 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94C  SER*     4.4     0.2    +      -       -      -
     95C  PRO*     3.2     3.0    -      -       -      +
     96C  ILE*     2.6    52.2    +      -       +      +
    104C  SER*     1.3    71.9    -      -       -      +
    106C  SER*     1.3    64.9    +      -       -      +
    107C  PHE*     3.6    27.5    -      -       +      -
    137C  ALA*     4.2     6.1    -      -       +      -
    138C  GLU      3.2    27.4    -      -       -      +
    139C  PHE*     4.4     4.9    -      -       +      +
    400C  VAL*     4.1    24.0    -      -       +      -
    404C  MET*     5.6     1.3    -      -       -      -
    414C  PRO*     4.0    19.3    -      -       +      -
    417C  LEU*     4.0    26.0    -      -       +      -
    418C  ILE*     4.2     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 106 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94C  SER*     3.2    15.7    -      -       -      -
     95C  PRO*     4.0    10.3    -      -       -      -
    105C  LEU*     1.3    77.4    -      -       -      +
    107C  PHE*     1.3    66.2    +      -       -      +
    136C  THR      4.0     1.0    -      -       -      +
    137C  ALA*     3.4     5.2    -      -       -      +
    138C  GLU*     3.2    43.9    +      -       -      +
    140C  ILE*     3.4    26.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 107 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90C  LEU*     4.0    31.9    -      -       +      +
     91C  TYR*     4.8     6.1    -      -       -      -
     93C  LEU*     3.5    33.9    -      -       +      -
     94C  SER*     2.5    26.8    +      -       -      +
     96C  ILE*     4.0    16.4    -      -       +      -
    105C  LEU*     3.6    26.0    -      -       +      -
    106C  SER*     1.3    74.6    -      -       -      +
    108C  SER*     1.3    66.1    +      -       -      +
    135C  VAL*     4.6    16.2    -      -       +      -
    136C  THR      3.9     2.5    -      -       -      +
    137C  ALA*     3.5    20.0    -      -       +      -
    154C  MET*     5.8     3.6    -      -       +      -
    393C  MET*     5.2     4.5    -      -       +      -
    396C  MET*     5.0    12.1    -      -       +      -
    400C  VAL*     5.5     0.2    -      -       +      -
    418C  ILE*     3.6    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 108 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90C  LEU*     4.2    10.4    -      -       -      +
     91C  TYR*     5.3    10.3    -      -       -      -
    107C  PHE*     1.3    77.5    -      -       -      +
    109C  ASP*     1.3    75.0    +      -       -      +
    110C  PRO*     3.9     0.7    -      -       -      -
    135C  VAL*     4.1     1.6    -      -       -      +
    136C  THR*     3.1    35.9    +      -       -      +
    138C  GLU*     6.1     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 109 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108C  SER*     1.3    84.6    -      -       -      +
    110C  PRO*     1.3    74.8    -      -       -      +
    111C  ARG*     2.9    43.6    +      -       -      +
    135C  VAL*     3.8     7.9    -      -       -      -
    136C  THR*     4.3     4.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 110 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65C  ILE      5.8     4.5    -      -       -      +
     86C  LEU*     4.5    23.3    -      -       +      -
     87C  GLU*     4.1    31.2    -      -       +      +
     90C  LEU*     4.8     9.4    -      -       +      -
    108C  SER      4.3     0.7    -      -       -      -
    109C  ASP*     1.3    91.4    -      -       -      +
    111C  ARG*     1.3    64.6    +      -       -      +
    112C  PHE*     5.5     2.2    -      -       +      -
    133C  LEU*     4.5    11.0    -      -       +      -
    134C  PHE      3.6     9.0    -      -       -      +
    135C  VAL*     4.5     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 111 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109C  ASP*     2.9    37.9    +      -       -      +
    110C  PRO*     1.3    76.3    -      -       -      +
    112C  PHE*     1.3    69.3    +      -       -      +
    132C  PRO      4.3     0.2    -      -       -      +
    133C  LEU*     3.9     3.0    -      -       -      +
    134C  PHE*     3.0    48.3    +      -       +      +
    135C  VAL      4.6     0.2    -      -       -      -
    136C  THR*     2.9    19.4    +      -       -      +
    151C  THR*     2.8    40.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 112 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65C  ILE*     3.8    42.4    -      -       +      -
     86C  LEU*     4.0    24.2    -      -       +      -
    110C  PRO*     5.7     0.9    -      -       +      -
    111C  ARG*     1.3    84.1    -      -       -      +
    113C  ASP*     1.3    73.2    +      -       -      +
    131C  ALA*     3.5    24.5    -      -       +      -
    132C  PRO      3.5     6.7    -      -       -      -
    133C  LEU*     3.9    13.0    -      -       +      -
    134C  PHE*     5.4     0.7    -      -       -      -
    157C  PHE*     3.6    37.0    -      +       +      -
    159C  MET*     4.7     8.3    -      -       +      -
----------------------------------------------------------
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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