Contacts of the strand formed by residues 140 - 146 (chain A) in PDB entry 1U54


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 VAL 140 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  ACP      3.7    63.0    -      -       +      +
    131A  LYS*     3.5     1.4    -      -       -      -
    132A  LEU*     3.2    31.1    +      -       +      -
    133A  GLY      2.8    27.9    +      -       -      +
    134A  ASP      4.1     0.9    -      -       -      -
    138A  GLY      5.7     0.2    -      -       -      +
    139A  VAL*     1.3    83.3    -      -       -      +
    141A  ARG*     1.3    69.5    +      -       -      +
    156A  ALA*     4.8     0.7    -      -       +      -
    157A  VAL      3.5    13.7    -      -       -      +
    158A  LYS*     4.4    20.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 141 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  LEU*     4.4    36.0    -      -       +      +
    129A  LEU      3.5    25.8    +      -       -      +
    130A  GLU      3.2     7.2    -      -       -      +
    131A  LYS*     3.5    36.5    -      -       -      +
    132A  LEU*     3.7     6.5    -      -       -      +
    139A  VAL*     4.1    11.7    -      -       +      +
    140A  VAL*     1.3    78.8    -      -       -      +
    142A  ARG*     1.3    62.3    +      -       -      +
    156A  ALA*     3.8     0.7    -      -       -      -
    157A  VAL*     2.9    39.0    +      -       -      +
    159A  CYS*     4.9     8.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  LEU*     4.1     0.6    -      -       -      -
    129A  LEU*     2.6    51.7    +      -       -      +
    130A  GLU*     3.0    40.4    +      -       -      +
    132A  LEU*     3.4    26.6    -      -       +      +
    141A  ARG*     1.3    72.1    -      -       -      +
    143A  GLY*     1.3    58.9    +      -       -      +
    154A  SER*     3.2    28.5    +      -       -      -
    155A  VAL      3.7    10.8    -      -       -      +
    157A  VAL*     4.7     0.4    -      -       -      -
    207A  LEU*     3.9    27.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  LEU*     5.5     0.7    -      -       -      -
    127A  ARG      3.4    12.1    -      -       -      -
    128A  LEU*     4.5     0.9    -      -       -      -
    129A  LEU*     4.3     3.6    -      -       -      -
    141A  ARG      4.0     0.4    +      -       -      -
    142A  ARG*     1.3    79.7    +      -       -      +
    144A  GLU*     1.3    67.2    +      -       -      +
    153A  VAL      3.5     1.9    -      -       -      +
    154A  SER*     3.6     7.6    +      -       -      -
    155A  VAL*     2.9    40.7    +      -       -      +
    157A  VAL*     4.2     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  ASP      3.4     1.6    -      -       -      +
    126A  LEU*     3.4     9.1    -      -       -      +
    127A  ARG*     3.2    51.1    +      -       +      +
    129A  LEU*     4.2    23.2    -      -       +      +
    143A  GLY*     1.3    77.0    -      -       -      +
    145A  TRP*     1.3    60.1    +      -       -      +
    146A  ASP*     3.8     2.1    +      -       -      +
    152A  THR*     4.3    27.2    -      -       +      +
    153A  VAL      3.4     5.8    -      -       -      +
    154A  SER*     5.2     5.2    -      -       -      +
    155A  VAL*     4.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  GLN*     5.6     8.1    -      -       -      -
    117A  LEU*     6.0     4.7    -      -       +      -
    119A  CYS*     4.0    16.4    -      -       -      -
    121A  ILE*     3.2    44.6    -      -       +      +
    125A  ASP*     3.4    14.1    -      -       +      +
    126A  LEU*     3.5    11.0    -      -       +      -
    144A  GLU*     1.3    70.1    -      -       -      +
    146A  ASP*     1.3    59.4    +      -       -      +
    147A  ALA*     2.6    41.8    +      -       +      +
    148A  PRO*     3.5    23.5    -      -       +      +
    151A  LYS      3.3     0.5    -      -       -      +
    152A  THR*     4.2     0.2    -      -       -      -
    153A  VAL*     2.8    43.2    +      -       +      +
    155A  VAL*     3.6    19.5    -      -       +      +
    193A  TYR*     3.9    44.9    -      +       +      -
    204A  VAL*     4.7     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  LYS      5.0     3.8    -      -       -      +
    125A  ASP*     2.9    41.4    +      -       +      +
    144A  GLU      3.8     1.9    +      -       -      -
    145A  TRP*     1.3    69.2    +      -       -      +
    147A  ALA*     1.3    67.3    +      -       -      +
    148A  PRO*     4.5     0.9    -      -       -      +
    150A  GLY      4.8     5.0    -      -       -      +
    151A  LYS      3.7     4.3    -      -       -      -
    152A  THR*     2.4    35.4    +      -       -      -
----------------------------------------------------------
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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