Contacts of the strand formed by residues 184 - 189 (chain B) in PDB entry 2PO5


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 184 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  LYS*     3.3     7.1    +      -       +      +
     69B  THR*     3.5    30.4    +      -       +      +
     70B  GLY*     2.8    28.2    +      -       -      -
    154B  THR*     3.7    21.2    -      -       -      +
    182B  LEU*     4.0     6.0    -      -       -      +
    183B  GLU*     1.3    83.3    -      -       +      +
    185B  ALA*     1.3    61.7    +      -       -      +
    186B  ILE*     4.2    16.8    -      -       +      +
    219B  MET*     4.7     0.2    -      -       -      -
    220B  LYS*     3.7    24.8    -      -       +      +
    222B  SER*     5.8     2.0    -      -       -      +
    389B  ILE*     3.7    35.1    +      -       -      +
    392B  ASN*     5.5     6.3    +      -       -      +
    423B  LEU*     5.5     9.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 185 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70B  GLY      3.6     3.6    -      -       -      -
    177B  MET*     3.8    17.0    -      -       +      -
    184B  ARG*     1.3    75.2    -      -       -      +
    186B  ILE*     1.3    64.0    +      -       -      +
    219B  MET*     3.8    17.5    -      -       +      +
    220B  LYS      2.9    11.7    +      -       -      +
    221B  TRP*     3.3    35.3    -      -       +      -
    222B  SER*     3.1    24.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 186 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69B  THR*     4.3     8.3    -      -       +      -
     70B  GLY      2.9    14.7    +      -       -      +
     71B  ILE*     3.6     7.4    -      -       +      -
     72B  LEU      2.8    27.8    +      -       -      -
    177B  MET*     4.7     0.6    -      -       -      +
    184B  ARG*     4.2    15.5    -      -       +      -
    185B  ALA*     1.3    74.3    -      -       -      +
    187B  ALA*     1.3    68.4    +      -       -      +
    188B  PHE*     3.1     9.7    +      -       +      +
    221B  TRP*     4.4     3.3    -      -       -      -
    222B  SER*     3.4    16.8    -      -       -      +
    224B  ILE*     4.2    27.4    -      -       +      +
    385B  VAL*     4.1    13.5    -      -       +      -
    388B  HIS*     4.1    12.3    -      -       +      +
    389B  ILE*     3.9    34.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 187 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  LEU*     3.8     6.3    -      -       -      -
     74B  LEU*     3.9    10.5    -      -       +      -
    186B  ILE*     1.3    67.5    -      -       -      +
    188B  PHE*     1.3    59.4    +      -       -      +
    189B  THR      3.6     1.0    +      -       -      -
    203B  LEU*     4.0     2.7    -      -       +      -
    206B  ILE*     3.7    30.3    -      -       +      -
    221B  TRP*     4.0    10.3    -      -       +      -
    222B  SER      2.8    17.2    +      -       -      +
    223B  THR*     2.8    35.4    +      -       -      +
    224B  ILE      3.0    13.7    +      -       -      +
    418B  PHE*     4.3     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 188 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71B  ILE*     3.7    20.9    -      -       +      -
     72B  LEU      2.7    15.8    +      -       -      +
     73B  MET*     3.4     0.4    -      -       -      -
     74B  LEU*     3.0    19.7    +      -       -      +
    143B  MET*     4.1     4.7    -      -       +      -
    186B  ILE*     3.1     6.3    +      -       +      +
    187B  ALA*     1.3    69.6    -      -       -      +
    189B  THR*     1.3    73.6    +      -       -      +
    190B  GLN*     3.0    15.4    +      -       -      +
    224B  ILE*     3.6    25.4    -      -       +      -
    227B  TRP*     3.5    24.7    -      +       -      -
    381B  LEU*     3.6    38.6    -      -       +      -
    384B  LEU*     3.8    22.4    -      -       +      -
    385B  VAL*     3.5    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 189 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74B  LEU*     3.9    17.6    +      -       -      +
    187B  ALA      3.6     2.4    +      -       -      -
    188B  PHE*     1.3    79.5    -      -       -      +
    190B  GLN*     1.3    62.4    +      -       -      +
    191B  TYR*     3.2    27.4    +      -       -      +
    199B  THR*     2.7    31.1    +      -       -      -
    203B  LEU*     5.9     0.2    -      -       -      -
    223B  THR*     5.8     0.4    -      -       -      -
    224B  ILE      3.1    21.4    +      -       -      +
    225B  ASP*     3.4    25.1    -      -       -      +
    226B  ARG      3.9     1.1    -      -       -      +
    227B  TRP*     3.0    19.3    +      -       -      +
----------------------------------------------------------
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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