Contacts of the strand formed by residues 21 - 25 (chain A) in PDB entry 3BB2


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 21 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  LEU      3.7     0.3    -      -       -      +
     15A  TYR*     3.6     1.0    -      -       -      -
     16A  CYS*     2.8    32.2    +      -       +      +
     19A  GLY*     3.5    10.7    +      -       -      -
     20A  GLY*     1.3    78.2    -      -       -      +
     22A  PHE*     1.3    64.4    +      -       -      +
     33A  GLY*     3.8    22.2    -      -       -      -
     34A  THR*     3.5    13.7    -      -       -      +
     35A  ARG*     3.6    40.3    +      -       +      +
    111A  LEU*     4.0    10.2    -      -       +      +
    112A  LYS      3.9     4.2    +      -       -      -
    113A  LYS      3.1    28.0    -      -       -      -
    114A  ASN      3.9     4.0    +      -       -      -
    115A  GLY*     3.3    30.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  LEU*     3.8    31.9    -      -       +      -
     14A  LEU      3.4     4.7    -      -       -      +
     15A  TYR*     3.6    37.0    -      +       +      -
     20A  GLY      5.1     2.2    -      -       -      -
     21A  HIS*     1.3    73.2    -      -       -      +
     23A  LEU*     1.3    64.8    +      -       -      +
     24A  ARG      3.4     0.5    +      -       -      -
     33A  GLY*     3.2     4.0    -      -       -      -
     34A  THR*     2.8    48.3    +      -       -      +
     35A  ARG*     3.8    23.3    -      -       -      -
     36A  ASP      4.4     0.7    -      -       -      -
     37A  ARG*     4.0    28.7    -      -       +      -
     42A  ILE*     3.8    32.3    -      -       +      -
    111A  LEU*     4.4     0.9    -      -       -      -
    135A  LEU*     4.1    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  LEU*     3.0    37.3    +      -       +      +
     21A  HIS      4.0     0.4    +      -       -      -
     22A  PHE*     1.3    71.5    -      -       -      +
     24A  ARG*     1.3    61.3    +      -       -      +
     25A  ILE*     5.4     2.7    -      -       +      -
     31A  VAL*     3.8    26.5    -      -       +      -
     32A  ASP      3.8     6.3    -      -       -      +
     41A  HIS      4.1     0.5    -      -       -      +
     42A  ILE*     3.5    22.3    -      -       -      +
     44A  LEU*     4.2    22.8    -      -       +      +
     56A  ILE*     5.0     1.1    -      -       +      -
     65A  LEU*     4.0    29.4    -      -       +      -
     73A  LEU*     4.8     0.9    -      -       +      -
    109A  VAL*     4.3    18.4    -      -       +      -
    111A  LEU*     4.0    24.3    -      -       +      +
    117A  CYS*     4.8     1.3    -      -       -      -
    132A  PHE*     4.7     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 24 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  PHE      4.2     3.1    -      -       -      +
     23A  LEU*     1.3    76.8    -      -       -      +
     25A  ILE*     1.3    69.1    +      -       -      +
     26A  ASP*     4.5     8.3    +      -       +      +
     30A  THR      4.0     0.5    -      -       -      +
     31A  VAL*     3.3     8.5    -      -       -      +
     32A  ASP*     2.8    73.8    +      -       -      +
     33A  GLY      4.1     2.0    +      -       -      -
     34A  THR*     3.7    27.1    +      -       +      -
     39A  ASP*     3.0    36.6    +      -       -      +
     41A  HIS*     3.5    22.4    -      -       +      +
     42A  ILE*     3.8     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 25 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  LEU*     5.4     3.4    -      -       +      -
     24A  ARG*     1.3    77.1    -      -       -      +
     26A  ASP*     1.3    65.0    +      -       -      +
     27A  PRO      3.8     0.2    -      -       -      -
     29A  GLY*     5.0     0.2    -      -       -      -
     30A  THR      3.8     6.5    -      -       -      +
     31A  VAL*     4.4    10.8    -      -       +      -
     41A  HIS*     3.1    30.4    +      -       -      +
     44A  LEU*     4.2    23.1    -      -       +      -
     56A  ILE*     4.5     2.2    -      -       +      +
     58A  SER*     4.3    14.7    +      -       -      +
     63A  GLN*     3.7    36.9    +      -       +      +
     65A  LEU*     3.9    40.6    -      -       +      +
     75A  GLY*     3.9    21.8    -      -       -      +
----------------------------------------------------------
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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