Contacts of the strand formed by residues 58 - 64 (chain A) in PDB entry 2B2T


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 ILE 58 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  CYS*     5.2     8.3    -      -       -      -
     23A  ARG      3.2     9.6    -      -       -      +
     24A  ILE*     4.2    17.5    -      -       +      -
     57A  GLU*     1.3    73.7    -      -       -      +
     59A  GLN*     1.3    58.2    +      -       -      +
     60A  TYR*     2.9    38.6    -      -       +      +
     76A  THR*     3.8    18.4    -      -       -      +
     77A  GLU*     4.7     2.5    +      -       +      +
     95A  LYS*     5.9     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  CYS*     3.5     5.5    -      -       -      -
     23A  ARG*     2.7    76.4    +      -       +      +
     25A  GLY*     3.6    10.4    +      -       -      -
     26A  ARG      3.1    25.6    +      -       -      -
     29A  ALA      3.2    18.6    +      -       -      +
     30A  THR*     3.4    10.0    -      -       +      +
     57A  GLU*     3.2    25.9    +      -       -      +
     58A  ILE*     1.3    77.4    -      -       -      +
     60A  TYR*     1.3    64.3    +      -       -      +
     74A  TRP*     4.0    11.0    -      -       +      -
     75A  GLU      3.1    11.4    -      -       -      +
     76A  THR*     3.9    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  PHE*     3.8    23.8    -      +       +      -
     21A  ASP      3.6     4.3    -      -       -      +
     22A  CYS*     4.1    16.2    -      -       -      -
     58A  ILE*     2.9    39.0    -      -       +      +
     59A  GLN*     1.3    77.2    -      -       -      +
     61A  LEU*     1.3    62.2    +      -       -      +
     62A  ILE*     3.5     8.1    +      -       +      +
     73A  THR      3.5     0.2    -      -       -      +
     74A  TRP*     3.1     7.0    -      -       -      -
     75A  GLU      2.7    44.4    +      -       -      +
     76A  THR*     4.6     1.1    -      -       -      -
     77A  GLU*     4.2    21.3    +      -       +      -
     80A  LEU*     5.1     2.2    -      -       +      -
     91A  LEU*     3.6    24.0    -      -       +      -
     94A  TYR*     4.0    30.5    -      +       -      -
     95A  LYS*     3.6    25.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  PHE*     3.8     2.9    -      -       -      -
     20A  MSE      2.9    49.1    +      -       +      +
     21A  ASP*     3.0    25.8    +      -       +      +
     60A  TYR*     1.3    71.6    -      -       -      +
     62A  ILE*     1.3    64.2    +      -       -      +
     72A  ASN*     3.7    29.4    -      -       +      +
     73A  THR      3.7    14.4    -      -       -      +
     74A  TRP*     3.3    39.9    -      -       +      +
    131A  GLN*     6.0     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  ILE*     3.5    24.2    -      -       +      -
     18A  ARG      3.9     4.7    -      -       -      +
     19A  PHE*     4.2    14.1    -      -       +      -
     60A  TYR*     3.7    15.7    -      -       +      +
     61A  LEU*     1.3    77.6    -      -       -      +
     63A  LYS*     1.3    71.6    +      -       -      +
     64A  TRP*     3.5    30.7    -      -       +      -
     72A  ASN*     3.2    29.2    -      -       -      -
     73A  THR      2.8    17.6    +      -       -      +
     75A  GLU*     3.6    35.9    -      -       +      -
     80A  LEU*     3.7    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  GLU*     2.9    59.1    +      -       +      +
     18A  ARG*     2.9    26.0    +      -       +      +
     20A  MSE      4.1    18.3    -      -       +      +
     61A  LEU      4.1     0.4    +      -       -      -
     62A  ILE*     1.3    73.3    -      -       -      +
     64A  TRP*     1.3    74.8    +      -       -      +
     66A  GLY      4.7     0.6    -      -       -      +
     67A  TRP      2.7    29.7    +      -       -      +
     68A  SER*     4.4     1.3    -      -       -      +
     69A  HIS*     3.5    40.4    -      -       +      +
     72A  ASN*     3.4    18.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  GLU*     3.9    16.2    -      -       +      +
     15A  THR      3.3    24.0    -      -       -      +
     16A  ILE*     3.7    24.5    -      -       +      -
     17A  GLU*     3.9     0.9    -      -       -      -
     62A  ILE*     3.5    26.4    +      -       +      -
     63A  LYS*     1.3   100.4    +      -       -      +
     65A  LYS*     1.3    66.4    +      -       -      +
     67A  TRP*     3.1    31.5    +      -       +      +
     71A  HIS      3.7    13.5    -      -       -      -
     72A  ASN*     4.4     1.4    +      -       -      -
     73A  THR*     3.0    27.9    +      -       -      -
     75A  GLU*     3.8    16.4    -      -       +      -
     80A  LEU*     4.1     8.1    -      -       +      -
     83A  GLN*     4.2     7.2    -      -       -      -
     85A  VAL*     3.9    28.7    -      -       +      -
      4D  M3L      3.4    30.1    -      -       -      -
----------------------------------------------------------
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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