Contacts of the strand formed by residues 140 - 145 (chain A) in PDB entry 4RZR


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
----------------------------------------------------------
      6A  VAL*     3.9    20.4    -      -       +      -
      7A  ASP      3.7     9.0    -      -       -      +
      8A  PHE*     3.5    29.4    -      -       +      -
      9A  ASP*     3.5    11.1    -      -       -      +
    128A  ILE*     5.1     0.2    -      -       +      -
    129A  LYS*     2.7    60.7    +      -       +      +
    132A  ILE*     4.1    29.4    -      -       +      -
    138A  ILE*     4.0     2.0    +      -       +      -
    139A  THR*     1.3    80.1    -      -       -      +
    141A  THR*     1.3    56.6    +      -       -      +
    142A  VAL*     4.3     5.2    -      -       +      -
    161A  ASN*     3.6     2.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 141 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  PHE      3.8     0.5    -      -       -      +
      6A  VAL*     3.6     2.3    -      -       -      +
      7A  ASP*     2.9    38.8    +      -       -      +
      9A  ASP*     2.8    22.1    +      -       -      -
    140A  VAL*     1.3    72.9    -      -       -      +
    142A  VAL*     1.3    63.9    +      -       -      +
    143A  GLY      4.3     0.3    +      -       -      -
    155A  ALA*     3.3    38.6    -      -       -      +
    158A  ALA*     3.8     9.2    -      -       +      -
    159A  LYS*     3.6    15.6    -      -       -      +
    160A  PRO*     3.4     5.9    -      -       -      +
    161A  ASN      3.1    14.9    +      -       -      -
    162A  GLY      3.2    11.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  LEU*     3.6    38.4    -      -       +      -
      5A  PHE      3.3     4.7    -      -       -      +
      6A  VAL*     4.5     6.1    -      -       +      -
    125A  GLY*     4.2    10.8    -      -       -      +
    128A  ILE*     5.0     2.9    -      -       +      -
    129A  LYS*     3.9    25.4    -      -       +      -
    140A  VAL*     4.3     8.3    -      -       +      -
    141A  THR*     1.3    79.7    -      -       -      +
    143A  GLY*     1.3    60.6    +      -       -      +
    144A  ILE*     3.9    17.5    -      -       +      -
    155A  ALA*     4.3     3.4    -      -       -      -
    162A  GLY      2.9     7.4    +      -       -      +
    163A  ILE*     3.1    15.8    +      -       +      -
    164A  LYS*     2.9    26.2    +      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
      4A  LEU*     3.5     2.8    -      -       -      -
      5A  PHE*     2.7    39.1    +      -       -      +
    142A  VAL*     1.3    73.2    -      -       -      +
    144A  ILE*     1.3    62.2    +      -       -      +
    151A  ALA*     3.3    24.9    -      -       -      +
    154A  ALA*     3.5     8.3    -      -       -      -
    155A  ALA*     3.7     7.4    -      -       -      +
    164A  LYS      3.4     5.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  ILE*     4.6     2.2    -      -       +      -
      3A  VAL      3.4     8.1    -      -       -      +
      4A  LEU*     3.8    19.5    -      -       +      -
    118A  TYR*     3.6    28.5    -      -       +      -
    121A  ALA*     3.6    40.4    -      -       +      +
    122A  TYR*     3.9    10.8    -      -       -      +
    142A  VAL*     3.9    15.5    -      -       +      -
    143A  GLY*     1.3    79.3    -      -       -      +
    145A  SER*     1.3    63.9    +      -       -      +
    151A  ALA*     4.4     1.3    -      -       -      -
    154A  ALA*     3.8     2.5    -      -       -      +
    163A  ILE*     4.5     9.2    -      -       +      -
    164A  LYS      2.8    12.3    +      -       -      +
    165A  VAL*     3.3    14.4    -      -       +      +
    166A  ILE*     2.9    28.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  ILE*     3.6     4.0    -      -       -      -
      3A  VAL      2.9    31.4    +      -       -      +
    118A  TYR*     3.3    12.9    +      -       -      -
    144A  ILE*     1.3    76.3    -      -       -      +
    146A  LYS*     1.3    63.2    +      -       -      +
    147A  ASN      3.3     4.9    -      -       -      -
    150A  PHE*     3.2    34.8    -      -       -      +
    151A  ALA*     3.5    13.1    -      -       -      +
    166A  ILE*     2.8    24.0    +      -       -      +
    171A  VAL*     3.7     9.0    -      -       -      +
----------------------------------------------------------
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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