Contacts of the strand formed by residues 496 - 503 (chain L) in PDB entry 2O93


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 THR 496 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397L  LEU*     3.8    22.9    -      -       +      -
    459L  PHE*     4.1    14.1    -      -       +      -
    460L  ILE      5.6     1.3    -      -       -      +
    470L  PRO*     3.2    28.6    -      -       +      +
    471L  HIS      4.9     3.1    +      -       -      -
    475L  GLN*     3.7     9.5    +      -       -      +
    492L  ILE*     4.5     1.6    -      -       -      -
    493L  VAL*     2.7    36.6    +      -       -      +
    494L  GLY      3.4     0.2    -      -       -      -
    495L  ASN*     1.3    80.1    +      -       -      +
    497L  LYS*     1.3    72.9    +      -       -      +
    498L  VAL*     3.3     7.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 497 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    425L  GLU*     6.0     0.4    +      -       -      -
    459L  PHE*     4.2     4.7    -      -       -      +
    475L  GLN*     3.4    32.4    +      -       +      +
    476L  VAL*     3.2    41.4    +      -       +      +
    477L  HIS*     5.5     7.2    -      -       -      -
    490L  GLU*     3.5    44.7    +      -       +      +
    491L  LYS      3.8     4.5    -      -       -      +
    492L  ILE*     4.3    20.2    -      -       +      +
    496L  THR*     1.3    77.5    -      -       -      +
    498L  VAL*     1.3    60.7    +      -       -      +
    519L  LEU*     5.4    10.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 498 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397L  LEU*     3.9    21.8    -      -       +      -
    457L  GLN*     4.2    26.0    -      -       +      +
    458L  ILE      3.2    20.0    -      -       -      +
    459L  PHE*     4.5     5.4    -      -       +      -
    476L  VAL*     4.4     1.1    -      -       -      -
    490L  GLU*     3.6     0.7    -      -       -      -
    491L  LYS*     2.6    52.5    +      -       +      +
    493L  VAL*     3.4    28.0    -      -       +      -
    496L  THR*     3.7     9.2    -      -       +      +
    497L  LYS*     1.3    77.3    -      -       -      +
    499L  LEU*     1.3    70.2    +      -       -      +
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Residues in contact with LEU 499 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    457L  GLN*     3.4     2.9    -      -       -      -
    458L  ILE*     2.7    54.6    +      -       +      +
    476L  VAL*     3.9    16.4    -      -       +      +
    477L  HIS      4.6     1.8    -      -       -      +
    478L  ARG*     3.5    40.6    -      -       +      +
    488L  SER*     4.3     6.7    -      -       -      -
    489L  TYR      3.3    11.2    -      -       -      +
    490L  GLU*     4.3     7.2    -      -       +      +
    498L  VAL*     1.3    75.4    -      -       -      +
    500L  GLU*     1.3    60.5    +      -       -      +
    501L  ILE*     4.2     0.9    -      -       +      -
    515L  CYS*     3.6    30.3    -      -       -      +
    516L  ALA*     3.8    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 500 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    455L  GLY*     4.5    11.6    -      -       -      -
    456L  LEU      3.2    15.0    -      -       -      +
    457L  GLN*     3.5    11.6    +      -       +      +
    489L  TYR*     2.5    62.2    +      -       +      +
    491L  LYS*     2.7    42.0    +      -       +      -
    499L  LEU*     1.3    75.5    -      -       -      +
    501L  ILE*     1.3    65.1    +      -       -      +
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Residues in contact with ILE 501 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    455L  GLY*     3.5     3.5    -      -       -      -
    456L  LEU*     2.7    72.9    +      -       +      +
    458L  ILE*     3.7    20.8    -      -       +      +
    486L  THR*     5.0     8.3    -      -       -      +
    487L  THR      3.4    15.0    -      -       -      +
    488L  SER*     4.2     2.9    -      -       -      -
    489L  TYR*     5.5     0.4    -      -       -      -
    499L  LEU*     4.8     0.9    -      -       +      -
    500L  GLU*     1.3    78.3    -      -       -      +
    502L  PRO*     1.3    68.1    -      -       +      +
    511L  ALA*     3.6    25.4    -      -       +      -
    512L  THR      5.4     0.9    -      -       -      +
    513L  ILE*     4.2    14.6    -      -       +      -
    515L  CYS*     3.8    19.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 502 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    453L  PRO*     6.2     0.9    -      -       +      -
    454L  LEU      3.6     6.5    -      -       -      +
    455L  GLY*     4.6     1.1    -      -       -      -
    486L  THR*     5.7     3.5    -      -       -      +
    487L  THR*     3.3    45.3    -      -       +      +
    489L  TYR*     4.9     8.7    -      -       +      -
    500L  GLU      4.6     0.9    -      -       -      +
    501L  ILE*     1.3    92.5    -      -       +      +
    503L  LEU*     1.3    63.3    +      -       -      +
    504L  GLU*     3.8    22.6    +      -       +      +
    510L  ARG      5.2     0.7    -      -       -      +
    511L  ALA*     4.5     8.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 503 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    410L  LEU*     5.2     2.2    -      -       +      -
    443L  VAL      4.9     1.6    -      -       -      +
    444L  GLN*     5.2     0.7    -      -       -      -
    445L  LEU*     4.2    15.3    -      -       +      +
    454L  LEU      2.6    44.0    +      -       -      +
    456L  LEU*     3.9    38.6    -      -       +      +
    501L  ILE      4.0     0.4    +      -       -      -
    502L  PRO*     1.3    70.5    -      -       -      +
    504L  GLU*     1.3    59.4    +      -       -      +
    509L  MET*     2.9    62.5    -      -       +      +
    510L  ARG*     3.6    13.9    -      -       -      +
    511L  ALA*     4.2    10.3    -      -       +      +
    548L  VAL*     4.5    14.8    -      -       +      -
----------------------------------------------------------
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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