Contacts of the strand formed by residues 409 - 414 (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 GLU 409 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    403L  SER*     3.4    11.0    -      -       -      +
    404L  GLN*     3.8    27.6    -      -       +      +
    408L  TYR*     1.3    77.7    -      -       -      +
    410L  LEU*     1.3    62.5    +      -       -      +
    411L  ARG*     3.2    49.4    +      -       +      +
    445L  LEU*     3.7     1.9    -      -       -      +
    446L  HIS*     2.9    45.1    +      -       +      +
    560L  LEU*     3.5     4.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 410 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    403L  SER*     2.9    20.5    +      -       -      +
    409L  GLU*     1.3    72.0    -      -       -      +
    411L  ARG*     1.3    59.9    +      -       -      +
    443L  VAL*     3.7    16.8    -      -       +      -
    444L  GLN      3.3    25.8    -      -       -      +
    445L  LEU*     3.9    12.1    -      -       +      +
    456L  LEU*     4.5     7.6    -      -       +      -
    503L  LEU*     5.2     1.8    -      -       +      -
    546L  PHE*     4.0    19.5    -      -       +      +
    547L  ARG*     4.2     4.5    -      -       -      -
    548L  VAL*     3.9    16.8    -      -       +      -
    560L  LEU*     3.7    34.5    -      -       +      +
    562L  THR*     3.3    33.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 411 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    403L  SER*     6.0     0.9    -      -       -      -
    409L  GLU*     3.2    52.1    +      -       +      +
    410L  LEU*     1.3    76.8    -      -       -      +
    412L  ILE*     1.3    64.7    +      -       -      +
    413L  GLU*     3.4    10.6    +      -       -      +
    443L  VAL*     4.0     3.5    -      -       -      +
    444L  GLN      3.3    29.6    +      -       -      +
    446L  HIS*     2.8    44.5    +      -       -      +
    562L  THR*     5.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 412 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    411L  ARG*     1.3    73.9    -      -       -      +
    413L  GLU*     1.3    65.4    +      -       -      +
    414L  VAL      4.1     3.8    -      -       -      +
    415L  GLN*     3.2    56.9    +      -       +      +
    416L  PRO*     5.0     0.9    -      -       +      -
    441L  PRO*     6.0     0.2    -      -       +      -
    442L  VAL      3.9     3.8    -      -       -      +
    443L  VAL*     3.9     9.0    -      -       +      -
    546L  PHE*     3.2    41.3    -      -       +      -
    562L  THR*     3.3    26.4    +      -       +      +
    563L  ALA      4.7     2.0    -      -       -      +
    564L  SER*     4.5    11.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 413 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    411L  ARG*     3.4     8.8    +      -       -      +
    412L  ILE*     1.3    75.5    -      -       -      +
    414L  VAL*     1.3    62.8    +      -       +      +
    415L  GLN*     4.1     1.0    +      -       -      +
    442L  VAL*     2.6    26.4    +      -       +      +
    444L  GLN*     2.7    39.6    -      -       +      +
    446L  HIS*     2.8    23.2    -      -       -      -
    510L  ARG*     3.3    30.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 414 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    412L  ILE*     4.1     4.9    -      -       -      +
    413L  GLU*     1.3    79.9    -      -       +      +
    415L  GLN*     1.3    61.8    +      -       -      +
    435L  ALA*     3.6    27.8    -      -       +      -
    436L  PRO*     5.3     1.1    -      -       +      -
    437L  THR*     4.4    13.9    -      -       +      -
    440L  HIS      3.7     4.0    -      -       -      +
    441L  PRO*     2.8    27.0    -      -       +      +
    442L  VAL*     2.9    43.8    +      -       +      +
    510L  ARG*     5.2     3.8    -      -       -      +
----------------------------------------------------------
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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