Contacts of the strand formed by residues 252 - 263 (chain A) in PDB entry 5TJA


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 ASP 252 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240A  ILE*     3.4     8.1    -      -       -      +
    241A  ASN*     2.8    38.4    +      -       +      +
    244A  SER*     4.3     2.7    +      -       -      +
    250A  ILE      3.4     5.2    +      -       -      +
    251A  PRO*     1.3    76.2    -      -       -      +
    253A  CYS*     1.3    60.9    +      -       -      +
    254A  TYR*     3.6    23.5    +      -       +      -
    281A  ILE*     3.6    22.7    -      -       -      +
    282A  GLN      3.4    16.2    -      -       -      +
    283A  GLU*     4.4     5.1    +      -       -      +
    284A  CYS*     3.6     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 253 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239A  THR      4.0     2.2    -      -       -      -
    240A  ILE*     3.5    18.6    -      -       -      -
    252A  ASP*     1.3    70.4    -      -       -      +
    254A  TYR*     1.3    62.4    +      -       -      +
    255A  THR*     5.4     0.4    +      -       -      -
    280A  HIS      3.7     1.6    -      -       -      +
    281A  ILE*     3.7     2.8    -      -       -      -
    282A  GLN*     2.9    50.6    +      -       +      +
    283A  GLU      4.1     2.2    -      -       -      +
    284A  CYS*     2.0    52.2    -      -       -      -
    285A  LYS      5.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 254 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  ALA*     3.3    34.7    +      -       -      +
     93A  PHE*     3.8    18.2    -      +       -      -
     94A  ARG*     5.0     3.4    -      -       +      -
    238A  LYS*     3.2     6.9    -      -       -      +
    239A  THR*     2.9    50.5    +      -       +      +
    241A  ASN*     3.7    25.4    +      -       +      -
    252A  ASP*     3.6    23.4    +      -       +      -
    253A  CYS*     1.3    78.8    -      -       -      +
    255A  THR*     1.3    61.8    +      -       -      +
    256A  PHE*     3.8    26.7    -      +       +      -
    279A  ALA*     4.3     9.4    -      -       +      -
    280A  HIS      3.5     2.9    -      -       -      -
    281A  ILE*     3.2    44.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  VAL*     4.6     4.3    -      -       +      -
    236A  ARG*     4.3    25.1    -      -       +      -
    237A  LEU      3.5     7.9    -      -       -      +
    238A  LYS*     3.4    27.4    -      -       +      +
    253A  CYS      5.4     0.3    +      -       -      -
    254A  TYR*     1.3    72.6    -      -       -      +
    256A  PHE*     1.3    64.9    +      -       -      +
    257A  SER*     3.9     1.7    +      -       -      -
    278A  GLN      3.7     0.5    -      -       -      +
    279A  ALA*     3.6     3.2    -      -       -      -
    280A  HIS*     3.0    51.7    +      -       +      +
    282A  GLN*     5.9     2.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 256 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  PHE*     4.2     2.5    -      +       -      -
     94A  ARG*     3.8    34.5    -      -       +      -
     97A  ASN*     3.5    38.4    -      -       +      -
     98A  THR*     5.0     0.2    -      -       -      -
    101A  PHE*     3.9    32.5    -      +       +      -
    147A  TYR*     5.0     1.3    -      +       -      -
    235A  PHE      3.9     0.2    -      -       -      +
    236A  ARG*     3.2     5.2    -      -       -      +
    237A  LEU      2.7    40.9    +      -       -      +
    239A  THR*     3.7    25.6    -      -       +      -
    254A  TYR*     3.8    18.6    -      +       +      -
    255A  THR*     1.3    74.3    -      -       -      +
    257A  SER*     1.3    60.6    +      -       -      +
    258A  VAL*     3.7     4.0    +      -       +      +
    277A  THR*     4.5    12.8    -      -       -      -
    278A  GLN      3.5     4.3    -      -       -      -
    279A  ALA*     3.8    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 257 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157A  TRP*     4.4     9.7    -      -       -      -
    235A  PHE      3.8     3.3    +      -       -      -
    236A  ARG*     3.9    18.4    -      -       -      +
    255A  THR*     3.9     2.3    +      -       -      -
    256A  PHE*     1.3    73.0    -      -       -      +
    258A  VAL*     1.3    62.1    +      -       -      +
    259A  LEU*     4.0     0.9    +      -       -      +
    276A  GLU      3.6     0.7    -      -       -      +
    277A  THR*     3.1     7.3    -      -       -      -
    278A  GLN*     2.9    52.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 258 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  PHE*     4.0    31.2    -      -       +      -
    233A  ILE      3.5     1.6    -      -       -      +
    234A  HIS*     3.4     5.7    -      -       -      +
    235A  PHE*     2.8    78.6    +      -       +      +
    237A  LEU*     4.9     1.3    -      -       +      -
    256A  PHE*     4.1     8.1    -      -       +      +
    257A  SER*     1.3    77.7    +      -       -      +
    259A  LEU*     1.3    61.4    +      -       -      +
    260A  ILE*     4.4     4.3    -      -       +      -
    275A  LEU*     4.0    31.4    -      -       +      -
    276A  GLU      3.6     3.8    -      -       -      +
    277A  THR*     4.4     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 259 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  THR*     3.8    17.0    -      -       +      -
    233A  ILE      3.4     7.9    -      -       -      +
    234A  HIS*     3.3    37.9    -      -       +      +
    257A  SER      4.0     0.6    +      -       -      +
    258A  VAL*     1.3    73.0    -      -       -      +
    260A  ILE*     1.3    63.6    +      -       -      +
    261A  THR*     3.9    16.7    +      -       -      +
    274A  SER      3.8     0.7    -      -       -      +
    275A  LEU*     3.4     1.4    -      -       -      -
    276A  GLU*     2.9    49.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 260 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  PHE*     3.9    28.7    -      -       +      -
    106A  LEU*     4.0    15.7    -      -       +      -
    132A  ALA*     4.1    17.3    -      -       +      -
    231A  VAL      3.9     0.3    -      -       -      +
    232A  THR*     3.2     7.6    -      -       -      -
    233A  ILE*     2.9    51.3    +      -       +      +
    235A  PHE*     4.4     8.1    -      -       +      -
    258A  VAL*     4.4     4.9    -      -       +      -
    259A  LEU*     1.3    77.4    -      -       -      +
    261A  THR*     1.3    61.2    +      -       -      +
    262A  PHE*     3.7    27.4    -      -       +      -
    273A  ILE*     4.3     4.0    -      -       +      -
    274A  SER      3.2     9.4    -      -       -      +
    275A  LEU*     4.0    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 261 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  ASN*     4.7     9.0    -      -       +      +
    231A  VAL      3.6     5.4    -      -       -      +
    232A  THR*     4.0    11.7    -      -       +      +
    259A  LEU*     3.9    21.5    +      -       -      +
    260A  ILE*     1.3    76.3    +      -       -      +
    262A  PHE*     1.3    65.1    +      -       -      +
    263A  ASP*     3.8    24.0    -      -       +      +
    272A  PRO      3.5     2.3    -      -       -      +
    273A  ILE*     3.2     6.1    -      -       -      +
    274A  SER*     2.9    44.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 262 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  LEU*     5.7     1.1    -      -       +      -
    125A  LEU*     3.8    18.4    -      -       +      -
    128A  ALA*     3.9    24.7    -      -       +      -
    129A  ILE*     3.9    24.7    -      -       +      -
    132A  ALA*     5.1     2.2    -      -       +      -
    228A  LEU*     5.6     1.0    -      -       -      +
    230A  ASN*     3.4     5.4    -      -       -      +
    231A  VAL*     2.8    56.1    +      -       +      +
    233A  ILE*     3.9    24.0    -      -       +      -
    260A  ILE*     3.7    25.1    -      -       +      -
    261A  THR*     1.3    72.8    -      -       -      +
    263A  ASP*     1.3    59.5    +      -       -      +
    264A  ASN*     3.6     1.2    +      -       -      +
    271A  ILE*     3.6    15.3    -      -       +      +
    272A  PRO      3.7     5.2    -      -       -      -
    273A  ILE*     3.5    33.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 263 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  VAL      3.9     2.4    -      -       -      +
    230A  ASN*     4.1     7.9    +      -       -      +
    261A  THR*     3.6    14.3    -      -       +      -
    262A  PHE*     1.3    70.4    -      -       -      +
    264A  ASN*     1.3    58.7    +      -       -      +
    265A  LYS*     2.9    56.9    +      -       -      +
    266A  ALA*     5.2     0.7    +      -       -      +
    270A  ARG      4.2     1.4    -      -       -      +
    271A  ILE*     3.5     6.2    -      -       -      +
    272A  PRO*     3.1    47.2    +      -       +      +
----------------------------------------------------------
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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