Contacts of the strand formed by residues 110 - 115 (chain D) in PDB entry 2YIN


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 ILE 110 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78D  PHE*     3.5    17.9    -      -       +      +
     80D  ILE*     4.1    23.3    -      -       +      -
     98D  TYR*     4.0    15.9    -      -       +      -
    101D  VAL*     3.7    24.0    -      -       +      -
    102D  ARG*     3.9    26.9    -      -       -      +
    108D  THR      4.1     6.1    -      -       -      +
    109D  PRO*     1.3    81.8    -      -       -      +
    111D  ILE*     1.3    74.1    +      -       -      +
    149D  ILE*     4.2     9.4    -      -       +      +
    150D  GLY      4.8     0.8    +      -       -      +
    151D  ALA*     3.3    22.5    -      -       +      +
    152D  VAL*     2.8    33.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 111 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77D  VAL*     4.4     7.4    -      -       +      -
     78D  PHE      2.8     8.9    +      -       -      +
     79D  LEU*     3.5    22.0    -      -       +      -
     80D  ILE*     2.8    28.4    +      -       -      +
    110D  ILE*     1.3    80.6    -      -       -      +
    112D  LEU*     1.3    69.5    +      -       -      +
    113D  VAL*     3.7     5.1    +      -       +      +
    152D  VAL*     5.0     2.5    -      -       +      -
    153D  LYS*     3.6    20.4    -      -       +      +
    155D  LEU*     4.1    18.2    -      -       +      -
    168D  VAL      4.4     2.2    -      -       -      +
    171D  GLU*     3.6    13.5    -      -       +      +
    172D  ALA*     3.2    43.3    -      -       +      +
    175D  ALA*     4.5     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 112 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80D  ILE*     3.4    31.0    -      -       +      +
     82D  PHE*     4.0    18.2    -      -       +      -
     93D  VAL*     3.9    16.6    -      -       +      -
    111D  ILE*     1.3    75.1    -      -       -      +
    113D  VAL*     1.3    63.0    -      -       -      +
    142D  GLY      3.5    24.7    -      -       -      +
    145D  MET*     3.9    17.9    -      -       +      -
    146D  ALA*     3.9     9.0    -      -       +      +
    149D  ILE*     3.9     9.4    -      -       +      -
    151D  ALA*     4.1    10.6    -      -       +      +
    153D  LYS      2.8    16.4    +      -       -      +
    154D  TYR*     3.4    16.7    -      -       +      -
    155D  LEU      2.9    26.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 113 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19D  LEU*     4.3    12.1    -      -       +      -
     79D  LEU*     4.0    18.6    -      -       +      -
     80D  ILE      2.5    19.5    +      -       -      +
     81D  CYS*     3.1    17.8    -      -       +      +
     82D  PHE*     2.9    34.5    +      -       -      +
    111D  ILE*     4.1     4.9    -      -       +      +
    112D  LEU*     1.3    80.0    -      -       -      +
    114D  GLY*     1.3    61.4    +      -       -      +
    115D  THR      4.8     0.7    -      -       -      +
    155D  LEU*     3.3     7.4    -      -       +      +
    157D  CYS*     3.8    28.7    -      -       -      -
    168D  VAL*     4.0    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 114 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82D  PHE*     3.5    23.0    -      -       -      -
     84D  LEU*     3.9    11.1    -      -       -      +
    112D  LEU      4.3     0.4    +      -       -      -
    113D  VAL*     1.3    72.7    -      -       -      +
    115D  THR*     1.3    62.6    +      -       -      +
    154D  TYR*     4.5     2.8    -      -       -      -
    155D  LEU      2.9    13.3    +      -       -      -
    156D  GLU*     3.4     5.0    -      -       -      +
    157D  CYS*     2.9    32.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 115 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14D  VAL*     2.9    46.9    -      -       -      +
     15D  GLY      4.4     9.0    -      -       -      +
     19D  LEU*     4.7    17.9    -      -       +      +
     81D  CYS*     4.0     7.8    -      -       -      +
     82D  PHE      2.8    13.2    +      -       -      -
     83D  SER*     4.0     4.3    -      -       -      -
     84D  LEU*     3.1    20.0    +      -       -      +
    113D  VAL*     4.8     2.9    -      -       -      +
    114D  GLY*     1.3    74.3    -      -       -      -
    116D  LYS*     1.3    87.6    +      -       +      +
    117D  LEU      3.0     4.1    +      -       -      -
    157D  CYS*     3.5     7.0    -      -       -      +
    159D  ALA*     5.6     2.9    -      -       +      +
----------------------------------------------------------
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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