Contacts of the strand formed by residues 71 - 82 (chain O) in PDB entry 5IY8


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 VAL 71 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66O  ARG      4.5     0.2    -      -       -      -
     67O  PHE*     3.1     6.9    -      -       -      -
     68O  CYS      2.8    34.1    +      -       -      +
     69O  ASP*     3.3    19.7    -      -       +      +
     70O  ASN*     1.3    78.3    -      -       -      +
     72O  TRP*     1.3    72.6    +      -       -      +
     73O  THR*     3.9     8.1    +      -       -      +
     96O  VAL*     3.9    13.9    -      -       +      -
     97O  ALA      3.7     2.7    -      -       -      +
     98O  CYS*     3.5    31.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 72 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339N  TYR*     3.5    45.4    -      +       +      -
    342N  ILE*     3.8    29.0    -      -       +      +
    349N  TRP*     5.1     0.7    -      +       -      -
     65O  TYR*     5.2     0.4    -      +       -      -
     66O  ARG      3.3    16.8    -      -       -      -
     67O  PHE*     3.3    44.8    -      +       +      -
     71O  VAL*     1.3    74.4    -      -       -      +
     73O  THR*     1.3    62.1    +      -       -      +
     74O  PHE*     3.2    43.5    -      +       +      -
     95O  ILE      4.4     0.4    -      -       -      -
     96O  VAL*     3.3     6.2    -      -       -      +
     97O  ALA*     2.8    46.7    +      -       +      +
    191P  GLU*     3.1    40.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 73 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64O  THR*     5.8     0.2    -      -       -      +
     65O  TYR*     3.2     1.9    -      -       -      -
     66O  ARG*     2.5    71.6    +      -       -      +
     71O  VAL*     3.9    12.7    +      -       -      +
     72O  TRP*     1.3    77.6    +      -       -      +
     74O  PHE*     1.3    68.6    +      -       -      +
     75O  VAL*     5.6     3.4    -      -       +      -
     94O  LYS*     6.0     4.3    -      -       +      -
     95O  ILE      3.6     1.8    -      -       -      -
     96O  VAL*     4.2    20.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 74 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342N  ILE*     4.6    24.0    -      -       +      -
    349N  TRP*     6.1     2.7    -      +       -      -
    351N  PHE*     4.7    18.8    -      +       -      -
    353N  LEU*     5.4     5.8    -      -       +      -
     62O  LEU*     4.6     6.1    -      -       +      -
     64O  THR*     3.7     4.9    -      -       -      +
     65O  TYR*     3.5    22.2    -      -       +      +
     72O  TRP*     3.2    51.6    -      +       +      -
     73O  THR*     1.3    83.2    -      -       -      +
     75O  VAL*     1.3    72.3    +      -       -      +
     76O  LEU*     3.6    21.1    -      -       +      -
     94O  LYS*     3.3     5.9    -      -       -      +
     95O  ILE*     2.6    54.8    +      -       +      +
     97O  ALA*     5.6     2.0    -      -       +      -
    191P  GLU*     5.3     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 75 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326N  GLN*     3.7    24.7    -      -       +      +
    327N  GLU*     4.3     6.5    -      -       +      +
    332N  GLU*     3.7    15.5    -      -       -      +
     62O  LEU*     4.0     0.3    -      -       -      +
     63O  ASN*     3.1    11.3    +      -       +      +
     64O  THR*     3.1    52.1    +      -       +      +
     73O  THR*     5.6     3.8    -      -       +      -
     74O  PHE*     1.3    81.5    -      -       -      +
     76O  LEU*     1.3    62.8    +      -       -      +
     92O  LYS*     4.0    19.1    -      -       +      -
     93O  VAL      3.3     9.6    -      -       -      +
     94O  LYS*     3.7    16.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 76 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    351N  PHE*     4.6     5.2    -      -       +      -
    374N  ALA*     4.1    24.9    -      -       +      -
     58O  PHE*     4.4    23.6    -      -       +      -
     60O  GLY*     4.9     4.3    -      -       -      +
     61O  SER      3.6     9.0    -      -       -      +
     62O  LEU*     3.8    14.4    -      -       +      -
     63O  ASN*     4.0     0.9    -      -       -      +
     74O  PHE*     3.6    30.1    -      -       +      -
     75O  VAL*     1.3    73.3    -      -       -      +
     77O  ASN*     1.3    60.7    +      -       -      +
     79O  VAL*     3.6    21.5    -      -       +      +
     92O  LYS*     3.1     7.8    -      -       -      +
     93O  VAL*     2.7    37.8    +      -       +      +
     95O  ILE*     3.6    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 77 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61O  SER*     2.7    44.2    +      -       -      +
     63O  ASN*     3.9    25.5    +      -       +      +
     76O  LEU*     1.3    73.5    -      -       -      +
     78O  ASP*     1.3    92.9    +      -       -      +
     79O  VAL*     3.4     2.8    +      -       -      +
     91O  ASP*     2.8    24.3    -      -       -      +
     92O  LYS*     4.2     6.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 78 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59O  ARG      4.2     0.3    -      -       -      +
     60O  GLY*     3.6    12.5    -      -       -      -
     61O  SER*     3.8     8.6    +      -       -      -
     77O  ASN*     1.3    92.2    +      -       -      +
     79O  VAL*     1.3    60.6    +      -       -      +
     80O  GLU*     4.0     0.7    +      -       -      +
     89O  LYS*     4.3    16.8    +      -       -      -
     90O  VAL      4.0     3.1    -      -       -      -
     91O  ASP*     2.6    14.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 79 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58O  PHE*     4.6     9.4    -      -       +      -
     59O  ARG      3.8     9.4    -      -       -      +
     60O  GLY*     4.2     2.9    -      -       -      -
     76O  LEU*     3.6    35.4    -      -       +      +
     77O  ASN      3.9     1.8    -      -       -      +
     78O  ASP*     1.3    76.5    -      -       -      +
     80O  GLU*     1.3    64.5    +      -       -      +
     81O  PHE*     3.3    33.7    -      -       +      -
     89O  LYS*     3.7     7.3    +      -       -      +
     90O  VAL*     3.0    38.9    +      -       +      +
     92O  LYS*     4.8     0.2    -      -       -      -
     93O  VAL*     3.5    28.5    -      -       +      +
     95O  ILE*     6.1     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 80 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57O  ASN      3.8     0.2    -      -       -      +
     58O  PHE*     3.2     3.8    -      -       -      -
     59O  ARG*     2.8    37.3    +      -       +      +
     78O  ASP      5.2     0.7    -      -       -      +
     79O  VAL*     1.3    77.0    -      -       -      +
     81O  PHE*     1.3    63.0    +      -       -      +
     82O  ARG*     2.4    53.4    +      -       +      +
     87O  LEU*     4.0    14.1    -      -       +      +
     88O  ILE      3.9     2.5    -      -       -      -
     89O  LYS*     2.6    46.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 81 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    335N  VAL*     4.3    10.5    -      -       +      -
    358N  MET*     3.5    28.5    -      -       +      -
    360N  LEU*     3.3    42.0    -      -       +      -
     56O  VAL*     4.2    11.9    -      -       +      -
     57O  ASN      3.6     2.2    -      -       -      -
     58O  PHE*     3.3    28.0    -      +       +      -
     79O  VAL*     3.3    26.2    -      -       +      -
     80O  GLU*     1.3    70.8    -      -       -      +
     82O  ARG*     1.3    60.7    +      -       -      +
     87O  LEU*     3.5     3.3    -      -       -      +
     88O  ILE*     2.7    60.1    +      -       +      +
     90O  VAL*     5.2     2.7    -      -       +      -
     93O  VAL*     4.4    15.0    -      -       +      -
     95O  ILE*     5.2     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 82 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56O  VAL*     3.6     2.7    -      -       -      +
     57O  ASN*     2.4    59.2    +      -       +      +
     58O  PHE*     5.4     1.1    -      -       -      +
     59O  ARG*     5.2    23.9    -      -       -      +
     80O  GLU*     2.4    47.5    +      -       -      +
     81O  PHE*     1.3    75.0    -      -       -      +
     83O  GLU*     1.3    61.9    +      -       -      +
     86O  GLU      4.3     2.0    -      -       -      -
     87O  LEU*     3.8    16.7    -      -       +      +
     88O  ILE*     5.2     0.2    -      -       -      -
----------------------------------------------------------
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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