Contacts of the strand formed by residues 452 - 458 (chain B) in PDB entry 4OE5


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 VAL 452 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318B  LYS*     5.1     0.3    +      -       -      -
    340B  ALA*     4.8     2.6    +      -       -      -
    341B  PHE*     4.1     0.6    -      -       -      -
    351B  CYS      5.1     0.2    -      -       -      +
    352B  SER*     3.9    19.9    -      -       -      +
    400B  ILE*     4.2    12.8    -      -       +      -
    403B  TRP*     5.2     5.2    -      -       +      +
    404B  LEU*     4.1    24.5    -      -       +      -
    432B  CYS*     3.4     4.0    -      -       +      +
    434B  VAL*     4.4    14.8    -      -       +      -
    443B  ILE*     4.2    17.3    -      -       +      -
    448B  ILE*     3.6    45.3    -      -       +      +
    450B  GLY      2.9    10.6    +      -       -      +
    451B  PRO*     1.3    79.8    -      -       +      +
    453B  LEU*     1.3    64.5    +      -       -      +
    454B  SER*     4.0     1.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 453 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336B  THR*     3.6    26.0    -      -       +      +
    337B  LEU*     5.3     0.2    -      -       +      -
    340B  ALA*     4.0    17.3    -      -       +      -
    341B  PHE*     4.1     7.6    -      -       +      -
    351B  CYS*     4.0    22.9    -      -       -      +
    352B  SER*     3.8    20.4    -      -       -      +
    353B  ARG      4.0     0.4    -      -       -      +
    354B  LEU*     4.2     7.2    -      -       +      -
    368B  LEU*     4.8     7.4    -      -       +      -
    432B  CYS      2.8    14.3    +      -       -      +
    433B  ILE*     4.3    16.8    -      -       +      +
    434B  VAL*     2.8    30.0    +      -       -      +
    451B  PRO      4.2     0.6    -      -       -      -
    452B  VAL*     1.3    74.0    -      -       -      +
    454B  SER*     1.3    73.5    +      -       -      +
    455B  VAL*     4.4    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 454 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318B  LYS*     4.8     1.0    +      -       -      -
    352B  SER      2.9    15.8    +      -       -      -
    353B  ARG*     3.4     1.7    -      -       -      +
    354B  LEU*     2.8    27.2    +      -       -      +
    434B  VAL*     3.2     7.6    -      -       -      +
    436B  SER*     5.4     1.1    -      -       -      -
    443B  ILE*     3.1    43.2    +      -       -      +
    444B  MET*     3.7    24.2    -      -       -      -
    452B  VAL*     4.8     2.3    +      -       -      +
    453B  LEU*     1.3    76.1    -      -       -      +
    455B  VAL*     1.3    63.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 455 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354B  LEU*     3.2    31.2    -      -       +      +
    356B  VAL*     3.9    14.8    -      -       +      -
    361B  TRP*     3.7    34.5    -      -       +      -
    368B  LEU*     4.9     0.9    -      -       +      -
    416B  LEU*     5.5     0.2    -      -       +      -
    433B  ILE*     4.1    22.2    -      -       +      -
    434B  VAL      2.8    15.9    +      -       -      +
    435B  GLU*     3.5     9.4    -      -       +      +
    436B  SER*     2.8    30.1    +      -       -      +
    444B  MET*     4.7     2.7    -      -       -      -
    453B  LEU*     4.4     5.6    -      -       +      -
    454B  SER*     1.3    80.0    -      -       -      +
    456B  TYR*     1.3    64.9    +      -       -      +
    457B  VAL*     4.4     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 456 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354B  LEU      2.7     9.7    +      -       -      -
    355B  TYR*     3.3    27.0    -      +       +      -
    356B  VAL      2.9    24.3    +      -       -      +
    436B  SER*     3.4    15.9    -      -       -      +
    437B  LYS*     3.6    12.5    +      -       -      -
    438B  ASP      4.3     0.2    -      -       -      -
    439B  PRO*     3.5    47.7    -      -       +      +
    444B  MET*     4.0    23.0    -      -       +      +
    454B  SER      4.3     0.2    -      -       -      -
    455B  VAL*     1.3    74.0    -      -       -      +
    457B  VAL*     1.3    72.7    +      -       -      +
    458B  TYR*     3.6    24.8    +      -       +      -
    459B  PRO*     4.6     9.5    -      -       -      +
    466B  THR*     4.8     1.3    -      -       +      -
    469B  LEU*     4.4    10.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 457 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356B  VAL*     3.1    14.4    -      -       +      +
    358B  HIS*     3.5    40.6    -      -       +      -
    361B  TRP*     3.6    41.7    -      -       +      -
    435B  GLU*     3.4    24.9    -      -       -      +
    436B  SER      4.5     2.8    +      -       -      -
    455B  VAL*     4.2     3.3    +      -       +      -
    456B  TYR*     1.3    88.8    +      -       -      +
    458B  TYR*     1.3    62.8    +      -       -      +
    459B  PRO*     4.3     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 458 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322B  PHE*     3.6    20.4    -      +       -      -
    323B  VAL      2.7    26.0    +      -       -      -
    324B  HIS*     3.9     6.9    -      -       -      -
    325B  ARG      4.6     0.3    +      -       -      -
    355B  TYR*     3.8     6.5    -      -       +      -
    356B  VAL      2.8    47.2    +      -       -      -
    357B  PRO*     3.3    19.5    -      -       +      +
    358B  HIS*     2.7    33.7    +      -       -      -
    456B  TYR*     3.7    15.9    -      -       +      -
    457B  VAL*     1.3    74.8    -      -       -      +
    459B  PRO*     1.3    87.7    -      -       +      +
    460B  ASP*     4.6     2.0    -      -       -      -
    463B  TYR*     3.6    28.3    -      -       +      +
    466B  THR*     3.4    34.8    -      -       +      +
----------------------------------------------------------
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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