Contacts of the strand formed by residues 204 - 210 (chain I) in PDB entry 5A31


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 THR 204 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111I  SER*     3.4    25.8    -      -       -      +
    181I  SER*     3.2    26.7    -      -       -      +
    203I  GLY*     1.3    72.6    -      -       -      -
    205I  CYS*     1.3    63.7    +      -       -      +
    206I  LEU*     4.0    15.2    +      -       +      +
    221I  THR*     3.4     0.2    -      -       -      -
    222I  GLU*     2.8    44.7    +      -       -      +
    570I  PHE*     5.8     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 205 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111I  SER*     2.8    23.1    +      -       -      -
    112I  CYS*     3.2    12.7    -      -       -      +
    179I  GLY*     5.0     2.2    -      -       -      -
    180I  GLY      3.9    19.4    +      -       -      +
    185I  ILE*     5.6     1.8    -      -       -      -
    201I  ILE*     3.2    35.0    -      -       -      -
    203I  GLY      4.6     0.9    -      -       -      -
    204I  THR*     1.3    75.4    -      -       -      +
    206I  LEU*     1.3    60.7    +      -       -      +
    207I  ALA      3.5     1.8    -      -       -      +
    208I  LEU*     4.8     8.5    -      -       +      -
    219I  VAL*     3.9    13.2    -      -       +      -
    220I  VAL      3.1     9.9    -      -       -      +
    221I  THR*     3.3    20.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 206 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111I  SER*     4.1     7.9    -      -       -      +
    112I  CYS*     3.6    15.4    -      -       -      +
    204I  THR*     4.0    15.0    +      -       +      +
    205I  CYS*     1.3    79.8    -      -       -      +
    207I  ALA*     1.3    61.2    +      -       +      +
    220I  VAL*     3.1    15.6    +      -       +      +
    222I  GLU*     4.9     7.9    -      -       +      +
    568I  ARG*     4.2    17.3    -      -       -      +
    570I  PHE*     3.3    80.5    -      -       +      +
    572I  PHE      4.3    13.7    -      -       -      +
    573I  PRO*     4.7    10.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 207 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112I  CYS*     3.9     2.4    -      -       -      -
    205I  CYS      3.5     1.4    -      -       -      -
    206I  LEU*     1.3    80.8    -      -       -      +
    208I  LEU*     1.3    67.4    +      -       -      +
    219I  VAL*     3.3     6.9    -      -       -      +
    220I  VAL*     2.9    44.5    +      -       +      -
    573I  PRO      4.2    15.0    -      -       -      +
    575I  LEU*     3.6    30.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 208 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112I  CYS*     3.7    25.1    -      -       +      +
    114I  HIS*     3.2    35.7    -      -       +      +
    177I  VAL*     3.6    36.8    -      -       +      +
    178I  LEU      3.8     0.2    -      -       -      -
    179I  GLY*     3.7    24.7    -      -       -      +
    185I  ILE*     4.2    14.4    -      -       +      -
    205I  CYS*     4.8     8.3    -      -       +      -
    207I  ALA*     1.3    81.4    -      -       -      +
    209I  CYS*     1.3    60.4    +      -       -      +
    217I  LEU*     4.8     1.8    -      -       +      -
    218I  SER      3.5     2.2    -      -       -      -
    219I  VAL*     3.7    28.3    -      -       +      -
    575I  LEU*     4.4     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 209 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114I  HIS*     4.5     7.2    -      -       -      -
    208I  LEU*     1.3    75.4    -      -       -      +
    210I  LEU*     1.3    59.5    +      -       -      +
    217I  LEU*     3.3     5.2    -      -       -      +
    218I  SER*     2.8    43.1    +      -       -      +
    575I  LEU*     4.0    18.6    -      -       +      -
    576I  TRP*     3.9     6.1    -      -       -      -
    577I  ASN*     3.3    34.3    -      -       -      -
    584I  HIS*     2.9    42.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 210 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114I  HIS*     3.9    17.4    +      -       -      +
    116I  MET*     3.1    39.7    -      -       +      +
    175I  ILE*     3.8    16.8    -      -       +      -
    177I  VAL*     3.6    26.2    -      -       +      +
    187I  LEU*     4.0    14.6    -      -       +      -
    209I  CYS*     1.3    76.6    -      -       -      +
    211I  SER*     1.3    67.4    +      -       -      +
    212I  SER      3.8     0.3    +      -       -      -
    214I  LEU*     4.0    17.3    -      -       +      -
    216I  SER      3.0    25.1    -      -       -      +
    217I  LEU*     3.9    18.4    -      -       +      +
    238I  THR*     4.5     7.4    -      -       +      +
    241I  LEU*     4.8     2.9    -      -       +      -
    577I  ASN*     4.2     4.2    -      -       -      +
    584I  HIS*     4.3     1.3    -      -       -      -
----------------------------------------------------------
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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