Contacts of the strand formed by residues 282 - 291 (chain E) in PDB entry 5TWV


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 282 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33E  ALA      3.8    18.5    -      -       -      +
     34E  ARG*     3.9     2.9    -      -       -      +
     35E  PHE*     3.8    28.9    +      -       +      +
     36E  VAL      3.9     5.5    -      -       -      +
    219E  VAL*     4.1     1.6    -      -       -      +
    220E  VAL*     3.0    46.1    +      -       +      +
    281E  LEU*     1.3    83.0    -      -       -      +
    283E  ILE*     1.3    66.1    +      -       -      +
    303E  SER*     2.8    31.3    +      -       -      +
    304E  TYR      3.9     7.0    -      -       -      +
    305E  LEU*     3.9    30.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 283 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198E  PHE*     5.1    22.0    -      -       +      -
    200E  LEU*     5.9     3.8    -      -       +      -
    217E  MET*     5.2     3.1    -      -       +      -
    218E  GLN      3.5    17.3    -      -       -      +
    219E  VAL*     4.1    26.5    -      -       +      -
    238E  ILE*     5.1    11.7    -      -       +      -
    267E  LEU*     4.7    23.3    -      -       +      -
    281E  LEU*     4.5     9.9    -      -       +      -
    282E  GLU*     1.3    79.5    -      -       -      +
    284E  ILE*     1.3    66.9    +      -       -      +
    285E  VAL*     4.1     1.3    +      -       +      +
    303E  SER*     3.5     4.4    +      -       -      -
    304E  TYR*     3.1    39.2    +      -       +      +
    309E  ILE*     4.6    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 284 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35E  PHE*     3.9    20.0    -      -       +      -
     36E  VAL*     3.9    20.2    -      -       +      -
    217E  MET*     3.5     7.4    -      -       -      +
    218E  GLN*     2.9    58.5    +      -       +      +
    220E  VAL*     5.0    12.1    -      -       +      -
    235E  GLN*     4.4    10.8    -      -       -      +
    282E  GLU      4.2     0.4    -      -       -      -
    283E  ILE*     1.3    72.9    -      -       -      +
    285E  VAL*     1.3    62.7    +      -       -      +
    286E  ILE*     3.9    16.4    -      -       +      +
    301E  ARG*     6.3     2.0    -      -       +      -
    302E  THR      3.5     4.9    -      -       -      +
    303E  SER*     3.6    16.4    -      -       -      +
    250G  PHE*     4.2    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 285 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183E  PHE*     4.0    25.6    -      -       +      -
    200E  LEU*     4.0    17.3    -      -       +      -
    215E  ILE*     4.7     8.5    -      -       +      -
    216E  HIS      4.4     0.7    -      -       -      -
    217E  MET*     4.3    26.0    -      -       +      -
    283E  ILE*     4.5     2.9    -      -       +      +
    284E  ILE*     1.3    75.7    -      -       -      +
    286E  ILE*     1.3    62.1    +      -       -      +
    300E  ALA      3.6     1.0    -      -       -      +
    301E  ARG*     3.3    28.2    -      -       -      +
    302E  THR*     2.9    29.8    +      -       -      +
    304E  TYR*     3.9    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 286 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214E  THR      3.8     0.7    -      -       -      +
    215E  ILE*     3.3     7.1    -      -       -      +
    216E  HIS*     2.8    62.6    +      -       +      +
    218E  GLN*     4.4     8.3    -      -       +      +
    284E  ILE*     3.9    35.2    -      -       +      +
    285E  VAL*     1.3    75.7    -      -       -      +
    287E  LEU*     1.3    58.0    +      -       -      +
    288E  GLU*     3.8    22.6    +      -       +      +
    299E  GLN*     3.4    21.8    -      -       +      +
    301E  ARG*     5.3     1.3    -      -       +      -
    250G  PHE*     4.1    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 287 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181E  LEU*     4.0    41.7    -      -       +      +
    183E  PHE*     3.7    29.4    -      -       +      -
    202E  VAL*     4.2    13.9    -      -       +      -
    210E  ILE*     5.1     7.0    -      -       +      -
    213E  ALA*     4.9     6.7    -      -       +      -
    215E  ILE*     3.7    30.7    -      -       +      -
    285E  VAL*     3.9     0.8    -      -       +      -
    286E  ILE*     1.3    71.1    -      -       -      +
    288E  GLU*     1.3    71.2    +      -       -      +
    298E  THR      3.9     0.2    -      -       -      +
    299E  GLN*     3.2    10.2    +      -       -      +
    300E  ALA*     2.9    40.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 288 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210E  ILE*     5.3     0.5    -      -       -      +
    213E  ALA*     2.7    33.4    -      -       -      +
    214E  THR*     3.1    36.6    +      -       -      +
    216E  HIS*     3.5    21.4    +      -       -      -
    286E  ILE*     3.9    16.3    -      -       +      +
    287E  LEU*     1.3    82.7    -      -       -      +
    289E  GLY*     1.3    53.1    +      -       -      +
    298E  THR*     3.5    10.5    -      -       -      +
    299E  GLN*     3.9    16.3    -      -       +      +
    211G  ILE*     3.6     8.6    -      -       +      +
    212G  SER*     3.1    38.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 289 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210E  ILE*     4.9     5.2    -      -       -      -
    211E  ILE      4.1     0.7    -      -       -      -
    212E  SER      4.3     2.7    -      -       -      -
    213E  ALA*     3.4    20.6    -      -       -      -
    288E  GLU*     1.3    79.8    -      -       -      +
    290E  VAL*     1.3    59.8    +      -       -      -
    297E  THR*     3.1    12.1    -      -       -      -
    298E  THR*     2.8    36.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 290 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297C  THR*     3.9    20.0    -      -       -      +
    210E  ILE*     3.1    12.1    -      -       -      -
    211E  ILE*     2.9    60.9    +      -       +      +
    212E  SER*     5.3     2.2    -      -       -      -
    289E  GLY*     1.3    73.7    -      -       -      -
    291E  VAL*     1.3    73.0    +      -       -      +
    294E  THR      3.5     8.1    -      -       -      +
    295E  GLY*     3.2    28.9    -      -       -      +
    296E  ILE      3.4     8.3    -      -       -      +
    297E  THR*     3.5    13.9    -      -       +      +
    298E  THR*     4.9     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 291 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296C  ILE*     5.2     2.6    -      -       -      +
    297C  THR      5.1     2.9    -      -       -      +
    174E  ALA*     5.4     3.1    -      -       +      -
    177E  ARG*     4.9    22.9    -      -       +      +
    209E  MET      4.3     4.5    -      -       -      -
    210E  ILE*     5.0     2.5    -      -       -      -
    211E  ILE*     5.0     0.2    -      -       -      +
    290E  VAL*     1.3    84.9    -      -       -      +
    292E  GLU*     1.3    61.1    +      -       -      +
    293E  THR*     3.1     8.1    -      -       -      +
    294E  THR*     2.7    46.6    +      -       -      +
    295E  GLY*     4.9     0.2    -      -       -      -
    296E  ILE      3.5     6.1    +      -       -      +
    298E  THR*     6.0     1.9    -      -       +      +
----------------------------------------------------------
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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