Contacts of the strand formed by residues 148 - 155 (chain Q) 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 THR 148 (chain Q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3151A    A      3.1    26.4    +      -       -      +
   3152A    C      3.1    17.1    +      -       -      -
     95L  ARG*     4.9     4.0    -      -       -      -
     79Q  GLU*     3.7     6.2    -      -       -      +
    140Q  ARG*     3.4     6.9    -      -       -      +
    141Q  SER*     2.7    43.7    +      -       -      -
    146Q  GLY      3.3     5.8    -      -       -      +
    147Q  ALA*     1.3    81.4    -      -       -      +
    149Q  PHE*     1.3    66.6    +      -       -      +
    150Q  ILE*     5.4     2.9    -      -       -      +
    163Q  CYS*     5.4     3.4    -      -       -      -
    164Q  PHE      3.2    12.1    -      -       -      +
    165Q  GLU*     3.7    20.4    -      -       +      -
    166Q  LEU*     4.4     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 149 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111Q  PHE*     3.7    16.2    -      +       +      -
    117Q  LEU*     3.6    14.4    -      -       +      -
    119Q  VAL*     3.5    28.0    -      -       +      -
    137Q  CYS*     3.9     7.2    -      -       -      -
    139Q  GLN      3.4     7.2    -      -       -      +
    140Q  ARG*     3.7    16.6    -      -       +      +
    148Q  THR*     1.3    74.5    -      -       -      +
    150Q  ILE*     1.3    65.2    +      -       -      +
    151Q  LEU*     3.6    35.0    -      -       +      -
    162Q  ILE      3.9     0.3    -      -       -      +
    163Q  CYS*     3.5     2.3    -      -       -      +
    164Q  PHE*     2.9    50.6    +      +       +      -
    166Q  LEU*     3.5    36.8    -      -       +      -
    174Q  ILE*     3.9    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 150 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3152A    C      4.6     8.7    -      -       -      +
   3153A    U      4.0    13.0    -      -       -      +
    137Q  CYS*     3.3     4.2    -      -       -      -
    138Q  ILE*     2.8    52.9    +      -       +      +
    139Q  GLN*     2.8    51.5    +      -       +      +
    141Q  SER*     5.4     2.5    -      -       -      +
    148Q  THR*     5.4     3.6    -      -       -      +
    149Q  PHE*     1.3    79.8    -      -       -      +
    151Q  LEU*     1.3    60.2    +      -       -      +
    161Q  GLU*     4.4    13.7    -      -       +      +
    162Q  ILE      3.3    13.9    -      -       -      +
    163Q  CYS*     3.7    27.6    -      -       +      -
    188Q  LEU*     6.2     0.2    -      -       +      -
    191Q  ARG*     6.0     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 151 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117Q  LEU*     4.0    18.4    -      -       +      +
    119Q  VAL*     3.5    31.4    -      -       +      -
    133Q  PHE*     3.5    23.1    -      -       +      +
    135Q  GLY*     3.6    30.7    -      -       -      +
    136Q  ILE      3.4     0.7    -      -       -      -
    137Q  CYS*     3.6    22.9    -      -       +      +
    138Q  ILE*     4.5     0.7    -      -       -      -
    149Q  PHE*     3.6    24.0    -      -       +      -
    150Q  ILE*     1.3    73.0    -      -       -      +
    152Q  ARG*     1.3    60.1    +      -       -      +
    161Q  GLU*     3.3     3.9    -      -       -      -
    162Q  ILE      2.9    31.2    +      -       -      -
    164Q  PHE*     3.7    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 152 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101L  ASP*     2.6    41.0    +      -       -      -
    133Q  PHE*     4.4     0.2    -      -       -      -
    135Q  GLY*     3.1     3.1    -      -       -      -
    136Q  ILE*     2.8    45.5    +      -       +      +
    138Q  ILE*     3.5    26.5    -      -       +      -
    151Q  LEU*     1.3    72.9    -      -       -      +
    153Q  ASN*     1.3    65.7    +      -       -      +
    154Q  VAL*     4.1    20.4    -      -       -      +
    159Q  GLY*     4.2     4.6    -      -       -      -
    160Q  VAL      3.3     5.2    -      -       -      +
    161Q  GLU*     2.9    31.8    +      -       +      +
    190Q  LEU*     4.1    26.8    +      -       +      +
    191Q  ARG*     3.9    27.4    +      -       -      +
    193Q  ALA      5.8     0.2    +      -       -      -
    195Q  PRO*     5.7     3.0    -      -       -      +
    197Q  TYR      5.0     7.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 153 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133Q  PHE*     3.9    13.0    -      -       +      -
    134Q  LEU*     2.9    38.0    +      -       -      +
    135Q  GLY*     4.5     2.0    -      -       -      -
    152Q  ARG*     1.3    79.7    -      -       -      +
    154Q  VAL*     1.3    78.1    +      -       -      +
    155Q  ILE*     3.7    18.2    -      -       +      +
    158Q  GLN      4.0     0.3    -      -       -      +
    159Q  GLY*     3.5     1.6    -      -       -      -
    160Q  VAL*     2.8    33.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 154 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101L  ASP*     5.6     0.4    -      -       -      +
    152Q  ARG*     4.1    15.5    -      -       -      +
    153Q  ASN*     1.3    85.8    +      -       -      +
    155Q  ILE*     1.3    68.1    +      -       -      +
    157Q  GLY*     4.0    25.8    -      -       -      +
    158Q  GLN      3.5     8.3    -      -       -      +
    159Q  GLY*     4.0    13.2    -      -       -      +
    195Q  PRO*     3.9    40.2    -      -       +      +
    197Q  TYR      5.3     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 155 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122L  PRO*     3.3    27.6    -      -       +      +
    143L  ASN*     5.5     5.6    -      -       -      +
    144L  PHE      5.0     4.0    -      -       -      +
    145L  VAL*     4.0    11.4    -      -       +      -
    133Q  PHE*     4.8    11.2    -      -       +      -
    153Q  ASN*     3.7    24.0    -      -       +      +
    154Q  VAL*     1.3    80.9    -      -       -      +
    156Q  GLU*     1.3    73.3    +      -       +      +
    157Q  GLY      3.1     0.9    -      -       -      -
    158Q  GLN      2.8    26.8    +      -       -      +
    160Q  VAL*     3.6    28.5    -      -       +      -
----------------------------------------------------------
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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