Contacts of the strand formed by residues 320 - 328 (chain A) in PDB entry 3ATA


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 THR 320 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    311A  GLU*     5.6     4.7    -      -       +      +
    312A  GLY*     3.3    20.6    +      -       -      +
    313A  MET*     4.2     9.7    -      -       -      +
    318A  GLY      4.2     0.2    +      -       -      -
    319A  MET*     1.3    77.4    -      -       -      +
    321A  CYS*     1.3    65.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 321 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  LEU*     6.3     1.6    -      -       -      -
    229A  LEU*     5.5     4.3    -      -       -      -
    234A  ILE*     4.6     9.9    -      -       -      -
    310A  LEU*     4.8    10.3    -      -       -      -
    311A  GLU*     3.6     3.8    -      -       -      +
    312A  GLY      2.8    39.0    +      -       -      +
    314A  VAL*     3.7    29.2    -      -       +      -
    317A  THR*     6.3     0.2    -      -       +      -
    319A  MET      3.5     1.4    +      -       -      -
    320A  THR*     1.3    79.9    -      -       -      +
    322A  GLN*     1.3    71.1    +      -       -      +
    323A  ALA*     5.0     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 322 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240A  ARG*     4.7     1.0    -      -       -      +
    309A  ILE*     3.5    23.6    -      -       +      +
    310A  LEU      3.3     8.3    -      -       -      +
    311A  GLU*     2.5    32.0    +      -       +      +
    321A  CYS*     1.3    79.4    -      -       -      +
    323A  ALA*     1.3    62.9    +      -       -      +
    324A  ARG*     2.7    45.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 323 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  THR*     6.0     0.9    -      -       -      +
    205A  LEU*     4.2    31.6    -      -       +      +
    207A  PHE*     3.9    17.4    -      -       +      -
    308A  VAL      3.9     0.2    -      -       -      +
    309A  ILE*     3.4     4.0    -      -       -      +
    310A  LEU*     2.8    36.7    +      -       +      +
    321A  CYS*     5.0     2.6    -      -       -      -
    322A  GLN*     1.3    74.1    -      -       -      +
    324A  ARG*     1.3    65.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 324 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207A  PHE*     3.6     8.7    -      -       -      -
    307A  VAL*     5.0     7.2    -      -       +      -
    308A  VAL      3.1     8.3    -      -       -      +
    309A  ILE*     4.1    17.5    -      -       +      -
    322A  GLN*     2.7    58.1    +      -       -      +
    323A  ALA*     1.3    79.4    -      -       -      +
    325A  SER*     1.3    66.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 325 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207A  PHE*     3.5    27.7    -      -       -      +
    208A  SER      4.9     2.6    +      -       -      -
    307A  VAL*     3.4    10.9    -      -       -      +
    308A  VAL*     3.0    35.4    +      -       -      +
    324A  ARG*     1.3    78.4    -      -       -      +
    326A  SER*     1.3    77.3    +      -       -      +
    327A  TYR*     4.9     5.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 326 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209A  THR      4.9     1.0    -      -       -      +
    305A  GLU*     2.6    37.0    +      -       -      +
    306A  ILE      3.3     5.8    -      -       -      -
    307A  VAL*     5.1     2.5    -      -       -      -
    325A  SER*     1.3    90.0    +      -       -      +
    327A  TYR*     1.3    73.7    +      -       -      +
    328A  ILE*     4.4     4.0    -      -       -      +
    331A  GLU*     3.4    11.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 327 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207A  PHE*     3.7    14.1    -      -       +      +
    208A  SER*     2.6    39.7    +      -       -      -
    209A  THR      3.3    20.0    -      -       -      -
    210A  HIS*     3.4    10.5    -      -       -      -
    211A  ALA*     3.8    17.0    -      -       +      -
    224A  PHE*     3.6    28.3    -      +       +      +
    225A  ARG      4.4     0.2    +      -       -      -
    304A  LEU      4.6     0.2    -      -       -      -
    305A  GLU*     3.2     2.9    -      -       -      -
    306A  ILE*     2.7    62.1    +      -       +      +
    308A  VAL*     3.7    26.2    -      -       +      -
    325A  SER*     4.9     3.1    -      -       -      -
    326A  SER*     1.3    80.5    +      -       -      +
    328A  ILE*     1.3    63.8    +      -       -      +
    331A  GLU*     3.4     6.3    -      -       +      -
    332A  ILE*     4.5    15.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 328 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304A  LEU      3.6     8.7    -      -       -      +
    305A  GLU*     3.9    25.1    -      -       +      +
    326A  SER*     4.4     3.6    -      -       -      +
    327A  TYR*     1.3    77.0    -      -       -      +
    329A  THR*     1.3    58.1    +      -       -      +
    330A  SER*     3.0    26.9    -      -       -      +
    331A  GLU*     2.6    59.2    +      -       -      +
    332A  ILE*     3.4     7.5    +      -       -      +
----------------------------------------------------------
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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