Contacts of the strand formed by residues 102 - 115 (chain I) 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 I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98I  LEU*     3.5     3.1    -      -       -      -
     99I  ASN      2.9    29.1    +      -       -      +
    100I  ASN*     4.4     9.6    -      -       -      +
    101I  GLY*     1.3    83.2    -      -       -      +
    103I  PHE*     1.3    62.8    +      -       -      +
    104I  TYR*     3.2    26.8    -      -       +      +
    131I  GLY*     3.1    37.4    +      -       -      +
    132I  LEU      3.7     2.9    -      -       -      -
    133I  LYS*     4.3    16.8    -      -       +      +
      2Z    C      3.0    57.7    +      -       -      +
      3Z    C      4.3     7.3    +      -       -      -
      4Z    C      4.2    10.5    -      -       -      +
      5Z    C      5.1     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 103 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96I  VAL*     4.3     8.1    -      -       +      -
     97I  ASP      3.3    13.0    -      -       -      -
     98I  LEU*     3.7    36.6    -      -       +      -
    101I  GLY      5.1     0.9    -      -       -      -
    102I  LYS*     1.3    71.9    -      -       -      +
    104I  TYR*     1.3    62.6    +      -       -      +
    105I  VAL*     4.2     4.5    -      -       +      -
    129I  SER      3.5     6.5    -      -       -      +
    131I  GLY      3.4    19.4    +      -       -      -
    132I  LEU      2.9    14.3    +      -       -      +
    133I  LYS*     3.3    29.4    -      -       -      -
    135I  LYS*     3.4    57.4    -      -       +      -
    138I  SER*     3.9    18.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 104 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95I  PHE*     3.1    22.8    -      -       +      -
     97I  ASP*     3.1    31.3    +      -       +      +
     99I  ASN*     3.8    30.9    +      -       +      +
    100I  ASN*     4.9     4.3    +      -       -      -
    102I  LYS*     3.2    46.0    -      -       +      +
    103I  PHE*     1.3    77.3    -      -       -      +
    105I  VAL*     1.3    61.2    +      -       -      +
    129I  SER      3.5     4.7    -      -       -      -
    130I  GLU*     3.7    33.2    -      -       +      +
    131I  GLY*     4.2     9.4    -      -       -      -
      2Z    C      4.8     3.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 105 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136H  ALA*     4.2     1.3    -      -       -      +
     95I  PHE*     3.5    14.1    -      -       -      +
     96I  VAL*     4.1    23.6    -      -       +      -
    103I  PHE*     4.8     2.0    -      -       +      -
    104I  TYR*     1.3    80.9    -      -       -      +
    106I  GLY*     1.3    61.3    +      -       -      +
    107I  VAL*     3.8    13.2    -      -       +      -
    127I  GLY      3.8     0.5    -      -       -      +
    128I  VAL*     3.6     9.7    -      -       -      +
    129I  SER*     3.1    29.9    +      -       -      +
    130I  GLU*     5.4     0.4    -      -       -      +
    135I  LYS*     5.3     0.9    -      -       +      +
    138I  SER*     3.9    27.8    -      -       -      +
    139I  LEU*     3.9    18.8    -      -       +      +
    142I  ALA*     3.7    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 106 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136H  ALA*     4.2     1.3    -      -       -      -
     93I  VAL      3.8     0.2    -      -       -      -
     94I  ASP*     2.8    31.7    +      -       -      +
     95I  PHE*     3.4    23.7    +      -       -      +
    105I  VAL*     1.3    74.8    -      -       -      +
    107I  VAL*     1.3    60.1    +      -       -      +
    126I  TYR*     3.6    24.5    -      -       -      -
    127I  GLY      3.7     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 107 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91I  GLN*     3.8    28.5    -      -       +      +
     92I  ASN      3.6     9.0    -      -       -      +
     93I  VAL*     3.7    23.6    -      -       +      +
    105I  VAL*     3.8     9.9    -      -       +      -
    106I  GLY*     1.3    78.6    -      -       -      +
    108I  CYS*     1.3    71.7    +      -       -      +
    126I  TYR*     3.4     7.5    -      -       -      -
    127I  GLY      2.8    35.8    +      -       -      -
    139I  LEU*     5.0     0.7    -      -       +      -
    142I  ALA*     3.8    26.5    -      -       +      +
    143I  ARG*     4.1    11.0    -      -       +      -
    146I  ALA*     3.3     8.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 108 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143H  ARG*     3.4    42.0    -      -       -      +
     91I  GLN*     3.4     1.9    -      -       -      -
     92I  ASN*     2.8    55.0    +      -       -      +
     94I  ASP*     4.0     0.8    +      -       -      -
    107I  VAL*     1.3    79.2    -      -       -      +
    109I  ALA*     1.3    61.5    +      -       -      +
    110I  PHE*     3.9    12.8    -      -       -      -
    124I  VAL*     4.1     5.2    -      -       +      -
    125I  GLY      3.3     8.5    -      -       -      +
    126I  TYR*     3.7    20.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 109 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88I  ILE*     4.8     2.0    -      -       +      -
     90I  GLN      3.3     8.7    -      -       -      +
     91I  GLN*     3.9    18.2    -      -       +      +
    108I  CYS*     1.3    74.5    -      -       -      +
    110I  PHE*     1.3    65.0    +      -       -      +
    111I  VAL*     3.9     6.2    +      -       +      -
    124I  VAL*     3.2     6.2    -      -       -      +
    125I  GLY      2.9    31.5    +      -       -      -
    146I  ALA      3.8    27.4    -      -       -      +
    147I  VAL*     4.0     9.9    -      -       +      +
    150I  GLY*     4.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 110 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88H  ILE*     3.9    21.1    -      -       +      -
     91H  GLN*     3.7    43.1    -      -       +      -
    143H  ARG*     4.3     5.8    -      -       -      -
     88I  ILE*     3.6     3.3    -      -       -      -
     89I  THR*     2.7    35.3    +      -       +      -
     90I  GLN*     2.7    50.3    +      -       +      +
    108I  CYS*     3.9    21.1    -      -       -      -
    109I  ALA*     1.3    74.7    -      -       -      +
    111I  VAL*     1.3    58.9    +      -       -      +
    122I  GLU*     3.7    15.7    -      -       -      +
    123I  ASP      3.5     5.2    -      -       -      +
    124I  VAL*     3.5    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86I  HIS*     3.8    30.3    -      -       +      -
     87I  SER      3.5     7.0    -      -       -      +
     88I  ILE*     4.7    11.4    -      -       +      -
    109I  ALA*     3.9     6.9    -      -       +      -
    110I  PHE*     1.3    76.7    -      -       -      +
    112I  ARG*     1.3    63.2    +      -       -      +
    113I  VAL*     4.1     2.0    -      -       +      -
    122I  GLU*     3.3     2.3    -      -       -      -
    123I  ASP      3.0    29.9    +      -       -      +
    147I  VAL*     3.6    32.5    -      -       +      +
    150I  GLY*     3.6    15.5    -      -       -      -
    151I  LEU*     3.7    23.6    -      -       +      +
    154I  ALA*     3.8     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 112 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87H  SER*     4.7     6.3    +      -       -      -
     85I  ALA      4.0     0.2    -      -       -      +
     86I  HIS*     3.2     2.9    -      -       -      -
     87I  SER*     3.0    40.5    +      -       -      +
     89I  THR*     4.0    13.0    -      -       -      +
    110I  PHE      4.1     0.4    +      -       -      -
    111I  VAL*     1.3    72.3    -      -       -      +
    113I  VAL*     1.3    70.2    +      -       -      +
    114I  GLN*     3.2    34.0    +      -       +      +
    120I  TYR*     3.7    46.4    -      -       +      +
    121I  HIS      3.4     3.8    -      -       -      +
    122I  GLU*     3.7    27.8    -      -       +      +
    120J  TYR*     4.6     6.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 113 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84I  TRP*     4.1    11.7    -      -       +      -
     85I  ALA      3.2    10.5    -      -       -      +
     86I  HIS*     3.9     3.8    -      -       +      -
    111I  VAL*     4.7     0.7    -      -       +      -
    112I  ARG*     1.3    74.3    -      -       -      +
    114I  GLN*     1.3    67.4    +      -       -      +
    120I  TYR*     3.1     5.2    -      -       -      +
    121I  HIS      2.7    42.3    +      -       -      +
    151I  LEU*     3.6    27.8    -      -       +      -
    154I  ALA*     3.6    22.9    -      -       +      -
    155I  LEU*     3.7    28.0    -      -       +      +
    158I  PHE*     3.8    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 114 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26I  PHE*     3.4    23.8    -      -       +      -
     27I  GLY*     4.7     5.8    -      -       -      -
     84I  TRP*     3.4     2.3    -      -       -      +
     85I  ALA      2.6    40.2    +      -       -      +
    112I  ARG*     3.2    26.8    +      -       -      +
    113I  VAL*     1.3    75.8    -      -       -      +
    115I  LEU*     1.3    71.7    +      -       -      +
    118I  GLY*     3.6    20.4    +      -       -      +
    119I  SER      3.2    15.9    -      -       -      +
    120I  TYR*     4.3     4.7    -      -       +      -
    158I  PHE*     5.5     0.2    -      -       -      -
    120J  TYR*     3.6    25.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 115 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81H  TYR*     3.9    19.1    -      -       +      -
     82H  ASN*     4.7     0.9    -      -       +      -
     26I  PHE*     3.6     7.4    -      -       -      -
     27I  GLY*     4.3     0.2    -      -       -      -
     31I  TYR*     4.5     5.2    -      -       +      +
     79I  PHE*     3.7    44.9    -      -       +      -
     83I  GLY      3.4     4.3    -      -       -      +
     84I  TRP*     3.9    18.4    -      -       +      -
    113I  VAL*     4.9     0.4    -      -       +      -
    114I  GLN*     1.3    83.7    -      -       -      +
    116I  LYS*     1.3    58.8    +      -       -      +
    117I  ASP*     2.9    28.9    +      -       -      +
    118I  GLY      3.0    12.2    +      -       -      -
    119I  SER*     2.7    14.9    +      -       -      +
    158I  PHE*     3.6    37.7    -      -       +      -
----------------------------------------------------------
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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