Contacts of the strand formed by residues 216 - 222 (chain A) in PDB entry 1TAD


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 CYS 216 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  LYS      3.2     2.0    +      -       -      -
     32A  LEU*     3.3    12.5    -      -       +      +
     33A  LEU      3.0    23.6    +      -       -      -
    214A  VAL*     3.4     5.0    -      -       -      +
    215A  THR*     1.3    83.6    -      -       -      +
    217A  ILE*     1.3    76.9    +      -       -      +
    218A  ILE*     4.4     6.5    -      -       -      -
    258A  THR*     4.0     0.4    -      -       -      -
    259A  SER*     3.2    21.1    -      -       -      +
    261A  VAL*     4.5     7.2    -      -       -      -
    335A  VAL*     4.4    14.6    -      -       -      -
    338A  ILE*     6.5     0.2    -      -       -      -
    339A  ILE*     4.1    36.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 217 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  LEU*     3.5    14.8    -      -       +      +
     35A  LEU*     3.9    19.3    -      -       +      -
    214A  VAL*     3.9    14.8    -      -       +      -
    216A  CYS*     1.3    77.6    -      -       -      +
    218A  ILE*     1.3    73.3    +      -       -      +
    219A  PHE*     4.1     6.1    -      -       +      +
    249A  ILE*     4.1    15.0    -      -       +      -
    255A  PHE*     3.5    50.5    -      -       +      -
    258A  THR*     4.0     5.4    -      -       +      -
    259A  SER      2.8     9.9    +      -       -      +
    260A  ILE*     3.4    16.6    -      -       +      -
    261A  VAL*     2.8    29.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 218 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  LEU*     3.6    32.8    -      -       +      -
     33A  LEU      2.9     7.4    +      -       -      +
     34A  LEU*     3.4    24.0    -      -       +      +
     35A  LEU      3.0    24.8    +      -       -      +
     45A  ILE*     5.6     1.3    -      -       +      -
    194A  MET*     4.9     1.1    -      -       +      -
    216A  CYS*     4.4     5.4    -      -       -      -
    217A  ILE*     1.3    74.4    -      -       -      +
    219A  PHE*     1.3    58.4    -      -       -      +
    220A  ILE*     3.9     5.6    +      -       +      +
    261A  VAL*     3.4    19.7    -      -       +      -
    263A  PHE*     3.6    49.8    -      -       +      -
    332A  PHE*     4.2    15.9    -      -       +      -
    335A  VAL*     4.3     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  LEU*     3.3    18.6    -      -       +      -
     36A  GLY*     4.0    15.9    -      -       -      -
     37A  ALA      4.8     0.4    -      -       -      -
    217A  ILE*     3.8     8.2    -      -       +      -
    218A  ILE*     1.3    72.7    -      -       -      +
    220A  ILE*     1.3    64.7    +      -       -      +
    221A  ALA*     4.3     2.9    -      -       +      -
    242A  SER*     3.7    24.2    -      -       -      -
    245A  LEU*     3.9    23.1    -      -       +      -
    246A  PHE*     3.6    62.8    -      +       +      -
    249A  ILE*     4.3    15.7    -      -       +      -
    260A  ILE*     5.1     1.6    -      -       +      -
    261A  VAL      2.8    14.6    +      -       -      +
    262A  LEU*     3.3    16.8    -      -       +      +
    263A  PHE      2.7    31.4    +      -       -      -
    303A  PHE*     4.5     0.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 220 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  LEU*     4.3    14.4    -      -       +      -
     35A  LEU      2.8    14.2    +      -       -      +
     36A  GLY*     3.6    11.3    -      -       -      -
     37A  ALA      4.4     1.2    +      -       -      -
     40A  SER*     3.4    47.5    +      -       -      +
     42A  LYS*     3.7    32.5    -      -       +      +
     45A  ILE*     3.8    22.9    -      -       +      -
    218A  ILE*     4.2     9.0    -      -       +      +
    219A  PHE*     1.3    80.2    -      -       -      +
    221A  ALA*     1.3    62.7    +      -       -      +
    242A  SER*     4.7     0.5    +      -       -      -
    263A  PHE*     3.5    16.6    -      -       +      +
    265A  ASN*     3.5    22.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 221 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  SER*     4.6     0.9    -      -       -      -
    219A  PHE*     4.0     1.5    +      -       +      -
    220A  ILE*     1.3    74.7    -      -       -      +
    222A  ALA*     1.3    58.7    +      -       -      +
    223A  LEU      3.4     0.2    +      -       -      -
    242A  SER*     3.4    23.3    -      -       -      +
    262A  LEU*     4.1    13.0    -      -       +      -
    263A  PHE      2.9     7.7    +      -       -      +
    264A  LEU*     3.4     8.4    -      -       +      +
    265A  ASN*     2.8    32.5    +      -       -      -
    303A  PHE*     3.6    26.9    -      -       +      -
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Residues in contact with ALA 222 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  GLU      5.6     0.2    -      -       -      -
     40A  SER*     4.4    15.1    -      -       -      +
    220A  ILE      4.3     0.4    -      -       -      -
    221A  ALA*     1.3    69.8    -      -       -      +
    223A  LEU*     1.3    64.8    +      -       -      +
    224A  SER*     4.5     0.7    -      -       -      +
    225A  ALA*     3.2    31.1    +      -       +      +
    239A  MET*     3.5    11.1    -      -       -      +
    242A  SER*     5.1     2.2    +      -       -      -
    265A  ASN*     3.7     8.1    -      -       -      -
    266A  LYS*     3.9    32.8    -      -       +      +
----------------------------------------------------------
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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