Contacts of the strand formed by residues 84 - 99 (chain I) in PDB entry 5XRZ


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 I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26I  PHE*     3.9     1.6    -      -       -      -
     72I  ILE*     4.3     7.9    -      -       +      -
     75I  ALA*     3.8    24.7    -      -       +      -
     76I  ASN*     3.1    31.9    +      -       -      +
     79I  PHE*     3.8    18.2    -      -       +      -
     80I  GLY      3.0    24.5    -      -       -      -
     81I  TYR      4.2     3.1    +      -       -      +
     83I  GLY*     1.3    77.9    -      -       -      +
     85I  ALA*     1.3    72.8    +      -       -      +
     86I  HIS*     4.2     4.9    -      -       +      -
    113I  VAL*     3.9    16.6    -      -       +      -
    114I  GLN      3.5     6.3    -      -       -      +
    115I  LEU*     4.1     7.6    -      -       +      -
    151I  LEU*     3.8    39.0    -      -       +      -
    155I  LEU*     4.1    12.1    -      -       +      -
    119J  SER*     3.4    15.6    +      -       -      -
    121J  HIS*     3.5    28.0    +      +       -      -
    157J  SER*     3.4    27.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 85 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26I  PHE*     3.5    19.7    -      -       +      -
     84I  TRP*     1.3    82.1    -      -       -      +
     86I  HIS*     1.3    58.6    +      -       -      +
    112I  ARG      3.8     0.3    -      -       -      +
    113I  VAL*     3.1     4.2    -      -       -      +
    114I  GLN*     2.6    37.9    +      -       -      +
    120J  TYR*     3.1    48.0    -      -       +      +
    121J  HIS*     3.7     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 86 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84I  TRP*     4.2     3.9    -      +       +      -
     85I  ALA*     1.3    74.6    -      -       -      +
     87I  SER*     1.3    63.1    +      -       -      +
     88I  ILE*     5.5     0.4    -      -       +      -
    111I  VAL*     3.7    21.1    -      -       +      -
    112I  ARG      3.2     9.6    -      -       -      +
    113I  VAL*     4.2     4.0    -      -       +      -
    147I  VAL*     5.0     4.9    -      -       +      +
    151I  LEU*     3.6    37.2    -      -       +      +
    120J  TYR*     3.3    20.9    +      -       -      +
    121J  HIS*     2.9    34.3    +      -       +      -
    122J  GLU      2.8    47.6    +      -       -      -
    123J  ASP*     4.2    11.4    +      -       +      -
    154J  ALA      5.4     0.4    -      -       -      -
    157J  SER*     3.9    14.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 87 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86I  HIS*     1.3    78.1    -      -       -      +
     88I  ILE*     1.3    66.3    +      -       -      +
     89I  THR*     3.5     2.3    +      -       -      -
    111I  VAL*     3.3     7.6    -      -       -      +
    112I  ARG*     2.9    49.2    +      -       -      +
    112J  ARG*     5.0     4.5    -      -       -      -
    120J  TYR*     3.5    24.6    +      -       -      -
    122J  GLU*     3.6    15.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 88 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86I  HIS*     5.5     0.4    -      -       +      -
     87I  SER*     1.3    72.1    -      -       -      +
     89I  THR*     1.3    68.1    +      -       -      +
     90I  GLN*     4.1    20.1    -      -       -      +
     91I  GLN*     4.2     5.2    -      -       +      +
    109I  ALA*     4.9     0.4    -      -       +      -
    110I  PHE      3.5    10.1    -      -       -      +
    111I  VAL*     4.7     3.6    -      -       +      +
    147I  VAL*     3.7    20.4    -      -       +      -
     89J  THR*     5.9     1.2    -      -       -      +
    110J  PHE*     3.7    35.7    -      -       +      -
    122J  GLU*     2.7    37.2    +      -       +      +
    123J  ASP*     3.7    21.1    -      -       -      +
    124J  VAL*     3.7    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 89 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88H  ILE      5.8     1.8    -      -       -      +
     87I  SER*     3.5     3.0    +      -       -      -
     88I  ILE*     1.3    74.0    -      -       -      +
     90I  GLN*     1.3    65.7    +      -       +      +
    110I  PHE*     2.7    17.5    +      -       +      -
    112I  ARG*     3.8    22.0    -      -       -      +
    122I  GLU*     3.0    28.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 90 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88I  ILE*     3.4     5.3    -      -       -      -
     89I  THR*     1.3    87.5    -      -       +      +
     91I  GLN*     1.3    70.9    +      -       -      +
     92I  ASN*     4.9     9.1    -      -       +      +
    110I  PHE*     2.9    48.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 91 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88I  ILE*     4.2     5.7    -      -       +      +
     90I  GLN*     1.3    80.1    -      -       -      +
     92I  ASN*     1.3    63.1    +      -       -      +
    107I  VAL*     4.2     8.6    -      -       +      +
    108I  CYS      3.5    11.9    +      -       -      +
    109I  ALA*     3.9     6.5    -      -       +      +
    143I  ARG*     2.4    67.9    +      -       -      +
    147I  VAL*     3.3    30.9    -      -       -      +
    110J  PHE*     3.3    26.9    -      -       +      -
    124J  VAL*     3.7     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 92 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143H  ARG*     4.9     5.1    -      -       -      +
     90I  GLN*     5.0    12.1    -      -       +      +
     91I  GLN*     1.3    75.2    -      -       -      +
     93I  VAL*     1.3    78.7    +      -       -      +
     94I  ASP*     3.4    15.2    +      -       -      +
    107I  VAL*     4.7     1.6    -      -       -      -
    108I  CYS*     3.2    41.3    +      -       -      +
    110I  PHE*     5.8     2.0    -      -       +      -
    143I  ARG*     5.4     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 93 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92I  ASN*     1.3    82.5    +      -       -      +
     94I  ASP*     1.3    66.3    +      -       -      +
     95I  PHE      3.8    15.7    -      -       -      +
     96I  VAL*     4.0    16.2    -      -       +      -
    106I  GLY      3.7     5.2    -      -       -      +
    107I  VAL*     3.7    28.5    -      -       +      -
    139I  LEU*     4.4     9.6    -      -       +      -
    143I  ARG*     3.8    32.7    -      -       -      +
     94J  ASP*     4.8     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 94 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93H  VAL*     4.8     5.5    -      -       -      +
    139H  LEU*     3.8    19.4    -      -       +      +
    143H  ARG*     2.8    34.4    +      -       -      -
     92I  ASN*     3.4    12.4    +      -       -      +
     93I  VAL*     1.3    74.8    -      -       -      +
     95I  PHE*     1.3    62.9    +      -       +      +
    106I  GLY      2.9    12.0    +      -       -      +
    108I  CYS*     3.9     4.2    +      -       -      +
    126I  TYR*     2.6    37.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 95 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135H  LYS*     3.5    34.8    -      -       +      +
    136H  ALA*     3.3    32.8    -      -       +      -
    139H  LEU*     3.6    32.5    -      -       +      -
     93I  VAL*     3.5     3.6    -      -       -      +
     94I  ASP*     1.3    80.3    -      -       +      +
     96I  VAL*     1.3    69.6    +      -       -      +
     97I  ASP*     3.1    25.8    -      -       -      +
    104I  TYR*     3.6    21.1    -      -       +      -
    105I  VAL*     3.6     2.0    -      -       -      -
    106I  GLY*     3.1    50.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 96 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93I  VAL*     4.0     9.6    -      -       +      -
     95I  PHE*     1.3    80.7    -      -       -      +
     97I  ASP*     1.3    70.6    +      -       -      +
    103I  PHE*     4.6     5.6    -      -       +      -
    104I  TYR      3.5     4.5    -      -       -      -
    105I  VAL*     3.9    22.0    -      -       +      -
    135I  LYS*     4.1    28.0    -      -       +      +
    139I  LEU*     3.9    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 97 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135H  LYS*     3.5    23.2    +      -       -      -
     95I  PHE*     3.1    27.5    -      -       -      +
     96I  VAL*     1.3    82.8    +      -       -      +
     98I  LEU*     1.3    62.7    +      -       -      +
     99I  ASN*     4.3     8.1    -      -       -      +
    103I  PHE*     3.4    11.1    -      -       -      -
    104I  TYR*     2.8    43.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 98 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97I  ASP*     1.3    76.6    -      -       -      +
     99I  ASN*     1.3    68.2    +      -       -      +
    100I  ASN      4.0     1.6    +      -       -      +
    101I  GLY*     3.7    15.9    -      -       -      +
    102I  ALA      3.3    31.2    -      -       -      +
    103I  PHE*     3.6    36.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 99 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97I  ASP*     5.0     7.0    -      -       -      +
     98I  LEU*     1.3    81.9    +      -       -      +
    100I  ASN*     1.3    86.7    +      -       -      +
    101I  GLY      3.3     1.1    -      -       -      -
    102I  ALA*     2.9    25.5    +      -       -      +
    104I  TYR*     3.2    35.6    +      -       +      +
----------------------------------------------------------
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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