Contacts of the strand formed by residues 22 - 28 (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 ILE 22 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  ASN      3.3     9.6    +      -       -      +
     21A  PRO*     1.3    78.4    -      -       -      +
     23A  LEU*     1.3    58.6    +      -       -      +
     68A  GLY*     2.6    41.3    +      -       -      +
     69A  GLY*     3.9     7.4    -      -       -      +
    103A  LEU*     3.8     8.7    -      -       -      +
    125A  GLY*     3.5     8.3    -      -       -      -
    126A  VAL*     3.5     7.4    -      -       -      -
    127A  CYS*     3.4    35.4    -      -       +      +
    140A  THR*     3.9    17.5    -      -       +      -
    142A  LEU*     4.1     9.6    -      -       +      -
    145A  CYS*     4.1     9.4    -      -       -      -
   1001A  MTP      3.7    44.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  ILE*     1.3    72.5    -      -       -      +
     24A  ASP*     1.3    66.5    +      -       -      +
     25A  LEU*     4.0     8.5    -      -       +      +
     65A  SER*     4.0    22.2    -      -       -      +
     66A  LEU      3.6    27.4    -      -       -      +
     67A  PRO*     4.6     0.2    -      -       +      -
     99A  ARG*     3.3    37.0    -      -       +      +
    102A  VAL*     4.2    22.4    -      -       +      +
    103A  LEU*     4.2    24.8    -      -       +      +
    106A  LEU*     5.3     2.2    -      -       +      -
    124A  THR*     5.2     0.4    -      -       +      -
    125A  GLY      3.0    13.6    +      -       -      +
    126A  VAL*     3.4     8.1    -      -       -      +
    127A  CYS      3.0    19.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 24 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  ILE*     3.7     0.9    +      -       -      +
     23A  LEU*     1.3    73.0    -      -       -      +
     25A  LEU*     1.3    61.2    +      -       -      +
     26A  VAL*     3.8     7.6    -      -       +      -
     64A  THR      3.3     4.0    -      -       -      +
     65A  SER*     3.5     2.9    -      -       -      -
     66A  LEU*     2.8    45.9    +      -       +      +
     67A  PRO      4.3     1.6    -      -       -      +
     68A  GLY*     3.6    10.0    -      -       -      -
    127A  CYS*     3.2    14.9    -      -       -      +
    129A  VAL*     4.1    15.7    -      -       +      -
    354A  PHE*     3.4    18.2    -      -       -      -
   1001A  MTP      2.6    46.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 25 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  LEU*     4.0    14.8    -      -       +      +
     24A  ASP*     1.3    75.9    -      -       -      +
     26A  VAL*     1.3    62.3    +      -       -      +
     55A  TYR*     4.5    18.4    -      -       +      +
     58A  LEU*     3.7    30.1    -      -       +      +
     59A  ASP*     5.9     2.5    -      -       -      +
     63A  PRO*     4.4    12.8    -      -       +      -
     64A  THR      3.6     3.1    -      -       -      +
     65A  SER*     3.4    26.0    -      -       -      +
     99A  ARG*     5.1     5.8    -      -       -      +
    126A  VAL*     3.7    27.8    -      -       +      -
    127A  CYS      2.8    12.5    +      -       -      +
    128A  ALA*     3.7     2.0    -      -       -      -
    129A  VAL      2.9    24.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 26 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  ASP*     4.6     7.9    -      -       +      -
     25A  LEU*     1.3    74.7    -      -       -      +
     27A  ALA*     1.3    69.0    +      -       -      +
     62A  ASN      4.3     0.7    -      -       -      +
     63A  PRO*     3.4     0.7    -      -       -      +
     64A  THR*     2.8    49.6    +      -       -      +
     66A  LEU*     4.4    18.2    -      -       +      -
    129A  VAL*     3.5    31.2    -      -       +      +
    131A  ILE*     3.7    25.4    -      -       +      -
    352A  VAL*     6.2     3.4    -      -       +      -
    353A  GLY*     6.2     2.9    -      -       -      -
    354A  PHE*     6.0     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  LEU      4.0     0.2    +      -       -      -
     26A  VAL*     1.3    82.9    -      -       -      +
     28A  GLU*     1.3    65.4    +      -       -      +
     29A  VAL*     3.7     3.2    +      -       -      +
     58A  LEU*     4.1    22.4    -      -       +      -
     61A  PHE*     3.8    21.3    -      -       +      +
     62A  ASN      4.3     2.0    -      -       -      +
     63A  PRO*     4.0    11.0    -      -       +      -
    129A  VAL      3.2     7.1    +      -       -      +
    130A  LEU*     3.7     4.0    -      -       -      +
    131A  ILE*     3.0    24.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  ALA*     1.3    73.4    -      -       -      +
     29A  VAL*     1.3    64.7    -      -       -      +
     61A  PHE*     4.0    17.2    +      -       -      +
    131A  ILE*     3.3    35.7    -      -       +      +
----------------------------------------------------------
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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