Contacts of the strand formed by residues 282 - 291 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  ALA      3.8    17.8    -      -       -      +
     34A  ARG*     3.9     3.3    -      -       -      +
     35A  PHE*     3.8    29.6    +      -       +      +
     36A  VAL      3.9     5.5    -      -       -      +
    219A  VAL*     4.0     1.9    -      -       -      +
    220A  VAL*     3.0    46.3    +      -       +      +
    281A  LEU*     1.3    82.1    -      -       -      +
    283A  ILE*     1.3    66.3    +      -       -      +
    303A  SER*     2.8    32.2    +      -       -      +
    304A  TYR      3.9     6.7    -      -       -      +
    305A  LEU*     3.9    31.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 283 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198A  PHE*     5.1    21.1    -      -       +      -
    200A  LEU*     5.9     3.4    -      -       +      -
    217A  MET*     5.2     4.0    -      -       +      -
    218A  GLN      3.5    16.8    -      -       -      +
    219A  VAL*     4.1    25.8    -      -       +      -
    238A  ILE*     5.1    12.3    -      -       +      -
    267A  LEU*     4.7    23.6    -      -       +      -
    281A  LEU*     4.5     9.4    -      -       +      -
    282A  GLU*     1.3    78.9    -      -       -      +
    284A  ILE*     1.3    67.3    +      -       -      +
    285A  VAL*     4.1     2.1    +      -       +      +
    303A  SER*     3.5     4.3    +      -       -      -
    304A  TYR*     3.1    39.6    +      -       +      +
    309A  ILE*     4.6    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 284 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  PHE*     3.9    20.4    -      -       +      -
     36A  VAL*     3.9    19.3    -      -       +      -
    217A  MET*     3.5     7.8    -      -       -      +
    218A  GLN*     2.9    56.9    +      -       +      +
    220A  VAL*     5.0    13.0    -      -       +      -
    235A  GLN*     4.4    10.5    -      -       -      +
    282A  GLU      4.2     0.4    -      -       -      -
    283A  ILE*     1.3    74.8    -      -       -      +
    285A  VAL*     1.3    61.9    +      -       -      +
    286A  ILE*     3.9    16.1    -      -       +      +
    301A  ARG*     6.3     1.6    -      -       +      -
    302A  THR      3.5     4.9    -      -       -      +
    303A  SER*     3.6    16.6    -      -       -      +
    250C  PHE*     4.2    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 285 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  PHE*     4.0    25.8    -      -       +      -
    200A  LEU*     4.0    17.5    -      -       +      -
    215A  ILE*     4.7     8.5    -      -       +      -
    216A  HIS      4.4     0.9    -      -       -      -
    217A  MET*     4.3    24.5    -      -       +      -
    283A  ILE*     4.5     2.9    -      -       +      +
    284A  ILE*     1.3    75.8    -      -       -      +
    286A  ILE*     1.3    63.9    +      -       -      +
    287A  LEU      3.9     0.2    -      -       -      -
    300A  ALA      3.6     0.7    -      -       -      +
    301A  ARG*     3.3    28.6    -      -       -      +
    302A  THR*     2.9    30.4    +      -       -      +
    304A  TYR*     3.9    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 286 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214A  THR      3.8     0.7    -      -       -      +
    215A  ILE*     3.3     6.7    -      -       -      -
    216A  HIS*     2.8    61.5    +      -       +      +
    218A  GLN*     4.4     8.5    -      -       +      +
    284A  ILE*     3.9    35.2    -      -       +      +
    285A  VAL*     1.3    76.5    -      -       -      +
    287A  LEU*     1.3    58.3    +      -       -      +
    288A  GLU*     3.8    21.8    +      -       +      +
    299A  GLN*     3.4    22.0    -      -       +      +
    301A  ARG*     5.3     1.3    -      -       +      -
    250C  PHE*     4.1    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 287 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181A  LEU*     4.0    42.5    -      -       +      +
    183A  PHE*     3.7    29.8    -      -       +      -
    202A  VAL*     4.2    13.9    -      -       +      -
    210A  ILE*     5.1     7.2    -      -       +      -
    213A  ALA*     4.9     6.1    -      -       +      +
    215A  ILE*     3.7    30.3    -      -       +      -
    285A  VAL      3.9     0.4    -      -       -      -
    286A  ILE*     1.3    70.9    -      -       -      +
    288A  GLU*     1.3    72.3    +      -       -      +
    298A  THR      3.9     0.3    -      -       -      +
    299A  GLN*     3.2     9.5    -      -       -      +
    300A  ALA*     2.9    39.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 288 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210A  ILE*     5.3     0.3    -      -       -      +
    213A  ALA*     2.7    33.4    -      -       -      +
    214A  THR*     3.1    36.9    +      -       -      +
    216A  HIS*     3.5    21.2    +      -       -      -
    286A  ILE*     3.9    16.5    -      -       +      +
    287A  LEU*     1.3    82.5    -      -       -      +
    289A  GLY*     1.3    51.2    +      -       -      +
    298A  THR      3.5     9.9    -      -       -      +
    299A  GLN*     3.9    16.6    -      -       +      +
    211C  ILE*     3.6     9.6    -      -       +      +
    212C  SER*     3.1    37.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 289 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210A  ILE*     4.9     4.7    -      -       -      -
    211A  ILE      4.1     0.9    -      -       -      -
    212A  SER      4.3     3.4    -      -       -      -
    213A  ALA*     3.4    19.7    -      -       -      -
    288A  GLU*     1.3    80.4    -      -       -      +
    290A  VAL*     1.3    60.3    +      -       -      -
    297A  THR*     3.1    11.9    -      -       -      -
    298A  THR*     2.8    35.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 290 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210A  ILE*     3.1    11.8    -      -       -      +
    211A  ILE*     2.9    61.6    +      -       +      +
    212A  SER*     4.9     3.1    +      -       -      -
    289A  GLY*     1.3    72.8    -      -       -      -
    291A  VAL*     1.3    74.3    +      -       -      +
    294A  THR      3.5     7.9    -      -       -      +
    295A  GLY*     3.2    29.2    -      -       -      +
    296A  ILE      3.4     8.1    -      -       -      +
    297A  THR*     3.5    13.7    -      -       +      -
    298A  THR*     6.0     1.8    -      -       -      -
    297G  THR*     3.9    17.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 291 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174A  ALA*     5.4     2.9    -      -       +      -
    177A  ARG*     4.9    22.9    -      -       +      +
    209A  MET      4.3     4.5    -      -       -      -
    210A  ILE*     5.0     2.7    -      -       -      -
    211A  ILE*     5.0     0.3    -      -       -      +
    290A  VAL*     1.3    86.2    -      -       -      +
    292A  GLU*     1.3    61.7    +      -       -      +
    293A  THR*     3.1     7.9    -      -       -      +
    294A  THR*     2.7    47.4    +      -       -      +
    295A  GLY*     4.9     0.2    -      -       -      -
    296A  ILE      3.5     6.8    +      -       -      +
    298A  THR*     6.0     2.1    -      -       +      +
    296G  ILE*     5.2     2.4    -      -       -      +
    297G  THR      5.1     3.3    -      -       -      +
----------------------------------------------------------
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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