Contacts of the helix formed by residues 74 - 82 (chain T) in PDB entry 2BKC


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 THR 74 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25R  VAL*     3.9     3.1    -      -       -      -
     29R  GLN*     4.2     0.2    -      -       -      +
     86R  GLU*     3.4    29.2    -      -       +      +
     87R  ALA*     3.8    31.2    -      -       -      +
     88R  PRO*     3.9     6.5    -      -       +      +
     73T  SER*     1.3    83.7    -      -       -      +
     75T  LEU*     1.3    64.5    +      -       -      +
     76T  LYS*     3.9     5.1    -      -       -      +
     77T  GLU*     2.6    40.7    +      -       -      +
     78T  PHE*     3.0    32.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 75 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21R  ASN      3.8    10.3    -      -       -      +
     22R  VAL*     3.8    18.2    -      -       +      -
     25R  VAL*     3.6    32.8    -      -       +      -
     75R  LEU*     3.7    29.4    -      -       +      +
     78R  PHE*     3.6    40.8    -      -       +      -
     79R  LEU*     3.8    15.5    -      -       +      -
     86R  GLU*     2.9    24.0    +      -       -      +
     74T  THR*     1.3    71.8    -      -       -      +
     76T  LYS*     1.3    61.4    +      -       -      +
     78T  PHE*     3.1    10.0    +      -       -      +
     79T  LEU*     3.0    23.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 76 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79R  LEU*     4.0    19.0    -      -       +      +
     86R  GLU*     3.1    14.2    +      -       -      +
     88R  PRO*     6.2     3.8    -      -       +      -
     74T  THR*     4.2     5.6    -      -       -      +
     75T  LEU*     1.3    80.1    -      -       -      +
     77T  GLU*     1.3    65.0    +      -       +      +
     79T  LEU*     3.5     3.4    +      -       -      +
     80T  GLU*     2.7    57.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 77 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88R  PRO*     3.6    24.2    -      -       +      +
     89R  TYR      5.2     0.9    +      -       -      -
     71T  PRO      5.3     0.5    -      -       -      +
     72T  PHE*     3.8    37.1    -      -       +      -
     73T  SER*     3.2    18.0    +      -       -      -
     74T  THR*     2.6    38.1    +      -       -      +
     76T  LYS*     1.3    76.2    -      -       +      +
     78T  PHE*     1.3    66.5    +      -       -      +
     80T  GLU*     3.5     9.1    +      -       -      +
     81T  ASN*     2.9    33.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 78 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25R  VAL*     3.6    24.0    -      -       +      -
     32R  TRP*     5.0     4.7    -      +       -      -
     75R  LEU*     3.7    14.6    -      -       +      -
     17T  VAL*     3.9     6.3    -      -       +      -
     18T  ALA*     3.5    29.7    -      -       -      +
     21T  ASN*     3.4    43.5    -      -       +      -
     22T  VAL*     4.7     1.6    -      -       +      -
     72T  PHE*     3.4    39.9    -      -       +      -
     73T  SER*     3.9     3.4    -      -       -      -
     74T  THR      3.0    27.4    +      -       -      -
     75T  LEU*     3.1    10.1    +      -       -      +
     77T  GLU*     1.3    76.0    -      -       -      +
     79T  LEU*     1.3    56.7    +      -       -      +
     82T  ALA*     2.9    36.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 79 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75R  LEU*     3.6    18.8    -      -       +      -
     76R  LYS*     3.8    35.9    -      -       +      +
     79R  LEU*     4.1    17.9    -      -       +      -
     22T  VAL*     4.8     6.5    -      -       +      -
     75T  LEU      3.0    16.2    +      -       -      +
     76T  LYS*     3.9     4.9    -      -       -      +
     78T  PHE*     1.3    78.2    -      -       -      +
     80T  GLU*     1.3    63.3    +      -       +      +
     81T  ASN      3.3     0.5    +      -       -      -
     82T  ALA*     4.0     9.8    +      -       -      +
     86T  GLU*     3.1    31.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 80 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76T  LYS*     2.7    57.0    +      -       +      +
     77T  GLU*     4.6     8.7    -      -       -      +
     78T  PHE      3.4     0.2    -      -       -      -
     79T  LEU*     1.3    78.9    -      -       +      +
     81T  ASN*     1.3    72.6    +      -       -      +
     82T  ALA      5.3     0.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 81 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15T  HIS*     3.2    31.7    +      -       +      -
     18T  ALA*     3.9     8.3    -      -       +      -
     72T  PHE*     3.5    44.1    -      -       +      -
     77T  GLU*     2.9    26.5    +      -       -      +
     79T  LEU      3.1     0.4    -      -       -      -
     80T  GLU*     1.3    91.1    +      -       -      +
     82T  ALA*     1.3    59.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 82 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15T  HIS*     4.6     0.4    -      -       -      -
     18T  ALA*     3.6     3.6    -      -       -      +
     19T  ASN*     3.4    22.2    -      -       -      +
     22T  VAL*     3.7    24.7    -      -       +      -
     78T  PHE      2.9    18.0    +      -       -      +
     79T  LEU*     4.0     7.8    +      -       -      +
     80T  GLU      3.8     0.9    -      -       -      +
     81T  ASN*     1.3    77.9    -      -       -      +
     83T  SER*     1.3    59.5    +      -       -      +
     84T  VAL      4.1    10.7    -      -       -      +
----------------------------------------------------------
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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