Contacts of the strand formed by residues 246 - 253 (chain A) in PDB entry 1DZI


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 246 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  LEU      2.9    16.9    +      -       -      -
    144A  ILE*     3.8     9.8    -      -       +      +
    145A  ASP      3.1    23.6    +      -       -      +
    244A  SER      3.7     2.0    +      -       -      -
    245A  ALA*     1.3    72.9    -      -       -      +
    247A  LYS*     1.3    66.3    +      -       -      +
    248A  VAL*     3.7     9.1    +      -       +      -
    274A  ASN      5.4     0.4    -      -       -      +
    276A  LEU*     3.8    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 247 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  ASP*     3.8     6.5    -      -       +      +
    231A  ARG      5.2     4.4    +      -       -      -
    235A  TYR*     3.9    43.1    +      -       +      +
    242A  ARG      6.0     1.8    -      -       -      -
    245A  ALA      3.7     8.5    +      -       -      +
    246A  THR*     1.3    74.1    -      -       -      +
    248A  VAL*     1.3    60.2    +      -       -      +
    273A  ASP*     4.0    29.3    +      -       -      +
    274A  ASN      4.1     7.7    +      -       -      +
    275A  ILE*     3.4    23.6    -      -       +      +
    276A  LEU*     2.9    31.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  ILE*     3.9    22.7    -      -       +      -
    145A  ASP      3.1     5.9    +      -       -      +
    146A  VAL*     3.4    24.1    -      -       +      -
    147A  VAL      2.9    19.8    +      -       -      -
    235A  TYR*     2.6    19.3    +      -       -      -
    246A  THR*     4.3    12.1    -      -       +      +
    247A  LYS*     1.3    80.5    -      -       -      +
    249A  MET*     1.3    61.2    +      -       -      +
    250A  VAL*     4.4     1.6    -      -       +      -
    275A  ILE*     4.2     0.4    -      -       -      -
    276A  LEU*     3.3    19.7    -      -       +      +
    278A  PHE*     4.0    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  VAL*     3.2    10.3    -      -       +      +
    149A  VAL*     3.7    19.7    -      -       +      -
    227A  ILE*     3.6    36.1    -      -       +      +
    230A  ALA*     3.5    28.7    -      -       +      -
    231A  ARG*     4.0    10.1    -      -       +      +
    235A  TYR*     3.3    20.4    -      -       +      +
    248A  VAL*     1.3    74.1    -      -       -      +
    250A  VAL*     1.3    67.2    +      -       -      +
    251A  VAL*     3.9    16.6    +      -       +      -
    270A  CYS*     4.7     4.9    -      -       -      -
    275A  ILE*     3.8    13.4    -      -       +      +
    276A  LEU      2.8     8.0    +      -       -      +
    277A  ARG*     3.4    15.0    -      -       +      +
    278A  PHE      3.0    23.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 250 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146A  VAL*     3.8    24.5    -      -       +      -
    147A  VAL      2.9     9.1    +      -       -      -
    148A  VAL*     3.4    17.1    -      -       +      +
    149A  VAL      2.7    30.1    +      -       -      +
    165A  PHE*     4.3    15.3    -      -       +      -
    169A  PHE*     4.0    18.2    -      -       +      -
    248A  VAL*     4.4     6.5    -      -       +      -
    249A  MET*     1.3    76.5    -      -       -      +
    251A  VAL*     1.3    58.0    +      -       -      +
    252A  VAL*     4.4     3.1    -      -       +      -
    278A  PHE*     3.9    17.5    -      -       +      -
    280A  ILE*     3.6    32.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 251 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  VAL*     3.3    14.6    -      -       +      +
    187A  TYR*     4.4     8.7    -      -       -      +
    223A  THR*     4.5     1.6    -      -       +      -
    227A  ILE*     4.1    13.2    -      -       +      -
    249A  MET*     3.9    27.8    -      -       +      +
    250A  VAL*     1.3    73.2    -      -       -      +
    252A  VAL*     1.3    61.8    +      -       -      +
    253A  THR*     3.9    23.3    +      -       +      +
    277A  ARG*     5.7     2.0    -      -       +      -
    278A  PHE      3.1    12.4    +      -       -      +
    279A  GLY*     3.7     1.9    -      -       -      -
    280A  ILE*     2.8    28.1    +      -       -      +
    303A  ILE*     3.7    34.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 252 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  VAL*     4.3    13.2    -      -       +      -
    149A  VAL      3.0     7.3    +      -       -      +
    150A  CYS*     4.2    18.4    -      -       -      -
    151A  ASP*     2.9    31.5    +      -       -      +
    162A  VAL*     4.7     7.0    -      -       +      -
    165A  PHE*     3.7    29.4    -      -       +      -
    166A  LEU*     4.7     3.1    -      -       +      -
    187A  TYR*     4.3     0.3    +      -       -      -
    250A  VAL*     4.3     8.7    -      -       +      +
    251A  VAL*     1.3    75.0    -      -       -      +
    253A  THR*     1.3    60.8    +      -       -      +
    280A  ILE*     3.5    20.4    -      -       +      +
    282A  VAL*     3.6    24.6    -      -       +      +
    315A  VAL*     4.6     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 253 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  ASP*     2.8    22.1    +      -       -      -
    156A  ILE*     4.4     0.4    -      -       -      -
    187A  TYR*     3.3    16.3    +      -       -      +
    221A  THR*     4.8     0.2    -      -       -      +
    223A  THR*     4.1     6.1    +      -       +      +
    251A  VAL*     3.9    21.5    -      -       +      +
    252A  VAL*     1.3    78.5    -      -       -      +
    254A  ASP*     1.3    68.4    +      -       -      +
    255A  GLY*     3.2    17.4    +      -       -      +
    256A  GLU      4.5     1.0    +      -       -      -
    280A  ILE      3.1     9.9    +      -       -      +
    282A  VAL*     3.0    26.2    +      -       -      -
    299A  GLU*     5.3     0.2    -      -       -      +
    300A  ILE*     3.4    18.3    -      -       +      +
    303A  ILE*     4.5    13.2    -      -       +      -
----------------------------------------------------------
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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