Contacts of the strand formed by residues 211 - 216 (chain A) in PDB entry 1ZSV


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 211 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  THR*     3.7    17.9    -      -       +      +
    146A  MET*     3.7    26.7    -      -       +      -
    170A  VAL*     3.7    24.1    -      -       +      +
    203A  LEU*     2.5    52.5    +      -       +      +
    206A  ALA*     3.6     7.3    -      -       -      +
    207A  SER*     3.6    25.6    +      -       -      -
    210A  GLY*     1.3    73.0    -      -       -      -
    212A  ASP*     1.3    62.8    +      -       -      +
    213A  CYS      4.0     9.6    -      -       -      +
    226A  VAL*     5.1     6.7    -      -       +      -
    229A  GLN*     3.1    31.0    +      -       +      -
    230A  MET*     3.5    19.2    -      -       -      +
    231A  LYS*     2.8    29.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 212 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  GLY      4.9     0.7    -      -       -      +
    143A  GLU*     3.6    30.6    -      -       +      +
    144A  THR*     2.9    30.1    +      -       -      +
    211A  TYR*     1.3    73.0    -      -       -      +
    213A  CYS*     1.3    59.9    +      -       -      +
    230A  MET*     3.9     0.9    -      -       -      -
    231A  LYS*     3.2    43.8    +      -       -      +
    234A  GLY*     3.3     7.0    -      -       -      -
    235A  ARG*     3.1    40.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 213 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  CYS*     4.0    21.5    -      -       +      -
    139A  VAL*     3.5    21.8    -      -       -      -
    143A  GLU*     4.5     3.1    -      -       -      -
    144A  THR      3.2     3.0    +      -       -      +
    145A  VAL*     3.4    18.5    -      -       +      -
    146A  MET*     2.9    26.4    +      -       -      +
    211A  TYR*     4.0     2.6    -      -       -      +
    212A  ASP*     1.3    85.6    -      -       -      +
    214A  TYR*     1.3    60.7    +      -       -      +
    230A  MET*     4.1     2.9    -      -       -      -
    235A  ARG*     3.3    37.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 214 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  CYS*     4.4     3.6    -      -       -      -
    146A  MET*     3.5    32.1    -      -       +      -
    148A  ASN*     2.7    33.4    +      -       +      -
    213A  CYS*     1.3    75.1    -      -       -      +
    215A  PHE*     1.3    65.9    +      -       -      +
    216A  ASP*     3.6    13.0    +      -       +      -
    222A  PHE*     3.6     4.5    -      -       -      -
    223A  SER*     2.7    40.6    +      -       -      -
    226A  VAL*     3.7    24.9    -      -       +      -
    227A  ILE*     5.2     1.3    -      -       +      -
    230A  MET*     3.8    17.5    -      -       +      -
    235A  ARG      3.0     8.1    +      -       -      +
    236A  ILE*     3.4    30.3    -      -       +      +
    237A  ALA*     2.9    26.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 215 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  THR      3.8     4.5    -      -       -      -
    129A  ALA      3.9     2.0    -      -       -      -
    132A  GLY*     3.6    12.1    -      -       -      -
    133A  LEU*     3.6    29.8    -      -       +      -
    137A  CYS*     4.6     5.8    -      -       -      -
    145A  VAL*     4.7     3.5    -      -       +      +
    146A  MET      2.9    13.6    +      -       -      +
    147A  VAL*     3.7     5.4    -      -       +      +
    148A  ASN*     3.4    26.0    +      -       -      +
    154A  VAL*     3.6    32.1    -      -       +      -
    158A  VAL*     3.7    37.5    -      -       +      -
    213A  CYS      4.2     0.6    -      -       -      -
    214A  TYR*     1.3    73.5    -      -       -      +
    216A  ASP*     1.3    57.5    +      -       -      +
    217A  ASN*     3.7    14.5    +      -       -      -
    237A  ALA*     3.9     9.9    -      -       +      -
    239A  CYS*     3.6    16.4    -      -       +      -
    270A  PHE*     3.8    18.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with ASP 216 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  ASN*     3.2     7.5    +      -       -      -
    214A  TYR*     3.5    20.9    +      -       +      -
    215A  PHE*     1.3    71.3    -      -       -      +
    217A  ASN*     1.3    60.6    +      -       -      +
    218A  VAL      3.0     8.0    +      -       -      -
    219A  GLY*     2.9    30.1    +      -       -      -
    223A  SER*     2.7    27.4    +      -       -      -
    236A  ILE*     4.4     6.3    -      -       +      +
    237A  ALA      2.9    15.9    +      -       -      +
    238A  ILE*     4.6    11.8    -      -       -      +
    239A  CYS*     2.9    32.7    +      -       -      +
    240A  GLY      3.2     8.0    +      -       -      +
----------------------------------------------------------
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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