Contacts of the strand formed by residues 297 - 302 (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 TYR 297 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    278A  GLN*     3.2    25.1    +      -       +      -
    279A  GLU*     5.0     5.4    +      -       -      +
    398A  GLN*     2.8    64.7    +      -       +      +
    401A  LEU*     3.8     5.6    -      -       -      +
    258B  ILE*     3.1    19.5    -      -       +      +
    260B  PHE*     3.9    13.9    -      +       +      -
    284B  VAL*     3.7    28.3    -      -       +      -
    285B  GLN*     3.4    19.3    +      -       -      -
    288B  MET*     3.5    41.7    -      -       +      -
    293B  TYR*     4.4     8.9    -      +       -      -
    296B  PRO*     1.3    75.4    -      -       -      +
    298B  ARG*     1.3    86.5    +      -       -      +
    299B  LEU      5.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 298 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  ARG*     5.7     0.2    -      -       -      +
    273A  GLY*     3.0    32.9    +      -       -      +
    274A  ASP      4.9     0.7    -      -       -      -
    275A  PRO*     3.3    32.0    -      -       -      +
    398A  GLN*     4.0    12.6    +      -       -      +
    401A  LEU*     3.0    50.1    +      -       +      +
    402A  SER      4.5     2.0    -      -       -      -
    403A  CYS*     3.8    20.8    -      -       -      +
    404A  PRO*     4.2    18.6    -      -       +      -
    258B  ILE      3.1     4.8    +      -       -      +
    259B  LEU*     3.6    19.2    -      -       +      +
    260B  PHE*     3.0    25.0    +      -       -      +
    297B  TYR*     1.3    90.9    +      -       -      +
    299B  LEU*     1.3    69.1    +      -       -      +
    300B  VAL*     3.7     5.9    +      -       +      -
    313B  PRO*     5.2     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 299 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    278A  GLN*     4.1    23.2    -      -       +      +
    260B  PHE*     3.4    21.8    -      -       +      +
    262B  ALA*     4.5     3.6    -      -       +      -
    280B  VAL*     3.9    15.3    -      -       +      -
    281B  SER*     3.6    36.8    -      -       -      +
    284B  VAL*     3.8    22.9    -      -       +      -
    297B  TYR*     4.6     2.0    -      -       -      -
    298B  ARG*     1.3    77.1    -      -       -      +
    300B  VAL*     1.3    68.3    +      -       -      +
    301B  TRP*     3.6    34.6    +      -       +      -
    313B  PRO*     4.2     8.7    -      -       -      +
    335B  ILE*     4.4     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 300 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    404A  PRO*     5.3     0.2    -      -       +      -
    259B  LEU*     4.0    24.7    -      -       +      -
    260B  PHE      2.7    26.6    +      -       -      +
    261B  SER*     3.3     2.0    -      -       -      -
    262B  ALA      3.0    22.7    +      -       -      -
    298B  ARG*     4.5     7.2    -      -       +      -
    299B  LEU*     1.3    81.2    -      -       -      +
    301B  TRP*     1.3    68.9    +      -       -      +
    313B  PRO*     3.6    19.3    -      -       +      +
    315B  THR*     3.4    30.7    -      -       +      +
    318B  SER*     3.3    29.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 301 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262B  ALA*     3.1    23.1    -      -       +      +
    263B  CYS      3.6    16.6    -      -       -      -
    264B  SER*     3.4    23.8    -      -       -      -
    276B  TYR*     3.8    24.2    -      +       -      -
    277B  PRO*     3.9    24.0    -      -       +      -
    280B  VAL*     4.1     7.2    -      -       +      -
    281B  SER*     5.0     1.3    -      -       -      -
    299B  LEU*     3.6    41.3    +      -       +      -
    300B  VAL*     1.3    76.5    -      -       -      +
    302B  GLN*     1.3    60.3    +      -       -      +
    304B  LYS*     6.0     0.5    -      -       -      +
    311B  LEU*     3.5    34.7    -      -       +      +
    312B  GLY      3.2    35.2    +      -       -      -
    313B  PRO*     2.9     7.4    +      -       -      +
    314B  GLN*     3.2    12.1    -      -       -      +
    315B  THR*     2.9    25.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 302 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261B  SER*     2.5    30.1    +      -       -      +
    262B  ALA      2.8    18.1    +      -       -      +
    263B  CYS*     3.7     4.4    -      -       -      -
    264B  SER*     2.8    25.6    +      -       -      -
    301B  TRP*     1.3    73.4    -      -       -      +
    303B  SER*     1.3    75.5    +      -       -      +
    304B  LYS      3.4     2.5    -      -       -      -
    314B  GLN*     6.0     0.2    -      -       -      -
    315B  THR*     3.4    18.8    +      -       -      +
    334B  PRO*     5.6     0.2    -      -       -      +
    337B  PHE*     4.8     4.9    -      -       -      -
    343B  GLU*     3.1    39.7    +      -       -      +
    347B  GLU*     3.4    22.4    +      -       -      +
    348B  LEU*     3.3    22.4    -      -       -      +
    352B  TYR*     4.3     3.6    -      -       +      -
----------------------------------------------------------
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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