Contacts of the strand formed by residues 129 - 133 (chain A) in PDB entry 3UXA


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 129 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  LEU*     4.2    23.1    -      -       +      -
    107A  ILE      3.1     4.2    +      -       -      +
    108A  LEU*     3.3    30.0    -      -       +      +
    109A  MET      3.1    22.0    +      -       -      -
    127A  ALA*     3.3     4.8    -      -       -      +
    128A  ASP*     1.3    80.2    -      -       +      +
    130A  VAL*     1.3    75.7    +      -       -      +
    154A  MET*     3.8    10.9    -      -       -      +
    155A  GLU      2.7    33.4    +      -       -      +
    156A  PRO*     3.0    11.8    -      -       +      +
    157A  ALA*     5.1     0.9    -      -       +      +
    176A  ILE*     5.8     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 130 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  LEU*     3.9     6.9    -      -       -      +
    109A  MET*     3.6    13.0    -      -       +      +
    113A  ILE*     4.0    20.2    -      -       +      -
    119A  ILE*     4.5    17.0    -      -       +      -
    122A  ALA*     3.5    29.8    -      -       +      -
    129A  THR*     1.3    87.3    +      -       -      +
    131A  GLY*     1.3    55.2    +      -       -      +
    132A  LEU*     4.4    16.2    -      -       +      -
    149A  ALA*     4.6     6.5    -      -       +      -
    154A  MET*     4.7     4.9    -      -       -      -
    156A  PRO*     3.3    23.8    -      -       +      +
    157A  ALA*     2.8    30.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  LEU*     3.9    11.5    -      -       -      +
    109A  MET      3.3    12.3    +      -       -      -
    110A  TRP*     5.1     7.2    -      -       -      -
    111A  ASP      4.2     7.0    -      -       -      +
    113A  ILE*     3.5    25.1    -      -       -      +
    130A  VAL*     1.3    72.7    -      -       -      +
    132A  LEU*     1.3    63.7    +      -       -      +
    133A  ILE*     4.0     6.1    +      -       -      +
    157A  ALA*     3.5     8.1    -      -       -      -
    159A  VAL*     4.8     9.6    -      -       -      -
    178A  ILE*     5.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  ILE*     4.1    24.9    -      -       +      -
    119A  ILE*     4.7     1.6    -      -       +      -
    130A  VAL*     4.4     8.7    -      -       +      -
    131A  GLY*     1.3    79.7    -      -       -      +
    133A  ILE*     1.3    63.7    +      -       -      +
    134A  VAL      3.8     1.3    +      -       -      -
    137A  LEU*     4.6     8.1    -      -       +      -
    142A  LEU*     4.0    24.5    -      -       +      +
    145A  LEU*     4.0    15.3    -      -       +      +
    146A  LEU*     3.8    39.9    -      -       +      +
    156A  PRO*     4.2    19.3    -      -       +      -
    157A  ALA      2.8    13.4    +      -       -      +
    158A  ILE*     3.4    11.6    -      -       +      +
    159A  VAL      2.9    26.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  TRP*     3.9    23.3    -      -       +      -
    111A  ASP      3.7    23.3    -      -       -      +
    112A  PHE*     3.8    27.6    -      -       +      -
    113A  ILE      5.1     4.7    +      -       -      +
    131A  GLY      4.0     4.0    +      -       -      +
    132A  LEU*     1.3    72.9    -      -       -      +
    134A  VAL*     1.3    66.3    +      -       -      +
    135A  LYS*     3.9    12.6    -      -       +      +
    136A  ILE*     3.3    38.1    +      -       +      +
    137A  LEU*     3.4    19.9    +      -       -      +
    142A  LEU*     5.3     0.2    -      -       -      -
    159A  VAL*     4.4    24.2    -      -       +      +
    184A  LEU*     4.2    12.6    -      -       +      -
----------------------------------------------------------
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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