Contacts of the strand formed by residues 131 - 138 (chain A) in PDB entry 1XUQ


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 GLY 131 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  ARG*     4.1     5.6    -      -       -      +
    129A  GLY      4.0     1.6    +      -       -      -
    130A  SER*     1.3    74.6    -      -       -      +
    132A  TRP*     1.3    61.5    +      -       -      -
    147A  THR      3.2    11.7    -      -       -      -
    149A  ASN      3.7    13.2    -      -       -      -
    166A  VAL*     2.8    36.8    +      -       -      +
    167A  TRP*     3.4    15.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  ASN*     3.6    40.1    -      -       +      +
     83A  HIS*     3.8    16.4    -      +       -      -
     85A  PHE*     5.4     0.7    -      +       -      -
     86A  PHE*     3.7    30.1    -      +       +      -
    127A  ARG*     4.4     1.0    -      -       -      +
    131A  GLY*     1.3    78.3    -      -       -      -
    133A  ALA*     1.3    59.0    +      -       -      +
    134A  TRP*     3.4    40.7    -      +       +      +
    146A  SER*     3.1     9.2    -      -       -      -
    147A  THR*     2.9    34.6    +      -       -      +
    149A  ASN      3.4    15.8    +      -       -      -
    150A  GLN*     2.9    21.1    +      -       -      +
    163A  GLY      4.6     1.3    -      -       -      -
    164A  LEU      3.4    14.4    -      -       -      -
    165A  ASP*     3.4    53.6    +      -       +      -
    166A  VAL*     3.9     4.7    -      -       -      +
    167A  TRP*     4.2     0.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  PHE*     3.5    25.1    -      -       +      +
    123A  ALA*     4.6     3.8    -      -       +      -
    124A  GLY*     3.9    31.9    -      -       -      +
    132A  TRP*     1.3    74.3    -      -       -      +
    134A  TRP*     1.3    61.6    +      -       -      +
    145A  THR      3.6     7.0    -      -       -      +
    146A  SER*     4.4     1.1    -      -       -      +
    163A  GLY*     3.1     4.5    -      -       -      -
    164A  LEU*     2.8    37.0    +      -       +      +
    166A  VAL*     4.6     2.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  ASN*     3.5    32.5    -      -       +      -
     85A  PHE*     3.9    26.2    -      +       +      -
    120A  PHE*     3.7     7.5    -      -       -      -
    132A  TRP*     3.4    39.5    -      +       +      +
    133A  ALA*     1.3    78.0    -      -       -      +
    135A  LEU*     1.3    60.5    +      -       -      +
    136A  VAL*     3.7    10.8    -      -       +      -
    144A  VAL*     3.3    10.6    -      -       -      +
    145A  THR*     2.9    53.9    +      -       -      +
    147A  THR*     2.9    30.1    +      -       +      -
    152A  SER*     5.5     0.2    -      -       -      -
    153A  PRO*     3.5    29.3    -      -       +      +
    160A  PRO*     3.8    20.6    -      -       +      -
    162A  ILE      3.4    19.3    -      -       -      +
    163A  GLY*     3.8     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  LEU*     4.4     8.5    -      -       +      -
    106A  ILE*     4.3    19.3    -      -       +      -
    110A  PHE*     4.1    19.3    -      -       +      -
    116A  PHE*     3.8    36.8    -      -       +      -
    120A  PHE*     3.9     1.4    -      -       -      -
    134A  TRP*     1.3    72.3    -      -       -      +
    136A  VAL*     1.3    61.4    -      -       -      +
    142A  LEU*     4.0    20.4    -      -       +      -
    143A  GLU      3.6    14.1    -      -       -      +
    144A  VAL*     4.5     0.4    -      -       +      +
    160A  PRO*     3.8     0.3    -      -       -      +
    161A  VAL*     2.8    45.5    +      -       +      +
    162A  ILE*     2.9    28.1    +      -       +      +
    192A  TRP*     4.9     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  TRP*     3.7    21.8    -      -       +      -
    135A  LEU*     1.3    79.0    -      -       -      +
    137A  VAL*     1.3    64.0    -      -       -      +
    142A  LEU*     3.3    10.1    -      -       -      +
    143A  GLU*     2.9    62.2    +      -       +      +
    145A  THR*     4.0     7.9    -      -       +      +
    153A  PRO*     3.9    25.1    -      -       +      -
    158A  LYS*     4.0    23.1    -      -       +      -
    159A  THR      3.2    14.1    -      -       -      +
    160A  PRO*     4.2     3.8    -      -       +      -
    161A  VAL*     4.3     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  VAL*     1.3    73.7    -      -       -      +
    138A  ASN*     1.3    60.0    +      -       -      +
    139A  ASN      4.0     2.5    +      -       -      +
    140A  GLY*     3.6    34.1    -      -       -      +
    141A  GLU      3.4     3.6    -      -       -      +
    142A  LEU*     4.0     7.0    -      -       +      -
    157A  GLY      4.6     0.3    -      -       -      +
    158A  LYS*     3.5     4.5    -      -       -      -
    159A  THR*     2.9    34.5    +      -       -      +
    161A  VAL*     3.7    22.7    -      -       +      -
    199A  TYR*     3.8    24.2    -      -       +      +
    202A  ALA*     4.2    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 138 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  VAL*     4.0     1.1    -      -       +      -
    137A  VAL*     1.3    71.4    -      -       -      +
    139A  ASN*     1.3    91.0    +      -       -      +
    141A  GLU*     2.8    28.9    +      -       +      +
    143A  GLU*     2.9    30.0    -      -       +      +
    156A  GLU      5.2     1.2    +      -       -      -
    157A  GLY      4.5     4.4    +      -       -      -
    158A  LYS*     3.5    33.5    +      -       +      +
----------------------------------------------------------
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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