Contacts of the strand formed by residues 143 - 147 (chain E) in PDB entry 3J7Y


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 ALA 143 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132E  TYR*     3.9    28.0    -      -       +      +
    133E  THR      3.5     5.4    -      -       -      -
    134E  SER*     3.9    12.3    -      -       -      +
    135E  LYS*     3.9     8.3    -      -       +      +
    142E  MET*     1.3    78.7    -      -       -      +
    144E  THR*     1.3    60.0    +      -       -      +
    180E  ASN*     3.7     1.0    -      -       -      -
    181E  ILE*     2.8    45.2    +      -       +      +
    183E  ASP*     4.8    13.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 144 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3206A    C      5.3     3.1    -      -       -      +
    131E  LYS      4.2     0.2    -      -       -      +
    132E  TYR*     3.4     6.9    -      -       -      -
    133E  THR*     2.6    64.8    +      -       -      -
    142E  MET*     3.7    11.6    +      -       +      +
    143E  ALA*     1.3    82.2    -      -       -      +
    145E  LEU*     1.3    64.7    +      -       -      +
    146E  SER      4.3     0.4    +      -       -      -
    178E  ILE*     3.6    16.5    -      -       +      +
    179E  PHE      3.2     7.4    -      -       -      +
    180E  ASN*     3.4    25.6    -      -       -      +
    181E  ILE*     3.9     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 145 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97E  VAL*     3.3    35.2    -      -       +      -
    129E  VAL*     3.8    21.1    -      -       +      -
    131E  LYS      3.7     0.7    -      -       -      -
    132E  TYR*     3.6    35.9    -      -       +      -
    144E  THR*     1.3    74.5    -      -       -      +
    146E  SER*     1.3    61.6    +      -       -      +
    147E  VAL*     3.5     8.8    +      -       +      -
    177E  LYS      3.7     0.2    -      -       -      +
    178E  ILE*     3.3     3.0    -      -       -      -
    179E  PHE*     2.8    45.1    +      -       +      +
    181E  ILE*     3.4    24.7    -      -       +      +
    186E  ALA*     4.7     3.8    -      -       -      -
    187E  ILE*     3.4    21.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 146 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129E  VAL*     3.7     3.8    -      -       -      +
    130E  LEU*     2.8    25.1    +      -       -      +
    131E  LYS*     2.8    50.7    +      -       -      +
    144E  THR      4.3     0.4    -      -       -      -
    145E  LEU*     1.3    71.3    -      -       -      +
    147E  VAL*     1.3    60.2    +      -       -      +
    176E  VAL*     3.7    20.9    -      -       -      -
    177E  LYS      3.6     5.8    -      -       -      -
    178E  ILE*     4.1    15.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 147 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97E  VAL*     3.7    20.9    -      -       +      -
     98E  GLY      4.4     2.2    -      -       -      +
    100E  ILE*     3.8    11.7    -      -       +      +
    127E  CYS*     4.4     8.5    -      -       +      -
    128E  HIS      3.7     7.9    -      -       -      +
    129E  VAL*     4.4     6.7    -      -       +      -
    130E  LEU*     4.2     2.9    -      -       -      -
    145E  LEU*     4.1     4.5    -      -       +      +
    146E  SER*     1.3    79.0    -      -       -      +
    148E  GLY*     1.3    71.4    +      -       -      +
    176E  VAL*     3.3     3.1    -      -       -      -
    177E  LYS      2.8    32.2    +      -       -      +
    179E  PHE*     3.4    35.4    -      -       +      -
    193E  LEU*     3.6    23.6    -      -       +      -
----------------------------------------------------------
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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