Contacts of the strand formed by residues 102 - 115 (chain T) 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 T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98T  LEU*     3.4     6.0    -      -       -      +
     99T  ASN      2.9    32.0    +      -       -      +
    100T  ASN*     4.5     9.9    -      -       -      +
    101T  GLY*     1.3    81.9    -      -       -      +
    103T  PHE*     1.3    59.7    +      -       -      +
    104T  TYR*     3.2    27.6    -      -       +      +
    131T  GLY*     3.3    34.3    +      -       -      +
    132T  LEU      3.7     3.1    -      -       -      -
    133T  LYS*     4.7    11.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 103 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96T  VAL*     4.2     8.3    -      -       +      -
     97T  ASP      3.3    13.0    -      -       -      -
     98T  LEU*     3.7    39.3    -      -       +      -
    101T  GLY      4.9     1.3    -      -       -      -
    102T  LYS*     1.3    70.5    -      -       -      +
    104T  TYR*     1.3    63.1    +      -       -      +
    105T  VAL*     4.8     3.8    -      -       +      -
    129T  SER      3.3    12.2    -      -       -      +
    131T  GLY      3.3    15.6    +      -       -      -
    132T  LEU      2.9    14.1    +      -       -      +
    133T  LYS*     3.3    29.8    -      -       -      -
    135T  LYS*     3.7    53.4    -      -       +      -
    138T  SER*     3.9    17.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 104 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136S  ALA*     6.5     0.4    -      -       +      -
     95T  PHE*     3.4    18.8    -      -       +      -
     96T  VAL*     3.7     0.2    -      -       -      -
     97T  ASP*     2.9    41.8    +      -       +      +
     99T  ASN*     3.7    35.6    +      -       +      +
    100T  ASN*     5.2     1.6    +      -       -      -
    102T  LYS*     3.2    44.1    -      -       +      +
    103T  PHE*     1.3    74.7    -      -       -      +
    105T  VAL*     1.3    60.7    +      -       -      +
    129T  SER      3.4     4.7    -      -       -      -
    130T  GLU*     3.4    38.8    -      -       +      +
    131T  GLY*     4.6     4.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 105 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136S  ALA*     4.3     0.9    -      -       -      +
     93T  VAL*     4.6     0.2    -      -       +      -
     95T  PHE*     3.5    13.9    -      -       -      +
     96T  VAL*     3.9    24.0    -      -       +      -
    103T  PHE*     4.8     2.0    -      -       +      -
    104T  TYR*     1.3    80.2    -      -       -      +
    106T  GLY*     1.3    60.7    +      -       -      +
    107T  VAL*     3.8    13.0    -      -       +      -
    127T  GLY      3.7     0.3    -      -       -      +
    128T  VAL*     3.5     9.9    -      -       -      +
    129T  SER*     3.1    29.3    +      -       -      +
    130T  GLU*     5.4     0.8    -      -       -      +
    135T  LYS*     5.3     0.7    -      -       +      +
    138T  SER*     3.8    27.1    -      -       -      +
    139T  LEU*     3.8    18.8    -      -       +      +
    142T  ALA*     3.7    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 106 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136S  ALA*     4.5     0.7    -      -       -      -
     93T  VAL      3.7     0.3    -      -       -      -
     94T  ASP*     2.8    32.1    +      -       -      +
     95T  PHE*     3.3    24.3    +      -       -      +
    105T  VAL*     1.3    74.4    -      -       -      +
    107T  VAL*     1.3    59.8    +      -       -      +
    126T  TYR*     3.4    24.9    -      -       -      -
    127T  GLY      3.6     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 107 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91T  GLN*     3.8    28.5    -      -       +      +
     92T  ASN      3.7     8.5    -      -       -      +
     93T  VAL*     3.7    22.7    -      -       +      -
    105T  VAL*     3.8     9.2    -      -       +      -
    106T  GLY*     1.3    80.8    -      -       -      +
    108T  CYS*     1.3    71.7    +      -       -      +
    126T  TYR*     3.2     9.5    -      -       -      -
    127T  GLY      2.7    34.6    +      -       -      -
    139T  LEU*     4.7     0.7    -      -       +      -
    142T  ALA*     3.6    26.9    -      -       +      +
    143T  ARG*     3.9    15.7    -      -       +      -
    146T  ALA*     3.3     3.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 108 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143S  ARG*     3.5    41.7    -      -       -      +
     91T  GLN*     3.4     7.1    -      -       -      +
     92T  ASN*     2.9    53.1    +      -       -      +
     94T  ASP*     3.9     1.7    +      -       -      -
    107T  VAL*     1.3    73.7    -      -       -      +
    109T  ALA*     1.3    61.3    +      -       -      +
    110T  PHE*     3.8    17.3    -      -       +      -
    124T  VAL*     5.0     2.2    -      -       +      -
    125T  GLY      3.3     7.4    -      -       -      +
    126T  TYR*     3.6    19.6    -      -       +      -
    146T  ALA*     4.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 109 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88T  ILE*     4.9     2.2    -      -       +      -
     90T  GLN      3.4     8.1    -      -       -      +
     91T  GLN*     3.7    22.2    -      -       +      +
    108T  CYS*     1.3    76.2    -      -       -      +
    110T  PHE*     1.3    65.7    +      -       -      +
    111T  VAL*     4.0     5.8    +      -       +      -
    123T  ASP      3.8     0.3    -      -       -      +
    124T  VAL*     3.3     5.0    -      -       -      +
    125T  GLY      2.7    35.5    +      -       -      -
    146T  ALA      3.7    23.3    -      -       -      +
    147T  VAL*     3.9    10.1    -      -       +      +
    150T  GLY*     4.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 110 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88S  ILE*     3.8    24.9    -      -       +      -
     91S  GLN*     3.6    46.7    -      -       +      -
    143S  ARG*     4.4     5.4    -      -       -      -
     88T  ILE*     3.4     3.1    -      -       -      -
     89T  THR*     2.6    43.5    +      -       +      -
     90T  GLN*     2.7    40.3    +      -       +      +
     92T  ASN*     5.7     1.6    -      -       +      -
    108T  CYS*     3.8    24.2    -      -       +      -
    109T  ALA*     1.3    77.1    -      -       -      +
    111T  VAL*     1.3    58.2    +      -       -      +
    122T  GLU*     3.8    15.3    -      -       -      +
    123T  ASP      3.5     4.9    -      -       -      +
    124T  VAL*     3.5    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86T  HIS*     3.9    25.4    -      -       +      -
     87T  SER      3.3    12.1    -      -       -      +
     88T  ILE*     4.7     6.7    -      -       +      -
    109T  ALA*     4.6     4.9    -      -       +      -
    110T  PHE*     1.3    77.4    -      -       -      +
    112T  ARG*     1.3    66.2    +      -       -      +
    113T  VAL*     4.1     1.8    -      -       +      -
    122T  GLU*     3.2     3.5    -      -       -      +
    123T  ASP      3.0    30.3    +      -       -      -
    147T  VAL*     3.5    36.6    -      -       +      +
    150T  GLY*     3.6    16.8    -      -       -      -
    151T  LEU*     3.7    22.7    -      -       +      +
    154T  ALA*     3.8     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 112 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87S  SER*     4.8     5.6    -      -       -      -
     86T  HIS*     3.2     2.1    -      -       -      -
     87T  SER*     2.8    43.2    +      -       -      +
     89T  THR*     3.8    16.8    -      -       -      +
    110T  PHE      4.2     0.4    +      -       -      -
    111T  VAL*     1.3    72.8    -      -       -      +
    113T  VAL*     1.3    69.8    +      -       -      +
    114T  GLN*     3.2    33.7    +      -       +      +
    120T  TYR*     3.8    45.8    -      -       +      +
    121T  HIS      3.5     3.4    -      -       -      +
    122T  GLU*     3.9    21.3    -      -       +      +
    120U  TYR*     4.7     7.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 113 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84T  TRP*     3.9    12.3    -      -       +      -
     85T  ALA      3.1    10.3    -      -       -      +
     86T  HIS*     3.7     5.4    -      -       +      -
    111T  VAL*     4.6     0.7    -      -       +      -
    112T  ARG*     1.3    73.9    -      -       -      +
    114T  GLN*     1.3    67.5    +      -       -      +
    120T  TYR*     3.0     6.1    -      -       -      +
    121T  HIS      2.8    36.6    +      -       -      +
    151T  LEU*     3.6    30.7    -      -       +      -
    154T  ALA*     3.6    19.5    -      -       +      -
    155T  LEU*     3.7    28.5    -      -       +      -
    158T  PHE*     3.9    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 114 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26T  PHE*     3.4    25.4    -      -       +      -
     27T  GLY*     4.9     4.8    -      -       -      -
     84T  TRP*     3.4     1.9    -      -       -      +
     85T  ALA*     2.6    41.3    +      -       -      +
    112T  ARG*     3.2    26.9    +      -       -      +
    113T  VAL*     1.3    75.0    -      -       -      +
    115T  LEU*     1.3    71.5    +      -       -      +
    118T  GLY*     3.6    23.8    +      -       -      +
    119T  SER      3.2    15.3    -      -       -      +
    120T  TYR*     4.3     5.2    -      -       +      -
    120U  TYR*     3.8    24.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 115 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81S  TYR*     4.0    19.3    -      -       +      -
     82S  ASN*     4.6     0.9    -      -       +      -
     26T  PHE*     3.7     7.4    -      -       -      -
     27T  GLY*     4.5     0.2    -      -       -      -
     31T  TYR*     4.3     6.3    -      -       +      +
     79T  PHE*     3.7    47.8    -      -       +      -
     83T  GLY      3.4     4.0    -      -       -      +
     84T  TRP*     3.9    14.8    -      -       +      -
    113T  VAL*     5.0     0.9    -      -       +      -
    114T  GLN*     1.3    83.2    -      -       -      +
    116T  LYS*     1.3    59.4    +      -       -      +
    117T  ASP*     2.9    26.8    +      -       -      +
    118T  GLY*     3.0    12.3    +      -       -      -
    119T  SER*     2.7    18.3    +      -       -      +
    158T  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