Contacts of the strand formed by residues 90 - 96 (chain A) in PDB entry 4A12


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 LYS 90 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  GLN*     3.2    16.3    +      -       -      +
     86A  ASN*     2.8    33.3    +      -       +      +
     89A  VAL*     1.4    87.7    -      -       +      +
     91A  ALA*     1.3    61.4    +      -       -      +
     92A  GLN*     3.8    33.6    -      -       -      +
    125A  LEU*     3.5     2.7    -      -       -      +
    153A  GLU*     4.2    17.2    +      -       -      -
    154A  ALA      3.3    13.2    -      -       -      +
    155A  ARG*     3.7    22.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  GLN*     3.3    13.0    -      -       -      +
     85A  VAL*     3.8    15.9    -      -       +      -
     90A  LYS*     1.3    75.1    -      -       -      +
     92A  GLN*     1.3    64.0    +      -       -      +
    121A  LEU*     3.8    19.6    -      -       +      +
    125A  LEU*     3.8    24.0    -      -       +      -
    153A  GLU*     3.4     2.9    -      -       -      +
    154A  ALA      2.8    35.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  LEU*     3.5     5.0    -      -       -      +
     83A  ILE*     2.8    40.5    +      -       +      +
     84A  GLN*     2.8    34.2    +      -       +      +
     90A  LYS*     3.8    20.2    -      -       -      +
     91A  ALA*     1.3    79.2    -      -       -      +
     93A  SER*     1.3    60.6    +      -       -      +
    121A  LEU*     3.7     2.7    -      -       -      -
    151A  ARG*     3.5    25.6    +      -       +      +
    152A  ALA      3.3     4.6    -      -       -      +
    153A  GLU*     3.0    36.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  PHE*     4.0    17.5    -      -       -      -
     81A  ASP      3.2    15.3    -      -       -      -
     82A  LEU*     4.2     0.4    -      -       -      -
     83A  ILE*     4.1     5.6    -      -       -      +
     92A  GLN*     1.3    75.2    -      -       -      +
     94A  ILE*     1.3    59.5    +      -       -      +
    117A  GLN*     3.2    30.1    +      -       -      +
    121A  LEU*     3.7    22.5    -      -       -      +
    150A  VAL      3.6     0.3    -      -       -      +
    151A  ARG*     3.7     2.6    -      -       -      +
    152A  ALA*     2.9    33.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 94 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  GLY*     3.4     1.2    -      -       -      -
     81A  ASP*     2.7    59.2    +      -       +      +
     83A  ILE*     3.5    22.4    -      -       +      +
     93A  SER*     1.3    71.5    -      -       -      +
     95A  LEU*     1.3    60.7    +      -       -      +
     96A  ASP*     4.3     7.6    -      -       -      +
    117A  GLN*     3.7     1.1    -      -       -      -
    149A  THR*     3.4    29.6    -      -       +      +
    150A  VAL      3.4     1.8    -      -       -      +
    151A  ARG*     3.8    37.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  ILE*     4.3     7.6    -      -       +      -
     80A  GLY*     3.7    24.2    -      -       -      +
     94A  ILE*     1.3    75.5    -      -       -      +
     96A  ASP*     1.3    68.3    +      -       -      +
     97A  ILE*     3.5    25.3    +      -       +      +
    101A  SER*     5.6     3.8    -      -       -      +
    113A  VAL*     3.9    23.3    -      -       +      +
    114A  LEU*     5.3     1.6    -      -       +      +
    117A  GLN*     3.5    39.3    -      -       +      +
    149A  THR*     3.4     3.1    -      -       -      -
    150A  VAL*     2.8    41.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ILE*     4.9     7.3    -      -       -      +
     95A  LEU*     1.3    79.2    -      -       -      +
     97A  ILE*     1.3    61.3    +      -       -      +
     98A  THR*     3.1    16.2    +      -       -      +
    101A  SER*     4.8     1.4    +      -       -      -
    147A  ASN      5.2     2.3    -      -       -      +
    148A  ASP      3.8     3.4    -      -       -      -
    149A  THR*     3.0    31.0    +      -       -      +
----------------------------------------------------------
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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