Contacts of the strand formed by residues 352 - 358 (chain A) in PDB entry 4RA4


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 LYS 352 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344A  VAL*     3.9    19.8    -      -       +      +
    346A  GLY      3.4    16.2    -      -       -      +
    347A  LYS*     4.2    12.1    -      -       +      +
    350A  PHE*     4.0     2.1    -      -       -      -
    351A  GLY*     1.3    73.2    -      -       -      -
    353A  VAL*     1.3    66.0    +      -       -      +
    354A  MET*     3.8    26.2    -      -       +      -
    367A  ILE      3.6     0.5    -      -       -      +
    368A  LYS*     3.6     4.5    -      -       -      +
    369A  ILE*     2.8    44.8    +      -       +      +
    370A  LEU*     5.3     0.2    -      -       -      +
    636A  VAL      5.6     2.2    -      -       -      -
    637A  LEU*     3.9    21.5    -      -       +      -
    638A  TPO      3.8    28.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 353 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344A  VAL*     3.7     2.8    -      -       -      +
    345A  LEU*     2.8    36.0    +      -       +      -
    346A  GLY      2.9    12.5    +      -       -      +
    350A  PHE*     3.7    11.2    -      -       +      -
    352A  LYS*     1.3    79.2    -      -       -      +
    354A  MET*     1.3    61.2    +      -       -      +
    366A  ALA*     4.3     5.2    -      -       +      -
    367A  ILE      3.4     5.6    -      -       -      +
    368A  LYS*     4.5     6.5    -      -       +      -
    701A  3KZ      3.2    88.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 354 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341A  PHE*     3.9    31.9    -      -       +      -
    343A  MET      3.9     4.0    -      -       -      +
    344A  VAL*     3.4    26.0    -      -       +      -
    345A  LEU*     4.1     4.3    -      -       -      -
    352A  LYS*     3.8    15.0    -      -       +      -
    353A  VAL*     1.3    73.6    -      -       -      +
    355A  LEU*     1.4    65.1    +      -       -      +
    356A  ALA      3.7     0.7    +      -       -      -
    365A  TYR      3.6     0.5    -      -       -      +
    366A  ALA*     3.4     3.1    -      -       -      -
    367A  ILE*     2.7    43.4    +      -       +      +
    369A  ILE*     3.7    21.5    -      -       +      -
    635A  PRO*     3.8    28.5    -      -       +      +
    636A  VAL      5.3     1.3    -      -       -      +
    637A  LEU*     3.8    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 355 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341A  PHE*     3.9     1.2    -      -       -      -
    342A  LEU*     2.8    47.3    +      -       +      +
    343A  MET*     2.8    40.7    +      -       +      +
    345A  LEU*     3.7    22.8    -      -       +      +
    354A  MET*     1.4    69.1    -      -       -      +
    356A  ALA*     1.3    57.1    +      -       -      +
    364A  LEU*     4.4    16.4    -      -       +      -
    365A  TYR      3.4    16.8    -      -       -      +
    419A  TYR*     3.7    42.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 356 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339A  PHE*     4.4     5.2    -      -       +      -
    340A  ASN      3.2    16.8    -      -       -      +
    341A  PHE*     3.6    23.6    -      -       +      -
    342A  LEU*     4.0     6.5    -      -       -      -
    354A  MET      3.7     0.6    +      -       -      +
    355A  LEU*     1.3    76.8    -      -       -      +
    357A  ASP*     1.3    57.0    +      -       -      +
    364A  LEU*     4.4     0.7    -      -       -      -
    365A  TYR*     2.8    41.6    +      -       -      +
    367A  ILE*     3.8    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 357 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339A  PHE*     3.5     6.8    -      -       -      -
    340A  ASN*     2.9    51.2    +      -       -      +
    342A  LEU*     3.4    19.8    -      -       -      +
    356A  ALA*     1.3    72.5    -      -       -      +
    358A  ARG*     1.3    72.1    +      -       -      +
    359A  LYS*     5.1     0.3    -      -       -      -
    360A  GLY      5.4     0.2    +      -       -      -
    361A  THR      3.4     9.7    -      -       -      +
    362A  GLU*     4.6     6.2    -      -       -      +
    363A  GLU      3.1    18.8    -      -       -      +
    364A  LEU*     3.8    15.0    -      -       +      -
    365A  TYR*     4.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 358 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338A  ASP*     3.6    19.3    -      -       +      +
    339A  PHE*     4.3    14.1    -      -       +      -
    357A  ASP*     1.3    78.6    -      -       -      +
    359A  LYS*     1.3    64.2    +      -       -      +
    361A  THR*     3.0    46.4    +      -       +      +
    363A  GLU*     2.8    38.9    +      -       -      +
    365A  TYR*     3.3    19.6    +      -       +      -
    404A  HIS*     3.2    30.2    +      -       -      -
    665A  HIS*     3.9     7.7    +      -       -      -
----------------------------------------------------------
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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