Contacts of the strand formed by residues 146 - 151 (chain A) in PDB entry 3I5Y


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 HIS 146 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  PRO      3.0    30.6    +      -       -      -
    140A  ILE      4.8     3.1    -      -       -      -
    142A  SER*     3.9    12.4    -      -       -      -
    144A  GLU*     3.0    40.7    +      -       +      +
    145A  ASP*     1.3    74.8    -      -       -      +
    147A  ASP*     1.3    64.9    +      -       -      +
    148A  VAL*     4.3    10.5    -      -       +      +
    300A  LYS*     3.5    21.7    -      -       +      +
    302A  LEU*     5.8     0.3    -      -       -      +
    322A  LYS*     3.9     8.0    -      -       -      +
    324A  GLU*     3.5    27.6    -      -       +      +
    326A  LEU*     3.2    33.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146A  HIS*     1.3    76.4    -      -       -      +
    148A  VAL*     1.3    67.7    +      -       -      +
    299A  ILE      4.4     1.2    -      -       -      +
    300A  LYS*     3.6     2.2    -      -       -      -
    301A  THR*     2.8    44.2    +      -       -      +
    302A  LEU*     5.4     0.2    -      -       -      -
    320A  MET*     3.6    21.9    -      -       +      +
    321A  ASN      3.7     1.7    +      -       -      -
    322A  LYS*     3.3    38.7    +      -       -      +
    324A  GLU      3.1     9.3    +      -       -      +
    325A  CYS*     3.9    18.1    -      -       -      +
    326A  LEU*     3.0    24.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  PRO      4.8     1.1    -      -       -      -
    140A  ILE*     4.2    26.2    -      -       +      +
    146A  HIS*     4.3    20.9    -      -       +      +
    147A  ASP*     1.3    80.2    -      -       -      +
    149A  ILE*     1.3    77.8    +      -       -      +
    150A  ALA*     4.6     6.7    -      -       +      -
    301A  THR      3.0    11.3    +      -       -      +
    302A  LEU*     3.4    21.0    -      -       +      -
    303A  LEU*     2.9    25.6    +      -       -      +
    304A  PHE*     5.3     3.4    -      -       +      -
    325A  CYS*     4.6     0.2    -      -       -      -
    326A  LEU*     3.5     9.6    -      -       +      +
    328A  LEU*     3.9    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  LEU*     4.2     8.7    -      -       +      -
    148A  VAL*     1.3    77.5    -      -       -      +
    150A  ALA*     1.3    61.7    +      -       -      +
    303A  LEU*     3.5    15.3    -      -       +      +
    308A  LEU*     3.6    37.9    -      -       +      -
    312A  VAL*     4.6     9.4    -      -       +      -
    313A  GLN*     4.1    26.9    -      -       +      -
    320A  MET*     4.1    11.9    -      -       +      -
    325A  CYS*     3.6    25.6    -      -       -      -
    326A  LEU      2.8    11.2    +      -       -      +
    327A  PHE*     4.4    14.6    -      -       +      -
    328A  LEU*     2.7    33.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  VAL*     4.8     3.6    -      -       +      -
    136A  THR*     4.0    15.0    -      -       +      -
    148A  VAL*     4.6     3.1    -      -       +      -
    149A  ILE*     1.3    77.4    -      -       -      +
    151A  ARG*     1.3    60.0    +      -       -      +
    152A  ALA      4.1     0.4    +      -       -      -
    303A  LEU      2.9     7.2    +      -       -      +
    304A  PHE*     3.3    42.7    -      -       +      -
    305A  SER      3.3    22.9    +      -       -      +
    308A  LEU*     4.1     5.8    -      -       -      +
    327A  PHE*     5.3     0.2    -      -       -      -
    328A  LEU*     3.2    11.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  VAL*     5.2     0.4    -      -       -      +
    150A  ALA*     1.3    73.2    -      -       -      +
    152A  ALA*     1.3    65.0    +      -       -      +
    305A  SER      3.3    12.1    -      -       -      +
    306A  ALA      3.9    12.6    -      -       -      +
    308A  LEU*     3.3    39.2    +      -       +      +
    309A  ASP*     5.8     1.6    -      -       -      +
    327A  PHE*     4.4     1.5    -      -       +      -
    328A  LEU      3.2     8.0    +      -       -      +
    329A  ASP*     3.0    38.2    +      -       -      +
    330A  THR*     2.9    28.4    +      -       -      +
    331A  VAL*     3.3    25.1    +      -       +      +
    332A  ASP      2.9    29.1    +      -       -      -
    333A  LYS*     4.3     9.5    +      -       -      +
    335A  GLU      5.0     2.6    +      -       -      -
    337A  GLU*     2.9    34.6    +      -       -      +
----------------------------------------------------------
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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