Contacts of the strand formed by residues 193 - 196 (chain C) 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 LEU 193 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192C  ILE*     1.3    75.1    -      -       -      +
    194C  PHE*     1.3    61.0    +      -       -      +
    195C  VAL*     3.8    17.5    -      -       +      -
    211C  ASP*     3.2    31.4    -      -       +      +
    212C  VAL      4.3     0.2    -      -       -      -
    213C  ALA*     3.9    21.3    -      -       +      -
    218C  VAL*     4.0     0.7    -      -       +      -
    222C  ASP*     3.7    23.6    -      -       +      +
    223C  LEU*     3.4    32.8    -      -       +      -
    231C  ARG*     3.7    24.1    -      -       +      +
    232C  LEU      3.4     4.8    +      -       -      -
    233C  THR*     3.2    12.2    -      -       +      +
    234C  VAL*     3.1    27.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 194 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144C  PHE*     3.5    37.9    -      +       +      -
    153C  VAL*     4.2     2.5    -      -       +      -
    157C  LEU*     3.7    35.4    -      -       +      -
    166C  ILE*     5.4     0.4    -      -       +      -
    192C  ILE*     3.7    29.8    -      -       +      -
    193C  LEU*     1.3    73.2    -      -       -      +
    195C  VAL*     1.3    62.1    +      -       -      +
    196C  THR*     3.8     2.1    +      -       -      +
    201C  SER*     4.7     3.9    +      -       -      -
    204C  ALA*     3.8    19.1    -      -       +      -
    207C  LEU*     3.8    10.1    -      -       +      -
    210C  ALA*     3.8    15.9    -      -       +      -
    211C  ASP      2.8    14.9    +      -       -      +
    212C  VAL*     3.5    11.2    -      -       +      +
    213C  ALA      2.8    26.4    +      -       -      +
    234C  VAL*     3.3    27.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 195 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144C  PHE*     5.9     0.2    -      -       -      -
    193C  LEU*     3.8    26.2    -      -       +      -
    194C  PHE*     1.3    74.6    -      -       -      +
    196C  THR*     1.3    62.6    +      -       -      +
    213C  ALA*     3.2     5.4    -      -       +      +
    214C  THR      3.7     5.2    -      -       -      +
    215C  ALA*     3.4    37.2    -      -       +      +
    218C  VAL*     4.2    15.9    -      -       +      -
    223C  LEU*     5.0     0.2    -      -       +      -
    233C  THR*     3.8    13.2    -      -       +      -
    234C  VAL      3.1     7.9    +      -       -      +
    235C  PHE*     3.6    25.8    -      -       +      -
    236C  THR*     3.3    24.1    +      -       -      -
    239C  ALA*     3.3     4.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 196 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144C  PHE*     4.0    27.8    -      -       +      -
    145C  GLU*     3.5    28.9    -      -       +      -
    194C  PHE      4.8     2.7    -      -       -      +
    195C  VAL*     1.3    77.9    -      -       -      +
    197C  SER*     1.3    61.9    +      -       -      +
    199C  GLU      2.5    29.7    +      -       -      +
    200C  PRO*     3.8     1.6    -      -       -      +
    201C  SER*     4.5    11.4    -      -       -      +
    213C  ALA      2.9    11.2    +      -       -      -
    214C  THR*     3.4     2.3    +      -       -      -
    215C  ALA      2.9    24.1    +      -       -      -
    236C  THR*     4.0     5.4    -      -       -      +
    239C  ALA*     3.6    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