Contacts of the strand formed by residues 324 - 331 (chain B) in PDB entry 3OPY


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 ASN 324 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182B  LYS*     3.4    41.4    -      -       -      +
    278B  ASP      3.4    15.9    +      -       -      +
    279B  ALA*     3.3    18.2    -      -       +      +
    280B  LEU      2.7    32.8    +      -       -      -
    322B  ASN*     3.5    16.3    +      -       -      +
    323B  LEU*     1.3    73.4    -      -       -      +
    325B  ILE*     1.3    55.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 325 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280B  LEU*     3.3    35.7    -      -       +      +
    282B  VAL*     4.3     2.9    -      -       +      -
    292B  ALA*     3.7    39.0    -      -       +      +
    293B  ASP*     6.2     0.2    -      -       -      -
    295B  PHE*     4.4     2.7    -      -       +      -
    296B  ARG*     4.2    28.9    -      -       +      -
    323B  LEU*     3.3    24.4    +      -       +      +
    324B  ASN*     1.3    74.3    -      -       -      +
    326B  CYS*     1.3    68.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 326 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280B  LEU      2.9     8.2    +      -       -      +
    281B  ILE*     3.4    22.0    -      -       +      +
    282B  VAL*     2.9    27.3    +      -       -      +
    325B  ILE*     1.3    79.2    -      -       -      +
    327B  GLY*     1.3    71.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 327 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281B  ILE*     5.8     0.7    -      -       -      -
    282B  VAL*     3.4     7.0    -      -       -      -
    289B  LEU*     3.7    20.4    -      -       -      -
    326B  CYS*     1.3    86.5    -      -       -      +
    328B  ALA*     1.3    60.4    +      -       -      +
    329B  VAL*     5.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 328 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199B  PHE*     3.5    39.3    -      -       +      -
    282B  VAL      3.0     7.1    +      -       -      +
    283B  CYS*     3.4     7.6    -      -       -      -
    284B  GLY      3.1    25.7    +      -       -      +
    289B  LEU*     4.1     4.0    -      -       -      +
    327B  GLY*     1.3    74.7    -      -       -      +
    329B  VAL*     1.3    63.2    +      -       -      +
    330B  GLY      3.3     0.3    +      -       -      -
    343B  ILE*     4.5     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 329 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284B  GLY      3.3    12.6    -      -       -      +
    285B  GLY*     4.3     4.5    -      -       -      -
    289B  LEU*     3.8    13.0    -      -       +      -
    328B  ALA*     1.3    72.2    -      -       -      +
    330B  GLY*     1.3    53.2    +      -       -      +
    331B  SER*     3.5    13.0    -      -       -      +
    336B  MET*     3.5    43.3    -      -       +      -
    339B  THR*     4.2    13.0    -      -       +      -
    342B  THR*     3.6    23.5    -      -       +      -
    343B  ILE*     2.7    42.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 330 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  SER      4.4     4.7    -      -       -      +
    190B  GLY*     5.9     0.3    -      -       -      -
    191B  GLY      4.5     4.5    -      -       -      +
    193B  SER*     3.7    14.3    -      -       -      -
    196B  MET*     4.6     5.3    -      -       -      +
    283B  CYS*     4.2    14.1    -      -       -      -
    284B  GLY*     2.7    32.0    +      -       -      +
    285B  GLY*     3.7     2.3    +      -       -      -
    328B  ALA      3.3     4.0    +      -       -      -
    329B  VAL*     1.3    69.9    -      -       -      +
    331B  SER*     1.4    59.2    +      -       -      -
    343B  ILE*     3.6    11.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 331 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191B  GLY      5.8     0.4    -      -       -      -
    193B  SER*     3.4     8.3    -      -       -      -
    285B  GLY*     4.4    10.5    -      -       -      -
    286B  ASP*     4.8     5.3    +      -       -      -
    329B  VAL*     3.5    12.5    +      -       -      +
    330B  GLY*     1.4    75.8    -      -       -      +
    332B  ILE*     1.3    56.8    +      -       -      +
    333B  ASP*     3.7    11.0    +      -       -      +
    334B  ASN      3.5    11.8    +      -       -      -
    335B  ASP      4.4     2.1    +      -       -      -
    342B  THR*     2.6    38.5    +      -       -      +
    343B  ILE      3.0    13.0    +      -       -      +
    345B  ALA      3.4     4.7    +      -       -      -
    469B  ARG*     6.0     2.0    -      -       -      +
----------------------------------------------------------
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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