Contacts of the strand formed by residues 38 - 44 (chain B) in PDB entry 1ZRF


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 38 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  GLU*     1.3    91.3    -      -       +      +
     39B  LEU*     1.3    60.8    +      -       -      +
     40B  TYR*     3.5    27.9    +      -       -      -
     71B  GLY      3.6     3.5    -      -       -      +
     82B  ARG*     3.0    30.6    +      -       -      +
     96B  GLU*     5.3     5.3    +      -       -      +
     97B  ILE      3.4    13.0    -      -       -      -
     98B  SER*     4.4     8.5    -      -       -      +
     99B  TYR*     3.6     6.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 39 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  PHE*     4.7     0.9    -      -       +      -
     38B  THR*     1.3    74.5    -      -       -      +
     40B  TYR*     1.3    67.2    +      -       -      +
     69B  PHE*     3.8    22.0    -      -       +      -
     70B  ILE      3.5    17.3    -      -       -      +
     71B  GLY      4.0     0.2    -      -       -      +
     72B  GLU*     3.7    31.6    -      -       +      -
     75B  LEU*     5.5     2.2    -      -       +      -
     95B  ALA      3.9     0.2    -      -       -      +
     96B  GLU*     3.3     4.7    -      -       -      +
     97B  ILE*     2.7    47.9    +      -       +      +
     99B  TYR*     3.8    14.5    -      -       +      -
    102B  PHE*     3.5    50.5    -      -       +      -
    116B  LEU*     5.0     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 40 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  PHE*     6.1     0.2    -      -       -      -
     23B  TYR*     4.1     9.3    +      +       -      -
     29B  LEU*     3.9    23.9    +      -       +      -
     30B  ILE*     3.9    26.6    -      -       +      +
     38B  THR*     3.5    32.1    +      -       -      -
     39B  LEU*     1.3    78.1    -      -       -      +
     41B  TYR*     1.3    61.2    +      -       -      +
     42B  ILE      4.3     0.4    -      -       -      -
     69B  PHE*     3.3    11.3    -      -       -      -
     70B  ILE*     2.9    54.3    +      -       +      +
     71B  GLY*     4.5     0.2    -      -       -      -
     82B  ARG*     3.8    11.6    +      -       -      -
     94B  VAL*     3.8    15.0    -      -       +      -
     95B  ALA      3.3     5.2    -      -       -      -
     96B  GLU*     3.5    41.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 41 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  LEU*     3.6    34.7    -      -       +      +
     14B  PHE*     3.9    22.9    -      +       +      -
     15B  LEU*     4.3    11.4    -      -       +      -
     40B  TYR*     1.3    74.4    -      -       -      +
     42B  ILE*     1.3    76.4    +      -       -      +
     43B  VAL*     3.3    17.2    +      -       +      -
     67B  GLY*     3.5    35.9    +      -       -      -
     68B  ASP      3.6     4.3    -      -       -      -
     69B  PHE*     3.9    34.5    -      +       +      -
     94B  VAL*     3.4     3.2    -      -       -      +
     95B  ALA*     2.8    42.4    +      -       +      +
    119B  GLN*     5.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 42 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  TYR*     1.3    78.6    -      -       -      +
     43B  VAL*     1.3    60.3    +      -       -      +
     44B  LYS      3.6    14.4    -      -       -      +
     45B  GLY      3.5    22.9    -      -       -      +
     47B  VAL*     4.0    23.3    -      -       +      +
     64B  LEU*     4.1    13.7    -      -       +      +
     65B  ASN      3.7    20.0    -      -       -      +
     66B  GLN*     3.7     7.6    -      -       -      -
     67B  GLY      2.8    27.5    +      -       -      -
     68B  ASP      2.9    13.1    +      -       -      +
     70B  ILE*     3.5    35.4    -      -       +      -
     92B  CYS*     5.2     2.7    -      -       -      -
     93B  GLU      3.9     4.0    -      -       -      +
     94B  VAL*     4.4     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 43 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  LEU*     4.3    16.2    -      -       +      -
     20B  ILE*     4.7     5.8    -      -       +      -
     41B  TYR*     3.3    24.0    +      -       +      +
     42B  ILE*     1.3    75.8    -      -       -      +
     44B  LYS*     1.3    71.1    +      -       +      +
     66B  GLN*     3.5    20.5    -      -       -      +
     93B  GLU*     2.8    40.3    +      -       -      +
     95B  ALA*     4.2    15.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 44 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  ILE*     3.5     4.2    -      -       -      +
     43B  VAL*     1.3    90.2    -      -       +      +
     45B  GLY*     1.3    62.3    +      -       -      +
     66B  GLN*     4.2     9.6    -      -       -      +
     91B  ALA      4.5     1.1    -      -       -      +
     92B  CYS*     3.2     6.3    -      -       -      +
     93B  GLU*     2.8    61.4    +      -       +      +
----------------------------------------------------------
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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