Contacts of the strand formed by residues 143 - 150 (chain Q) in PDB entry 5A0Q


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 TYR 143 (chain Q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108Q  GLU*     5.3     8.7    -      -       +      -
    140Q  ASP*     3.0    29.8    +      -       -      +
    142Q  HIS*     1.3    89.5    -      -       +      +
    144Q  GLY*     1.3    61.6    +      -       -      +
    145Q  PHE      3.9     5.2    +      -       -      +
    146Q  GLN*     3.1    15.0    -      -       -      +
    148Q  TYR*     5.1     6.3    -      -       -      -
     71Y  ASN      4.9     1.4    +      -       -      -
     72Y  GLY*     5.1     2.3    +      -       -      -
     73Y  TYR*     3.7    37.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLY 144 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139Q  TRP*     2.9    28.7    -      -       -      -
    140Q  ASP*     3.0    32.4    +      -       -      +
    141Q  LYS      4.4     2.4    +      -       -      -
    142Q  HIS      3.9     0.6    -      -       -      -
    143Q  TYR*     1.3    80.0    -      -       -      +
    145Q  PHE*     1.4    62.6    +      -       -      -
    146Q  GLN*     3.7     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 145 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38Q  LEU*     3.6    12.6    -      -       +      +
     39Q  ALA      4.4    14.6    -      -       -      +
     40Q  ASN      4.8     2.9    -      -       -      -
     41Q  ASP*     2.7    42.6    -      -       -      -
     42Q  GLY*     3.3     6.7    -      -       -      +
     43Q  VAL*     3.6    16.2    -      -       +      -
    138Q  GLY      3.3    14.4    -      -       -      -
    139Q  TRP*     2.8    37.8    -      +       +      -
    143Q  TYR*     3.9     5.6    +      -       -      +
    144Q  GLY*     1.4    71.7    -      -       -      -
    146Q  GLN*     1.3    60.4    +      -       -      +
    216Q  LEU*     3.6    25.6    -      -       +      -
    217Q  THR      4.0     1.1    -      -       -      -
    218Q  ARG*     3.6    34.8    -      -       +      -
    223Q  THR*     4.4     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 146 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38Q  LEU*     3.7     9.4    -      -       -      +
     43Q  VAL*     4.2     3.9    -      -       -      +
    107Q  CYS*     3.6     8.8    -      -       +      +
    108Q  GLU*     3.5    24.9    -      -       -      +
    136Q  TYR      4.1     0.2    -      -       -      -
    137Q  ILE*     3.6     1.6    -      -       -      -
    138Q  GLY      2.9    40.8    +      -       -      +
    140Q  ASP*     2.7    43.5    +      -       -      +
    143Q  TYR*     3.1    19.8    -      -       +      +
    144Q  GLY      3.7     3.9    -      -       -      +
    145Q  PHE*     1.3    74.6    -      -       -      +
    147Q  LEU*     1.3    61.3    +      -       -      +
    148Q  TYR*     3.5    29.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 147 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36Q  GLY*     3.8    25.4    -      -       -      +
     37Q  ILE      4.5     0.2    -      -       -      +
     38Q  LEU*     4.1     9.6    -      -       +      +
     43Q  VAL*     4.1    10.8    -      -       +      -
    135Q  LEU*     4.2    16.4    -      -       +      -
    136Q  TYR      2.8    19.1    -      -       -      +
    137Q  ILE*     4.0    17.3    -      -       +      -
    146Q  GLN*     1.3    73.2    -      -       -      +
    148Q  TYR*     1.3    78.6    +      -       -      +
    158Q  GLY*     3.4     3.1    -      -       -      -
    159Q  TRP*     2.7    53.1    +      -       +      +
    160Q  LYS      3.8    12.1    -      -       -      +
    161Q  ALA*     3.9     2.7    -      -       -      +
    162Q  THR*     4.3    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 148 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107Q  CYS*     5.4     2.2    -      -       -      -
    108Q  GLU*     3.2    40.0    -      -       +      +
    111Q  VAL*     4.2    11.7    -      -       +      -
    135Q  LEU*     3.0     6.4    -      -       -      +
    136Q  TYR*     2.5    58.1    +      -       +      -
    143Q  TYR*     5.1     5.5    -      -       -      -
    146Q  GLN*     3.5    41.5    +      -       +      +
    147Q  LEU*     1.3    82.1    -      -       -      +
    149Q  GLN*     1.3    59.3    +      -       -      +
    156Q  TYR*     4.5    12.6    -      +       +      -
    157Q  GLY      3.5    10.8    -      -       -      +
    158Q  GLY*     3.5    28.7    -      -       -      -
    159Q  TRP*     4.6     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 149 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133Q  SER*     4.9     4.2    +      -       -      -
    134Q  LEU      3.3    11.9    -      -       -      +
    135Q  LEU*     3.7    15.9    -      -       +      -
    136Q  TYR*     4.7     0.9    -      -       -      -
    148Q  TYR*     1.3    75.6    -      -       -      +
    150Q  SER*     1.3    66.5    +      -       -      +
    151Q  ASP*     3.9     6.2    +      -       -      +
    155Q  ASN*     5.8     0.2    +      -       -      -
    156Q  TYR*     3.2    23.7    -      -       -      -
    157Q  GLY      3.2    13.1    +      -       -      +
    159Q  TRP*     4.3    17.9    +      -       +      +
    162Q  THR*     2.9    27.6    +      -       +      -
    163Q  CYS      4.5     4.2    +      -       -      -
    164Q  ILE*     3.7    29.1    -      -       +      +
    168Q  SER*     5.6     0.4    +      -       -      -
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Residues in contact with SER 150 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115Q  CYS*     3.1    25.2    -      -       -      -
    118Q  LYS*     3.1    20.4    +      -       -      -
    133Q  SER*     3.2     7.6    -      -       -      -
    134Q  LEU*     2.8    33.0    +      -       -      -
    136Q  TYR*     3.8    28.1    +      -       -      -
    149Q  GLN*     1.3    72.7    -      -       -      +
    151Q  ASP*     1.3    65.9    +      -       -      +
    155Q  ASN      4.0     6.1    -      -       -      -
    156Q  TYR*     4.6     0.2    -      -       -      +
----------------------------------------------------------
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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