Contacts of the strand formed by residues 189 - 195 (chain G) in PDB entry 3EXF


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 CYS 189 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145G  GLY      4.0    12.6    -      -       -      -
    146G  ALA*     4.0     7.0    -      -       -      -
    149G  ALA*     3.6    14.4    -      -       +      -
    161G  CYS      3.4     4.7    -      -       -      -
    163G  THR*     3.6    22.2    -      -       -      -
    182G  ALA*     5.1     1.1    -      -       +      -
    187G  LEU*     2.7    19.0    +      -       +      +
    188G  PRO*     1.3    71.5    -      -       -      +
    190G  ILE*     1.3    63.8    +      -       -      +
    191G  PHE*     3.2    42.4    +      -       +      -
    244G  CYS*     4.0     4.2    -      -       -      -
    250G  PRO*     3.7    19.0    -      -       +      +
    251G  ILE      3.7     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 190 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160G  VAL*     3.7    28.3    -      -       +      -
    161G  CYS      3.0     7.2    +      -       -      +
    162G  LEU*     3.7    23.7    -      -       +      -
    163G  THR*     3.0    29.6    +      -       -      -
    189G  CYS*     1.3    70.5    -      -       -      +
    191G  PHE*     1.3    62.2    +      -       -      +
    192G  ILE*     3.3    27.8    -      -       +      -
    237G  THR*     5.6     1.1    -      -       +      +
    240G  ALA*     3.9    18.4    -      -       +      +
    241G  ALA*     3.9    10.5    -      -       -      +
    244G  CYS*     3.6    25.4    -      -       +      -
    251G  ILE*     3.7    11.7    -      -       +      +
    253G  MET*     4.1    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 191 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142G  VAL*     3.3    35.0    -      -       +      -
    146G  ALA*     4.7     2.7    -      -       +      -
    163G  THR*     3.7     9.6    -      -       +      -
    165G  TYR*     4.4     6.7    -      +       +      -
    178G  ALA*     3.8    14.4    -      -       +      -
    179G  TYR*     3.8    28.9    -      +       +      -
    182G  ALA*     3.6    31.2    -      -       +      -
    189G  CYS*     3.2    33.6    +      -       -      -
    190G  ILE*     1.3    70.4    -      -       -      +
    192G  ILE*     1.3    59.6    +      -       -      +
    220G  ILE*     4.2     4.5    -      -       +      -
    250G  PRO*     4.1    12.8    -      -       +      -
    251G  ILE      2.8    15.5    +      -       -      +
    252G  LEU*     3.3    23.5    -      -       +      +
    253G  MET      2.9    25.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 192 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75G  LEU*     4.5     5.4    -      -       +      -
    162G  LEU*     3.4    45.8    -      -       +      -
    163G  THR      3.0     9.3    +      -       -      +
    164G  LEU*     3.3    29.7    -      -       +      +
    165G  TYR*     3.1    27.4    +      -       -      +
    190G  ILE*     3.3    20.2    -      -       +      +
    191G  PHE*     1.3    70.3    -      -       -      +
    193G  CYS*     1.3    64.8    +      -       -      +
    194G  GLU*     3.7     0.6    +      -       +      +
    253G  MET*     3.2    25.1    -      -       +      +
    255G  LEU*     3.8    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 193 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165G  TYR*     3.3    24.2    -      -       +      +
    166G  GLY      4.0    23.3    -      -       -      -
    167G  ASP*     4.1     5.4    -      -       -      -
    191G  PHE      4.0     1.0    +      -       -      -
    192G  ILE*     1.3    74.8    -      -       -      +
    194G  GLU*     1.3    58.7    +      -       -      +
    195G  ASN*     3.2     9.5    +      -       -      -
    213G  TYR*     3.9    35.9    -      -       +      +
    252G  LEU*     5.5     2.2    -      -       +      -
    253G  MET      2.7    11.2    +      -       -      +
    254G  GLU*     3.5    10.6    -      -       -      +
    255G  LEU      2.6    31.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 194 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68G  GLN*     3.0    28.8    -      -       -      +
     71G  CYS*     4.1    23.7    -      -       -      +
     87G  THR*     4.3     7.3    +      -       -      -
     90G  ARG*     5.1     9.5    -      -       -      +
     94G  PHE*     4.2    11.3    -      -       -      -
    164G  LEU*     3.7    31.9    -      -       +      +
    165G  TYR*     2.7    17.4    +      -       -      +
    166G  GLY*     3.3    12.3    +      -       -      -
    167G  ASP*     3.1    15.9    -      -       -      +
    192G  ILE*     3.7     0.6    +      -       +      -
    193G  CYS*     1.3    68.5    -      -       -      +
    195G  ASN*     1.3    59.5    -      -       -      +
    196G  ASN*     3.4     4.4    +      -       -      +
    255G  LEU*     4.0    11.2    -      -       +      -
    257G  THR*     4.8     3.8    -      -       +      -
   1010G   MG      3.8     2.1    -      -       -      -
   1012G  TPP      4.8     8.9    +      -       -      +
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Residues in contact with ASN 195 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167G  ASP*     3.4    20.7    -      -       -      +
    193G  CYS*     3.2     4.7    +      -       -      +
    194G  GLU*     1.3    70.5    -      -       -      +
    196G  ASN*     1.3    59.1    +      -       -      +
    197G  ARG*     3.0    24.8    +      -       -      +
    204G  VAL*     3.7     6.0    -      -       -      +
    211G  THR      5.0     1.4    +      -       -      -
    213G  TYR*     3.6    17.8    -      -       -      -
    254G  GLU*     3.1    32.5    +      -       +      +
    255G  LEU      2.8    17.4    +      -       -      +
    256G  GLN*     3.8     9.2    -      -       -      +
    257G  THR*     2.9    29.3    +      -       -      +
----------------------------------------------------------
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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