Contacts of the strand formed by residues 75 - 81 (chain O) in PDB entry 1YIT


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 75 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56O  GLU      5.1     1.2    +      -       -      -
     57O  THR*     3.4    28.0    -      -       +      +
     58O  VAL*     2.7    33.3    +      -       -      +
     74O  VAL*     1.3    76.8    -      -       -      +
     76O  VAL*     1.3    57.5    +      -       -      +
     94O  GLU*     3.3    18.3    +      -       -      +
     96O  VAL*     3.9    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 76 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48O  ILE*     4.0    36.8    -      -       +      -
     58O  VAL*     3.4    12.8    -      -       +      +
     60O  VAL*     4.4     3.8    -      -       +      -
     64O  VAL*     4.0    16.6    -      -       +      -
     70O  LEU*     5.2     0.2    -      -       +      -
     74O  VAL*     4.3    10.1    -      -       +      -
     75O  THR*     1.3    76.8    -      -       -      +
     77O  ALA*     1.3    63.6    +      -       -      +
     81O  PHE*     3.5    25.8    -      -       +      -
     89O  ILE*     4.1    20.2    -      -       +      -
     94O  GLU      2.9     8.9    +      -       -      +
     96O  VAL*     2.7    34.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 77 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57O  THR*     4.2     8.1    -      -       +      -
     58O  VAL      2.7    12.5    +      -       -      +
     59O  VAL*     3.4    13.0    -      -       +      -
     60O  VAL      2.8    25.9    +      -       -      -
     75O  THR      4.1     0.2    +      -       -      -
     76O  VAL*     1.3    74.4    -      -       -      +
     78O  ALA*     1.3    58.8    +      -       -      +
     96O  VAL*     3.1    13.2    -      -       +      +
     98O  LEU*     3.0    19.4    -      -       +      +
    101O  ALA*     4.0    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 78 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60O  VAL*     3.5     9.2    -      -       +      -
     62O  GLY      3.8     5.6    -      -       -      +
     64O  VAL*     3.3    33.9    -      -       +      -
     77O  ALA*     1.3    73.7    -      -       -      +
     79O  VAL*     1.3    64.8    +      -       -      +
     80O  ASP*     3.1    13.2    +      -       -      +
     81O  PHE*     3.5    11.4    -      -       +      -
     96O  VAL      3.3     8.9    +      -       -      +
     97O  SER*     3.9     4.2    -      -       -      -
     98O  LEU*     3.1    24.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 79 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7O  LEU*     4.4    14.4    -      -       +      -
     10O  LEU*     3.8    23.5    -      -       +      +
     33O  LEU*     3.7    22.0    -      -       +      -
     62O  GLY*     2.8    37.3    +      -       -      +
     78O  ALA*     1.3    74.0    -      -       -      +
     80O  ASP*     1.3    64.4    +      -       +      +
     97O  SER*     5.8     1.9    -      -       -      -
     98O  LEU*     4.0    19.1    -      -       +      -
     99O  GLU*     5.2     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 80 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    6580    C      4.5    12.5    +      -       -      -
    6590    A      5.4     0.2    +      -       -      -
     62O  GLY      3.5     1.6    +      -       -      -
     63O  LYS*     3.2    26.7    -      -       +      +
     64O  VAL      2.8    24.6    +      -       -      -
     78O  ALA*     3.1     5.7    -      -       -      +
     79O  VAL*     1.3    86.8    -      -       +      +
     81O  PHE*     1.3    98.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 81 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    6590    A      4.4     2.3    +      -       -      -
     63O  LYS*     4.1     2.9    -      -       -      -
     64O  VAL*     3.4    20.4    -      -       +      -
     76O  VAL*     3.5    32.5    -      -       +      -
     78O  ALA*     3.5    26.2    -      -       +      -
     80O  ASP*     1.3    93.7    +      -       -      +
     82O  SER*     1.3    72.6    +      -       -      +
     83O  GLY*     3.5     1.7    +      -       -      -
     85O  ALA*     4.0     0.9    -      -       +      -
     86O  GLU*     3.7    36.5    -      -       +      +
     89O  ILE*     3.9    14.6    -      -       +      -
     95O  ALA*     3.9    12.3    -      -       +      -
     96O  VAL      3.2    38.8    -      -       -      -
     97O  SER*     4.6     1.6    -      -       -      -
----------------------------------------------------------
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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