Contacts of the strand formed by residues 40 - 48 (chain B) in PDB entry 1BTE


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 40 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  THR*     4.0     7.0    -      -       -      +
     11B  CYS*     4.0     1.0    -      -       -      -
     38B  ARG*     3.6    16.4    +      -       -      +
     39B  ARG*     1.3    80.9    +      -       -      +
     41B  CYS*     1.3    65.0    +      -       -      +
     59B  CYS*     3.6     5.4    -      -       -      +
     60B  TRP*     2.8    41.3    +      -       +      +
     62B  ASP      4.7     4.3    -      -       -      -
     63B  ASP*     5.8     0.4    -      -       -      -
     64B  ILE*     3.5    36.6    +      -       +      -
     66B  CYS*     3.5    25.4    -      -       +      -
     85B  CYS*     4.6     1.8    -      -       +      -
     86B  CYS      3.3    11.9    +      -       -      +
     87B  GLU*     3.4    38.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 41 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  THR*     3.6    14.6    -      -       -      -
     10B  GLU      3.7     2.9    -      -       -      -
     11B  CYS*     2.1    48.7    -      -       -      -
     40B  HIS*     1.3    74.5    -      -       -      +
     42B  PHE*     1.3    61.9    +      -       -      +
     58B  GLY      3.3     6.1    -      -       -      -
     60B  TRP*     4.8     0.4    -      -       -      -
     85B  CYS*     3.2     7.8    -      -       -      +
     86B  CYS*     2.9    31.0    +      -       -      -
     88B  GLY      3.9     3.4    -      -       -      -
     91B  CYS*     3.6    22.7    -      -       -      -
     92B  ASN*     3.5    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 42 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  GLU*     5.5     0.2    -      -       -      -
     41B  CYS*     1.3    76.4    -      -       -      +
     43B  ALA*     1.3    67.0    +      -       -      +
     44B  THR*     4.0    10.3    -      -       +      -
     56B  LYS*     4.0    37.9    -      -       +      -
     57B  GLN*     3.4     1.4    -      -       -      -
     58B  GLY*     2.9    51.1    +      -       -      -
     59B  CYS      3.5    23.1    -      -       -      -
     60B  TRP*     3.8    30.1    -      +       +      -
     72B  CYS*     4.5     0.9    -      -       -      -
     83B  PHE*     3.8    26.9    -      +       +      -
     84B  CYS      3.2    15.0    -      -       -      +
     85B  CYS*     4.2     3.4    -      -       +      +
     92B  ASN*     2.9    25.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 43 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  PHE*     1.3    79.6    -      -       -      +
     44B  THR*     1.3    59.6    +      -       -      +
     45B  TRP*     3.6    11.2    -      -       +      -
     54B  ILE*     6.1     0.2    -      -       +      -
     56B  LYS      3.4     7.2    -      -       -      -
     57B  GLN*     3.9    16.2    -      -       +      -
     72B  CYS*     4.2     2.4    -      -       -      -
     83B  PHE*     3.4     4.5    -      -       -      -
     84B  CYS*     3.0    46.8    +      -       -      +
     92B  ASN      4.6     3.1    -      -       -      +
     95B  PHE*     4.0    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 44 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  PHE*     4.0     9.6    -      -       +      -
     43B  ALA*     1.3    75.3    -      -       -      +
     45B  TRP*     1.3    63.4    +      -       -      +
     54B  ILE*     3.9     2.8    -      -       -      +
     55B  VAL*     2.9    34.9    +      -       +      +
     56B  LYS*     2.9    43.4    +      -       +      +
     81B  VAL*     3.4    18.0    -      -       -      +
     82B  TYR      2.9    17.6    +      -       -      -
     83B  PHE*     4.4    11.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 45 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43B  ALA*     3.6    23.1    -      -       +      -
     44B  THR*     1.3    80.7    +      -       -      +
     46B  LYS*     1.3    83.3    +      -       -      +
     47B  ASN*     4.3     2.0    -      -       +      -
     52B  ILE*     3.9    13.0    -      -       +      -
     53B  GLU      3.3    18.4    -      -       -      +
     54B  ILE*     4.1     3.8    -      -       -      -
     55B  VAL*     4.0     4.9    -      -       -      +
     74B  GLU*     4.0    17.7    -      -       +      -
     81B  VAL*     3.8     3.7    -      -       -      +
     82B  TYR*     2.8    61.1    +      +       +      +
     83B  PHE      4.0     3.1    -      -       -      -
     84B  CYS*     3.7    26.0    -      -       -      -
     95B  PHE*     3.5    38.6    -      +       +      -
     96B  SER      4.1    14.1    -      -       -      -
    147B  NAG      2.9    34.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 46 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  TRP*     1.3    84.0    -      -       -      +
     47B  ASN*     1.4    60.9    +      -       -      +
     48B  ILE*     4.1    15.5    -      -       +      -
     51B  SER      4.2     0.9    -      -       -      +
     52B  ILE*     3.4     3.8    -      -       -      -
     53B  GLU*     2.8    59.9    +      -       +      +
     55B  VAL*     4.2    16.8    -      -       +      -
     80B  GLU      4.6    12.3    -      -       -      +
     81B  VAL*     4.9    15.3    -      -       +      -
     82B  TYR*     4.5     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 47 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  TRP*     4.3     2.7    -      -       +      -
     46B  LYS*     1.4    76.1    -      -       -      +
     48B  ILE*     1.3    63.2    +      -       -      +
     49B  SER      3.5     2.6    +      -       -      -
     50B  GLY*     3.0    26.0    +      -       -      -
     51B  SER      3.5     5.4    -      -       -      -
     52B  ILE*     5.1     2.5    -      -       -      -
     80B  GLU      5.2     1.2    +      -       -      -
     82B  TYR*     3.5    35.4    +      -       +      -
    147B  NAG      1.4    70.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 48 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46B  LYS*     4.6    13.2    -      -       +      -
     47B  ASN*     1.3    77.6    -      -       -      +
     49B  SER*     1.3    75.1    +      -       -      +
     50B  GLY      3.3     0.2    -      -       -      -
     51B  SER*     3.1    33.2    +      -       -      +
----------------------------------------------------------
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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