Contacts of the strand formed by residues 233 - 245 (chain A) in PDB entry 3RT0


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 HIS 233 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214A  LYS*     2.9    53.6    -      -       +      +
    215A  LEU      3.0    24.2    -      -       -      +
    216A  PRO*     4.2     2.0    -      -       +      -
    217A  ILE*     3.4     9.5    -      -       -      +
    232A  THR*     1.3   103.3    +      -       -      +
    234A  LEU*     1.3    63.0    +      -       -      +
    235A  THR*     4.3     2.3    +      -       -      -
    270A  LYS*     6.2     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 234 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182A  TYR*     3.2    56.1    -      -       +      +
    184A  LEU      6.0     1.1    -      -       -      +
    214A  LYS*     3.7     1.7    -      -       -      -
    215A  LEU*     2.9    31.8    +      -       +      +
    217A  ILE*     3.2    23.2    -      -       +      +
    220A  LEU*     3.8    16.8    -      -       +      -
    233A  HIS*     1.3    81.0    -      -       -      +
    235A  THR*     1.3    67.2    -      -       -      +
    335A  CYS*     4.1    12.1    -      -       +      -
    336A  SER*     4.4     9.4    -      -       -      +
    337A  SER*     3.7    20.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186A  CYS*     4.9     9.0    -      -       -      +
    211A  HIS*     3.5    46.6    +      -       +      +
    213A  LEU      3.5     8.3    -      -       -      +
    214A  LYS*     5.0     4.3    -      -       -      +
    233A  HIS*     4.3     2.8    +      -       -      -
    234A  LEU*     1.3    72.3    -      -       -      +
    236A  GLY*     1.3    60.9    +      -       -      +
    237A  HIS*     4.0    11.7    +      -       +      -
    334A  VAL      4.0     0.3    -      -       -      +
    335A  CYS*     3.3    23.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211A  HIS      3.9     0.5    -      -       -      -
    212A  PHE*     3.1    10.0    +      -       -      +
    213A  LEU*     2.8    41.5    +      -       -      +
    215A  LEU*     3.8    20.9    -      -       -      -
    234A  LEU      3.5     1.6    +      -       -      -
    235A  THR*     1.3    75.3    -      -       -      +
    237A  HIS*     1.3    63.9    +      -       -      -
    333A  LEU*     5.9     0.7    -      -       -      -
    334A  VAL      3.5     6.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186A  CYS*     3.0    40.5    +      -       -      +
    188A  PRO*     3.5    30.4    -      -       +      +
    209A  SER      3.8     3.6    -      -       -      -
    210A  PRO*     3.7     5.4    -      -       +      -
    211A  HIS*     2.8    49.7    +      -       -      -
    213A  LEU*     5.6     0.4    -      -       -      -
    235A  THR*     4.0     9.2    +      -       +      +
    236A  GLY*     1.3    74.0    -      -       -      -
    238A  PHE*     1.3    61.4    +      -       -      +
    239A  PHE*     3.7    22.9    -      +       +      -
    332A  ALA      3.5     1.7    -      -       -      +
    333A  LEU*     3.2     8.9    -      -       -      +
    334A  VAL*     2.9    43.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207A  ALA*     3.9    12.3    -      -       +      -
    208A  VAL*     3.4     2.9    -      -       -      +
    209A  SER*     2.9    47.5    +      -       -      +
    212A  PHE*     4.4    10.5    -      -       +      -
    213A  LEU*     4.8     3.6    -      -       +      -
    236A  GLY      4.2     0.2    +      -       -      -
    237A  HIS*     1.3    72.5    -      -       -      +
    239A  PHE*     1.3    69.4    +      -       -      +
    240A  GLY      3.8    12.3    -      -       -      -
    242A  TYR*     3.3    26.5    -      -       -      -
    258A  LEU*     4.3     4.3    -      -       +      -
    259A  HIS*     3.5    44.2    -      +       +      -
    262A  LEU*     3.9    18.4    -      -       +      -
    331A  VAL*     4.0    24.9    -      -       +      -
    332A  ALA      3.7     2.0    -      -       -      -
    333A  LEU*     3.9    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188A  PRO*     4.8     7.4    -      -       +      -
    189A  LEU      5.5     0.2    -      -       -      -
    190A  TRP*     3.8    29.4    -      +       +      -
    207A  ALA      3.6     4.0    -      -       -      -
    208A  VAL*     3.6    32.5    -      -       +      -
    210A  PRO*     6.1     0.4    -      -       +      -
    237A  HIS*     3.7    30.1    -      +       +      -
    238A  PHE*     1.3    82.8    -      -       -      +
    240A  GLY*     1.3    57.9    +      -       -      +
    331A  VAL*     3.3     3.8    -      -       -      +
    332A  ALA*     2.8    47.2    +      -       +      +
    334A  VAL*     3.9    18.2    -      -       +      -
    429A  LEU*     3.6    15.8    -      -       +      +
    497A  ILE*     4.0    10.1    -      -       +      -
    499A  ILE*     3.6    38.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206A  PHE*     3.3     5.9    -      -       -      +
    207A  ALA      2.9    35.1    +      -       -      +
    238A  PHE*     3.8     2.8    -      -       -      -
    239A  PHE*     1.3    76.5    -      -       -      +
    241A  VAL*     1.3    64.8    +      -       -      +
    242A  TYR*     3.8    22.4    -      -       -      -
    330A  VAL      3.4     8.1    -      -       -      -
    331A  VAL*     4.2     1.8    -      -       -      -
    429A  LEU*     4.4     0.2    -      -       -      -
    497A  ILE*     3.7     3.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  ASP*     5.6     0.2    -      -       -      +
    205A  ALA      3.9     4.0    -      -       -      +
    206A  PHE*     4.6     4.3    -      -       +      -
    240A  GLY*     1.3    76.4    -      -       -      +
    242A  TYR*     1.3    69.2    +      -       -      +
    243A  ASP      4.1     1.4    +      -       -      +
    328A  THR*     4.5     1.6    +      -       -      -
    329A  ALA*     3.6     1.0    -      -       -      -
    330A  VAL*     2.9    44.0    +      -       +      +
    347A  SER*     4.9     1.5    +      -       -      +
    429A  LEU*     3.8    23.1    -      -       +      +
    430A  ALA*     4.1     1.8    -      -       -      -
    431A  SER*     3.8    30.7    -      -       -      +
    495A  SER*     4.2    20.0    -      -       -      +
    497A  ILE*     3.5    27.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  ASP*     3.6     2.3    -      -       -      +
    205A  ALA      2.8    45.3    +      -       -      +
    206A  PHE*     4.1     0.2    -      -       -      -
    207A  ALA*     4.3     8.0    -      -       +      +
    238A  PHE*     3.3    32.2    -      -       -      -
    240A  GLY*     3.8    17.4    -      -       -      -
    241A  VAL*     1.3    83.2    -      -       -      +
    243A  ASP*     1.3    61.4    +      -       -      +
    244A  GLY      3.3     4.9    +      -       -      -
    251A  ALA*     3.6    16.9    -      -       +      +
    254A  CYS*     3.6    24.0    +      -       +      -
    255A  ARG*     3.7    30.5    -      -       -      -
    258A  LEU*     3.9    14.8    -      -       +      +
    259A  HIS*     5.0     0.5    +      -       -      -
    327A  SER*     3.4    12.1    -      -       -      +
    328A  THR      3.5     3.1    -      -       -      -
    329A  ALA*     3.7    26.0    -      -       +      -
    331A  VAL*     3.9     9.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  ASP*     3.2    16.0    -      -       -      +
    241A  VAL      4.1     0.4    -      -       -      -
    242A  TYR*     1.3    71.2    -      -       -      +
    244A  GLY*     1.3    69.7    +      -       -      +
    245A  HIS*     3.8     5.9    +      -       -      -
    327A  SER*     3.3     3.6    +      -       -      -
    328A  THR*     3.0    41.6    +      -       -      +
    346A  ASP*     4.9     2.6    -      -       -      +
    347A  SER*     3.3    11.0    +      -       -      +
    431A  SER*     3.8    11.4    -      -       -      -
    432A  ASP*     3.1    26.2    +      -       -      +
    512A   MG      2.6    30.2    -      -       -      -
     81C  SER*     5.0     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 244 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  GLU*     2.8    31.5    +      -       -      +
    242A  TYR      3.3     2.6    +      -       -      -
    243A  ASP*     1.3    84.6    +      -       -      +
    245A  HIS*     1.3    59.3    +      -       -      +
    247A  GLY      3.9     8.1    -      -       -      -
    251A  ALA*     3.9     6.3    -      -       -      +
    326A  GLY      3.5    10.8    -      -       -      -
    327A  SER*     3.5     7.8    +      -       -      -
     81C  SER*     3.1    14.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 245 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  GLU*     3.5     4.0    -      -       -      -
    243A  ASP      3.8     8.7    +      -       -      -
    244A  GLY*     1.3    73.9    -      -       -      +
    246A  GLY*     1.3    60.1    +      -       -      +
    247A  GLY      3.1     6.5    +      -       -      +
    324A  THR      5.1     1.3    -      -       -      -
    325A  VAL*     3.6     0.2    -      -       -      -
    326A  GLY*     2.9    34.2    +      -       -      +
    327A  SER*     3.5    20.9    -      -       -      -
    328A  THR      4.1     1.1    -      -       -      -
    394A  LEU*     4.2    16.6    -      -       +      +
    396A  MET*     3.8    33.7    -      -       +      +
    399A  SER*     3.8     9.4    -      -       -      -
    402A  ASP*     2.5    40.0    +      -       -      -
    404A  TYR*     5.8     0.2    -      -       -      -
     81C  SER*     3.5    12.8    -      -       -      +
     82C  GLY*     4.0    12.8    -      -       -      -
----------------------------------------------------------
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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