Contacts of the strand formed by residues 140 - 150 (chain E) in PDB entry 5HHM


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 140 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163D  MET*     4.5    15.7    -      -       +      -
    166D  MET*     5.1    13.0    -      -       -      -
    168D  PHE*     3.8    51.4    -      -       +      -
    134E  GLU*     3.6     8.8    -      -       -      +
    135E  ILE*     3.4    25.6    +      -       -      -
    138E  THR*     3.2    31.8    +      -       -      +
    139E  GLN*     1.3    82.6    +      -       -      +
    141E  ALA*     1.3    59.7    +      -       -      +
    195E  ARG*     3.5    25.4    -      -       -      +
    196E  VAL      3.7     4.7    -      -       -      +
    197E  SER*     5.2     1.8    -      -       -      -
    198E  ALA*     4.1     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 141 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130E  PRO*     3.8    16.8    -      -       +      +
    134E  GLU*     3.7     3.1    -      -       -      -
    135E  ILE*     4.1     9.6    -      -       +      -
    140E  LYS*     1.3    75.2    -      -       -      +
    142E  THR*     1.3    64.7    +      -       -      +
    143E  LEU      3.9     0.6    +      -       -      -
    194E  LEU      3.7     1.2    -      -       -      +
    195E  ARG*     3.3     1.8    -      -       -      -
    196E  VAL*     2.8    45.6    +      -       +      +
    198E  ALA*     4.3     5.2    -      -       -      -
    201E  TRP*     3.7    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 142 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123D  LEU*     3.3    21.0    -      -       -      +
    135D  LEU*     3.8    25.1    -      -       +      +
    137D  THR*     5.2     2.0    +      -       -      +
    161D  LEU*     5.0     2.5    -      -       +      -
    172D  SER*     5.6     0.9    -      -       -      +
    130E  PRO*     3.4    13.5    -      -       -      +
    134E  GLU*     2.6    34.9    +      -       -      +
    141E  ALA*     1.3    72.1    -      -       -      +
    143E  LEU*     1.3    70.9    +      -       -      +
    144E  VAL*     4.4     0.9    -      -       +      -
    193E  ARG*     4.0    23.1    -      -       +      -
    194E  LEU      3.4     7.2    -      -       -      +
    195E  ARG*     3.0    23.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 143 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127E  VAL*     3.8    23.8    -      -       +      -
    128E  PHE      3.6     5.4    -      -       -      +
    129E  GLU*     4.3     2.0    -      -       -      -
    130E  PRO*     3.8    15.7    -      -       +      -
    141E  ALA      3.9     0.6    +      -       -      +
    142E  THR*     1.3    73.5    -      -       -      +
    144E  VAL*     1.3    60.8    +      -       -      +
    145E  CYS      4.2     0.2    -      -       -      -
    159E  TRP*     3.9    15.1    -      -       +      -
    193E  ARG*     3.3     5.2    -      -       -      -
    194E  LEU*     2.6    52.5    +      -       +      +
    196E  VAL*     5.0     7.0    -      -       +      -
    201E  TRP*     3.8    25.8    -      -       +      -
    208E  PHE*     3.5    44.6    -      -       +      -
    239E  ALA*     4.7     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 144 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123D  LEU*     3.8    18.8    -      -       +      -
    133D  VAL*     4.0    22.9    -      -       +      -
    135D  LEU*     4.1    18.2    -      -       +      -
    174D  VAL*     3.8    30.7    -      -       +      -
    127E  VAL*     3.7     0.7    -      -       -      -
    128E  PHE*     2.8    43.6    +      -       +      +
    142E  THR*     4.1     3.6    +      -       +      -
    143E  LEU*     1.3    77.5    -      -       -      +
    145E  CYS*     1.3    70.1    +      -       -      +
    146E  LEU*     5.3     1.1    -      -       +      -
    159E  TRP*     4.3     3.1    -      -       -      -
    191E  SER*     4.8     0.7    -      -       -      -
    192E  SER      3.6     4.7    -      -       -      +
    193E  ARG*     4.1    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 145 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125E  VAL*     4.1    14.8    -      -       -      -
    126E  ALA      3.7     5.6    -      -       -      -
    127E  VAL*     4.6     1.6    -      -       +      +
    144E  VAL*     1.3    73.4    -      -       -      +
    146E  LEU*     1.3    68.8    +      -       -      +
    147E  ALA      4.2     0.7    -      -       -      -
    157E  LEU*     4.1     9.0    -      -       -      -
    159E  TRP*     3.3    27.9    -      -       +      -
    191E  SER*     3.1    11.1    -      -       -      -
    192E  SER*     2.7    37.2    +      -       -      +
    210E  CYS*     2.5    40.4    -      -       +      -
    212E  VAL*     5.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 146 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131D  LYS*     5.9     5.6    -      -       +      -
    133D  VAL*     4.4     9.2    -      -       +      -
    174D  VAL*     5.5     1.3    -      -       +      -
    176D  TRP*     3.6    58.1    -      -       +      +
    124E  GLU      3.4    10.9    -      -       -      +
    125E  VAL*     4.7     0.2    -      -       -      -
    126E  ALA*     3.0    23.3    +      -       +      +
    128E  PHE*     3.8    29.6    -      -       +      -
    144E  VAL*     5.3     0.7    -      -       +      -
    145E  CYS*     1.3    77.2    -      -       -      +
    147E  ALA*     1.3    60.8    -      -       -      +
    148E  THR*     3.7    19.2    +      -       +      +
    189E  SER*     3.8     7.4    -      -       -      +
    190E  LEU      3.6    13.9    -      -       -      +
    191E  SER*     4.2     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 147 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123E  PRO*     4.4     9.9    -      -       +      -
    124E  GLU      3.5     7.6    -      -       -      -
    125E  VAL*     4.4     3.1    -      -       +      -
    145E  CYS*     4.2     2.8    -      -       -      -
    146E  LEU*     1.3    70.7    -      -       -      +
    148E  THR*     1.3    57.5    +      -       -      +
    150E  PHE*     4.0    17.9    -      -       +      -
    157E  LEU*     4.8     4.0    -      -       +      -
    189E  SER*     3.1     4.3    +      -       -      -
    190E  LEU*     2.7    48.4    +      -       +      +
    212E  VAL*     4.1    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 148 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131D  LYS*     6.1     1.2    -      -       -      -
    176D  TRP*     4.4     7.0    -      -       +      +
    122E  PRO      4.2     0.7    -      -       -      +
    123E  PRO*     3.5     1.6    -      -       -      +
    124E  GLU*     3.0    47.5    +      -       -      +
    146E  LEU*     3.7    28.9    +      -       +      +
    147E  ALA*     1.3    74.6    -      -       -      +
    149E  GLY*     1.3    65.5    +      -       -      +
    150E  PHE*     3.4     3.1    -      -       -      -
    179E  GLU*     3.3     8.7    -      -       -      +
    188E  TYR      3.4     3.4    -      -       -      -
    189E  SER*     2.9    22.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 149 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121E  PHE*     3.3    12.0    -      -       -      +
    122E  PRO      3.5     5.1    -      -       -      +
    148E  THR*     1.3    72.7    -      -       -      +
    150E  PHE*     1.3    56.8    +      -       -      -
    179E  GLU*     2.9    26.2    +      -       -      -
    187E  ARG*     3.0    37.9    +      -       -      -
    188E  TYR      2.7    11.2    +      -       -      -
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Residues in contact with PHE 150 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121E  PHE      3.5     6.5    -      -       -      +
    122E  PRO      4.2     0.2    -      -       -      -
    123E  PRO*     3.7    38.1    -      -       +      -
    147E  ALA*     3.8    26.2    -      -       +      -
    148E  THR      4.1     4.3    -      -       -      -
    149E  GLY*     1.3    78.2    -      -       -      +
    151E  TYR*     1.3    61.3    +      -       -      +
    152E  PRO      3.4    15.5    -      -       -      -
    153E  ASP*     3.7    13.7    -      -       +      -
    155E  VAL*     3.4    38.8    -      -       +      -
    176E  PRO*     4.4     3.6    -      -       +      -
    187E  ARG*     4.2     0.2    -      -       -      -
    188E  TYR*     2.6    69.1    +      -       +      -
    189E  SER      4.3     0.4    -      -       -      -
    190E  LEU*     4.0    16.4    -      -       +      -
    214E  PHE*     4.3     3.8    -      -       +      -
----------------------------------------------------------
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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