Contacts of the strand formed by residues 155 - 161 (chain A) in PDB entry 3BU0


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 PHE 155 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  THR*     3.6    20.2    -      -       +      -
    115A  TYR      3.4    10.8    -      -       -      -
    116A  GLY*     4.1     0.4    -      -       -      -
    120A  LEU*     4.2    16.8    -      -       +      -
    121A  THR      5.1     0.7    -      -       -      -
    122A  TYR*     3.5    43.7    -      +       +      -
    129A  LEU      5.0     0.2    -      -       -      -
    131A  PRO*     3.9    26.7    -      -       +      -
    134A  TRP*     3.6     6.3    -      -       -      -
    153A  PHE*     3.6     0.7    -      -       -      +
    154A  ASN*     1.3    81.3    -      -       -      +
    156A  VAL*     1.3    86.7    +      -       -      +
    157A  LEU*     3.9    11.4    -      -       +      -
    253A  PHE*     3.3     8.5    -      -       -      +
    254A  ARG*     2.9    37.5    +      -       -      +
    256A  ILE*     3.5    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  ALA      3.9     0.3    -      -       -      +
    114A  THR*     3.4     4.9    -      -       -      -
    115A  TYR*     2.7    58.3    +      -       +      +
    134A  TRP*     3.9    13.7    -      -       +      -
    138A  LEU*     4.1    12.8    -      -       +      -
    155A  PHE*     1.3    81.9    -      -       -      +
    157A  LEU*     1.3    63.4    +      -       -      +
    158A  ILE*     4.0     7.5    +      -       +      +
    251A  LEU*     3.8    26.5    -      -       +      -
    252A  THR      3.5    12.3    -      -       -      +
    253A  PHE*     3.6    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  GLN*     4.3    21.1    -      -       +      +
    113A  ALA      3.6    10.1    -      -       -      +
    114A  THR*     3.9    13.7    -      -       +      -
    122A  TYR*     3.4    32.5    -      -       +      +
    124A  PHE*     5.8     0.7    -      -       +      -
    129A  LEU*     4.7     3.6    -      -       +      -
    155A  PHE*     3.9    14.4    -      -       +      -
    156A  VAL*     1.3    71.9    -      -       -      +
    158A  ILE*     1.3    66.2    +      -       -      +
    159A  ASN*     3.4    11.6    +      -       -      +
    250A  ASN*     3.5     2.4    +      -       -      +
    251A  LEU*     3.5     0.7    -      -       -      -
    252A  THR*     2.8    47.5    +      -       -      +
    254A  ARG*     3.6    12.1    -      -       -      +
    301A  AKG      3.1    28.0    -      -       -      +
      7B  2YR      5.9     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  LEU*     5.3     0.4    -      -       +      -
     89A  VAL*     3.9    12.8    -      -       +      -
     91A  TYR*     3.7    28.0    -      -       +      +
    111A  LYS      3.6     0.5    -      -       -      +
    112A  GLN*     3.1     9.4    -      -       -      +
    113A  ALA*     2.8    41.8    +      -       +      +
    115A  TYR*     3.7    33.0    -      -       +      -
    138A  LEU*     3.9    23.3    -      -       +      -
    156A  VAL*     4.4    14.1    -      -       +      -
    157A  LEU*     1.3    76.4    -      -       -      +
    159A  ASN*     1.3    63.9    +      -       -      +
    249A  VAL*     3.7    20.2    -      -       +      -
    250A  ASN      3.2     4.3    -      -       -      +
    251A  LEU*     4.5     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  ARG*     2.9    27.5    +      -       -      -
    111A  LYS      3.4     2.0    -      -       -      -
    112A  GLN*     3.1    16.1    +      -       -      +
    157A  LEU*     3.4    18.0    +      -       -      +
    158A  ILE*     1.3    76.2    -      -       -      +
    160A  ARG*     1.3    59.4    +      -       -      +
    161A  TYR*     3.4    33.2    -      -       +      +
    249A  VAL*     3.6     0.7    -      -       -      -
    250A  ASN*     2.8    41.5    +      -       +      +
    301A  AKG      2.5    37.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  GLU*     2.7    39.6    +      -       -      -
     91A  TYR*     3.5    47.3    -      -       +      +
    110A  ARG*     3.4     7.1    -      -       -      +
    111A  LYS*     2.8    57.6    +      -       +      +
    158A  ILE      4.1     0.4    -      -       -      -
    159A  ASN*     1.3    73.0    -      -       -      +
    161A  TYR*     1.3    63.4    +      -       -      +
    162A  LYS*     3.6    28.5    +      -       -      +
    166A  ASP*     3.9     1.7    -      -       -      +
    247A  PRO*     3.6    19.4    -      -       -      +
    248A  ARG      3.3    11.2    -      -       -      +
    249A  VAL*     3.9     6.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  ARG*     3.7    13.5    -      -       +      -
    159A  ASN*     3.4    35.5    -      -       +      +
    160A  ARG*     1.3    72.6    -      -       -      +
    162A  LYS*     1.3    63.3    +      -       -      +
    163A  ASP*     3.2     2.9    +      -       -      -
    166A  ASP*     3.5     8.3    -      -       +      -
    167A  HIS*     3.5    43.3    -      -       -      -
    168A  ILE*     3.4    16.4    -      -       +      +
    193A  ARG*     3.7    18.2    -      -       -      +
    238A  LEU*     3.6    15.9    -      -       +      -
    246A  ALA      4.1     0.5    -      -       -      +
    247A  PRO*     3.1     0.5    -      -       -      +
    248A  ARG*     2.8    72.7    +      -       +      +
    250A  ASN*     4.4     0.4    -      -       +      -
    301A  AKG      2.5    23.8    +      -       -      +
----------------------------------------------------------
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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