Contacts of the strand formed by residues 133 - 144 (chain B) in PDB entry 5UHE


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 LYS 133 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57B  ASP*     5.0     5.8    -      -       -      -
     66B  VAL*     4.4     3.5    -      -       -      +
     67B  PRO      3.5    19.1    +      -       -      +
    100B  GLN*     3.6    33.8    +      -       +      +
    128B  LEU*     4.5     1.7    -      -       -      +
    131B  LYS      3.9     4.1    +      -       -      +
    132B  GLY*     1.3    71.5    -      -       -      -
    134B  LEU*     1.3    74.6    +      -       -      +
    135B  GLU*     3.0    31.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  ILE*     4.8     6.1    -      -       +      -
     66B  VAL*     3.6    32.1    -      -       +      -
     69B  VAL*     3.8    11.4    -      -       +      -
     76B  ILE*     6.1     3.8    -      -       +      -
     97B  LEU      3.8     1.5    -      -       -      +
     98B  ARG*     3.4     3.8    -      -       -      -
     99B  LYS*     3.1    40.5    +      -       +      +
    105B  VAL*     4.4    15.0    -      -       +      -
    125B  ILE*     6.3     0.7    -      -       +      -
    126B  ALA*     4.5    13.2    -      -       +      -
    128B  LEU*     3.8    26.9    -      -       +      -
    133B  LYS*     1.3    78.8    -      -       -      +
    135B  GLU*     1.3    64.2    +      -       -      +
    136B  VAL*     4.3    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  ARG      3.8     2.4    -      -       -      +
     56B  ILE*     3.9     1.6    -      -       -      +
     57B  ASP*     3.0    53.8    +      -       +      +
     97B  LEU      3.8     3.1    -      -       -      -
     98B  ARG*     3.9    29.9    -      -       +      +
    133B  LYS*     3.0    34.2    +      -       +      +
    134B  LEU*     1.3    79.7    -      -       -      +
    136B  VAL*     1.3    67.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  ILE*     4.5     9.2    -      -       +      -
     55B  ARG      3.4    15.0    -      -       -      +
     56B  ILE*     4.9    12.3    -      -       +      -
     76B  ILE*     6.4     1.8    -      -       +      -
     80B  LEU*     5.1     4.5    -      -       +      -
     95B  MET      4.1     0.2    -      -       -      +
     96B  TYR*     3.6     8.3    -      -       -      -
     97B  LEU*     3.0    45.8    +      -       +      +
     98B  ARG*     5.0     1.0    -      -       -      +
    134B  LEU*     4.5    18.8    -      -       +      -
    135B  GLU*     1.3    84.1    -      -       -      +
    137B  GLU*     1.3    64.0    +      -       -      +
    138B  LEU*     3.6    27.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  ILE*     3.4     7.1    -      -       -      +
     55B  ARG*     3.1    75.9    +      -       +      -
     94B  THR*     3.7    24.8    +      -       +      +
     95B  MET      3.9     2.5    -      -       -      -
     96B  TYR*     3.7    27.0    +      -       +      -
    136B  VAL*     1.3    74.6    -      -       -      +
    138B  LEU*     1.3    64.6    +      -       -      +
    139B  VAL*     4.5    10.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 138 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  VAL*     5.0     9.4    -      -       +      -
     53B  SER      4.1     1.3    -      -       -      +
     54B  ILE*     3.6    25.8    -      -       +      -
     80B  LEU*     4.1    17.3    -      -       +      -
     83B  LEU*     4.8     7.9    -      -       +      -
     94B  THR*     3.2    12.3    -      -       -      +
     95B  MET*     2.8    69.4    +      -       +      +
     97B  LEU*     5.1     9.0    -      -       +      -
    110B  ILE*     4.6    18.2    -      -       +      -
    136B  VAL*     3.6    24.7    -      -       +      +
    137B  GLU*     1.3    74.5    -      -       -      +
    139B  VAL*     1.3    63.6    +      -       -      +
    140B  VAL*     4.0     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 139 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  VAL*     3.7     3.9    -      -       -      +
     52B  THR*     2.9    36.3    +      -       +      -
     53B  SER*     2.9    40.1    +      -       -      +
     54B  ILE*     5.4     1.1    -      -       -      -
     55B  ARG*     6.1     2.9    -      -       +      -
     92B  PRO*     4.7    14.6    -      -       +      -
     93B  VAL      3.8     8.7    -      -       -      +
     94B  THR*     4.4     9.0    -      -       -      +
    137B  GLU*     4.5    14.6    -      -       +      +
    138B  LEU*     1.3    76.2    -      -       -      +
    140B  VAL*     1.3    63.2    +      -       -      +
    141B  GLU*     4.7     4.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 140 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  ALA*     4.2    15.3    -      -       +      -
     50B  ALA      3.6    12.8    -      -       -      +
     51B  VAL*     4.9    11.2    -      -       +      -
     85B  VAL*     4.3    13.2    -      -       +      -
     87B  SER*     4.2    15.8    +      -       -      -
     91B  GLU      4.7     0.3    -      -       -      +
     92B  PRO*     3.3     5.9    -      -       -      +
     93B  VAL*     3.1    43.0    +      -       +      +
     95B  MET*     3.8    38.4    -      -       +      -
    138B  LEU*     4.0     1.5    -      -       +      -
    139B  VAL*     1.3    73.8    -      -       -      +
    141B  GLU*     1.3    72.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 141 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  ILE*     3.3    38.0    -      -       +      +
    186A  ARG*     4.9     5.6    +      -       -      -
     49B  ALA*     3.4    24.8    -      -       -      +
     50B  ALA      3.2    12.1    +      -       -      -
     52B  THR*     3.3    35.7    +      -       -      +
     87B  SER*     5.7     0.2    -      -       -      -
     90B  ASP      4.9     2.5    -      -       -      +
     92B  PRO*     3.8    28.6    -      -       +      +
    139B  VAL*     3.9     6.3    +      -       +      +
    140B  VAL*     1.3    79.0    -      -       -      +
    142B  ARG*     1.3    65.4    +      -       -      +
    152B  ASN*     5.2     0.2    -      -       -      +
    168B  TYR*     3.8     9.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 142 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  ILE*     3.5    23.7    -      -       -      +
      5A  GLN*     5.6     4.0    -      -       -      +
     47B  PRO*     4.4    25.6    +      -       +      +
     48B  GLY*     3.4    27.3    +      -       -      +
     49B  ALA*     4.2     6.3    -      -       +      -
     86B  SER*     5.5     1.6    -      -       -      +
     87B  SER*     2.8    38.6    +      -       -      +
     88B  GLU      4.9     2.8    +      -       -      -
     89B  GLU      3.5    27.6    -      -       -      +
     90B  ASP*     3.6    34.9    +      -       -      +
    141B  GLU*     1.3    79.3    -      -       -      +
    143B  GLY*     1.3    58.8    +      -       -      +
    168B  TYR*     3.7     4.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 143 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  ILE*     4.9    10.3    -      -       -      -
     47B  PRO*     3.2     7.4    -      -       -      +
     48B  GLY      3.2    25.5    +      -       -      -
    142B  ARG*     1.3    76.3    -      -       -      +
    144B  ARG*     1.3    64.8    +      -       -      -
    168B  TYR*     3.2    27.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 144 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  ILE      5.7     2.0    -      -       -      +
      4A  SER      4.9     5.9    +      -       -      -
      5A  GLN*     3.1    39.0    -      -       -      +
     27A  GLU*     3.6    28.9    +      -       -      +
     44B  SER      3.1    17.5    -      -       -      +
     45B  SER*     3.8    14.7    +      -       -      +
     46B  ILE      3.8     4.7    -      -       -      +
     47B  PRO*     3.2    42.8    -      -       +      +
    143B  GLY*     1.3    80.4    -      -       -      +
    145B  GLY*     1.3    64.8    +      -       -      +
    146B  TYR      3.3     3.3    +      -       -      +
    147B  VAL*     4.6     6.1    -      -       -      +
    168B  TYR*     3.6    11.1    -      -       -      -
    624D  ARG*     5.2     2.8    +      -       -      -
----------------------------------------------------------
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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