Contacts of the strand formed by residues 80 - 87 (chain E) in PDB entry 1YI2


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 TRP 80 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71E  ASN*     3.0    60.0    +      -       -      -
     74E  HIS*     3.6    31.2    -      +       +      -
     75E  GLY*     3.4     9.6    -      -       -      -
     79E  GLY*     1.3    70.9    -      -       -      -
     81E  GLU*     1.3    63.5    +      -       -      +
     82E  TYR*     4.9     0.7    -      -       +      -
    133E  VAL      4.3     0.2    -      -       -      -
    134E  SER*     2.9    27.1    -      -       -      -
    135E  GLY      2.9    21.5    +      -       -      +
    136E  PRO      3.4    20.4    +      -       -      -
    138E  ILE*     3.6    38.2    -      -       +      +
    141E  VAL*     3.9    15.4    -      -       +      +
    172E  PRO*     3.6    40.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 81 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78E  GLU      6.0     0.9    -      -       -      +
     79E  GLY      4.3     2.4    +      -       -      -
     80E  TRP*     1.3    82.0    -      -       -      +
     82E  TYR*     1.3    64.8    +      -       -      +
     83E  GLY      4.3     0.2    +      -       -      -
    125E  GLU*     5.7     0.9    -      -       -      +
    132E  THR*     3.8    18.6    +      -       -      +
    133E  VAL      3.0     4.9    -      -       -      +
    134E  SER*     3.4    20.7    +      -       -      -
    170E  ARG*     4.0    14.5    +      -       -      +
    172E  PRO*     3.3    28.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 82 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   27800    C      5.1     0.2    -      -       -      -
   27810    U      2.7    36.9    +      -       -      -
     80E  TRP*     4.9     2.2    -      -       +      -
     81E  GLU*     1.3    79.4    -      -       -      +
     83E  GLY*     1.3    61.6    +      -       -      +
     84E  MET*     4.0     0.4    +      -       -      -
    131E  LEU      3.8     0.2    -      -       -      +
    132E  THR*     3.3     4.6    +      -       -      -
    133E  VAL*     2.7    36.2    +      -       +      +
    138E  ILE*     4.0    14.1    -      -       +      +
    141E  VAL*     3.7    22.2    -      -       +      -
    142E  GLY*     3.6    29.4    -      -       -      -
    145E  ALA*     3.9    26.2    -      -       +      -
    168E  ILE*     4.3    16.6    -      -       +      -
    170E  ARG*     3.2    10.8    -      -       -      +
    171E  LYS*     4.4    10.5    -      -       +      -
    172E  PRO*     3.7    28.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 83 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82E  TYR*     1.3    74.5    -      -       -      +
     84E  MET*     1.3    54.9    +      -       -      +
    131E  LEU      3.4     5.8    -      -       -      -
    168E  ILE*     3.4     3.8    -      -       -      +
    169E  THR*     2.4    37.6    +      -       -      -
    170E  ARG*     2.9    40.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 84 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82E  TYR      4.8     0.7    -      -       -      +
     83E  GLY*     1.3    78.1    -      -       -      +
     85E  GLU*     1.3    64.5    +      -       -      +
    130E  GLU*     3.4     6.1    -      -       -      +
    131E  LEU*     2.7    59.2    +      -       +      +
    133E  VAL*     3.1    34.1    -      -       +      -
    145E  ALA*     3.9     7.6    -      -       -      +
    148E  ILE*     3.2    46.2    -      -       +      -
    149E  GLU      4.8     1.8    -      -       -      -
    166E  VAL*     3.9     8.3    -      -       +      -
    167E  TYR      2.9    16.6    -      -       -      +
    168E  ILE*     3.7    25.6    -      -       +      -
    169E  THR*     4.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 85 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84E  MET*     1.3    76.1    -      -       -      +
     86E  VAL*     1.3    63.3    +      -       -      +
     87E  PHE*     3.6     4.2    +      -       +      +
    129E  GLU*     3.6    13.6    -      -       -      +
    130E  GLU*     4.7    12.7    -      -       +      +
    165E  GLY      3.8     0.7    -      -       -      +
    166E  VAL*     3.6     2.5    -      -       -      -
    167E  TYR*     2.8    35.7    +      -       +      +
    169E  THR*     3.2    32.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 86 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84E  MET      4.2     0.6    -      -       -      -
     85E  GLU*     1.3    74.0    -      -       -      +
     87E  PHE*     1.3    62.8    +      -       -      +
     88E  TYR*     4.6     1.6    -      -       +      -
     93E  MET*     4.0    33.4    -      -       +      +
     95E  VAL*     4.1    16.8    -      -       +      -
    126E  ILE*     5.9     1.3    -      -       +      -
    128E  GLY      4.2     4.3    -      -       -      +
    129E  GLU*     3.3    59.4    +      -       -      +
    130E  GLU*     4.2     1.3    -      -       -      +
    131E  LEU*     5.5     6.7    -      -       +      +
    165E  GLY      3.9     3.8    -      -       -      -
    166E  VAL*     4.1    16.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 87 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85E  GLU*     3.6     5.3    +      -       +      +
     86E  VAL*     1.3    74.8    -      -       -      +
     88E  TYR*     1.3    86.2    +      -       -      +
     89E  SER*     4.7    10.3    -      -       -      -
     93E  MET*     3.1     6.2    -      -       -      +
    163E  GLN*     3.7    42.8    -      -       +      -
    164E  ASP*     3.3     0.6    -      -       -      -
    165E  GLY      2.7    41.8    +      -       -      +
    167E  TYR*     4.8     7.6    -      +       +      -
----------------------------------------------------------
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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