Contacts of the strand formed by residues 155 - 159 (chain A) in PDB entry 1J71


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 155 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  ILE*     4.6     2.9    -      -       -      +
    153A  LYS*     2.9    15.8    +      -       +      +
    154A  ASN*     1.3    76.2    +      -       -      +
    156A  TYR*     1.3    62.2    +      -       -      +
    172A  PHE*     3.7     1.2    -      -       -      -
    173A  GLY*     2.6    33.0    +      -       -      -
    310A  VAL*     5.0     1.1    -      -       +      -
    311A  TYR      3.0    15.5    -      -       -      +
    312A  ASP*     3.7    16.8    -      -       +      +
    313A  LEU      4.5     0.2    -      -       -      +
    334A  LEU*     3.8    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  THR*     4.0     7.6    -      -       +      +
    126A  ILE*     2.7    53.3    +      -       +      +
    142A  PRO*     4.3     6.1    -      -       +      -
    154A  ASN*     4.7     4.0    -      -       -      -
    155A  ALA*     1.3    80.0    -      -       -      +
    157A  SER*     1.3    64.4    +      -       -      +
    158A  LEU*     5.5     0.9    -      -       +      -
    170A  ILE*     4.0    18.6    -      -       +      -
    171A  ILE      3.1    14.4    -      -       -      +
    172A  PHE*     3.9    24.2    -      +       +      -
    173A  GLY      4.2     0.4    -      -       -      +
    174A  GLY      4.6     2.0    -      -       -      -
    195A  LEU*     3.7    19.8    -      -       -      +
    309A  ILE      3.8     0.5    -      -       -      +
    310A  VAL*     3.5     3.4    -      -       -      +
    311A  TYR*     2.8    58.7    +      +       +      -
    313A  LEU*     3.8    18.4    -      -       +      +
    334A  LEU*     5.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  TYR*     1.3    74.1    -      -       -      +
    158A  LEU*     1.3    60.0    +      -       -      +
    169A  LYS      4.0     0.6    -      -       -      +
    170A  ILE*     3.2    10.1    -      -       -      +
    171A  ILE*     2.9    34.6    +      -       -      +
    174A  GLY      2.7    24.3    +      -       -      -
    175A  VAL*     3.4    16.7    -      -       -      +
    308A  TYR*     3.2    27.5    +      -       -      -
    309A  ILE      3.1     6.5    -      -       -      -
    310A  VAL*     3.5    10.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  LEU*     3.8    19.1    -      -       +      -
     31A  ILE*     5.1     6.7    -      -       +      -
     33A  THR*     4.7     3.6    -      -       +      -
    156A  TYR*     5.5     0.9    -      -       +      -
    157A  SER*     1.3    73.8    -      -       -      +
    159A  TYR*     1.3    60.4    +      -       -      +
    160A  LEU*     3.7    34.9    +      -       +      -
    169A  LYS      3.9     0.2    -      -       -      -
    170A  ILE*     4.3    18.2    -      -       +      -
    219A  SER*     4.2    19.7    -      -       -      -
    304A  LEU*     4.7     7.0    -      -       +      -
    307A  ALA      4.0     6.8    -      -       -      +
    308A  TYR*     4.0     4.8    -      -       -      -
    309A  ILE*     2.8    38.4    +      -       +      +
    311A  TYR*     4.1    35.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  LEU*     4.3     0.2    -      -       -      +
    157A  SER      5.8     0.4    -      -       -      -
    158A  LEU*     1.3    74.0    -      -       -      +
    160A  LEU*     1.3    61.9    +      -       -      +
    161A  ASN*     3.4    40.3    +      -       +      -
    168A  GLY*     4.6     1.6    -      -       -      -
    169A  LYS*     2.7    58.8    +      -       +      +
    171A  ILE*     6.5     0.4    -      -       +      -
    179A  LYS*     3.5    35.8    -      -       +      -
    307A  ALA      5.3     1.6    -      -       -      -
    308A  TYR*     4.0    22.7    -      +       +      -
    323A  VAL*     3.5    33.2    -      -       +      -
    324A  LYS      3.9     2.2    -      -       -      -
    325A  TYR*     3.4    24.2    -      +       -      -
    326A  THR      3.5     9.2    +      -       -      -
----------------------------------------------------------
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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