Contacts of the strand formed by residues 154 - 159 (chain A) in PDB entry 1UCU


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 154 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  THR*     4.2    11.4    -      -       -      +
    145A  ILE      3.1    18.6    -      -       -      +
    146A  GLN*     3.7    26.9    -      -       +      +
    147A  VAL*     4.2     2.5    -      -       -      +
    152A  GLY*     3.0    18.9    +      -       -      +
    153A  GLU*     1.3    79.3    -      -       -      +
    155A  ILE*     1.3    67.0    +      -       -      +
    156A  ASP*     3.2    15.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  LEU      3.7     1.0    -      -       -      +
    145A  ILE*     2.9    32.7    +      -       -      +
    147A  VAL*     3.7    15.5    -      -       +      -
    154A  THR*     1.3    77.6    -      -       -      +
    156A  ASP*     1.3    66.2    -      -       -      +
    428A  VAL*     4.3    14.1    -      -       +      +
    431A  ARG*     4.0    10.3    -      -       +      +
    432A  PHE*     3.3    57.1    -      -       +      -
    435A  ALA*     3.4    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  THR*     3.7    19.4    -      -       +      +
    143A  LEU      3.3     3.1    -      -       -      -
    144A  THR*     3.4    26.1    -      -       -      +
    154A  THR*     3.2    19.4    +      -       -      -
    155A  ILE*     1.3    85.3    -      -       -      +
    157A  ILE*     1.3    64.1    +      -       -      +
    158A  ASP*     3.9     8.7    +      -       -      +
    428A  VAL*     4.5     9.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  GLY*     3.8    28.5    -      -       -      +
     73A  ILE*     4.6    15.0    -      -       +      +
     74A  ALA*     4.9     4.9    -      -       +      +
    141A  ASN      3.6     0.2    -      -       -      +
    142A  THR*     4.3     0.4    -      -       -      -
    143A  LEU*     2.8    49.9    +      -       +      +
    145A  ILE*     4.4    11.0    -      -       +      -
    156A  ASP*     1.3    75.5    -      -       -      +
    158A  ASP*     1.3    58.5    +      -       -      +
    159A  LEU*     3.3    21.8    +      -       +      +
    425A  LEU*     3.5    30.1    -      -       +      -
    428A  VAL*     4.0    18.8    -      -       +      -
    432A  PHE*     3.9    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  ASN      3.8     4.3    -      -       -      -
    142A  THR*     2.7    33.5    +      -       -      +
    156A  ASP*     3.9     8.4    +      -       -      +
    157A  ILE*     1.3    70.6    -      -       -      +
    159A  LEU*     1.3    63.0    -      -       -      +
    160A  LYS*     3.9    28.4    +      -       -      +
    421A  LEU      5.5     1.2    -      -       -      +
    424A  ASP*     4.6    18.5    -      -       +      +
    425A  LEU*     4.1    14.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  ILE*     4.9     2.7    -      -       +      -
     77A  THR*     3.7    26.9    -      -       +      +
    134A  VAL*     4.3     7.6    -      -       +      -
    135A  LYS      5.4     0.7    -      -       -      +
    136A  VAL*     3.5    37.7    -      -       +      +
    139A  GLN      3.9     6.5    -      -       -      +
    140A  ASP*     3.3     1.9    -      -       -      -
    141A  ASN*     2.7    42.1    +      -       +      +
    143A  LEU*     4.0    35.7    -      -       +      -
    157A  ILE*     3.9    25.4    -      -       +      +
    158A  ASP*     1.3    73.1    -      -       -      +
    160A  LYS*     1.3    67.4    +      -       -      +
    425A  LEU*     4.5     2.2    -      -       +      -
----------------------------------------------------------
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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