Contacts of the strand formed by residues 234 - 244 (chain A) in PDB entry 3ATF


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 234 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  LEU*     3.8    29.2    -      -       +      -
    229A  LEU*     3.8    28.9    -      -       +      +
    232A  SER      4.3     0.9    -      -       -      +
    233A  HIS*     1.3    80.4    +      -       -      +
    235A  VAL*     1.3    62.1    +      -       -      +
    236A  GLU      3.8     0.3    +      -       -      -
    237A  ALA*     3.5    22.8    +      -       +      +
    273A  LEU      5.2     1.0    -      -       -      +
    275A  LEU*     4.4    27.5    +      -       +      +
    310A  LEU*     4.6     5.6    -      -       +      -
    311A  GLU      5.0     0.4    -      -       -      -
    312A  GLY*     3.6    28.3    -      -       -      +
    313A  MET      3.2    12.8    -      -       -      +
    314A  VAL*     5.0     5.2    -      -       +      -
    321A  CYS*     4.8     8.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233A  HIS*     5.2     1.8    -      -       +      -
    234A  ILE*     1.3    72.0    -      -       -      +
    236A  GLU*     1.3    80.3    +      -       +      +
    237A  ALA      3.1     1.4    +      -       -      -
    312A  GLY*     3.4     0.7    -      -       -      -
    313A  MET*     2.8    52.3    +      -       +      +
    315A  GLU*     3.8    33.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A   CS      3.0    33.7    -      -       -      -
    234A  ILE      3.8     0.2    +      -       -      -
    235A  VAL*     1.3    87.8    -      -       +      +
    237A  ALA*     1.3    61.0    +      -       -      +
    311A  GLU      3.4     2.1    -      -       -      +
    312A  GLY*     3.7     1.3    -      -       -      -
    313A  MET*     4.9     5.8    -      -       +      +
    382A   MG      3.9    16.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  ILE*     3.5    27.7    +      -       +      +
    235A  VAL      3.1     3.0    +      -       -      -
    236A  GLU*     1.3    78.9    -      -       -      +
    238A  SER*     1.3    62.3    +      -       -      +
    272A  ARG*     3.5     8.1    -      -       -      +
    273A  LEU*     3.1    46.5    +      -       +      +
    275A  LEU*     4.9     7.0    -      -       +      +
    310A  LEU*     4.5     9.9    -      -       +      -
    311A  GLU      3.4     6.3    -      -       -      +
    312A  GLY*     4.2     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A   CS      2.9    27.9    -      -       -      -
    237A  ALA*     1.3    77.5    -      -       -      +
    239A  ILE*     1.3    63.3    +      -       -      +
    240A  ARG*     5.4     4.1    -      -       -      +
    271A  ASP*     3.1    19.3    -      -       -      -
    272A  ARG*     4.7     4.7    -      -       -      -
    273A  LEU*     4.4     1.1    -      -       -      +
    309A  ILE      3.8     0.9    -      -       -      +
    310A  LEU*     3.4     7.5    -      -       -      +
    311A  GLU*     2.9    35.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207A  PHE*     4.3    14.4    -      -       +      -
    224A  PHE*     3.9    34.5    -      -       +      -
    226A  VAL*     5.1     2.5    -      -       +      -
    238A  SER*     1.3    77.1    -      -       -      +
    240A  ARG*     1.3    72.2    +      -       -      +
    264A  VAL*     3.6    13.8    -      -       +      +
    270A  ASP      5.0     0.2    -      -       -      +
    271A  ASP*     3.1    38.9    +      -       -      +
    273A  LEU*     3.7    26.2    -      -       +      -
    281A  ILE*     4.4    17.7    -      -       +      -
    309A  ILE      3.6    19.1    -      -       -      +
    310A  LEU*     4.4     7.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238A  SER*     5.4     4.7    -      -       -      +
    239A  ILE*     1.3    83.6    -      -       -      +
    241A  ALA*     1.3    63.2    +      -       -      +
    242A  LYS*     4.9    16.3    -      -       -      +
    261A  ASP*     4.7    14.2    +      -       -      +
    264A  VAL*     4.0     7.6    -      -       -      -
    308A  VAL*     3.7     1.2    -      -       -      -
    309A  ILE*     3.0    57.8    +      -       +      +
    311A  GLU*     2.7    43.7    +      -       +      +
    322A  GLN*     5.3     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224A  PHE*     4.9     4.3    -      -       +      -
    240A  ARG*     1.3    77.3    -      -       -      +
    242A  LYS*     1.3    64.9    +      -       -      +
    261A  ASP*     3.5     8.3    -      -       -      +
    262A  ILE*     3.0    45.7    +      -       +      +
    264A  VAL*     4.5    12.7    -      -       +      +
    306A  ILE*     4.5     9.0    -      -       +      -
    307A  VAL      3.0    12.1    -      -       -      +
    308A  VAL*     4.4    12.3    -      -       +      -
    309A  ILE*     5.4     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240A  ARG*     4.9    18.2    -      -       +      +
    241A  ALA*     1.3    78.2    -      -       -      +
    243A  LEU*     1.3    61.9    +      -       -      +
    244A  ILE*     3.9    12.3    -      -       +      -
    259A  GLN*     3.9    32.6    -      -       +      +
    260A  THR*     3.4     5.7    -      -       -      +
    261A  ASP*     2.7    42.1    +      -       -      +
    262A  ILE*     3.9     5.1    -      -       -      +
    306A  ILE*     3.4     5.0    -      -       -      -
    307A  VAL*     2.8    37.7    +      -       +      +
    309A  ILE*     4.5    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242A  LYS*     1.3    71.4    -      -       -      +
    244A  ILE*     1.3    60.5    +      -       -      +
    245A  LYS*     4.2    20.1    -      -       +      +
    258A  ASN      3.0    14.6    -      -       -      +
    259A  GLN*     3.3     1.4    -      -       -      -
    260A  THR*     2.7    43.0    +      -       -      +
    262A  ILE*     3.9    14.8    -      -       +      +
    290A  PRO*     3.5    31.9    -      -       +      -
    291A  PHE*     4.5    14.8    -      -       +      -
    304A  LEU*     3.9    36.1    -      -       +      -
    305A  GLU      3.7    10.8    -      -       -      +
    306A  ILE*     4.7     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 244 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242A  LYS*     4.5     6.1    -      -       +      -
    243A  LEU*     1.3    73.0    -      -       -      +
    245A  LYS*     1.3    65.0    +      -       -      +
    257A  LEU*     3.6    43.1    -      -       +      +
    258A  ASN      3.4     1.3    -      -       -      +
    259A  GLN*     3.7    35.4    -      -       +      +
    304A  LEU*     3.5     3.3    -      -       -      +
    305A  GLU*     2.9    39.9    +      -       +      +
    307A  VAL*     3.8    30.1    -      -       +      -
    384A  EOH      3.6    15.5    +      -       -      +
----------------------------------------------------------
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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