Contacts of the strand formed by residues 40 - 48 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  THR*     4.1     5.6    -      -       -      -
     11A  CYS*     3.8     1.9    -      -       -      -
     31A  CYS*     4.3     1.4    -      -       -      -
     38A  ARG*     3.8    20.0    +      -       +      +
     39A  ARG*     1.3    78.0    +      -       -      +
     41A  CYS*     1.3    66.5    +      -       -      +
     59A  CYS*     3.4     7.4    -      -       -      +
     60A  TRP*     2.8    43.4    +      -       +      +
     62A  ASP      5.0     2.9    -      -       -      -
     63A  ASP*     6.1     0.2    -      -       -      -
     64A  ILE*     3.7    33.7    +      -       +      -
     66A  CYS*     3.5    25.2    -      -       -      -
     85A  CYS*     4.4     4.0    -      -       +      -
     86A  CYS      3.4     9.8    +      -       -      +
     87A  GLU*     3.5    34.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  THR*     3.6    11.0    -      -       -      +
     10A  GLU      3.6     7.4    -      -       -      -
     11A  CYS*     2.1    48.5    -      -       -      -
     40A  HIS*     1.3    73.2    -      -       -      +
     42A  PHE*     1.3    62.0    +      -       -      +
     58A  GLY      3.3     5.6    -      -       -      +
     60A  TRP*     4.7     0.4    -      -       -      -
     85A  CYS*     3.1     9.0    -      -       -      +
     86A  CYS*     2.9    30.4    +      -       -      -
     88A  GLY      3.8    12.1    -      -       -      -
     91A  CYS*     3.6    13.9    -      -       -      -
     92A  ASN*     3.5    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  CYS*     1.3    76.8    -      -       -      +
     43A  ALA*     1.3    65.6    +      -       -      +
     44A  THR*     4.0    11.0    -      -       +      -
     56A  LYS*     3.9    41.1    -      -       +      -
     57A  GLN*     3.4     1.7    -      -       -      -
     58A  GLY*     2.9    53.8    +      -       -      -
     59A  CYS      3.4    24.7    -      -       -      -
     60A  TRP*     3.8    27.1    -      +       +      -
     72A  CYS*     4.5     0.9    -      -       -      -
     83A  PHE*     3.7    27.6    -      +       +      -
     84A  CYS      3.1    14.8    -      -       -      +
     85A  CYS*     4.1     0.9    -      -       +      +
     92A  ASN*     3.0    25.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  PHE*     1.3    76.9    -      -       -      +
     44A  THR*     1.4    65.5    +      -       -      +
     45A  TRP*     3.6     6.0    -      -       +      -
     54A  ILE*     6.1     0.2    -      -       +      -
     56A  LYS      3.4     6.7    -      -       -      -
     57A  GLN*     3.9    15.7    -      -       +      -
     72A  CYS*     4.1     2.6    -      -       -      -
     83A  PHE*     3.4     4.3    -      -       -      -
     84A  CYS*     3.0    43.0    +      -       -      +
     92A  ASN      4.5     3.1    -      -       -      +
     95A  PHE*     4.0    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  PHE*     4.0     9.6    -      -       +      -
     43A  ALA*     1.4    73.1    -      -       -      +
     45A  TRP*     1.3    65.2    +      -       -      +
     54A  ILE*     3.8     3.5    -      -       -      +
     55A  VAL*     2.8    33.4    +      -       -      +
     56A  LYS*     2.8    33.7    +      -       -      +
     60A  TRP*     5.9     1.1    -      -       +      -
     81A  VAL*     4.3    11.2    -      -       +      -
     82A  TYR      3.1    10.5    -      -       -      +
     83A  PHE*     3.4    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  ALA*     3.6    14.4    -      -       +      -
     44A  THR*     1.3    82.0    -      -       -      +
     46A  LYS*     1.3    77.5    +      -       -      +
     47A  ASN*     4.2     0.4    -      -       +      -
     52A  ILE*     3.9    15.9    -      -       +      -
     53A  GLU      3.4    13.9    -      -       -      +
     54A  ILE*     4.1     6.3    -      -       -      -
     55A  VAL*     4.0     4.7    -      -       -      +
     74A  GLU*     3.9    13.9    -      -       +      -
     81A  VAL*     3.8     4.3    -      -       -      +
     82A  TYR*     2.8    65.2    +      +       +      +
     83A  PHE      4.0     2.5    -      -       -      -
     84A  CYS*     3.6    32.8    -      -       -      -
     95A  PHE*     3.5    36.1    -      +       +      -
     96A  SER      3.9    23.6    -      -       -      -
     97A  TYR      4.8     0.2    -      -       -      -
    147A  NAG      3.0    28.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  TRP*     1.3    82.0    -      -       -      +
     47A  ASN*     1.3    61.4    +      -       -      +
     48A  ILE*     4.1    14.8    -      -       +      -
     51A  SER      3.6     1.1    -      -       -      +
     52A  ILE*     3.3     4.7    -      -       -      -
     53A  GLU*     2.9    55.6    +      -       +      +
     55A  VAL*     4.1    19.3    -      -       +      -
     80A  GLU*     4.5    16.3    +      -       -      +
     81A  VAL*     4.1    23.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  TRP*     4.2     1.6    -      -       +      -
     46A  LYS*     1.3    76.0    -      -       -      +
     48A  ILE*     1.3    68.4    +      -       -      +
     49A  SER      4.0     1.2    +      -       -      -
     50A  GLY*     2.9    23.4    +      -       -      -
     51A  SER      3.4     3.6    -      -       -      -
     52A  ILE*     3.4    11.7    -      -       +      -
     80A  GLU      5.2     0.6    +      -       -      -
     82A  TYR*     3.7    35.7    +      -       +      -
    147A  NAG      1.4    68.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  LYS*     4.9    13.2    -      -       +      -
     47A  ASN*     1.3    82.8    -      -       -      +
     49A  SER*     1.3    81.4    +      -       -      +
     51A  SER*     2.9    30.4    +      -       -      +
     80A  GLU      5.8     3.8    -      -       -      +
----------------------------------------------------------
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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