Contacts of the strand formed by residues 189 - 201 (chain A) in PDB entry 4OIP


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 ARG 189 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  SER*     2.6    55.2    +      -       -      +
      5A  LYS      4.1     6.9    +      -       -      +
      6A  LEU*     3.5    33.9    -      -       -      +
     29A  GLU*     4.5     5.8    +      -       -      -
    185A  ARG*     3.2    23.3    -      -       -      +
    186A  LEU*     3.0    28.9    +      -       -      +
    187A  GLY      4.3     0.7    -      -       -      +
    188A  GLN*     1.3    79.8    -      -       +      +
    190A  THR*     1.3    60.6    +      -       -      +
    192A  LEU*     3.8    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 190 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  ARG*     3.5    32.3    -      -       +      +
    188A  GLN      3.6     8.6    +      -       -      +
    189A  ARG*     1.3    77.3    -      -       -      +
    191A  ASP*     1.3    75.8    +      -       -      +
    192A  LEU*     3.2    11.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 191 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  ARG*     3.2    41.7    -      -       -      +
    183A  ASP*     3.3    17.3    +      -       -      +
    184A  THR      3.9     1.8    +      -       -      -
    190A  THR*     1.3    83.2    -      -       -      +
    192A  LEU*     1.3    60.4    +      -       -      +
    938C  LYS*     3.2    27.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 192 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  LEU*     4.5     5.6    -      -       +      -
     27A  PRO*     4.2    10.8    -      -       +      -
     28A  LEU      3.5    13.5    -      -       -      +
     29A  GLU*     4.2    17.3    -      -       -      +
     30A  ARG*     4.1    14.4    -      -       +      +
    184A  THR*     2.9    38.7    +      -       +      +
    186A  LEU*     3.7    35.0    -      -       +      +
    189A  ARG*     3.8    25.8    -      -       +      -
    190A  THR      3.9    12.8    -      -       -      +
    191A  ASP*     1.3    78.8    -      -       -      +
    193A  ASP*     1.3    58.4    +      -       -      +
    938C  LYS*     2.8    19.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 193 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  LEU      4.0     0.2    -      -       -      +
     27A  PRO*     3.6     1.9    -      -       -      +
     28A  LEU*     2.7    51.1    +      -       +      +
     29A  GLU      3.9     4.0    -      -       -      +
     30A  ARG*     4.1     0.9    -      -       -      -
     31A  GLY*     2.6    34.2    +      -       -      -
     32A  PHE      3.3     0.3    +      -       -      -
     33A  GLY*     3.3    22.7    +      -       -      +
    181A  VAL*     3.5    15.6    -      -       +      +
    182A  GLU      3.8     1.3    -      -       -      -
    184A  THR*     3.6     4.6    -      -       -      +
    192A  LEU*     1.3    72.7    -      -       -      +
    194A  LYS*     1.3    59.0    +      -       -      +
    195A  LEU      4.0     0.2    -      -       -      -
    938C  LYS*     2.4    42.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  ARG*     6.1     1.3    -      -       -      +
     24A  VAL*     3.8    21.5    -      -       +      -
     25A  LEU      3.8     3.4    -      -       -      -
     26A  GLU*     3.5    40.4    +      -       +      +
    180A  GLN      3.1     5.4    -      -       -      +
    181A  VAL*     3.5     1.4    -      -       -      -
    182A  GLU*     2.9    62.0    +      -       +      +
    183A  ASP      5.8     0.9    -      -       -      +
    184A  THR*     3.8    14.6    -      -       -      +
    193A  ASP*     1.3    72.9    -      -       -      +
    195A  LEU*     1.3    61.1    +      -       -      +
    196A  THR*     4.4     6.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  PHE      3.6     2.0    -      -       -      +
     24A  VAL*     3.1     6.8    -      -       -      +
     25A  LEU*     2.9    41.3    +      -       +      +
     28A  LEU*     3.8    21.1    -      -       +      -
     33A  GLY*     3.3    31.9    -      -       -      +
     36A  LEU*     3.9    16.8    -      -       +      -
     37A  GLY*     3.8    16.6    -      -       -      +
    179A  PHE*     3.6    28.0    -      -       +      -
    180A  GLN      3.5     4.9    -      -       -      +
    181A  VAL*     4.1     2.5    -      -       +      +
    193A  ASP      4.0     1.2    -      -       -      -
    194A  LYS*     1.3    69.7    -      -       -      +
    196A  THR*     1.3    75.1    +      -       -      +
    197A  LEU*     4.8    12.3    -      -       +      +
    225B  PHE*     5.2     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  ARG*     4.3     2.5    -      -       -      +
     22A  GLU*     4.6     4.3    -      -       +      -
     23A  PHE      3.4     8.1    -      -       -      +
     24A  VAL*     3.7    28.1    -      -       +      +
    179A  PHE*     3.1     7.0    -      -       -      -
    180A  GLN*     2.9    45.0    +      -       -      +
    182A  GLU*     4.5     7.3    +      -       -      -
    194A  LYS*     4.4     6.4    +      -       -      +
    195A  LEU*     1.3    79.3    +      -       -      +
    197A  LEU*     1.3    65.1    +      -       -      +
    198A  ARG*     3.7     4.3    +      -       +      +
    934C  PHE*     3.4    37.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  GLU*     3.3     5.0    -      -       -      -
     23A  PHE*     2.9    54.3    +      -       +      +
     37A  GLY*     4.1    15.0    -      -       -      +
     40A  LEU*     3.7    35.0    -      -       +      -
     41A  ARG      5.0     0.9    -      -       -      +
     44A  LEU*     5.6     1.3    -      -       +      -
    177A  VAL*     4.5    15.5    -      -       +      -
    178A  ALA      3.7     5.8    -      -       -      +
    179A  PHE*     3.6    22.4    -      -       +      -
    195A  LEU*     4.3    11.9    -      -       +      -
    196A  THR*     1.3    70.5    -      -       -      +
    198A  ARG*     1.3    62.6    +      -       -      +
    199A  ILE*     4.4     7.2    -      -       +      -
    211A  LEU*     3.7    20.6    -      -       +      -
    225B  PHE*     4.5     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  TYR*     3.1    22.5    +      -       -      +
     21A  GLY      3.5     4.3    -      -       -      -
     22A  GLU*     4.2     3.7    +      -       +      +
    176A  ARG*     5.4     0.2    -      -       -      +
    177A  VAL*     3.4     4.9    -      -       -      +
    178A  ALA*     2.9    45.3    +      -       +      +
    179A  PHE*     5.4     0.7    -      -       -      -
    180A  GLN*     5.7     3.6    -      -       +      +
    196A  THR*     4.4     8.3    -      -       +      +
    197A  LEU*     1.3    73.2    -      -       -      +
    199A  ILE*     1.3    61.7    +      -       -      +
    200A  TRP*     3.5    40.3    -      -       +      -
    863C  ASP*     4.7    18.2    +      -       -      +
    929C  ARG*     6.2     0.6    -      -       -      +
    932C  GLU*     3.0    35.5    +      -       -      +
    934C  PHE*     3.4    43.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  TYR*     3.2     6.6    -      -       -      -
     21A  GLY      2.9    37.2    +      -       -      +
     23A  PHE*     3.7    26.5    -      -       +      -
     44A  LEU*     3.7    26.0    -      -       +      -
    174A  VAL*     4.7     2.5    -      -       +      -
    176A  ARG      3.8     2.0    -      -       -      -
    177A  VAL*     4.0    20.6    -      -       +      -
    197A  LEU*     4.2    14.4    -      -       +      +
    198A  ARG*     1.3    78.3    -      -       -      +
    200A  TRP*     1.3    65.3    +      -       -      +
    201A  THR*     3.9    12.3    -      -       +      -
    207A  PRO*     3.5    36.0    -      -       +      +
    210A  ALA*     5.1     2.5    -      -       +      -
    211A  LEU*     4.2     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  GLU      3.5     4.7    -      -       -      +
     20A  TYR*     3.3    41.3    -      +       +      -
    174A  VAL*     3.6     3.5    -      -       -      +
    175A  ARG*     2.7    35.2    +      -       +      -
    176A  ARG*     2.9    89.6    +      -       +      +
    178A  ALA*     4.1     4.7    -      -       +      -
    198A  ARG*     3.5    60.1    -      -       +      -
    199A  ILE*     1.3    72.7    -      -       -      +
    201A  THR*     1.3    57.0    +      -       -      +
    863C  ASP      4.0     8.1    -      -       -      -
    932C  GLU*     6.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  ARG      3.1    17.3    +      -       -      -
     19A  GLU*     2.8    23.7    +      -       -      +
    173A  PRO      3.3    16.4    -      -       -      +
    174A  VAL*     4.1    14.8    -      -       +      -
    175A  ARG*     3.8    12.0    -      -       -      +
    199A  ILE*     3.9    19.1    -      -       +      -
    200A  TRP*     1.3    79.8    -      -       -      +
    202A  ASP*     1.3    61.6    +      -       -      +
    203A  GLY      3.4     0.9    +      -       -      -
    205A  VAL*     2.8    30.4    +      -       +      +
    206A  THR      4.4     1.3    -      -       -      +
    207A  PRO*     3.5    13.4    -      -       +      +
    210A  ALA*     4.7     1.3    -      -       +      -
----------------------------------------------------------
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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