Contacts of the strand formed by residues 162 - 169 (chain A) in PDB entry 1RHM


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 MET 162 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  MET*     3.0    52.2    -      -       -      +
    156A  TYR      5.3     4.0    -      -       -      +
    162A  GLU*     1.3    74.1    -      -       -      +
    163A  GLY*     1.3    58.6    +      -       -      +
    196A  LEU      3.4    20.9    -      -       -      -
    197A  LYS*     3.5    26.7    +      -       -      -
    198A  TYR*     3.6    21.4    +      -       -      -
    228A  SER*     3.9     5.0    +      -       -      -
    229A  SER*     3.0    32.6    +      -       -      -
    400B  PHE*     5.3    14.4    -      -       -      -
    401B  TYR*     5.8     2.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  MET*     1.3    88.8    -      -       -      +
    164A  LEU*     1.3    67.6    +      -       -      -
    197A  LYS      4.9     0.4    +      -       -      -
    198A  TYR*     3.4     6.2    -      -       -      -
    199A  GLU*     3.1    25.6    +      -       -      +
    227A  ARG*     3.8    19.3    -      -       -      -
    229A  SER      3.2    12.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  GLU*     5.0     0.2    -      -       -      +
    163A  GLY*     1.3    78.1    -      -       -      -
    165A  CYS*     1.3    63.0    +      -       -      +
    166A  ILE*     4.2     6.7    -      -       +      -
    198A  TYR*     3.4     8.5    -      -       -      -
    199A  GLU*     3.9    23.8    -      -       +      +
    201A  ARG*     3.2    35.2    -      -       -      +
    218A  VAL*     3.7    26.5    -      -       +      -
    221A  GLU*     4.0     1.6    -      -       -      +
    224A  HIS*     4.4     3.1    +      -       +      -
    227A  ARG*     3.3    45.2    -      -       -      +
    229A  SER      3.8     4.2    +      -       -      -
    230A  PHE*     4.1    15.0    -      -       +      +
    231A  VAL      3.0    23.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  LEU*     1.3    77.6    -      -       -      +
    166A  ILE*     1.3    65.8    +      -       -      +
    167A  ILE*     3.6    18.3    +      -       -      -
    193A  PHE*     3.6    35.2    -      -       -      -
    198A  TYR*     4.0    22.0    -      -       +      -
    199A  GLU      3.5     6.1    +      -       -      -
    200A  VAL*     3.5    10.0    -      -       +      +
    201A  ARG      3.1    23.0    +      -       -      +
    231A  VAL*     2.9    20.6    -      -       +      -
    233A  VAL*     4.8     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  LEU*     4.2    16.6    -      -       +      -
    165A  CYS*     1.3    74.2    -      -       -      +
    167A  ILE*     1.3    56.6    +      -       -      +
    168A  ILE*     3.6    28.3    -      -       +      -
    201A  ARG*     3.7    40.2    -      -       +      +
    203A  LYS*     5.0     4.0    -      -       +      -
    214A  LEU*     4.1     8.5    -      -       +      -
    215A  MET*     3.9    15.9    -      -       +      -
    218A  VAL*     4.4    13.2    -      -       +      -
    230A  PHE*     4.0    24.0    -      -       +      -
    231A  VAL      2.8     7.3    +      -       -      +
    232A  CYS*     3.3     5.4    -      -       -      -
    233A  VAL*     2.7    33.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165A  CYS*     4.1    17.9    -      -       -      +
    166A  ILE*     1.3    77.8    -      -       -      +
    168A  ILE*     1.3    64.5    +      -       -      +
    169A  ASN*     4.6     4.3    -      -       +      -
    186A  ALA*     4.0     9.0    -      -       -      +
    189A  LEU*     3.8    27.4    -      -       +      -
    190A  ARG*     3.8    12.8    -      -       -      +
    200A  VAL*     3.8    17.5    -      -       +      -
    201A  ARG      3.0    12.2    +      -       -      +
    202A  ASN*     4.1    17.0    -      -       -      +
    203A  LYS*     3.1    25.1    +      -       -      +
    233A  VAL*     3.6    16.8    -      -       +      -
    235A  LEU*     4.3    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  ILE*     3.6    16.2    -      -       +      -
    167A  ILE*     1.3    72.1    -      -       -      +
    169A  ASN*     1.3    59.5    +      -       -      +
    170A  ASN*     4.0    14.1    -      -       -      +
    203A  LYS*     3.9     8.1    -      -       +      +
    206A  LEU*     3.8    22.9    -      -       +      -
    211A  ILE*     4.0    24.5    -      -       +      -
    214A  LEU*     3.2    35.4    -      -       +      -
    215A  MET*     4.5     7.2    -      -       +      -
    232A  CYS*     4.8     1.8    -      -       -      -
    233A  VAL      2.8     9.9    +      -       -      +
    234A  LEU*     3.5    27.6    -      -       +      -
    235A  LEU*     2.9    29.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  ILE*     4.6     4.9    -      -       +      +
    168A  ILE*     1.3    73.9    -      -       -      +
    170A  ASN*     1.3    60.2    +      -       -      +
    171A  LYS*     3.7     4.7    +      -       -      +
    182A  THR*     2.6    57.9    +      -       -      +
    183A  ASP*     4.0     5.5    -      -       -      +
    186A  ALA*     3.4    14.8    -      -       +      +
    202A  ASN*     5.6     0.7    -      -       -      +
    203A  LYS      2.9    15.1    +      -       -      +
    204A  ASN*     3.2    21.1    +      -       -      +
    205A  ASP      3.1    17.8    +      -       -      -
    235A  LEU*     2.9    21.7    -      -       +      +
----------------------------------------------------------
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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