Contacts of the strand formed by residues 194 - 199 (chain A) in PDB entry 1RPJ


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 ILE 194 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  GLU*     3.6    16.1    +      -       +      +
    136A  VAL*     3.7     4.7    -      -       -      +
    137A  ALA*     3.4    42.6    -      -       +      +
    168A  VAL*     4.3     6.3    -      -       +      -
    187A  VAL*     3.9    12.6    -      -       +      -
    188A  LEU*     3.4    32.5    -      -       +      -
    191A  ASN*     3.1    21.5    +      -       +      +
    192A  PRO      4.3     5.3    -      -       -      +
    193A  ASN*     1.3    79.6    -      -       -      +
    195A  LYS*     1.3    64.5    +      -       -      +
    196A  ALA      3.7    13.9    -      -       -      +
    197A  ILE*     3.8    11.9    -      -       +      -
    217A  LYS*     5.7     0.2    -      -       -      +
    220A  LYS      4.5     0.5    -      -       -      +
    221A  VAL*     3.3    17.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  LEU*     3.7    27.1    -      -       +      +
    133A  GLY      4.8     4.5    -      -       -      +
    134A  GLY*     4.5    15.0    -      -       -      -
    135A  GLU      2.8    15.9    +      -       -      +
    193A  ASN*     2.8    47.7    +      -       -      +
    194A  ILE*     1.3    73.7    +      -       -      +
    196A  ALA*     1.3    60.0    +      -       -      +
    220A  LYS      3.7    14.0    -      -       -      +
    221A  VAL*     3.6     4.1    -      -       -      -
    222A  LEU*     2.9    27.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  ILE*     3.4    34.8    -      -       +      -
    129A  LEU*     4.3     2.2    -      -       +      -
    135A  GLU      3.7     1.8    +      -       -      -
    136A  VAL*     3.2    13.3    -      -       +      -
    137A  ALA      3.0    21.8    +      -       -      -
    194A  ILE*     3.7     3.8    -      -       -      +
    195A  LYS*     1.3    81.6    -      -       -      +
    197A  ILE*     1.3    68.5    +      -       -      +
    198A  TYR      4.3     0.2    -      -       -      -
    221A  VAL*     4.1     1.1    -      -       -      +
    222A  LEU*     3.2    24.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  ILE*     4.1     4.4    -      -       -      +
    137A  ALA*     3.2    13.2    -      -       +      +
    139A  ILE*     3.5    31.4    -      -       +      -
    184A  ALA*     4.6     9.6    -      -       +      -
    187A  VAL*     5.0     4.7    -      -       +      -
    188A  LEU*     4.5    13.7    -      -       +      -
    194A  ILE*     3.8    19.1    -      -       +      -
    196A  ALA*     1.3    82.8    -      -       -      +
    198A  TYR*     1.3    64.4    -      -       -      +
    199A  CYS*     4.0     4.0    -      -       -      -
    208A  VAL*     3.8    28.3    -      -       +      -
    212A  VAL*     4.6     2.0    -      -       +      -
    221A  VAL*     4.1    19.7    -      -       +      -
    222A  LEU      2.8     8.7    +      -       -      +
    223A  VAL*     3.5     2.8    -      -       -      -
    224A  VAL      3.0    24.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  VAL*     3.5    15.5    -      -       -      +
    118A  GLY*     4.2     6.3    -      -       -      -
    121A  GLY*     4.2    19.7    -      -       -      -
    122A  ALA      5.2     0.7    -      -       -      +
    125A  ILE*     3.9    17.3    -      -       +      +
    137A  ALA      2.9     9.9    +      -       -      +
    138A  ILE*     3.3    20.3    -      -       +      -
    139A  ILE      2.9    23.9    +      -       -      -
    151A  ARG*     3.5    32.8    -      -       +      +
    155A  ALA*     3.9    16.4    -      -       +      -
    159A  PHE*     4.6     7.4    -      -       +      -
    197A  ILE*     1.3    74.6    -      -       -      +
    199A  CYS*     1.3    81.5    +      -       -      +
    200A  ALA*     3.8     6.9    -      -       +      -
    224A  VAL*     3.8    16.6    -      -       +      -
    225A  GLY      3.8     6.5    -      -       -      -
    226A  THR*     2.7    25.1    +      -       -      -
    245A  VAL*     4.7     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  ILE*     3.4     7.6    -      -       +      +
    197A  ILE*     4.0    15.3    -      -       -      -
    198A  TYR*     1.3    93.5    -      -       -      +
    200A  ALA*     1.3    60.1    +      -       -      +
    201A  ASN      3.1    10.0    +      -       -      +
    204A  MET*     4.5     4.3    -      -       +      -
    205A  ALA*     3.6    29.6    -      -       +      +
    208A  VAL*     3.6    35.0    -      -       -      -
    223A  VAL*     4.2     2.9    -      -       -      -
    224A  VAL      2.7    21.9    +      -       -      +
    225A  GLY      3.5     7.6    -      -       -      -
----------------------------------------------------------
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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