Contacts of the strand formed by residues 54 - 58 (chain H) in PDB entry 1Y1V


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 SER 54 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9H  ILE*     4.2    12.7    -      -       -      +
     10H  PHE      3.8     4.7    -      -       -      -
     11H  GLN*     5.8     1.1    -      -       -      +
     53H  ASP*     1.3    75.0    +      -       -      +
     55H  LEU*     1.3    61.6    +      -       -      +
     56H  THR*     4.7     1.9    +      -       -      -
    145H  ARG      4.0     3.8    -      -       -      +
    146H  ARG*     3.8    20.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 55 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9H  ILE*     2.9    19.4    -      -       -      +
     10H  PHE*     3.0    28.2    +      -       +      +
     12H  VAL*     4.5    18.2    -      -       +      -
     26H  ILE*     5.3     5.8    -      -       +      -
     42H  ILE*     5.0    11.7    -      -       +      -
     47H  PHE*     3.8    12.1    -      -       +      -
     49H  VAL*     4.7    17.3    -      -       +      -
     53H  ASP*     3.6    12.1    +      -       +      -
     54H  SER*     1.3    75.4    -      -       -      +
     56H  THR*     1.3    62.8    +      -       -      +
     57H  VAL*     4.1     7.8    +      -       +      -
    144H  ILE*     3.5    31.0    -      -       +      -
    145H  ARG      4.2     0.9    -      -       -      +
    146H  ARG*     3.6    20.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 56 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7H  ASP*     4.3    12.6    -      -       -      +
      8H  ASP      3.5    11.9    -      -       -      +
      9H  ILE*     4.5    11.6    -      -       +      +
     54H  SER      4.7     1.2    +      -       -      -
     55H  LEU*     1.3    76.0    -      -       -      +
     57H  VAL*     1.3    65.5    +      -       -      +
     58H  THR*     4.6     7.4    -      -       -      +
     93H  TYR*     4.7     1.8    -      -       +      -
    143H  LEU      3.3     1.0    -      -       -      +
    144H  ILE*     3.0    27.2    +      -       -      +
    145H  ARG*     3.4    57.6    +      -       +      +
    146H  ARG*     4.3    11.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 57 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6H  PHE*     3.5    11.9    -      -       +      +
      7H  ASP*     3.4     7.4    -      -       -      +
      8H  ASP      3.0    27.9    +      -       -      +
     10H  PHE*     3.5    36.3    -      -       +      -
     38H  LEU*     4.3    13.7    -      -       +      -
     40H  LEU*     6.2     1.6    -      -       +      -
     55H  LEU*     4.8     6.7    -      -       +      +
     56H  THR*     1.3    80.1    -      -       -      +
     58H  THR*     1.3    72.0    +      -       -      +
     59H  ILE*     5.2     2.2    -      -       +      -
    123H  MET*     4.7     7.9    -      -       +      -
    125H  LEU*     6.0     2.9    -      -       +      -
    142H  LEU*     3.8    24.5    -      -       +      -
    143H  LEU      3.6     4.7    -      -       -      +
    144H  ILE*     4.9     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 58 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4H  THR*     3.5    25.6    -      -       +      -
      6H  PHE      3.0    19.5    -      -       -      +
      7H  ASP*     4.8     9.3    +      -       -      +
     56H  THR*     4.6     3.6    -      -       -      +
     57H  VAL*     1.3    78.7    +      -       -      +
     59H  ILE*     1.3    79.9    +      -       -      +
     60H  ALA*     5.4     0.2    -      -       +      -
     93H  TYR*     3.3    32.2    +      -       -      +
    142H  LEU*     3.2    17.2    -      -       -      +
    143H  LEU*     3.4    30.0    +      -       +      -
----------------------------------------------------------
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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