Contacts of the strand formed by residues 305 - 314 (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 GLU 305 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242A  LYS      3.5     1.2    -      -       -      +
    243A  LEU*     3.5     3.9    -      -       -      +
    244A  ILE*     2.7    52.2    +      -       +      +
    304A  LEU*     1.3    77.4    -      -       -      +
    306A  ILE*     1.3    68.6    +      -       -      +
    307A  VAL*     4.4    12.5    -      -       +      +
    326A  SER*     2.6    34.9    +      -       -      +
    327A  TYR      3.2     6.5    -      -       -      +
    328A  ILE*     4.3    15.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 306 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211A  ALA*     5.3     0.7    -      -       +      -
    222A  LEU*     3.6    28.9    -      -       +      -
    224A  PHE*     5.4     3.8    -      -       +      -
    241A  ALA*     4.4     3.6    -      -       +      -
    242A  LYS      3.4     3.8    -      -       -      -
    243A  LEU*     4.3     2.5    -      -       +      -
    262A  ILE*     3.8    28.3    -      -       +      -
    291A  PHE*     3.8    15.3    -      -       +      -
    304A  LEU*     4.6     1.1    -      -       +      -
    305A  GLU*     1.3    73.2    -      -       -      +
    307A  VAL*     1.3    65.4    +      -       -      +
    308A  VAL*     3.9    20.9    -      -       +      -
    326A  SER*     3.4     2.6    -      -       -      -
    327A  TYR*     2.8    50.5    +      -       +      +
    332A  ILE*     3.5    33.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 307 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241A  ALA*     3.1     8.8    -      -       -      +
    242A  LYS*     2.8    42.8    +      -       +      +
    244A  ILE*     3.5    33.4    -      -       +      -
    305A  GLU*     4.4    13.9    -      -       +      +
    306A  ILE*     1.3    73.5    -      -       -      +
    308A  VAL*     1.3    64.9    +      -       -      +
    309A  ILE*     3.9    22.6    +      -       +      +
    324A  ARG*     5.0    10.1    -      -       +      -
    325A  SER      3.5    10.8    -      -       -      +
    326A  SER*     5.0     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 308 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207A  PHE*     3.2    40.1    -      -       +      -
    224A  PHE*     3.7    28.9    -      -       +      -
    240A  ARG      4.0     2.5    -      -       -      -
    241A  ALA*     4.7     1.3    -      -       +      -
    306A  ILE*     3.9     6.7    -      -       +      -
    307A  VAL*     1.3    76.3    -      -       -      +
    309A  ILE*     1.3    63.2    +      -       -      +
    310A  LEU      4.2     0.2    -      -       -      -
    323A  ALA      3.7     0.7    -      -       -      +
    324A  ARG*     3.2     6.4    -      -       -      +
    325A  SER*     2.9    41.4    +      -       -      +
    327A  TYR*     3.4    31.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 309 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238A  SER      3.8     0.2    -      -       -      +
    239A  ILE*     3.3    15.7    -      -       -      +
    240A  ARG*     3.1    51.1    +      -       +      +
    242A  LYS*     4.2    22.2    -      -       +      +
    307A  VAL*     3.9    23.8    -      -       +      +
    308A  VAL*     1.3    80.0    -      -       -      +
    310A  LEU*     1.3    59.3    +      -       -      +
    311A  GLU*     4.0    10.3    -      -       +      +
    322A  GLN*     3.8    36.8    -      -       +      +
    323A  ALA      3.4     3.6    -      -       -      +
    324A  ARG*     4.4     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 310 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  LEU*     3.7    25.8    -      -       +      -
    207A  PHE*     3.9    17.7    -      -       +      -
    226A  VAL*     3.8    22.7    -      -       +      -
    234A  ILE*     4.7    11.4    -      -       +      -
    237A  ALA*     5.5     3.8    -      -       +      -
    238A  SER      3.6     7.9    -      -       -      +
    239A  ILE*     4.1     4.9    -      -       +      -
    273A  LEU*     4.0    24.7    -      -       +      -
    275A  LEU*     4.2    11.0    -      -       +      -
    309A  ILE*     1.3    71.9    -      -       -      +
    311A  GLU*     1.3    69.3    +      -       -      +
    312A  GLY      4.7     0.2    -      -       -      +
    321A  CYS*     4.4    19.5    -      -       -      -
    322A  GLN*     3.2     5.7    -      -       -      +
    323A  ALA*     2.8    38.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 311 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  GLU      3.7     3.3    -      -       -      +
    237A  ALA*     3.4     1.0    -      -       -      -
    238A  SER*     2.8    44.8    +      -       -      +
    240A  ARG*     2.5    36.9    +      -       -      +
    309A  ILE*     4.0     7.4    -      -       +      +
    310A  LEU*     1.3    83.9    -      -       -      +
    312A  GLY*     1.3    58.5    +      -       -      +
    320A  THR*     5.9     4.5    -      -       +      +
    321A  CYS      3.7     8.5    -      -       -      +
    322A  GLN*     2.6    35.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 312 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  ILE*     3.4    19.9    -      -       -      +
    235A  VAL      3.5     7.9    -      -       -      -
    236A  GLU*     3.9     3.8    -      -       -      -
    237A  ALA*     3.9     2.5    -      -       -      -
    311A  GLU*     1.3    74.7    -      -       -      +
    313A  MET*     1.3    54.8    +      -       -      -
    320A  THR*     3.5    10.3    -      -       -      +
    321A  CYS*     2.7    42.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 313 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  ILE*     3.4     2.5    -      -       -      -
    235A  VAL*     2.8    55.8    +      -       +      +
    236A  GLU*     5.2     5.1    -      -       +      +
    312A  GLY*     1.3    72.1    -      -       -      -
    314A  VAL*     1.3    92.5    +      -       -      +
    315A  GLU*     3.3    16.9    +      -       +      +
    318A  GLY*     3.2    31.6    -      -       -      +
    319A  MET      3.7     9.2    -      -       -      +
    320A  THR*     4.0     9.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 314 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  LEU*     4.9    15.9    -      -       +      -
    232A  SER*     3.4    26.2    -      -       -      +
    233A  HIS      3.9     4.5    -      -       -      +
    234A  ILE*     4.7     4.7    -      -       +      +
    313A  MET*     1.3    75.4    -      -       -      +
    315A  GLU*     1.3    64.8    +      -       -      +
    316A  ALA*     3.3     3.1    +      -       +      +
    317A  THR*     3.5    29.6    -      -       +      +
    318A  GLY      2.9    22.2    +      -       -      -
    319A  MET      3.0     9.6    +      -       -      +
    321A  CYS*     3.8    30.7    -      -       +      -
----------------------------------------------------------
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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