Contacts of the strand formed by residues 102 - 115 (chain R) 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 LYS 102 (chain R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98R  LEU*     3.3     6.9    -      -       -      +
     99R  ASN      2.9    28.0    +      -       -      +
    100R  ASN*     3.8    12.6    -      -       -      +
    101R  GLY*     1.3    83.0    -      -       -      +
    103R  PHE*     1.3    59.9    +      -       -      +
    104R  TYR*     3.4    25.8    -      -       +      +
    131R  GLY*     3.1    30.9    -      -       -      +
    132R  LEU      3.7     4.0    -      -       -      -
    133R  LYS*     5.1     5.2    -      -       +      +
      4W    C      3.1    22.4    +      -       -      -
      5W    C      3.1    43.4    +      -       -      +
      6W    C      3.1    32.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 103 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96R  VAL*     4.2    11.2    -      -       +      -
     97R  ASP      3.5    11.9    -      -       -      -
     98R  LEU*     3.8    34.1    -      -       +      -
    101R  GLY      4.9     1.8    -      -       -      -
    102R  LYS*     1.3    72.3    -      -       -      +
    104R  TYR*     1.3    62.6    +      -       -      +
    105R  VAL*     4.2     3.8    -      -       +      -
    129R  SER      3.4     7.1    -      -       -      +
    131R  GLY      3.1    21.1    +      -       -      -
    132R  LEU      2.7    15.9    +      -       -      +
    133R  LYS*     3.3    30.1    -      -       -      -
    135R  LYS*     3.5    55.4    -      -       +      -
    138R  SER*     3.8    17.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 104 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95R  PHE*     3.2    23.2    -      -       +      -
     97R  ASP*     3.1    33.4    +      -       +      +
     99R  ASN*     3.8    23.4    +      -       +      +
    100R  ASN*     5.0     1.0    +      -       -      -
    102R  LYS*     3.4    42.8    -      -       +      +
    103R  PHE*     1.3    76.3    -      -       -      +
    105R  VAL*     1.3    60.4    +      -       -      +
    129R  SER      3.4     4.5    -      -       -      -
    130R  GLU*     3.5    30.1    -      -       +      +
    131R  GLY      3.9     3.8    -      -       -      -
      3W    C      3.3    25.8    -      -       +      -
      4W    C      3.1    33.1    +      -       -      -
      5W    C      4.2     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 105 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136Q  ALA*     4.3     0.7    -      -       -      +
     93R  VAL*     4.7     0.2    -      -       +      -
     95R  PHE*     3.5    14.1    -      -       -      +
     96R  VAL*     4.0    23.8    -      -       +      -
    103R  PHE*     4.7     2.2    -      -       +      -
    104R  TYR*     1.3    81.9    -      -       -      +
    106R  GLY*     1.3    61.3    +      -       -      +
    107R  VAL*     3.7    14.1    -      -       +      -
    127R  GLY      3.8     0.2    -      -       -      +
    128R  VAL*     3.6     9.0    -      -       -      +
    129R  SER      2.9    30.1    +      -       -      +
    130R  GLU*     5.2     0.8    -      -       -      +
    135R  LYS*     5.5     0.4    -      -       +      +
    138R  SER*     4.0    25.1    -      -       -      +
    139R  LEU*     3.9    21.1    -      -       +      +
    142R  ALA*     3.7    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 106 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136Q  ALA*     4.5     1.6    -      -       -      -
     94R  ASP*     2.8    26.9    +      -       -      +
     95R  PHE*     3.4    25.5    +      -       -      +
    105R  VAL*     1.3    74.0    -      -       -      +
    107R  VAL*     1.3    64.2    +      -       -      +
    126R  TYR*     3.6    24.2    -      -       -      -
    127R  GLY      3.5     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 107 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91R  GLN*     3.8    24.7    -      -       +      +
     92R  ASN      3.7     9.0    -      -       -      +
     93R  VAL*     3.8    22.4    -      -       +      -
    105R  VAL*     3.7    11.0    -      -       +      -
    106R  GLY*     1.3    79.5    -      -       -      +
    108R  CYS*     1.3    70.6    +      -       -      +
    126R  TYR*     3.3     7.3    -      -       -      -
    127R  GLY      2.6    37.7    +      -       -      -
    139R  LEU*     4.9     0.4    -      -       +      -
    142R  ALA*     3.7    27.6    -      -       +      +
    143R  ARG*     4.0    11.4    -      -       +      -
    146R  ALA*     3.4    10.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 108 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143Q  ARG*     3.4    42.0    -      -       -      +
     91R  GLN*     3.4     5.2    -      -       -      +
     92R  ASN*     2.9    55.6    +      -       -      +
     94R  ASP*     4.0     1.1    +      -       -      -
    107R  VAL*     1.3    74.7    -      -       -      +
    109R  ALA*     1.3    60.6    +      -       -      +
    110R  PHE*     3.7    12.3    -      -       -      -
    124R  VAL*     4.3     4.5    -      -       +      -
    125R  GLY      3.2     7.6    -      -       -      +
    126R  TYR*     3.5    21.4    -      -       +      -
    146R  ALA*     4.1     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 109 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88R  ILE*     5.0     2.0    -      -       +      -
     90R  GLN      3.4     8.1    -      -       -      +
     91R  GLN*     3.8    18.2    -      -       +      +
    108R  CYS*     1.3    75.6    -      -       -      +
    110R  PHE*     1.3    64.6    +      -       -      +
    111R  VAL*     4.0     5.3    +      -       +      -
    124R  VAL*     3.3     4.2    -      -       -      +
    125R  GLY      2.6    37.5    +      -       -      -
    146R  ALA      3.7    27.1    -      -       -      +
    147R  VAL*     3.9    10.8    -      -       +      +
    150R  GLY*     4.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 110 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88Q  ILE*     3.8    31.9    -      -       +      -
     91Q  GLN*     3.4    47.3    -      -       +      -
    143Q  ARG*     4.3     5.6    -      -       -      -
     88R  ILE*     3.6     2.9    -      -       -      -
     89R  THR*     2.7    40.9    +      -       +      -
     90R  GLN*     2.7    38.4    +      -       +      +
     92R  ASN*     5.4     0.2    -      -       +      -
    108R  CYS*     3.7    24.2    -      -       -      -
    109R  ALA*     1.3    74.9    -      -       -      +
    111R  VAL*     1.3    59.2    +      -       -      +
    122R  GLU*     3.9    13.9    -      -       -      +
    123R  ASP      3.5     4.9    -      -       -      +
    124R  VAL*     3.8    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86R  HIS*     3.8    26.7    -      -       +      -
     87R  SER      3.4    11.2    -      -       -      +
     88R  ILE*     4.9     7.2    -      -       +      -
    109R  ALA*     4.0     2.7    +      -       +      -
    110R  PHE*     1.3    79.1    -      -       -      +
    112R  ARG*     1.3    64.8    +      -       -      +
    113R  VAL*     4.1     2.0    -      -       +      -
    122R  GLU*     3.3     3.4    -      -       -      +
    123R  ASP      3.1    30.5    +      -       -      +
    147R  VAL*     3.5    35.7    -      -       +      +
    150R  GLY*     3.6    16.8    -      -       -      +
    151R  LEU*     3.6    22.4    -      -       +      +
    154R  ALA*     3.7     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 112 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87Q  SER*     5.0     3.6    -      -       -      -
     86R  HIS*     3.1     2.5    -      -       -      -
     87R  SER*     2.9    43.0    +      -       -      +
     89R  THR*     3.9    17.3    -      -       -      +
    110R  PHE      4.2     0.4    +      -       -      -
    111R  VAL*     1.3    73.3    -      -       -      +
    113R  VAL*     1.3    69.7    +      -       -      +
    114R  GLN*     3.6    31.4    +      -       -      +
    118R  GLY      4.7     0.2    +      -       -      -
    120R  TYR*     3.2    48.9    -      -       +      +
    121R  HIS      3.6     4.5    -      -       -      +
    122R  GLU*     4.0    20.4    -      -       +      -
    120S  TYR*     4.7    11.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 113 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84R  TRP*     3.9    12.1    -      -       +      -
     85R  ALA      3.1     9.9    -      -       -      +
     86R  HIS*     3.8     5.8    -      -       +      -
    111R  VAL*     4.6     0.7    -      -       +      -
    112R  ARG*     1.3    72.0    -      -       -      +
    114R  GLN*     1.3    67.1    +      -       -      +
    120R  TYR*     3.1     6.2    -      -       -      +
    121R  HIS      2.8    37.3    +      -       -      +
    151R  LEU*     3.7    27.6    -      -       +      -
    154R  ALA*     3.6    22.4    -      -       +      -
    155R  LEU*     3.6    27.8    -      -       +      +
    158R  PHE*     3.7    18.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 114 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26R  PHE*     3.5    22.7    -      -       +      -
     27R  GLY*     4.5     6.9    -      -       -      -
     84R  TRP*     3.2     2.9    -      -       -      +
     85R  ALA      2.5    41.0    +      -       -      +
    112R  ARG*     3.6    26.1    +      -       -      +
    113R  VAL*     1.3    76.0    -      -       -      +
    115R  LEU*     1.3    72.0    -      -       -      +
    118R  GLY*     3.4    25.2    +      -       -      +
    119R  SER      3.2    11.9    -      -       -      +
    120R  TYR*     4.4     3.1    -      -       +      -
    120S  TYR*     2.9    29.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 115 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81Q  TYR*     3.6    33.0    -      -       +      -
     82Q  ASN*     4.6     0.2    -      -       +      -
     26R  PHE*     3.5     7.3    -      -       -      -
     31R  TYR*     4.0     6.3    -      -       -      +
     79R  PHE*     3.6    37.2    -      -       +      -
     83R  GLY      3.3     9.4    -      -       -      +
     84R  TRP*     4.0     7.6    -      -       +      -
    113R  VAL*     5.1     0.2    -      -       +      -
    114R  GLN*     1.3    82.5    -      -       -      +
    116R  LYS*     1.3    59.8    +      -       -      +
    117R  ASP*     2.9    23.4    +      -       -      +
    118R  GLY      3.0    12.0    +      -       -      -
    119R  SER*     2.7    22.1    +      -       -      +
    158R  PHE*     3.6    36.3    -      -       +      -
----------------------------------------------------------
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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