Contacts of the strand formed by residues 120 - 132 (chain V) in PDB entry 5XS0


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 TYR 120 (chain V).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26U  PHE*     4.1    12.8    -      +       -      -
     85U  ALA*     3.1    37.6    -      -       +      +
     86U  HIS      3.3    30.7    -      -       -      -
     87U  SER*     3.6    17.9    +      -       -      -
    112U  ARG*     4.7     6.9    +      -       -      -
    114U  GLN*     3.6    29.4    +      -       -      +
    112V  ARG*     4.0    42.2    -      -       +      +
    113V  VAL      3.0    12.8    -      -       -      +
    114V  GLN*     4.3     4.7    -      -       +      -
    118V  GLY      3.4    15.9    -      -       -      +
    119V  SER*     1.3    76.0    +      -       -      +
    121V  HIS*     1.3    75.4    +      -       -      +
    158V  PHE*     4.8     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 121 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81U  TYR      4.3     1.8    +      -       -      -
     84U  TRP*     3.5    55.9    +      +       -      -
     85U  ALA*     3.9     1.6    -      -       -      -
     86U  HIS*     2.8    30.5    +      -       +      -
    112V  ARG*     4.3     1.3    -      -       -      -
    113V  VAL*     2.7    39.8    +      -       -      +
    119V  SER*     5.1     0.2    -      -       -      -
    120V  TYR*     1.3    83.6    +      -       -      +
    122V  GLU*     1.3    57.8    +      -       -      +
    154V  ALA*     3.6    23.6    -      -       -      +
    157V  SER*     3.8    19.7    +      -       -      -
    158V  PHE*     3.3    44.2    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLU 122 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86U  HIS*     3.0    21.5    +      -       -      +
     87U  SER*     3.5    19.1    -      -       -      -
     88U  ILE*     3.0    49.0    +      -       +      +
     89V  THR*     3.0    38.1    +      -       -      +
    110V  PHE*     3.9     7.3    -      -       -      +
    111V  VAL      3.2    15.5    -      -       -      +
    112V  ARG*     3.7    19.8    +      -       +      -
    121V  HIS*     1.3    74.2    -      -       -      +
    123V  ASP*     1.3    75.3    +      -       -      +
    154V  ALA*     4.7     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 123 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72U  ILE*     5.9     0.7    -      -       -      +
     86U  HIS*     3.5     8.8    +      -       -      -
     88U  ILE*     3.7     7.1    -      -       -      +
    147U  VAL*     3.2    22.6    -      -       -      +
    148U  THR*     5.7     0.2    +      -       -      -
    151U  LEU*     5.5     3.0    -      -       -      +
    110V  PHE*     3.5     3.6    -      -       -      +
    111V  VAL*     3.0    32.6    +      -       -      +
    122V  GLU*     1.3    81.8    -      -       -      +
    124V  VAL*     1.3    65.0    +      -       -      +
    150V  GLY      4.6     1.7    -      -       -      +
    153V  ARG*     2.8    53.0    +      -       +      +
    154V  ALA*     3.9     3.5    -      -       -      +
    156V  ARG*     5.9     0.3    -      -       -      -
    157V  SER*     3.5    12.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 124 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88U  ILE*     3.5     6.1    -      -       +      -
     91U  GLN*     4.2    13.7    -      -       -      +
    143U  ARG*     4.4    13.5    -      -       +      +
    144U  LYS*     4.1     8.3    -      -       +      -
    147U  VAL*     3.4    31.1    -      -       +      +
    108V  CYS*     4.3    13.5    -      -       +      -
    109V  ALA      3.3    11.9    -      -       -      +
    110V  PHE*     3.5    26.5    -      -       +      -
    123V  ASP*     1.3    76.4    +      -       -      +
    125V  GLY*     1.3    70.2    +      -       -      +
    126V  TYR*     5.5     0.7    -      -       +      -
    150V  GLY*     4.0     2.9    -      -       -      -
    153V  ARG*     2.6    36.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 125 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144U  LYS*     4.5     1.1    -      -       -      -
    108V  CYS*     3.3     4.0    -      -       -      -
    109V  ALA      2.8    31.7    +      -       -      +
    124V  VAL*     1.3    80.3    -      -       -      +
    126V  TYR*     1.3    60.2    +      -       -      +
    146V  ALA*     3.6     7.9    -      -       -      -
    149V  ASP*     3.4     6.7    -      -       -      -
    150V  GLY*     3.3    28.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 126 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136U  ALA      3.4    16.2    -      -       -      -
    139U  LEU*     3.3    25.4    -      -       +      +
    140U  GLU*     3.6    45.4    -      -       +      +
    143U  ARG*     4.1    11.4    -      -       +      -
    144U  LYS*     4.0     2.6    -      -       +      +
     94V  ASP*     2.7    36.2    +      -       -      +
     95V  PHE*     3.8     1.0    -      -       -      -
    106V  GLY*     3.6    12.9    -      -       -      -
    107V  VAL      3.4    11.0    -      -       -      -
    108V  CYS*     3.5    22.7    -      -       +      -
    124V  VAL*     5.5     0.7    -      -       +      -
    125V  GLY*     1.3    72.8    -      -       -      -
    127V  GLY*     1.3    75.8    +      -       -      +
    128V  VAL*     3.7    17.0    -      -       +      +
    145V  GLU*     3.8     2.4    -      -       -      +
    146V  ALA*     3.5    11.1    -      -       -      -
    149V  ASP*     3.1    20.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 127 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106V  GLY*     3.4     4.7    -      -       -      -
    107V  VAL      2.7    36.8    +      -       -      -
    126V  TYR*     1.3    74.1    -      -       -      +
    128V  VAL*     1.3    63.2    +      -       -      +
    142V  ALA*     3.3    29.8    -      -       -      +
    145V  GLU*     4.2     6.1    -      -       -      -
    146V  ALA*     3.4     5.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 128 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136U  ALA*     3.6    27.1    -      -       +      +
    137U  LEU*     4.8     8.3    -      -       +      -
    140U  GLU*     4.5    12.1    -      -       -      +
    105V  VAL      3.4     4.5    -      -       -      +
    126V  TYR*     3.7    19.3    -      -       +      -
    127V  GLY*     1.3    80.2    -      -       -      +
    129V  SER*     1.3    65.2    +      -       -      +
    130V  GLU*     3.6    29.4    -      -       +      +
    141V  LYS*     3.0    26.2    +      -       -      +
    142V  ALA*     4.2     3.3    -      -       -      +
    145V  GLU*     3.7     6.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 129 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103V  PHE      3.3     3.3    -      -       -      +
    104V  TYR*     3.3     3.1    -      -       -      -
    105V  VAL*     2.8    37.7    +      -       -      +
    128V  VAL*     1.3    76.8    -      -       -      +
    130V  GLU*     1.3    60.0    +      -       -      +
    132V  LEU*     3.7    14.6    -      -       -      +
    138V  SER*     3.2    47.4    +      -       -      -
    141V  LYS*     3.7    15.5    -      -       -      +
    142V  ALA*     4.4     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 130 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134U  SER*     4.0    22.5    +      -       -      -
    135U  LYS      5.7     0.2    +      -       -      -
    136U  ALA*     4.8     4.9    +      -       +      +
    137U  LEU*     4.7     5.9    -      -       -      +
     95V  PHE*     6.1     0.2    -      -       -      -
    103V  PHE      3.6     3.1    -      -       -      -
    104V  TYR*     3.7    32.9    -      -       +      +
    105V  VAL      5.3     0.4    -      -       -      +
    128V  VAL*     3.6    25.0    -      -       +      +
    129V  SER*     1.3    77.9    +      -       -      +
    131V  GLY*     1.3    58.8    +      -       -      +
    132V  LEU*     3.5     4.9    +      -       -      +
    141V  LYS*     5.9     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 131 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102V  LYS*     3.3    39.0    -      -       -      +
    103V  PHE      3.1     8.9    +      -       -      -
    104V  TYR*     4.5     7.3    -      -       -      -
    130V  GLU*     1.3    72.2    -      -       -      +
    132V  LEU*     1.3    67.3    +      -       -      +
    133V  LYS*     3.6     2.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 132 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103V  PHE*     2.7    37.1    +      -       -      +
    129V  SER*     3.7    17.9    -      -       -      +
    130V  GLU      3.5     4.2    -      -       -      +
    131V  GLY*     1.3    76.9    -      -       -      +
    133V  LYS*     1.3    61.4    +      -       -      +
    134V  SER*     3.5     5.6    -      -       -      +
    137V  LEU*     4.1    20.9    -      -       +      +
    138V  SER*     3.2    29.6    -      -       -      +
    141V  LYS*     4.7    12.1    -      -       +      -
----------------------------------------------------------
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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