Contacts of the strand formed by residues 113 - 119 (chain A) in PDB entry 2AA0


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 ALA 113 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  MET*     4.1    20.2    -      -       +      -
     86A  GLY*     3.9    17.9    -      -       -      -
     88A  ALA      3.1    17.0    +      -       -      +
     89A  GLY*     3.1     2.3    -      -       -      -
     90A  TYR      2.9    24.3    +      -       -      -
    111A  GLY      3.6     2.2    +      -       -      -
    112A  LEU*     1.3    71.5    -      -       -      +
    114A  THR*     1.3    61.2    +      -       -      +
    157A  PHE*     3.9     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  TYR*     3.3    15.9    -      -       +      -
    104A  LYS*     5.3     1.2    -      -       -      +
    107A  CYS*     4.5     4.4    -      -       +      +
    108A  ASP*     4.2    13.5    +      -       -      -
    112A  LEU*     3.4    35.7    +      -       +      +
    113A  ALA*     1.3    80.4    -      -       -      +
    115A  ARG*     1.3    63.6    +      -       -      +
    116A  PHE*     3.3    38.1    -      -       +      -
    157A  PHE*     4.0     9.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  TYR      3.1     6.0    +      -       -      -
     91A  MET*     3.5    49.2    -      -       +      +
     92A  GLY      3.6     3.3    -      -       -      +
    114A  THR*     1.3    75.8    -      -       -      +
    116A  PHE*     1.3    63.6    +      -       -      +
    117A  MET*     3.7    27.4    +      -       -      +
    151A  PRO*     3.4    16.2    -      -       -      +
    153A  ASP*     2.9    43.8    +      -       -      -
    157A  PHE*     4.0    29.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  PRO*     3.8    27.4    -      -       +      -
     72A  LEU*     5.0     1.1    -      -       +      -
     90A  TYR*     3.8    20.0    -      +       -      -
     92A  GLY      3.4     5.8    -      -       -      -
     94A  ILE*     3.6    37.5    -      -       +      -
    103A  LEU*     4.9     5.2    -      -       +      -
    104A  LYS*     3.5    55.7    +      -       +      +
    107A  CYS*     3.9    24.0    -      -       +      -
    114A  THR*     3.3    32.3    -      -       +      -
    115A  ARG*     1.3    76.7    -      -       -      +
    117A  MET*     1.3    63.7    +      -       -      +
    118A  VAL*     3.5     6.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  MET*     5.5     0.2    -      -       -      +
     92A  GLY      2.9    17.2    +      -       -      +
     93A  ALA*     3.1    12.3    -      -       +      +
     94A  ILE      2.7    31.5    +      -       -      +
    115A  ARG*     3.7    34.1    -      -       -      +
    116A  PHE*     1.3    70.9    -      -       -      +
    118A  VAL*     1.3    59.0    +      -       -      +
    148A  PHE*     3.8    23.3    -      -       +      -
    149A  ARG      4.9     7.2    -      -       -      +
    151A  PRO*     4.4    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ILE*     3.4    22.7    -      -       +      -
     95A  GLY      4.6     1.1    -      -       -      +
     96A  ASP*     3.5    36.6    -      -       +      +
    104A  LYS*     5.0     5.6    -      -       -      +
    116A  PHE      3.5     7.4    +      -       -      +
    117A  MET*     1.3    74.0    -      -       -      +
    119A  ALA*     1.3    63.7    +      -       -      +
    120A  PRO*     3.5    13.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ILE      2.9    16.2    +      -       -      +
     95A  GLY*     3.9     0.3    -      -       -      -
     96A  ASP      3.8     9.4    +      -       -      -
    117A  MET      5.0     0.2    -      -       -      +
    118A  VAL*     1.3    75.8    -      -       -      +
    120A  PRO*     1.3    69.6    -      -       -      +
    121A  GLY      3.4     0.5    +      -       -      -
    122A  GLN*     3.1    36.0    +      -       -      +
    144A  ALA*     4.0     3.6    -      -       +      -
    147A  SER*     3.4    27.4    -      -       -      +
----------------------------------------------------------
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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