Contacts of the strand formed by residues 163 - 169 (chain A) in PDB entry 4BU2


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 GLY 163 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  GLN*     3.5    15.5    -      -       -      -
    141A  GLN*     3.8     1.8    -      -       -      -
    151A  GLN*     3.6     4.1    +      -       -      -
    161A  LEU      4.1     1.2    -      -       -      -
    162A  VAL*     1.3    75.5    -      -       -      +
    164A  SER*     1.3    63.9    -      -       -      -
    165A  ASN*     5.7     0.2    -      -       -      -
    256A  ILE*     3.5     3.5    -      -       -      +
    257A  SER*     3.0    35.4    +      -       -      -
    405A  MSE      3.9    17.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  GLN*     2.9    37.7    +      -       -      +
    140A  PRO*     3.1    23.8    -      -       -      +
    141A  GLN*     3.3     0.7    +      -       -      -
    151A  GLN*     2.7    28.6    +      -       -      +
    163A  GLY*     1.3    74.2    -      -       -      -
    165A  ASN*     1.3    66.6    +      -       -      +
    254A  VAL*     3.7    12.7    -      -       -      +
    255A  THR      3.1    13.2    -      -       -      -
    256A  ILE*     4.0     5.8    -      -       -      -
    257A  SER*     5.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  GLN*     3.2    17.3    +      -       +      +
    137A  PHE      3.5     4.8    -      -       -      +
    138A  HIS*     2.9    37.8    +      -       -      +
    139A  GLN*     4.3     9.7    +      -       -      +
    140A  PRO*     4.3     0.2    -      -       -      -
    164A  SER*     1.3    81.0    +      -       -      +
    166A  VAL*     1.3    64.1    +      -       -      +
    167A  TYR*     4.0    11.0    -      -       +      -
    254A  VAL*     3.2     2.8    -      -       -      +
    255A  THR*     2.7    36.5    +      -       -      -
    257A  SER*     5.3     3.0    +      -       -      -
    902A  EDO      3.5    31.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  PHE*     3.8    37.9    -      -       +      -
    135A  ILE      3.6     0.7    -      -       -      +
    136A  GLN*     3.2     9.0    -      -       -      +
    137A  PHE*     2.9    41.8    +      -       +      +
    140A  PRO*     3.7    29.8    -      -       +      -
    147A  LEU*     5.3     0.2    -      -       +      -
    165A  ASN*     1.3    76.8    -      -       -      +
    167A  TYR*     1.3    64.1    +      -       -      +
    168A  ILE*     4.1    17.3    -      -       +      -
    190A  LEU*     5.4     0.2    -      -       +      -
    252A  THR*     4.4     6.1    -      -       +      -
    253A  HIS      3.4    10.3    -      -       -      +
    254A  VAL*     3.8    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  THR*     4.2    18.2    -      -       +      -
    135A  ILE      3.5     2.2    -      -       -      -
    136A  GLN*     3.6    36.2    +      -       +      -
    165A  ASN*     4.0    10.3    -      -       +      -
    166A  VAL*     1.3    73.7    -      -       -      +
    168A  ILE*     1.3    63.7    +      -       -      +
    169A  THR*     4.2     1.1    -      -       -      -
    176A  LEU*     4.3    11.8    -      -       +      +
    194A  LYS*     4.9     1.9    +      -       -      +
    251A  SER      3.6     1.0    -      -       -      +
    252A  THR*     3.3     5.5    -      -       -      -
    253A  HIS*     2.8    65.2    +      +       +      +
    255A  THR*     3.4    22.7    -      -       -      -
    701A  AKG      3.4    34.2    -      -       +      +
    902A  EDO      2.8    32.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  PHE*     4.4     8.3    -      -       +      -
     83A  LEU*     3.6    32.8    -      -       +      -
     86A  LEU*     3.8    33.7    -      -       +      -
    133A  ALA      4.2     0.5    -      -       -      +
    134A  THR*     3.7     0.7    -      -       -      +
    135A  ILE*     2.8    55.7    +      -       +      +
    137A  PHE*     5.7     1.1    -      -       +      -
    166A  VAL*     4.1    18.4    -      -       +      -
    167A  TYR*     1.3    78.8    -      -       -      +
    169A  THR*     1.3    67.6    +      -       -      +
    170A  PRO*     4.5     0.9    -      -       +      +
    250A  HIS*     4.1     7.2    -      -       +      -
    251A  SER      3.3     8.1    -      -       -      +
    252A  THR*     3.6    13.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  ALA      3.6     4.0    -      -       -      +
    134A  THR*     3.4    29.2    +      -       -      +
    167A  TYR      4.2     0.4    -      -       -      -
    168A  ILE*     1.3    76.7    +      -       -      +
    170A  PRO*     1.3    76.1    -      -       +      +
    173A  SER*     3.3    22.7    -      -       -      +
    174A  GLN      4.0     6.5    -      -       -      +
    175A  GLY*     4.9     0.2    -      -       -      -
    194A  LYS*     2.8    23.3    +      -       -      +
    243A  ASP*     6.2     0.2    -      -       -      -
    244A  THR*     3.3    17.8    +      -       -      +
    250A  HIS*     3.3     3.7    -      -       -      +
    251A  SER      2.8    35.6    +      -       -      -
    701A  AKG      4.7     0.2    +      -       -      -
----------------------------------------------------------
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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