Contacts of the strand formed by residues 84 - 93 (chain G) in PDB entry 5IYB


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 84 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99D  CYS*     3.9    17.1    -      -       -      -
    102D  ASN*     6.0     0.7    -      -       -      +
    103D  LEU*     3.6    37.4    -      -       +      +
    114D  LEU*     4.2    30.1    -      -       +      +
     82G  GLY      3.7     1.8    +      -       -      +
     83G  GLU*     1.3    73.4    -      -       -      +
     85G  VAL*     1.3    70.9    +      -       -      +
    144G  ARG*     4.9     4.5    -      -       +      -
    145G  LEU      3.4    13.5    -      -       -      +
    146G  LYS*     3.6    36.8    -      -       +      -
    167G  TYR      5.5     0.4    -      -       -      +
    168G  LEU*     4.0    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 85 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67D  TYR*     5.3     2.0    -      -       -      +
    102D  ASN*     6.6     0.4    -      -       +      -
    103D  LEU*     4.3     4.3    -      -       -      -
     77G  PHE*     6.2     3.4    -      -       +      -
     79G  PRO*     6.0     3.1    -      -       +      -
     83G  GLU*     3.8    28.9    -      -       +      +
     84G  VAL*     1.3    80.8    -      -       -      +
     86G  ASP*     1.3    67.9    +      -       -      +
     87G  ALA      3.9     0.3    +      -       -      -
    101G  ILE*     4.0    28.0    -      -       +      -
    144G  ARG*     3.6     1.3    -      -       -      +
    145G  LEU*     2.9    53.1    +      -       +      +
    147G  ILE*     4.2    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 86 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67D  TYR*     3.1    24.3    +      -       -      +
     71D  PHE*     3.5    25.6    -      -       +      +
     73D  ARG*     3.2    26.3    +      -       -      -
    102D  ASN      4.1     9.4    -      -       -      +
    103D  LEU*     3.8    15.9    -      -       -      +
     85G  VAL*     1.3    74.5    -      -       -      +
     87G  ALA*     1.3    59.8    +      -       -      +
    101G  ILE*     3.6     6.1    -      -       -      +
    142G  GLU*     6.1     0.2    -      -       +      -
    143G  ILE      3.4     7.4    -      -       -      +
    144G  ARG*     3.5    20.8    -      -       -      +
    171G  VAL*     4.1    14.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 87 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71D  PHE*     4.1     3.5    -      -       -      -
     85G  VAL      3.9     0.6    +      -       -      +
     86G  ASP*     1.3    75.4    -      -       -      +
     88G  VAL*     1.3    64.5    +      -       -      +
     99G  THR*     3.4    30.3    -      -       +      +
    100G  GLU      3.7    11.7    -      -       -      +
    101G  ILE*     4.1     9.0    -      -       +      -
    142G  GLU*     3.4     5.2    -      -       -      -
    143G  ILE*     2.8    33.0    +      -       +      +
    145G  LEU*     3.7    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 88 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67D  TYR*     5.3     3.6    -      -       +      -
     70D  ARG*     3.2    42.0    -      -       -      +
     71D  PHE*     3.5    26.9    -      -       +      -
     87G  ALA*     1.3    75.4    -      -       -      +
     89G  VAL*     1.3    75.5    +      -       -      +
     90G  THR*     3.4     4.1    +      -       +      +
     99G  THR*     3.1     3.8    -      -       -      -
    100G  GLU*     2.7    42.3    +      -       +      +
    140G  ASP*     3.7     4.5    -      -       -      +
    141G  ASP      3.1    14.6    -      -       -      +
    142G  GLU*     3.9     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 89 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88G  VAL*     1.3    72.6    -      -       -      +
     90G  THR*     1.3    60.4    +      -       -      +
     91G  GLN      3.8    19.3    -      -       -      +
     92G  VAL*     4.6     1.3    -      -       +      -
     97G  LEU*     3.8    31.6    -      -       +      -
     98G  PHE      3.2    13.5    -      -       -      +
     99G  THR*     4.0     1.3    -      -       +      +
    137G  ILE*     3.9    17.9    -      -       +      -
    138G  GLN      3.4    25.1    -      -       -      +
    140G  ASP*     2.6    34.7    +      -       -      -
    141G  ASP*     2.8    19.0    +      -       +      +
    143G  ILE*     4.0    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 90 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88G  VAL*     3.9    12.6    -      -       +      +
     89G  VAL*     1.3    77.0    -      -       -      +
     91G  GLN*     1.3    65.4    +      -       -      +
     98G  PHE*     3.1    29.2    +      -       -      +
     99G  THR      4.3     1.7    +      -       -      -
    100G  GLU*     4.0    28.7    -      -       +      +
    139G  GLN*     3.6    22.0    +      -       -      +
    140G  ASP      4.8     0.9    -      -       -      +
    145Q  PHE*     5.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 91 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89G  VAL*     3.8     2.8    -      -       -      -
     90G  THR*     1.3    83.2    +      -       -      +
     92G  VAL*     1.3    93.2    +      -       -      +
     93G  ASN*     4.2     1.2    +      -       +      -
     96G  GLY      4.3     0.2    -      -       -      +
     97G  LEU*     3.8     8.7    -      -       -      +
     98G  PHE*     3.2    46.1    +      -       +      +
    126G  PRO*     5.8     0.9    -      -       -      +
    139G  GLN*     2.5    38.7    +      -       -      +
    145Q  PHE*     3.4    38.9    -      -       +      -
    147Q  PRO*     4.9     5.7    +      -       -      +
    150Q  GLY*     3.9    16.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 92 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89G  VAL*     4.6     1.6    -      -       +      -
     91G  GLN*     1.3    86.8    +      -       -      +
     93G  ASN*     1.3    61.1    +      -       -      +
     96G  GLY      4.4     1.3    -      -       -      -
     97G  LEU*     4.3     8.1    -      -       +      -
    119G  PHE*     4.1    13.5    -      -       +      -
    126G  PRO*     3.2    43.3    -      -       +      +
    127G  CYS*     3.8     6.5    -      -       -      +
    128G  TYR*     4.0    19.7    -      -       +      -
    137G  ILE      4.0    19.1    -      -       -      +
    138G  GLN*     4.5    13.7    -      -       -      -
    139G  GLN*     5.0     3.3    -      -       +      +
    150Q  GLY      3.4    16.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 93 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91G  GLN*     5.4     2.9    -      -       +      +
     92G  VAL*     1.3    75.0    -      -       -      +
     94G  LYS*     1.3    84.0    +      -       -      +
     95G  VAL*     2.9    13.0    +      -       -      +
     96G  GLY      3.1    20.3    +      -       -      +
     98G  PHE*     5.5     3.8    -      -       +      -
    119G  PHE*     4.0     9.1    -      -       -      -
    128G  TYR*     2.9    25.1    +      -       -      -
    150Q  GLY      4.2     6.5    -      -       -      +
    151Q  THR*     3.1    23.9    -      -       -      +
    152Q  PHE*     3.2    57.1    -      -       +      +
    161Q  VAL      5.8     0.8    +      -       -      -
----------------------------------------------------------
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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