Contacts of the strand formed by residues 253 - 259 (chain A) in PDB entry 3RJH


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 253 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  ASP      4.6     1.7    +      -       -      -
    146A  PHE*     4.0     7.2    -      -       -      -
    148A  LYS*     3.8    20.8    +      -       -      +
    149A  ARG      2.8    28.3    +      -       -      -
    150A  ILE*     3.4    36.6    -      -       +      +
    151A  PRO*     3.9     4.9    -      -       -      +
    154A  GLU*     2.6    37.6    +      -       -      -
    158A  MET*     4.1    13.2    -      -       +      -
    238A  VAL*     3.1     5.2    -      -       -      +
    239A  CYS*     2.7    55.1    +      -       -      +
    240A  GLN*     5.2     2.5    -      -       -      -
    241A  LEU*     5.9     0.9    -      -       +      +
    250A  TYR*     5.7     0.2    -      -       -      +
    251A  PRO*     3.7    33.9    +      -       -      +
    252A  HIS*     1.3    84.6    -      -       -      +
    254A  ARG*     1.3    64.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 254 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  SER*     4.6     8.6    +      -       -      -
    146A  PHE*     3.8    38.1    -      -       +      -
    189A  GLY      4.9     4.9    +      -       -      +
    190A  ASP*     3.3    20.9    +      -       +      +
    191A  MET*     3.2    22.7    +      -       -      +
    228A  LEU*     3.5    23.1    -      -       -      +
    236A  MET*     3.4    21.2    -      -       -      +
    237A  GLY      3.1    22.2    +      -       -      +
    239A  CYS*     4.7     0.3    -      -       -      -
    253A  ARG*     1.3    77.7    -      -       -      +
    255A  ILE*     1.3    74.7    +      -       -      +
    256A  ASP*     2.7    34.8    +      -       -      -
      9P    G      4.0     1.8    +      -       -      -
     10P    A      2.6    30.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  VAL*     4.4     7.0    -      -       +      -
    191A  MET*     3.4    19.5    -      -       +      +
    193A  VAL*     4.4    10.3    -      -       +      -
    218A  LEU*     5.2     0.4    -      -       +      -
    223A  PHE*     3.9    27.1    -      -       +      -
    224A  ILE*     4.6     6.1    -      -       +      -
    235A  PHE*     3.9    11.5    -      -       +      +
    236A  MET*     3.7     0.7    -      -       -      -
    237A  GLY*     2.8    51.3    +      -       -      -
    238A  VAL      3.8    15.5    -      -       -      +
    239A  CYS*     3.8    12.3    -      -       +      -
    254A  ARG*     1.3    80.3    +      -       -      +
    256A  ASP*     1.3    67.3    +      -       -      +
    257A  ILE*     4.2    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 256 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190A  ASP*     2.8     6.6    -      -       -      +
    191A  MET      2.9     6.8    +      -       -      +
    192A  ASP*     3.4    10.3    -      -       -      +
    193A  VAL*     2.7    32.2    +      -       -      +
    234A  LYS*     6.0     2.9    -      -       +      -
    235A  PHE      3.3     4.9    -      -       -      +
    236A  MET*     3.2    13.6    -      -       -      +
    254A  ARG*     2.7    33.2    +      -       -      -
    255A  ILE*     1.3    71.4    -      -       -      +
    257A  ILE*     1.3    61.2    +      -       -      +
    272A  PHE*     4.4     9.9    -      -       +      -
    403A   MG      2.0    33.4    -      -       -      -
     10P    A      2.8    17.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 257 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  VAL*     5.8     1.1    -      -       +      -
    193A  VAL*     3.3    24.0    -      -       +      +
    195A  LEU*     4.3    19.1    -      -       +      -
    211A  LEU*     3.8    19.5    -      -       +      +
    214A  VAL*     4.9     7.9    -      -       +      -
    215A  VAL*     5.0     3.8    -      -       +      -
    218A  LEU*     4.2    25.6    -      -       +      -
    224A  ILE*     4.6     3.8    -      -       +      -
    233A  THR      3.7     0.7    -      -       -      +
    234A  LYS*     3.3     4.9    -      -       -      +
    235A  PHE*     2.7    63.8    +      -       +      +
    255A  ILE*     4.2    17.7    -      -       +      -
    256A  ASP*     1.3    80.3    -      -       -      +
    258A  ARG*     1.3    64.0    +      -       -      +
    259A  LEU      4.1     0.2    +      -       -      -
    272A  PHE*     4.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 258 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  VAL      2.8     8.5    +      -       -      -
    194A  LEU*     3.6     3.0    -      -       -      -
    195A  LEU*     2.9    25.6    +      -       -      -
    233A  THR*     3.2    24.3    +      -       -      -
    234A  LYS*     3.9    20.2    -      -       +      +
    257A  ILE*     1.3    73.6    -      -       -      +
    259A  LEU*     1.3    61.7    +      -       -      +
    260A  ILE*     3.5    21.9    +      -       +      +
    271A  TYR*     3.7    27.9    +      -       +      -
    272A  PHE*     3.8    28.0    -      -       +      -
    295A  GLU*     2.6    35.3    +      -       -      +
    296A  TYR*     2.7    30.7    +      -       -      -
      9T    G      3.2    20.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 259 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  LEU*     3.2    39.7    -      -       +      +
    196A  THR*     4.1    11.9    -      -       -      -
    197A  HIS*     4.6     5.2    -      -       +      +
    200A  PHE*     3.6    31.7    -      -       +      -
    210A  LEU*     3.9    28.5    -      -       +      -
    211A  LEU*     4.2    14.8    -      -       +      +
    232A  GLU      3.8    16.6    -      -       -      +
    233A  THR*     2.6    41.3    +      -       -      +
    257A  ILE*     4.1     2.0    -      -       -      +
    258A  ARG*     1.3    70.4    +      -       -      +
    260A  ILE*     1.3    62.2    +      -       -      +
    261A  PRO*     4.5     0.7    -      -       -      +
    296A  TYR*     5.6     1.0    -      -       -      -
----------------------------------------------------------
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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