Contacts of the strand formed by residues 84 - 99 (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 TRP 84 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26T  PHE*     4.0     4.1    -      -       -      -
     72T  ILE*     4.0    14.4    -      -       +      -
     75T  ALA*     3.6    28.5    -      -       +      -
     76T  ASN*     2.8    25.9    +      -       -      +
     79T  PHE*     3.9    10.3    -      +       +      -
     80T  GLY      3.1    24.0    -      -       -      -
     81T  TYR      4.2     6.6    -      -       -      +
     82T  ASN      4.7     0.5    -      -       -      -
     83T  GLY*     1.3    81.7    +      -       -      +
     85T  ALA*     1.3    72.5    +      -       -      +
     86T  HIS*     4.4     4.5    -      -       +      -
    113T  VAL*     3.9    15.9    -      -       +      -
    114T  GLN      3.4     5.8    -      -       -      +
    115T  LEU*     3.9    17.9    -      -       +      -
    151T  LEU*     3.8    35.4    -      -       +      -
    155T  LEU*     3.8    17.0    -      -       +      -
    119U  SER*     4.7     3.1    -      -       -      -
    120U  TYR      4.4     0.5    -      -       -      +
    121U  HIS*     3.6    37.5    +      +       -      -
    157U  SER*     3.8    15.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 85 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26T  PHE*     3.5    20.4    -      -       +      -
     84T  TRP*     1.3    79.7    -      -       -      +
     86T  HIS*     1.3    56.7    +      -       -      +
    113T  VAL*     3.1     7.6    -      -       -      +
    114T  GLN      2.6    36.3    +      -       -      +
    120U  TYR*     3.1    50.0    -      -       +      +
    121U  HIS*     3.9     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 86 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84T  TRP*     4.4     2.3    -      -       +      -
     85T  ALA*     1.3    77.3    -      -       -      +
     87T  SER*     1.3    60.0    +      -       -      +
     88T  ILE*     5.6     0.4    -      -       +      -
    111T  VAL*     3.9    15.7    -      -       +      -
    112T  ARG      3.2     6.7    -      -       -      +
    113T  VAL*     3.7    10.5    -      -       +      -
    147T  VAL*     5.4     4.1    -      -       +      +
    151T  LEU*     3.6    44.4    -      -       +      +
    120U  TYR*     3.3    13.9    +      -       -      -
    121U  HIS*     2.8    42.7    +      -       +      -
    122U  GLU      2.9    44.2    +      -       -      -
    123U  ASP*     4.3     7.4    +      -       +      -
    157U  SER*     3.7    15.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 87 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86T  HIS*     1.3    74.6    -      -       -      +
     88T  ILE*     1.3    67.8    +      -       -      +
     89T  THR*     3.6     2.1    +      -       -      -
    111T  VAL*     3.3     6.9    -      -       -      +
    112T  ARG*     2.8    45.9    +      -       -      +
    112U  ARG*     5.0     6.3    -      -       -      -
    120U  TYR*     3.5    24.0    +      -       -      -
    122U  GLU*     3.6    17.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 88 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86T  HIS*     5.6     0.2    -      -       +      -
     87T  SER*     1.3    72.9    -      -       -      +
     89T  THR*     1.3    65.1    +      -       -      +
     90T  GLN*     4.0    22.2    -      -       -      +
     91T  GLN*     4.2     4.5    -      -       +      +
    109T  ALA*     4.9     2.2    -      -       +      -
    110T  PHE      3.5     8.5    -      -       -      +
    111T  VAL*     4.5     6.7    -      -       +      +
    147T  VAL*     3.7    33.9    -      -       +      -
     89U  THR*     5.9     1.4    -      -       -      +
    110U  PHE*     4.0    21.7    -      -       +      -
    122U  GLU*     3.1    32.0    +      -       +      +
    123U  ASP*     3.8    33.0    -      -       -      +
    124U  VAL*     3.8     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 89 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88S  ILE      5.7     2.5    -      -       -      +
     87T  SER*     3.6     3.0    +      -       -      -
     88T  ILE*     1.3    74.5    -      -       -      +
     90T  GLN*     1.3    64.9    +      -       +      +
    110T  PHE*     2.6    18.7    +      -       +      -
    112T  ARG*     3.8    16.3    -      -       -      +
    122T  GLU*     2.8    32.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 90 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88T  ILE*     3.3     6.2    -      -       -      -
     89T  THR*     1.3    88.3    -      -       +      +
     91T  GLN*     1.3    68.6    +      -       -      +
     92T  ASN*     5.0    11.3    +      -       +      +
    110T  PHE*     2.7    54.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 91 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88T  ILE*     4.2     5.9    -      -       +      +
     90T  GLN*     1.3    79.9    -      -       -      +
     92T  ASN*     1.3    63.8    +      -       -      +
     93T  VAL      4.5     0.2    +      -       -      -
    107T  VAL*     3.8    14.1    -      -       +      +
    108T  CYS      3.4     8.7    -      -       -      +
    109T  ALA*     3.7    10.0    -      -       +      +
    143T  ARG*     2.6    72.1    +      -       -      +
    147T  VAL*     3.3    17.4    -      -       -      +
    110U  PHE*     3.5    33.8    -      -       +      -
    124U  VAL*     3.8     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 92 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143S  ARG*     4.9     5.0    -      -       -      +
     90T  GLN*     4.3    13.9    -      -       -      +
     91T  GLN*     1.3    74.9    -      -       -      +
     93T  VAL*     1.3    73.1    +      -       -      +
     94T  ASP*     3.1    26.5    +      -       -      +
    107T  VAL*     3.7     2.2    -      -       -      -
    108T  CYS*     2.9    46.7    +      -       -      -
    110T  PHE*     5.7     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 93 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91T  GLN      4.3     0.4    +      -       -      -
     92T  ASN*     1.3    79.9    +      -       -      +
     94T  ASP*     1.3    66.2    +      -       -      +
     95T  PHE*     3.9     9.6    -      -       -      +
     96T  VAL*     3.8    28.7    -      -       +      -
    106T  GLY      3.9     2.9    -      -       -      -
    107T  VAL*     3.7    22.7    -      -       +      -
    139T  LEU*     4.2     7.4    -      -       +      -
    143T  ARG*     3.2    39.4    -      -       -      +
     94U  ASP*     5.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 94 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93S  VAL*     5.2     0.2    -      -       -      +
    139S  LEU*     3.9    11.5    -      -       +      +
    143S  ARG*     2.7    34.7    +      -       -      -
     92T  ASN*     3.1    23.9    +      -       -      +
     93T  VAL*     1.3    74.2    -      -       -      +
     95T  PHE*     1.3    68.8    +      -       +      +
    106T  GLY      2.8    16.5    +      -       -      +
    108T  CYS*     3.9     1.8    -      -       -      -
    126T  TYR*     2.9    34.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 95 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135S  LYS*     3.6    22.7    -      -       +      +
    136S  ALA*     3.6    30.3    -      -       +      -
    139S  LEU*     3.5    33.0    -      -       +      -
     93T  VAL*     3.4     4.1    -      -       -      +
     94T  ASP*     1.3    81.2    -      -       +      +
     96T  VAL*     1.3    69.3    +      -       -      +
     97T  ASP*     3.1    27.8    -      -       -      +
    104T  TYR*     3.4    28.7    -      -       +      -
    105T  VAL*     3.5     3.1    -      -       -      +
    106T  GLY*     3.3    41.4    +      -       -      +
    126T  TYR*     3.7     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 96 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93T  VAL*     3.8    18.4    -      -       +      -
     95T  PHE*     1.3    79.6    -      -       -      +
     97T  ASP*     1.3    65.6    +      -       -      +
     98T  LEU      4.3     0.3    +      -       -      -
    103T  PHE*     4.2    11.9    -      -       +      -
    104T  TYR      3.7     3.6    -      -       -      -
    105T  VAL*     3.9    15.9    -      -       +      -
    135T  LYS*     3.8    29.2    -      -       +      +
    139T  LEU*     3.9    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 97 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135S  LYS*     2.9    38.2    +      -       -      -
     95T  PHE*     3.1    12.6    -      -       -      +
     96T  VAL*     1.3    80.0    +      -       -      +
     98T  LEU*     1.3    61.8    +      -       -      +
     99T  ASN*     4.1    11.7    -      -       -      +
    102T  LYS      3.7     0.5    -      -       -      +
    103T  PHE*     3.3     9.2    -      -       -      -
    104T  TYR*     2.9    44.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 98 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96T  VAL      4.3     0.4    +      -       -      -
     97T  ASP*     1.3    73.0    -      -       -      +
     99T  ASN*     1.3    63.7    +      -       -      +
    100T  ASN      4.1     1.1    +      -       -      +
    101T  GLY*     3.6    30.7    -      -       -      +
    102T  LYS      3.4    16.4    -      -       -      +
    103T  PHE*     3.7    35.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 99 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97T  ASP*     4.1    10.6    -      -       -      +
     98T  LEU*     1.3    76.7    -      -       -      +
    100T  ASN*     1.3    84.5    +      -       -      +
    101T  GLY      3.2     0.9    -      -       -      -
    102T  LYS*     2.9    24.6    +      -       -      +
    104T  TYR*     3.7    33.6    +      -       +      +
----------------------------------------------------------
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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