Contacts of the strand formed by residues 334 - 341 (chain I) in PDB entry 6RAR


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 ARG 334 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B    A      4.9     8.3    +      -       -      -
    300D  AMP      4.0    10.1    +      -       -      -
    147I  LEU*     3.7    44.1    -      -       +      +
    148I  ALA      2.4    42.3    +      -       -      +
    149I  HIS*     3.2    37.7    +      -       +      +
    187I  ARG*     5.1     6.5    -      -       -      +
    333I  LYS*     1.3    85.2    -      -       -      +
    335I  THR*     1.3    59.6    +      -       -      +
    340I  LYS*     4.8     2.4    -      -       -      +
    501I  SO4      5.0     4.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 335 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146I  PRO*     5.0     3.4    -      -       +      -
    147I  LEU      3.2    17.4    +      -       -      +
    149I  HIS*     3.5    11.1    -      -       -      -
    329I  MET      5.9     0.9    -      -       -      +
    331I  GLU*     3.5    28.1    +      -       +      +
    333I  LYS*     3.6    14.8    -      -       -      +
    334I  ARG*     1.3    76.8    -      -       -      +
    336I  HIS*     1.3    63.5    +      -       -      +
    337I  SER*     3.1    31.0    +      -       -      -
    338I  TRP*     3.2    24.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 336 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B    G      4.1    15.9    -      -       +      -
      6B    A      3.7    23.8    +      -       -      -
    149I  HIS*     3.5    24.5    +      +       +      -
    154I  HIS*     3.3    33.3    +      +       -      -
    157I  LYS*     3.6    44.4    +      -       +      +
    162I  LYS*     4.7     7.6    +      -       -      -
    323I  ILE      5.0     0.2    -      -       -      +
    325I  ASP*     5.2     0.2    -      -       -      +
    335I  THR*     1.3    72.1    +      -       -      +
    337I  SER*     1.3    65.1    +      -       -      +
    338I  TRP      3.1     3.0    +      -       -      -
    339I  LEU*     3.6    24.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 337 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162I  LYS*     5.5     0.2    +      -       -      -
    266I  GLN*     5.5     1.6    -      -       -      -
    323I  ILE      3.5     1.6    -      -       -      +
    324I  LYS*     3.1     8.3    -      -       -      -
    325I  ASP*     3.0    38.0    +      -       -      +
    328I  GLY*     3.7    26.5    -      -       -      -
    329I  MET      4.4     7.3    +      -       -      -
    331I  GLU*     4.4     6.2    +      -       -      -
    335I  THR*     3.1    22.3    +      -       -      -
    336I  HIS*     1.3    78.5    -      -       -      +
    338I  TRP*     1.3    67.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 338 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300D  AMP      3.9    19.5    -      +       -      -
    146I  PRO*     3.8    32.5    -      -       +      -
    147I  LEU*     4.2    10.3    -      -       -      +
    148I  ALA*     3.2    14.4    -      -       +      -
    149I  HIS      2.9    23.2    +      -       -      -
    172I  ARG*     3.4    35.4    -      -       -      -
    218I  ASP*     4.0     5.4    -      -       -      -
    249I  PHE*     3.9    13.9    -      +       -      -
    250I  ASP*     3.5    23.3    -      -       +      -
    266I  GLN*     2.9    24.8    +      -       -      -
    269I  ARG*     4.5     4.2    -      -       -      +
    322I  MET*     4.3     7.0    -      -       +      -
    323I  ILE      3.9     1.8    -      -       -      -
    324I  LYS*     3.7    27.2    -      -       +      +
    330I  TYR*     5.2     0.2    -      +       -      -
    335I  THR*     3.2    11.5    +      -       +      +
    336I  HIS      3.1     0.2    -      -       -      -
    337I  SER*     1.3    93.1    -      -       -      +
    339I  LEU*     1.3    63.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 339 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148I  ALA*     4.8     0.2    -      -       -      -
    149I  HIS*     3.1    33.9    -      -       +      +
    151I  SER*     4.1    14.1    -      -       -      +
    154I  HIS*     4.4    10.8    -      -       +      +
    157I  LYS*     4.4    21.8    -      -       +      +
    158I  MET*     3.5    28.5    -      -       +      -
    162I  LYS*     4.5     8.1    -      -       -      +
    322I  MET*     3.4     8.8    -      -       -      +
    323I  ILE*     2.7    47.0    +      -       +      +
    336I  HIS*     3.6    32.5    -      -       +      +
    338I  TRP*     1.3    74.2    -      -       -      +
    340I  LYS*     1.3    59.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 340 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33D    A      3.6    25.8    +      -       -      -
    300D  AMP      2.9    42.2    +      -       -      +
    148I  ALA*     3.9     7.2    +      -       +      -
    149I  HIS*     2.9    29.4    +      -       -      +
    150I  ASP*     3.3    25.6    -      -       -      +
    151I  SER*     2.7    31.6    +      -       -      -
    167I  LYS*     4.1    10.3    -      -       +      -
    321I  VAL      3.6     5.2    -      -       -      +
    322I  MET*     4.0    18.8    -      -       +      -
    323I  ILE*     4.3     1.1    -      -       -      -
    334I  ARG*     4.8     2.2    -      -       -      +
    339I  LEU*     1.3    75.8    -      -       -      +
    341I  ALA*     1.3    56.5    +      -       -      +
    342I  LYS*     4.1    18.4    -      -       +      +
    501I  SO4      4.9     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 341 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150I  ASP*     5.0     1.6    -      -       -      -
    151I  SER*     3.6    13.7    -      -       -      +
    167I  LYS*     5.1     0.2    -      -       -      +
    306I  PHE*     4.6     7.0    -      -       +      -
    310I  ASN*     4.3     9.0    -      -       -      +
    320I  GLY*     3.3     5.2    -      -       -      -
    321I  VAL*     3.0    49.0    +      -       +      +
    323I  ILE*     4.0     7.4    -      -       +      -
    340I  LYS*     1.3    73.6    -      -       -      +
    342I  LYS*     1.3    64.8    +      -       -      +
----------------------------------------------------------
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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