Contacts of the strand formed by residues 176 - 185 (chain H) in PDB entry 1RZK


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 TYR 176 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87H  THR*     4.4     8.5    -      -       -      +
    110H  THR*     3.6    20.4    -      -       +      +
    112H  SER*     5.7     2.4    -      -       -      -
    144H  ASP*     3.3     4.5    +      -       -      -
    145H  TYR*     3.0    52.9    +      -       +      -
    146H  PHE*     3.5    26.3    -      +       -      -
    147H  PRO      3.4    22.0    -      -       -      -
    148H  GLU*     3.2    26.0    -      -       -      -
    168H  ALA*     4.0     7.4    -      -       +      -
    169H  VAL*     3.0     8.5    -      -       -      +
    170H  LEU*     3.4    45.9    -      -       +      +
    171H  GLN*     4.3     0.7    -      -       -      -
    175H  LEU*     1.3    76.2    -      -       -      +
    177H  SER*     1.3    64.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 177 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141H  LEU*     4.7     6.2    -      -       -      +
    142H  VAL      3.0    17.8    +      -       -      -
    143H  LYS*     3.4    14.6    -      -       -      +
    145H  TYR*     4.3     2.7    -      -       -      -
    168H  ALA*     3.7     1.1    -      -       -      -
    169H  VAL*     2.8    35.8    +      -       -      +
    171H  GLN*     2.8    29.6    +      -       -      -
    176H  TYR*     1.3    75.3    -      -       -      +
    178H  LEU*     1.3    63.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 178 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141H  LEU*     3.7     2.6    -      -       -      +
    142H  VAL*     3.0    56.1    +      -       +      +
    145H  TYR*     4.2     5.5    -      -       +      +
    150H  VAL*     3.3    34.8    -      -       +      +
    152H  VAL*     4.5     9.2    -      -       +      -
    165H  THR*     4.0    13.9    -      -       +      -
    166H  PHE*     3.3    24.0    -      -       -      +
    167H  PRO*     4.3     3.6    -      -       +      -
    168H  ALA*     3.5    14.8    -      -       +      +
    177H  SER*     1.3    80.7    +      -       -      +
    179H  SER*     1.3    93.8    +      -       -      +
    180H  SER      4.4     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 179 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124H  LEU*     5.6     0.7    -      -       -      -
    140H  CYS      3.5    11.9    -      -       -      -
    141H  LEU*     2.8    22.0    -      -       -      +
    165H  THR*     3.4     2.6    -      -       -      +
    166H  PHE*     2.7    53.3    +      -       -      +
    178H  LEU*     1.3    93.7    +      -       -      +
    180H  SER*     1.3    60.0    +      -       -      +
    181H  VAL*     5.1     2.5    -      -       -      -
    133L  VAL*     4.6     8.0    -      -       -      +
    176L  SER*     4.5    10.4    +      -       -      -
    178L  THR*     4.9     1.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 180 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139H  GLY*     4.1     0.7    -      -       -      -
    140H  CYS*     2.8    37.9    +      -       -      +
    142H  VAL*     5.9     0.9    -      -       -      -
    152H  VAL*     3.1    24.3    -      -       -      +
    154H  TRP*     2.8    29.7    +      -       -      -
    163H  VAL*     5.0     0.7    -      -       -      +
    165H  THR*     2.9    27.5    +      -       -      +
    178H  LEU*     4.4     1.5    -      -       -      +
    179H  SER*     1.3    74.3    -      -       -      +
    181H  VAL*     1.3    68.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 181 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124H  LEU*     4.8    13.0    -      -       +      -
    137H  ALA*     5.6     0.9    -      -       +      -
    138H  LEU      3.2    14.4    -      -       -      +
    139H  GLY*     3.8     5.2    -      -       -      -
    154H  TRP*     4.8     1.6    -      -       -      -
    163H  VAL*     3.0     8.4    -      -       -      +
    164H  HIS*     2.9    52.1    +      -       +      +
    166H  PHE*     4.0    12.1    -      -       +      -
    179H  SER*     5.0     1.8    -      -       -      -
    180H  SER*     1.3    84.8    +      -       -      +
    182H  VAL*     1.3    65.1    +      -       -      +
    183H  THR*     5.5     1.3    -      -       -      +
    118L  PHE*     4.9     2.5    -      -       +      -
    133L  VAL*     5.9     1.6    -      -       +      -
    135L  LEU*     3.2    37.5    -      -       +      -
    137L  ASN*     4.1     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 182 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137H  ALA*     4.3     0.4    -      -       -      -
    138H  LEU*     2.8    43.3    +      -       +      +
    154H  TRP*     4.1    26.7    -      -       +      -
    159H  LEU*     3.6    17.3    -      -       +      -
    161H  SER      3.6     5.6    -      -       -      +
    162H  GLY*     3.0    18.2    -      -       -      +
    163H  VAL*     3.4    19.3    -      -       +      -
    181H  VAL*     1.3    76.9    -      -       -      +
    183H  THR*     1.3    57.9    +      -       -      +
    184H  VAL*     3.1    29.5    +      -       +      -
    194H  TYR*     5.6     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 183 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135H  THR*     3.3    25.8    +      -       -      +
    136H  ALA      3.6    16.2    -      -       -      +
    137H  ALA*     3.1    19.8    -      -       +      +
    162H  GLY*     3.3    14.2    +      -       -      +
    181H  VAL*     5.5     0.9    -      -       -      +
    182H  VAL*     1.3    68.3    -      -       -      +
    184H  VAL*     1.3    62.9    +      -       -      +
    185H  PRO*     4.8     0.3    -      -       -      +
    116L  PHE*     4.5     8.9    -      -       +      -
    137L  ASN*     3.2    28.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 184 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135H  THR*     3.3     5.4    -      -       -      -
    136H  ALA*     2.6    38.2    +      -       -      +
    138H  LEU*     3.7    22.0    -      -       +      -
    159H  LEU*     3.4    21.1    -      -       +      -
    182H  VAL*     3.4    28.9    -      -       +      -
    183H  THR*     1.3    74.3    -      -       -      +
    185H  PRO*     1.3    70.1    -      -       +      +
    186H  SER*     3.5     0.3    +      -       -      -
    189H  LEU*     4.8     2.7    -      -       +      +
    194H  TYR*     3.1    33.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 185 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134H  GLY      3.6     6.5    -      -       -      +
    135H  THR*     3.2    27.3    -      -       +      -
    183H  THR      4.8     0.4    -      -       -      +
    184H  VAL*     1.3    90.7    -      -       +      +
    186H  SER*     1.3    65.6    +      -       -      +
    187H  SER*     4.2    12.6    -      -       -      +
    188H  SER*     3.1    29.3    +      -       -      -
    189H  LEU*     4.3     1.9    -      -       -      +
    194H  TYR*     4.2     3.3    +      -       -      -
----------------------------------------------------------
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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