Contacts of the strand formed by residues 279 - 284 (chain A) in PDB entry 3ATB


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 LEU 279 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  TYR*     5.5     2.0    -      -       -      +
    225A  ARG*     3.4     3.0    -      -       -      +
    226A  VAL*     3.0    34.6    +      -       +      +
    273A  LEU*     4.4    22.0    -      -       +      -
    274A  PHE      4.0    24.0    -      -       -      +
    275A  LEU*     3.6    21.5    -      -       +      -
    277A  SER*     3.4    21.3    -      -       -      +
    278A  PRO*     1.3    77.0    -      -       -      +
    280A  ILE*     1.3    66.5    +      -       -      +
    281A  ILE*     3.6    12.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 280 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216A  ARG*     3.9    31.5    +      -       -      +
    223A  MET*     3.7    20.4    -      -       +      -
    224A  PHE      3.8     6.3    -      -       -      +
    225A  ARG*     4.0    24.0    -      -       -      +
    279A  LEU*     1.3    76.0    -      -       -      +
    281A  ILE*     1.3    77.5    +      -       -      +
    282A  SER*     4.1     2.6    +      -       -      -
    338A  PHE*     3.5    38.8    -      -       +      +
    339A  THR      5.4     0.2    -      -       -      +
    340A  PRO*     6.4     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 281 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  MET*     3.2    28.8    -      -       -      +
    224A  PHE*     2.9    51.2    +      -       +      +
    226A  VAL*     4.1    24.5    -      -       +      -
    239A  ILE*     4.3    13.5    -      -       +      -
    264A  VAL*     3.9    26.7    -      -       +      +
    273A  LEU*     4.0    26.5    -      -       +      -
    279A  LEU*     4.2     9.6    -      -       +      -
    280A  ILE*     1.3    79.0    -      -       -      +
    282A  SER*     1.3    64.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 282 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216A  ARG*     3.9    19.5    +      -       -      -
    221A  CYS*     3.9    24.8    -      -       -      +
    222A  LEU      3.5     4.3    -      -       -      -
    223A  MET*     3.7    10.0    -      -       -      +
    264A  VAL*     4.3    16.4    -      -       -      -
    280A  ILE      4.1     1.8    +      -       -      -
    281A  ILE*     1.3    80.2    -      -       -      +
    283A  HIS*     1.3    61.1    +      -       -      +
    284A  GLU      4.0     1.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 283 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221A  CYS*     3.6     0.7    -      -       -      -
    222A  LEU*     3.0    49.4    +      -       +      +
    224A  PHE*     6.2     1.1    -      -       +      -
    262A  ILE*     3.4    17.6    -      -       +      +
    263A  ASN*     2.7    48.0    +      -       +      +
    264A  VAL*     3.7    11.6    -      -       +      +
    282A  SER*     1.3    74.7    +      -       -      +
    284A  GLU*     1.3    69.9    +      -       -      +
    285A  ILE*     3.4    12.6    +      -       +      +
    286A  ASN*     5.2     0.9    -      -       -      -
    289A  SER*     2.5    44.5    +      -       -      -
    290A  PRO*     4.3     2.4    -      -       +      +
    291A  PHE*     4.2     6.1    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLU 284 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219A  LYS*     3.5    46.6    -      -       +      +
    220A  LEU      4.0     4.0    -      -       -      +
    221A  CYS*     4.0     8.7    -      -       -      -
    263A  ASN*     4.6     1.8    +      -       -      +
    282A  SER*     4.0     3.6    +      -       -      +
    283A  HIS*     1.3    85.2    +      -       -      +
    285A  ILE*     1.3    65.2    +      -       -      +
    286A  ASN*     3.0    38.6    +      -       +      +
----------------------------------------------------------
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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