Contacts of the strand formed by residues 133 - 137 (chain S) 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 VAL 133 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97S  ALA*     4.1     3.6    -      -       +      -
     98S  VAL      3.8     3.8    -      -       -      -
     99S  VAL*     3.6    19.7    -      -       +      -
    130S  LEU      4.4     8.1    -      -       -      +
    131S  GLU*     5.9     0.4    -      -       -      -
    132S  LYS*     1.3    74.1    -      -       -      +
    134S  LEU*     1.3    59.6    +      -       -      +
    135S  LEU      3.3     3.6    -      -       -      +
    136S  VAL*     4.0    10.8    -      -       +      -
    149S  LEU*     3.3    40.7    +      -       +      +
    150S  GLY      5.2     1.1    -      -       -      +
    154S  VAL*     4.0    33.2    -      -       +      +
    155S  ARG*     5.2     0.9    -      -       -      +
    156S  VAL*     3.4    35.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 134 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95R  VAL*     5.7     1.0    -      -       -      +
     96R  GLU      4.5     8.3    -      -       -      +
     97R  LEU*     3.5    21.9    -      -       +      +
     98S  VAL*     3.1    45.7    +      -       +      +
     99S  VAL      5.1     0.2    -      -       -      -
    100S  HIS*     4.7     6.5    -      -       +      -
    105S  GLN*     3.9    30.7    -      -       +      +
    132S  LYS      3.4     6.3    -      -       -      +
    133S  VAL*     1.3    72.6    -      -       -      +
    135S  LEU*     1.3    60.9    +      -       -      +
    144S  LEU*     3.8     6.4    -      -       -      +
    145S  GLY      3.5    19.6    +      -       -      +
    147S  PRO*     3.2    27.2    -      -       +      +
    148S  LEU*     4.1    17.3    -      -       +      +
    149S  LEU*     4.8     0.2    -      -       -      -
     43j  LEU*     4.2    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 135 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97R  LEU*     4.1    25.6    -      -       +      -
    105R  LEU*     5.1     2.0    -      -       +      -
    112R  THR*     4.4    15.7    -      -       +      -
    116R  LEU*     5.1     1.1    -      -       +      -
     96S  PHE*     3.6    29.8    -      -       +      -
     97S  ALA*     3.2     4.5    -      -       -      +
     98S  VAL*     2.8    51.7    +      -       +      +
    133S  VAL      4.3     1.5    -      -       -      -
    134S  LEU*     1.3    76.8    -      -       -      +
    136S  VAL*     1.3    82.7    +      -       -      +
    137S  GLY*     4.4     1.6    -      -       -      -
    142S  THR*     4.7     2.7    -      -       -      -
    143S  LEU      3.6     3.8    -      -       -      +
    144S  LEU*     3.4    40.4    -      -       +      -
    149S  LEU*     4.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 136 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95S  LEU*     5.0     4.9    -      -       +      -
     96S  PHE      3.3     9.0    -      -       -      +
     97S  ALA*     4.3     6.3    -      -       +      -
    133S  VAL*     4.0    10.3    -      -       +      -
    135S  LEU*     1.3    83.2    -      -       -      +
    137S  GLY*     1.3    63.1    +      -       -      +
    141S  PHE*     5.8     1.0    -      -       +      -
    142S  THR*     3.7     0.2    -      -       -      -
    143S  LEU*     2.8    42.8    +      -       +      +
    149S  LEU*     3.5    24.9    -      -       +      -
    154S  VAL*     3.6    38.8    -      -       +      -
    198S  ILE*     4.8     8.3    -      -       +      -
    200S  ILE*     4.1    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 137 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95S  LEU*     3.4     5.7    -      -       -      +
     96S  PHE*     2.8    60.2    +      -       -      +
    136S  VAL*     1.3    76.1    -      -       -      +
    138S  ALA*     1.3    64.1    +      -       -      +
    141S  PHE*     3.9     3.6    -      -       -      -
    142S  THR*     3.8    12.1    -      -       -      -
----------------------------------------------------------
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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