Contacts of the strand formed by residues 259 - 264 (chain A) in PDB entry 1Z6T


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 GLN 259 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  LEU*     3.4    33.0    -      -       +      +
    144A  LYS      4.5     0.2    +      -       -      -
    145A  GLY*     3.5    28.2    +      -       -      -
    146A  GLU      3.2    23.6    -      -       -      +
    148A  GLY      3.7     4.3    -      -       -      -
    177A  CYS      4.9     2.1    +      -       -      +
    178A  PHE*     3.8    16.3    -      -       +      -
    231A  MET*     5.9     0.6    -      -       -      +
    237A  ARG*     4.1    11.1    -      -       -      +
    238A  SER      3.5    33.5    +      -       -      +
    239A  LEU*     3.4     7.9    -      -       +      +
    240A  LEU*     3.0    25.8    +      -       -      +
    258A  CYS*     1.3    74.3    -      -       -      +
    260A  ILE*     1.3    63.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 260 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  LEU*     4.8     1.3    -      -       -      +
    148A  GLY      3.0     8.8    +      -       -      +
    149A  TRP*     3.4    39.9    -      -       +      -
    150A  VAL*     2.9    28.6    +      -       -      +
    239A  LEU*     3.9     4.0    -      -       -      +
    240A  LEU*     3.3    18.8    -      -       +      +
    242A  LEU*     3.8    18.8    -      -       +      -
    254A  PHE*     3.4    37.0    -      -       +      +
    258A  CYS*     3.8    18.6    -      -       +      +
    259A  GLN*     1.3    81.0    -      -       -      +
    261A  LEU*     1.3    73.1    +      -       -      +
    262A  LEU*     4.2     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 261 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  ILE*     4.1     9.6    -      -       +      -
    140A  LEU*     4.2    15.9    -      -       +      -
    150A  VAL*     3.4    34.8    -      -       +      +
    152A  ILE*     3.8    24.2    -      -       +      -
    164A  ALA*     4.0    35.0    -      -       +      +
    168A  VAL*     5.0     0.9    -      -       +      -
    239A  LEU*     3.7    24.1    -      -       +      +
    240A  LEU      2.9     7.2    +      -       -      +
    241A  ILE*     3.1    19.3    -      -       +      +
    242A  LEU      2.8    23.9    +      -       -      -
    260A  ILE*     1.3    75.9    -      -       -      +
    262A  LEU*     1.3    60.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 262 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  TRP*     3.9    30.7    -      -       +      -
    150A  VAL      3.0    12.6    +      -       -      +
    151A  THR*     3.5    31.4    -      -       +      +
    152A  ILE*     2.9    29.3    +      -       -      +
    241A  ILE*     5.3     0.4    -      -       -      -
    242A  LEU*     3.1    22.4    -      -       +      +
    245A  VAL*     4.2     6.3    -      -       +      -
    251A  LEU*     4.1    18.6    -      -       +      -
    260A  ILE*     4.2     5.2    -      -       +      -
    261A  LEU*     1.3    75.4    -      -       -      +
    263A  THR*     1.3    71.6    +      -       -      +
    264A  THR*     4.3     0.7    -      -       -      -
    269A  VAL*     3.9    28.7    -      -       +      -
    270A  THR*     5.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 263 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  ILE*     3.2    16.4    -      -       +      -
    160A  LYS*     3.8    41.6    -      -       +      +
    164A  ALA*     4.2    14.6    -      -       +      -
    184A  TRP*     6.0     0.2    -      -       +      -
    241A  ILE*     5.8     1.6    -      -       +      -
    242A  LEU      3.0     7.6    +      -       -      +
    243A  ASP*     2.8    18.7    +      -       -      +
    244A  ASP*     2.7    29.5    +      -       -      +
    245A  VAL*     3.0    26.2    +      -       -      +
    262A  LEU*     1.3    78.2    -      -       -      +
    264A  THR*     1.3    63.0    +      -       -      +
    900A  ADP      5.3     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 264 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  THR*     3.4    31.4    -      -       +      -
    152A  ILE      3.0     5.5    +      -       -      +
    153A  HIS*     3.1    29.9    -      -       +      -
    154A  GLY      3.2     4.7    +      -       -      +
    160A  LYS*     3.6     9.1    -      -       -      +
    244A  ASP*     4.6     3.6    -      -       -      -
    245A  VAL      2.9    23.5    +      -       -      +
    262A  LEU*     4.3     1.6    -      -       -      -
    263A  THR*     1.3    76.7    -      -       -      +
    265A  ARG*     1.3    56.8    +      -       -      +
    266A  ASP*     2.9    40.2    +      -       -      +
    267A  LYS*     4.1     0.2    -      -       -      -
    269A  VAL*     3.7    11.3    -      -       +      +
----------------------------------------------------------
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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