Contacts of the strand formed by residues 171 - 177 (chain A) in PDB entry 1RL3


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 ASN 171 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  PHE*     3.8    17.1    -      -       -      -
    169A  GLY      3.8     1.2    -      -       -      -
    170A  ASP*     1.3   104.6    +      -       -      +
    172A  PHE*     1.3    57.6    +      -       -      +
    173A  TYR*     2.6    63.9    +      -       -      -
    199A  GLY      4.3     0.2    -      -       -      +
    203A  LEU*     3.7    13.1    -      -       -      +
    209A  ARG*     3.7    14.4    +      -       -      -
    224A  ILE      2.3    39.4    -      -       -      +
    225A  ASP*     3.7     2.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 172 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  LEU*     5.2    14.8    -      -       +      -
    136A  PHE*     5.7     1.8    -      +       -      -
    151A  MET*     6.2     0.2    -      -       -      -
    171A  ASN*     1.3    70.5    -      -       -      +
    173A  TYR*     1.3    75.2    +      -       -      +
    174A  VAL*     3.6    24.7    -      -       +      -
    197A  SER*     3.0    29.4    -      -       -      -
    198A  PHE*     3.1    27.8    -      -       -      -
    199A  GLY      4.3     1.6    -      -       -      -
    200A  GLU*     3.6    29.4    -      -       +      -
    203A  LEU*     3.4     8.8    -      -       +      +
    223A  GLY*     3.1    21.2    -      -       -      -
    224A  ILE*     3.1    20.8    +      -       +      -
    229A  TYR*     3.4    44.0    -      +       +      -
    233A  LEU*     4.2    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 173 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  PHE*     4.9     4.8    -      +       -      -
    154A  VAL*     4.1    20.2    -      -       +      +
    156A  PHE*     4.6     8.3    -      +       -      -
    162A  VAL*     3.7    23.3    -      -       +      +
    163A  ILE*     5.2     0.9    -      -       +      -
    170A  ASP*     3.8     8.1    +      -       -      -
    171A  ASN*     2.6    50.6    +      -       -      -
    172A  PHE*     1.3    85.9    -      -       -      +
    174A  VAL*     1.3    64.0    +      -       -      +
    197A  SER*     3.0     5.8    -      -       -      -
    198A  PHE*     2.7    74.1    +      +       +      +
    209A  ARG*     4.8     5.8    -      -       -      -
    221A  LEU*     3.7    23.1    -      -       +      -
    222A  TRP      3.2    12.8    -      -       -      -
    223A  GLY*     4.4     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 174 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  ALA*     5.5     5.8    -      -       +      -
    133A  ASN*     3.9    21.3    -      -       +      +
    135A  LEU*     6.5     0.2    -      -       +      -
    136A  PHE*     4.4    20.0    -      -       +      -
    151A  MET*     5.1     5.4    -      -       +      -
    172A  PHE*     3.6    25.1    -      -       +      -
    173A  TYR*     1.3    78.1    -      -       -      +
    175A  ILE*     1.3    70.9    +      -       -      +
    176A  ASP      3.5     0.6    +      -       -      -
    195A  GLY*     4.8     1.3    -      -       -      +
    196A  GLY      3.7    11.7    -      -       -      +
    197A  SER*     4.1     3.6    -      -       -      -
    221A  LEU*     3.4     7.3    -      -       -      +
    222A  TRP*     2.9    52.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 175 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174A  VAL*     1.3    74.7    -      -       -      +
    176A  ASP*     1.3    64.2    +      -       -      +
    177A  GLN      3.8    14.1    -      -       -      +
    178A  GLY      3.8    12.3    -      -       -      +
    180A  MET*     3.3    20.9    -      -       +      +
    192A  VAL*     3.3    35.4    -      -       +      +
    193A  GLY      3.1    23.8    -      -       -      +
    194A  GLU*     3.3    20.4    -      -       -      -
    195A  GLY*     3.2    18.1    +      -       -      +
    196A  GLY      3.0    16.6    +      -       -      +
    198A  PHE*     3.8     8.5    -      -       +      -
    219A  VAL*     5.6     0.2    -      -       +      -
    221A  LEU*     3.6    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 176 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  ALA*     4.3     6.3    -      -       -      +
    129A  ALA*     4.0    10.8    -      -       -      +
    132A  LYS*     5.4     3.5    +      -       -      -
    174A  VAL*     3.5     4.6    +      -       -      -
    175A  ILE*     1.3    73.7    -      -       -      +
    177A  GLN*     1.3    64.5    +      -       -      +
    194A  GLU*     3.1    19.7    -      -       -      +
    220A  LYS*     3.1    38.8    +      -       +      +
    222A  TRP*     2.4    48.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 177 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175A  ILE*     3.4     4.9    -      -       -      +
    176A  ASP*     1.3    87.4    +      -       +      +
    178A  GLY*     1.3    62.5    +      -       -      +
    194A  GLU*     3.0    20.6    -      -       -      +
    218A  ASN      5.1     0.4    -      -       -      -
    219A  VAL*     3.3    22.5    -      -       -      +
    220A  LYS*     3.3    21.2    +      -       +      +
----------------------------------------------------------
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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