Contacts of the strand formed by residues 67 - 73 (chain A) in PDB entry 1BMZ


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 GLY 67 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  ARG*     3.6    13.7    -      -       -      -
     35A  LYS      5.7     0.2    -      -       -      -
     65A  VAL      3.5     1.8    +      -       -      -
     66A  GLU*     1.3    76.8    -      -       -      +
     68A  ILE*     1.3    65.3    +      -       -      -
     69A  TYR*     3.6    11.1    -      -       -      -
     96A  THR*     3.4     7.3    -      -       -      +
     97A  ALA      2.9    28.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  ARG*     3.5     4.3    -      -       -      +
     35A  LYS*     2.8    60.2    +      -       +      +
     41A  TRP*     3.6    19.2    -      -       +      -
     67A  GLY*     1.3    74.4    -      -       -      -
     69A  TYR*     1.3    61.0    +      -       -      +
     94A  VAL*     3.9    16.8    -      -       +      -
     95A  PHE      3.5     8.1    -      -       -      +
     96A  THR*     3.8    18.6    -      -       +      +
     89B  GLU*     4.0    17.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  LEU*     6.2     0.2    -      -       +      -
     32A  VAL*     4.2    16.8    -      -       +      -
     33A  PHE      3.3    15.9    -      -       -      +
     34A  ARG*     3.3    35.1    +      -       +      -
     41A  TRP*     3.7     2.5    -      -       -      -
     44A  PHE*     4.0    14.6    -      +       -      -
     64A  PHE*     3.6    28.9    -      +       -      -
     65A  VAL*     2.7    41.1    +      -       -      +
     67A  GLY      3.6    21.5    -      -       -      -
     68A  ILE*     1.3    74.7    -      -       -      +
     70A  LYS*     1.3    59.7    +      -       -      +
     71A  VAL      4.2     0.4    -      -       -      -
     93A  VAL      3.7     0.9    -      -       -      +
     94A  VAL*     3.3     5.9    -      -       -      +
     95A  PHE*     2.8    51.2    +      -       +      +
     97A  ALA*     3.7    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  HIS      3.7     0.9    -      -       -      +
     32A  VAL*     3.3     4.6    -      -       -      +
     33A  PHE*     2.8    54.1    +      -       +      +
     41A  TRP*     3.5    53.8    -      -       +      +
     69A  TYR*     1.3    73.8    -      -       -      +
     71A  VAL*     1.3    68.7    +      -       -      +
     72A  GLU*     4.2    10.2    +      -       +      +
     92A  GLU*     3.8    29.3    +      -       +      +
     93A  VAL      3.3     4.5    -      -       -      -
     94A  VAL*     3.8    18.2    -      -       +      -
     92B  GLU*     5.0     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  LEU*     5.0     7.0    -      -       +      -
     14A  VAL*     4.3    13.7    -      -       +      -
     30A  VAL*     3.7    25.8    -      -       +      -
     31A  HIS      3.7     2.5    -      -       -      +
     32A  VAL*     4.4    16.6    -      -       +      +
     70A  LYS*     1.3    75.4    -      -       -      +
     72A  GLU*     1.3    62.0    +      -       -      +
     73A  ILE*     4.1    13.8    +      -       +      +
     91A  ALA      3.6     1.6    -      -       -      +
     92A  GLU*     3.2     3.8    -      -       -      -
     93A  VAL*     2.7    47.2    +      -       +      +
     95A  PHE*     3.8    26.7    -      -       +      -
    107A  ILE*     4.5    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  ALA      4.0     0.2    -      -       -      +
     30A  VAL*     3.2     7.1    -      -       -      +
     31A  HIS*     2.8    51.9    +      -       +      +
     33A  PHE*     3.9    27.4    -      -       +      -
     70A  LYS*     4.0     8.5    +      -       +      -
     71A  VAL*     1.3    73.1    -      -       -      +
     73A  ILE*     1.3    62.9    +      -       -      +
     74A  ASP*     4.0     0.6    +      -       -      +
     90A  HIS*     3.6    32.2    +      -       +      -
     91A  ALA      3.4     2.0    -      -       -      -
     92A  GLU*     2.8    27.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  VAL*     4.5    14.8    -      -       +      -
     16A  VAL*     4.5    14.1    -      -       +      -
     28A  VAL*     3.6    25.8    -      -       +      -
     29A  ALA      3.7     2.9    -      -       -      +
     30A  VAL*     4.5     9.6    -      -       +      +
     71A  VAL*     4.3    15.3    -      -       +      +
     72A  GLU*     1.3    76.8    -      -       -      +
     74A  ASP*     1.3    58.2    +      -       -      +
     75A  THR*     2.8    25.3    +      -       +      -
     90A  HIS*     3.0    17.5    -      -       -      +
     91A  ALA*     2.8    24.2    +      -       +      +
     93A  VAL*     4.9    11.2    -      -       +      -
    107A  ILE*     5.2     2.9    -      -       +      -
    109A  ALA*     3.7    27.8    -      -       +      -
    111A  LEU*     5.0     0.9    -      -       +      -
----------------------------------------------------------
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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