Contacts of the strand formed by residues 169 - 180 (chain A) in PDB entry 3BXB


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 HIS 169 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  GLU*     3.3    29.9    +      -       +      +
    161A  ALA*     3.7    22.2    -      -       +      -
    162A  LEU      3.4     5.2    -      -       -      +
    163A  LYS*     3.8    22.7    -      -       +      +
    164A  LEU*     3.8    10.0    -      -       -      +
    168A  GLY*     1.3    84.6    -      -       -      -
    170A  LEU*     1.3    59.0    +      -       -      +
    171A  ILE*     3.9    23.0    +      -       +      +
    148B  TYR*     4.2    24.9    -      +       +      +
    149B  PRO*     4.8     9.8    +      -       +      -
    192B  VAL*     3.7    19.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  TYR*     3.9    26.0    -      -       +      -
     97A  GLU*     4.5     3.8    -      -       +      +
     98A  ASP*     3.6    47.8    -      -       +      +
    131A  PRO*     4.4    14.1    -      -       +      -
    132A  VAL*     4.1    19.7    -      -       +      -
    140A  TRP*     4.7     0.9    -      -       -      -
    160A  MET      4.0     0.3    -      -       -      +
    161A  ALA*     3.7     0.3    -      -       -      -
    162A  LEU*     2.9    45.7    +      -       +      +
    164A  LEU*     3.8    18.6    -      -       +      +
    169A  HIS*     1.3    71.0    -      -       -      +
    171A  ILE*     1.3    66.7    +      -       -      +
    172A  CYS*     4.0     0.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 171 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  TYR*     4.0     0.5    -      -       -      -
     97A  GLU*     3.1    56.8    +      -       -      +
    159A  ASP*     5.0     2.5    -      -       +      +
    160A  MET      3.4     8.3    -      -       -      +
    161A  ALA*     3.6    27.6    -      -       +      -
    169A  HIS*     4.0     6.7    +      -       +      +
    170A  LEU*     1.3    79.2    -      -       -      +
    172A  CYS*     1.3    73.2    +      -       -      +
    146B  MET*     4.3     3.4    -      -       +      -
    148B  TYR*     3.0    51.1    -      -       +      +
    157B  ARG*     3.8    19.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 172 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  THR*     3.7    20.6    -      -       +      -
     95A  THR      3.3    13.7    -      -       -      +
     96A  TYR*     3.7    19.7    -      -       +      -
     97A  GLU*     5.0     1.6    -      -       -      -
    140A  TRP*     3.8    33.2    -      -       -      -
    159A  ASP*     3.5     4.7    -      -       -      +
    160A  MET*     2.9    37.5    +      -       -      +
    171A  ILE*     1.3    81.2    -      -       -      +
    173A  ASN*     1.3    61.1    +      -       -      +
    174A  LEU*     3.8    11.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 173 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  VAL      3.8     1.2    -      -       -      +
     94A  THR*     3.3     3.1    -      -       -      -
     95A  THR*     2.8    43.2    +      -       -      +
     97A  GLU*     5.9     1.8    -      -       +      +
    157A  ARG*     5.4     1.9    -      -       -      +
    158A  SER      3.2    10.6    +      -       -      -
    159A  ASP*     2.7    24.4    +      -       -      +
    171A  ILE*     6.2     0.2    -      -       +      -
    172A  CYS*     1.3    76.2    -      -       -      +
    174A  LEU*     1.3    66.3    +      -       -      +
    175A  LYS*     3.5    30.8    +      -       -      +
    159B  ASP*     3.5    17.8    +      -       -      -
    173B  ASN*     3.8    12.3    -      -       -      +
    175B  LYS*     5.8     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 174 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  THR*     4.7     5.6    -      -       -      +
     63A  NRQ      4.7    10.1    -      -       +      -
     92A  ARG*     3.8    28.0    -      -       -      +
     93A  VAL      3.7     2.7    -      -       -      -
     94A  THR*     3.4    30.5    -      -       +      +
    156A  GLY      3.8     0.6    -      -       -      +
    157A  ARG*     3.5    10.4    -      -       -      -
    158A  SER*     2.8    48.1    +      -       -      +
    160A  MET*     4.1    28.5    -      -       +      -
    172A  CYS*     3.8    15.5    -      -       -      +
    173A  ASN*     1.3    83.0    +      -       -      +
    175A  LYS*     1.3    62.9    +      -       -      +
    176A  THR*     4.3     3.6    -      -       -      +
    197A  ARG*     4.8     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 175 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  GLU      4.0     0.2    -      -       -      +
     92A  ARG*     3.3     4.6    -      -       -      +
     93A  VAL*     3.0    49.9    +      -       +      +
     95A  THR*     5.7     4.2    +      -       -      -
    156A  GLY      3.6     4.5    -      -       -      -
    157A  ARG*     3.5    34.3    -      -       -      +
    173A  ASN*     3.5    20.7    +      -       -      +
    174A  LEU*     1.3    75.7    -      -       -      +
    176A  THR*     1.3    61.8    +      -       -      +
     97B  GLU*     3.6    20.3    +      -       -      +
     99C  GLY      5.6     0.9    -      -       -      -
    101C  VAL*     6.1     3.4    -      -       -      -
    124C  VAL*     5.5     0.3    -      -       -      +
    125C  ASN*     4.2    23.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 176 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  TRP*     4.3     5.2    -      -       +      -
     91A  GLU      3.2    17.7    -      -       -      +
     92A  ARG*     3.2    34.3    +      -       +      +
    145A  GLU*     4.1     6.1    +      -       -      -
    155A  GLU*     3.2     8.2    -      -       -      +
    156A  GLY*     2.7    38.2    +      -       -      +
    157A  ARG*     4.1     1.6    +      -       -      +
    174A  LEU*     4.7     4.5    -      -       -      +
    175A  LYS*     1.3    77.1    +      -       -      +
    177A  THR*     1.3    62.7    +      -       -      +
    178A  TYR*     3.5    42.9    +      -       +      +
    125C  ASN*     6.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 177 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  THR      4.1     0.3    -      -       -      +
     90A  TRP*     3.3     6.1    -      -       -      +
     91A  GLU*     3.0    48.5    +      -       -      +
    154A  LEU      3.7     2.7    -      -       -      +
    155A  GLU*     3.7    26.3    +      -       +      +
    176A  THR*     1.3    73.9    -      -       -      +
    178A  TYR*     1.3    66.1    +      -       -      +
    179A  ARG*     3.7    39.8    +      -       +      +
    125C  ASN*     4.2    13.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 178 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  LYS*     3.2    36.8    +      -       +      -
     79A  PHE*     4.1    11.2    -      -       +      -
     80A  PHE*     3.6    26.5    -      +       +      -
     88A  PHE*     5.6     0.7    -      +       +      -
     89A  THR      3.6     4.7    -      -       -      +
     90A  TRP*     3.6    21.8    -      +       +      -
     92A  ARG*     3.8     5.5    +      -       -      -
    145A  GLU*     2.8    24.6    +      -       -      -
    147A  LEU*     3.8    17.9    -      -       +      -
    153A  GLY*     3.4     7.6    -      -       -      -
    154A  LEU*     2.6    58.3    +      -       +      +
    156A  GLY      4.0    12.3    -      -       -      -
    176A  THR*     3.5    24.6    -      -       +      +
    177A  THR*     1.3    75.9    -      -       -      +
    179A  ARG*     1.3    63.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 179 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  PHE*     4.3     0.9    -      -       -      -
     88A  PHE*     3.3     6.4    -      -       -      +
     89A  THR*     2.8    47.0    +      -       -      +
     91A  GLU*     2.7    37.8    +      -       -      +
    153A  GLY*     5.0     3.1    -      -       -      -
    177A  THR*     3.7    22.5    +      -       +      +
    178A  TYR*     1.3    79.0    -      -       -      +
    180A  SER*     1.3    64.6    +      -       -      +
    181A  LYS*     5.1     1.1    -      -       +      +
     20C  ASN*     3.5    40.6    +      -       -      +
     21C  ASN*     3.7    22.6    -      -       -      +
    125C  ASN*     6.1     0.2    -      -       -      +
    126C  PHE      5.0     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 180 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  PHE*     3.7    14.3    -      -       -      -
     83A  SER*     2.8    31.4    +      -       -      -
     88A  PHE*     4.2     6.7    -      -       -      -
    152A  GLY      5.3     3.3    +      -       -      -
    153A  GLY*     5.3     1.4    -      -       -      -
    179A  ARG*     1.3    76.8    -      -       -      +
    181A  LYS*     1.3    63.7    +      -       -      +
    182A  LYS*     3.4    12.5    +      -       -      +
    187A  LEU*     3.5    29.1    -      -       -      +
----------------------------------------------------------
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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