Contacts of the strand formed by residues 193 - 199 (chain B) in PDB entry 1HDZ


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 SER 193 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  VAL*     3.2    21.5    -      -       -      +
    190B  THR*     2.5    31.0    +      -       -      -
    191B  PRO      3.2     1.8    +      -       -      -
    192B  GLY*     1.3    77.5    -      -       -      +
    194B  THR*     1.3    60.7    +      -       -      +
    195B  CYS*     4.1     0.6    -      -       -      -
    216B  ALA*     3.4     3.0    -      -       -      -
    217B  ALA      2.7    30.3    +      -       -      +
    218B  ARG      3.2     3.1    +      -       -      -
    263B  ASP*     3.5    15.7    -      -       -      -
    264B  PHE*     3.3    21.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 194 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  ARG*     5.8     0.9    -      -       -      +
    192B  GLY      4.7     1.9    +      -       -      -
    193B  SER*     1.3    75.3    +      -       -      +
    195B  CYS*     1.3    62.2    +      -       -      +
    217B  ALA*     5.0     1.7    -      -       -      +
    218B  ARG*     3.3    31.9    +      -       +      +
    220B  ILE*     4.7     1.1    -      -       +      -
    258B  THR*     3.6    22.7    -      -       +      +
    261B  GLY      4.9     1.1    -      -       -      +
    262B  VAL*     3.5    27.4    -      -       +      -
    263B  ASP*     2.8    42.1    +      -       -      +
    264B  PHE      3.2     2.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 195 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  VAL*     3.6    25.4    -      -       -      -
    193B  SER*     4.1     2.5    -      -       -      -
    194B  THR*     1.3    78.0    -      -       -      +
    196B  ALA*     1.3    60.8    +      -       -      +
    211B  CYS*     3.9    24.9    -      -       +      -
    216B  ALA*     3.4    29.6    -      -       -      -
    218B  ARG      2.8     8.1    +      -       -      +
    219B  ILE*     3.3     6.9    -      -       +      -
    220B  ILE*     3.0    25.9    +      -       -      +
    262B  VAL*     3.9     4.3    -      -       -      +
    264B  PHE*     3.1    18.8    -      -       +      +
    266B  PHE*     4.2     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 196 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195B  CYS*     1.3    73.9    -      -       -      +
    197B  VAL*     1.4    61.4    +      -       -      +
    198B  PHE*     4.3    20.0    -      -       +      -
    220B  ILE*     3.3    10.5    -      -       +      +
    222B  VAL*     5.1     1.3    -      -       +      -
    254B  LEU*     4.5    12.8    -      -       +      -
    262B  VAL*     3.9    24.4    -      -       +      +
    264B  PHE      3.0     4.9    +      -       -      -
    265B  SER*     3.5     2.9    -      -       -      -
    266B  PHE*     3.1    27.8    +      -       -      -
    281B  CYS*     4.4     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 197 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196B  ALA*     1.4    76.1    -      -       -      +
    198B  PHE*     1.3    63.6    +      -       -      +
    199B  GLY      3.6    13.8    +      -       -      +
    200B  LEU*     4.6     4.7    -      -       +      +
    204B  GLY      3.8    19.5    -      -       -      +
    207B  ALA*     4.0     3.6    -      -       +      -
    208B  VAL*     4.1    30.1    -      -       +      +
    211B  CYS*     4.3     6.1    -      -       -      -
    219B  ILE*     4.3    14.1    -      -       +      -
    220B  ILE      2.9     9.9    +      -       -      +
    221B  ALA*     3.8     0.6    -      -       -      -
    222B  VAL*     2.8    29.1    +      -       -      +
    266B  PHE*     3.8    16.8    -      -       +      -
    268B  VAL*     3.9    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 198 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196B  ALA*     4.3     7.6    -      -       +      -
    197B  VAL*     1.3    77.5    -      -       -      +
    199B  GLY*     1.3    58.2    +      -       -      +
    222B  VAL*     3.8    26.7    -      -       +      -
    243B  PRO*     5.8     0.7    -      -       +      -
    250B  ILE*     4.1    10.8    -      -       +      -
    254B  LEU*     3.7    26.7    -      -       +      -
    265B  SER*     5.0     0.7    -      -       -      -
    266B  PHE      2.9    21.7    +      -       -      +
    267B  GLU*     4.0     8.1    -      -       +      -
    268B  VAL      2.8    22.6    +      -       -      -
    269B  ILE*     3.1    17.9    -      -       +      +
    274B  THR*     3.8    22.9    -      -       +      -
    277B  ALA*     4.0    32.5    -      -       +      -
    278B  SER*     4.1    14.8    -      -       -      -
    281B  CYS*     4.0    18.8    -      -       -      -
    377B  NAD      5.2     0.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLY 199 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197B  VAL*     3.6     4.3    +      -       -      +
    198B  PHE*     1.3    76.0    -      -       -      +
    200B  LEU*     1.3    68.1    +      -       -      +
    201B  GLY      3.7     2.7    -      -       -      -
    204B  GLY*     3.2    20.5    -      -       -      -
    222B  VAL      2.8    16.2    +      -       -      -
    223B  ASP*     3.9     1.6    -      -       -      -
    268B  VAL*     3.9     5.3    -      -       -      +
    269B  ILE*     3.5    18.7    -      -       -      +
    377B  NAD      3.8    10.1    -      -       -      -
----------------------------------------------------------
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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