Contacts of the strand formed by residues 141 - 148 (chain A) in PDB entry 1XRE


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 GLU 141 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  TYR*     3.6    25.4    -      -       +      +
    136A  VAL      3.6     0.3    -      -       -      +
    137A  LEU*     3.4     3.5    -      -       -      -
    138A  ASP*     2.8    44.5    +      -       +      +
    139A  GLY      3.4     0.2    -      -       -      -
    140A  GLU*     1.3    77.7    -      -       -      +
    142A  LEU*     1.3    79.0    +      -       -      +
    143A  SER*     3.9    10.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  VAL*     4.5     3.6    -      -       +      -
    105A  VAL*     3.5    50.0    -      -       +      +
    106A  ILE*     3.8    19.5    -      -       +      +
    109A  TYR*     3.7    18.9    -      -       +      +
    110A  PHE*     3.9    22.3    -      -       +      -
    135A  LEU*     4.2    13.5    -      -       +      -
    136A  VAL      3.3     3.4    -      -       -      +
    137A  LEU*     3.4    29.4    -      -       +      -
    141A  GLU*     1.3    85.0    -      -       -      +
    143A  SER*     1.3    59.5    +      -       -      +
    161A  LEU*     3.8    20.0    -      -       +      -
    199A  TYR*     4.3     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  PHE*     4.2     4.9    -      -       -      -
    135A  LEU*     3.5     6.7    -      -       -      +
    136A  VAL*     2.9    50.0    +      -       -      +
    138A  ASP*     4.4    12.5    +      -       -      +
    141A  GLU*     3.9    11.9    +      -       -      -
    142A  LEU*     1.3    75.1    -      -       -      +
    144A  VAL*     1.3    68.0    +      -       -      +
    145A  MET*     5.7     0.3    -      -       -      +
    158A  LYS*     4.9     6.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  PHE*     4.2    11.9    -      -       +      -
    116A  LEU*     3.8    28.7    -      -       +      -
    119A  GLN*     3.7    17.5    -      -       +      +
    120A  LEU*     3.7    20.0    -      -       +      +
    123A  ALA*     3.5    28.5    -      -       +      -
    134A  TRP      3.2    12.6    -      -       -      +
    135A  LEU*     4.4     2.9    -      -       +      -
    143A  SER*     1.3    81.8    -      -       -      +
    145A  MET*     1.3    67.6    +      -       -      +
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Residues in contact with MET 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  ALA*     4.3     9.1    -      -       -      +
    133A  GLY*     3.6     2.4    -      -       -      -
    134A  TRP*     2.7    46.8    +      -       +      +
    136A  VAL*     4.2     9.2    -      -       +      -
    143A  SER*     5.9     0.2    -      -       -      +
    144A  VAL*     1.3    78.5    -      -       -      +
    146A  SER*     1.3    73.9    +      -       -      +
    147A  THR*     3.9    15.9    -      -       +      -
    153A  PRO*     4.0    17.7    -      -       +      -
    156A  GLU*     3.4    27.1    -      -       -      +
    158A  LYS*     3.7    36.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  ALA*     3.7    26.3    +      -       -      +
    126A  SER      5.6     0.2    -      -       -      -
    127A  ARG*     3.0    37.3    +      -       -      +
    132A  TYR      3.2    15.7    -      -       -      -
    134A  TRP*     4.1     0.9    -      -       -      -
    145A  MET*     1.3    86.1    -      -       -      +
    147A  THR*     1.3    69.0    +      -       -      +
    148A  PRO*     4.8     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  ARG*     3.5    10.0    +      -       -      +
    131A  GLY*     3.2     3.8    -      -       -      -
    132A  TYR*     3.0    34.4    +      -       -      +
    134A  TRP*     2.9    30.4    +      -       +      +
    145A  MET*     3.9    14.1    -      -       +      -
    146A  SER*     1.3    77.9    -      -       -      +
    148A  PRO*     1.4    70.3    +      -       +      +
    151A  ASP*     2.7    34.8    +      -       +      +
    152A  THR      4.1    11.9    -      -       -      +
    156A  GLU*     5.4     1.1    -      -       -      +
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Residues in contact with PRO 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  ARG*     3.5    25.3    -      -       -      +
    128A  PHE      6.1     0.2    -      -       -      +
    130A  SER      3.5     8.1    -      -       -      +
    147A  THR*     1.4    89.5    -      -       +      +
    149A  ASN*     1.3    80.8    +      -       -      +
    150A  GLN      3.3     0.2    +      -       -      -
    151A  ASP*     3.0    38.3    +      -       +      +
----------------------------------------------------------
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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