Contacts of the strand formed by residues 189 - 198 (chain A) in PDB entry 3I5D


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 THR 189 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  LYS      3.8     1.6    -      -       -      +
     71A  VAL*     3.4     3.1    -      -       -      -
     72A  LYS*     2.7    52.7    +      -       +      +
    187A  ASN      4.9     3.1    -      -       -      +
    188A  PHE*     1.3    81.0    -      -       -      +
    190A  VAL*     1.3    57.1    +      -       -      +
    191A  LEU      4.1     0.2    -      -       -      -
    221A  VAL*     5.1     7.7    -      -       +      +
    232A  ILE*     2.9    30.6    +      -       +      +
    233A  PHE      3.1    14.5    +      -       -      -
    234A  ARG*     4.0     5.9    +      -       -      -
    235A  LEU*     4.4     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 190 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  THR*     4.0    13.0    -      -       -      -
     70A  LYS      3.6     3.4    -      -       -      +
     71A  VAL*     3.7    26.0    -      -       +      +
    102A  PHE*     3.7    19.1    -      -       +      -
    189A  THR*     1.3    74.2    +      -       -      +
    191A  LEU*     1.3    73.8    +      -       -      +
    192A  ILE*     3.6    22.0    +      -       +      +
    231A  PRO      3.6     0.7    -      -       -      +
    232A  ILE*     3.6     3.0    -      -       -      -
    233A  PHE*     2.8    38.2    +      -       +      +
    235A  LEU*     4.1    17.5    -      -       +      +
    238A  ILE*     4.2     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 191 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  THR      3.5     1.0    -      -       -      +
     69A  THR*     3.1     7.7    -      -       -      -
     70A  LYS*     2.9    44.3    +      -       +      +
    189A  THR      4.1     0.8    +      -       -      -
    190A  VAL*     1.3    72.1    -      -       -      +
    192A  ILE*     1.3    66.2    +      -       -      +
    193A  LYS*     3.9    22.4    -      -       +      -
    208A  ILE*     5.9     0.7    -      -       +      -
    231A  PRO*     3.9    17.7    -      -       +      +
    232A  ILE*     3.7    32.6    -      -       +      +
    291C  VAL*     3.9    24.2    -      -       +      -
    292C  ALA*     3.5    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  VAL*     5.2     1.8    -      -       +      -
     68A  THR      3.5     4.5    -      -       -      +
     69A  THR*     4.4     5.8    -      -       +      -
    102A  PHE*     5.2     2.5    -      -       +      -
    190A  VAL*     3.8    28.0    -      -       +      +
    191A  LEU*     1.3    79.0    -      -       -      +
    193A  LYS*     1.3    61.4    +      -       -      +
    194A  ASN*     5.2     0.4    -      -       +      -
    207A  ASN*     2.7    29.8    +      -       -      +
    231A  PRO*     3.2    18.0    +      -       -      +
    233A  PHE*     3.8    25.3    -      -       +      -
    238A  ILE*     5.1     0.9    -      -       +      -
    258A  VAL*     4.3    24.2    -      -       +      -
    260A  ILE*     4.3    22.4    -      -       +      -
    277A  TYR*     5.8     0.4    -      -       +      -
    324A  VAL*     4.5    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  VAL*     3.3     6.2    -      -       -      +
     68A  THR*     2.8    54.5    +      -       +      +
    191A  LEU*     3.9    24.9    -      -       +      -
    192A  ILE*     1.3    77.0    -      -       -      +
    194A  ASN*     1.3    59.9    +      -       -      +
    195A  ASN      4.3     0.9    -      -       -      -
    207A  ASN*     3.6     5.2    -      -       -      +
    208A  ILE*     3.6    26.7    -      -       +      -
    231A  PRO*     6.2     0.2    -      -       +      -
    283C  ASP*     4.7     9.7    -      -       -      +
    284C  ASN*     4.6    13.3    +      -       -      +
    290C  ASN*     3.4    24.2    -      -       -      +
    291C  VAL      3.5    18.6    +      -       -      +
    292C  ALA*     4.0    12.8    +      -       +      +
    293C  PRO*     5.1     0.8    -      -       -      +
    294C  GLY      5.2     2.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  SER*     3.2    17.2    +      -       -      -
     66A  SER      2.9    20.7    +      -       -      -
     67A  VAL*     3.7    12.2    -      -       +      +
    192A  ILE*     5.2     0.4    -      -       +      -
    193A  LYS*     1.3    76.7    -      -       -      +
    195A  ASN*     1.3    64.3    +      -       -      +
    196A  ILE*     3.4     4.9    +      -       -      +
    206A  ARG*     3.5     3.5    -      -       -      -
    207A  ASN*     2.6    47.2    +      -       +      +
    260A  ILE*     3.8    14.9    -      -       +      +
    262A  TRP*     3.0    28.6    +      -       -      -
    326A  VAL*     3.5    14.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  SER      3.9     0.5    -      -       -      -
     66A  SER*     3.1    35.6    +      -       -      +
    193A  LYS      4.3     0.6    -      -       -      -
    194A  ASN*     1.3    74.3    +      -       -      +
    196A  ILE*     1.3    87.1    +      -       -      +
    204A  ASN*     4.6     2.6    -      -       -      +
    205A  LYS      3.7     7.9    -      -       -      +
    206A  ARG*     4.3    21.0    -      -       +      +
    280C  ARG*     4.1    13.8    +      -       -      +
    281C  ARG      4.7     1.0    +      -       -      -
    282C  LEU*     2.8    60.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  VAL*     3.6    20.6    -      -       +      -
     64A  LEU      3.5     3.6    -      -       -      -
     65A  SER*     3.7    13.0    -      -       -      +
    194A  ASN*     3.4    18.4    -      -       -      +
    195A  ASN*     1.3    84.0    +      -       -      +
    197A  ARG*     1.3    62.5    +      -       -      +
    198A  TYR*     4.2    22.7    -      -       +      -
    203A  PHE*     5.1     1.3    -      -       +      -
    204A  ASN*     3.0    20.0    -      -       -      +
    205A  LYS*     3.0    34.1    +      -       +      +
    262A  TRP*     3.5    52.5    -      -       +      +
    273A  CYS*     5.3     0.2    -      -       -      -
    280C  ARG*     5.1     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  VAL*     4.0     3.0    -      -       -      -
     64A  LEU*     3.0    38.9    +      -       +      +
    196A  ILE*     1.3    77.7    -      -       -      +
    198A  TYR*     1.3    66.3    +      -       -      +
    199A  PRO*     3.5     5.7    -      -       +      +
    203A  PHE      3.4     7.0    -      -       -      +
    204A  ASN*     3.5    17.5    -      -       +      +
    259C  GLN*     5.8     0.2    -      -       -      +
    280C  ARG*     3.6    24.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  ASP*     3.3    37.5    -      -       +      +
     62A  THR      3.9     8.1    -      -       -      -
     63A  VAL*     3.5    22.1    -      -       +      +
    196A  ILE*     4.2    13.7    -      -       +      -
    197A  ARG*     1.3    71.9    -      -       -      +
    199A  PRO*     1.3    70.7    -      -       -      +
    200A  LYS      3.3     0.4    -      -       -      -
    201A  PHE*     3.3    15.1    +      +       +      -
    202A  ASN*     3.1    17.8    +      -       -      -
    203A  PHE*     2.7    48.5    +      +       +      +
    262A  TRP*     2.7    38.3    +      -       +      +
    264A  CYS*     4.3     7.2    +      -       +      +
    266A  LEU*     4.7     1.6    -      -       +      -
    329A  GLN      3.7     3.1    +      -       -      -
    330A  ALA*     3.7    27.1    -      -       +      +
----------------------------------------------------------
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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