Contacts of the strand formed by residues 219 - 225 (chain S) in PDB entry 3SDI


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 THR 219 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45S  HIS*     3.5    24.3    +      -       +      -
    214S  ILE*     4.4    20.2    -      -       +      -
    215S  VAL*     3.6     5.7    -      -       -      +
    216S  GLY      2.9    41.0    +      -       -      +
    218S  ASP*     1.3    79.6    +      -       -      +
    220S  PRO*     1.3    78.5    -      -       +      +
    221S  PHE      3.7     0.2    +      -       -      -
    222S  THR*     4.6     3.8    -      -       -      +
    224S  TYR*     5.6     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 220 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72S  GLU*     3.4    34.3    -      -       +      +
    214S  ILE      3.5     2.8    -      -       -      +
    218S  ASP      3.7     9.4    -      -       -      +
    219S  THR*     1.3    91.0    -      -       +      +
    221S  PHE*     1.3    66.6    +      -       -      +
    222S  THR*     3.1    22.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 221 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48S  LEU*     4.4     0.9    -      -       +      -
     67S  ILE*     3.9    10.3    -      -       +      -
     69S  LYS*     3.8    51.8    +      -       +      +
     71S  ASP      4.0    11.0    -      -       -      +
     72S  GLU      3.1    16.2    +      -       -      +
     74S  MET      3.7     6.7    -      -       -      +
     75S  GLY*     3.3    37.0    -      -       -      -
     76S  LEU      4.0     0.9    -      -       -      -
    139S  ILE*     3.7    24.5    -      -       +      -
    213S  ALA*     3.8    18.4    -      -       +      -
    214S  ILE      3.3     9.4    -      -       -      -
    215S  VAL*     3.8    22.6    -      -       +      +
    219S  THR      3.7     1.8    +      -       -      -
    220S  PRO*     1.3    70.4    -      -       -      +
    222S  THR*     1.3    65.4    +      -       -      +
    223S  ILE*     4.0    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 222 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212S  ILE      3.9     0.2    -      -       -      +
    213S  ALA*     3.2     5.0    -      -       -      +
    214S  ILE*     3.1    43.2    +      -       -      +
    219S  THR*     4.6     3.1    -      -       -      +
    220S  PRO*     3.2    20.2    +      -       +      +
    221S  PHE*     1.3    80.8    -      -       -      +
    223S  ILE*     1.3    65.1    +      -       -      +
    224S  TYR*     3.9    22.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 223 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67S  ILE*     3.5    47.3    -      -       +      +
     68S  ILE*     4.7     0.2    -      -       -      -
     69S  LYS*     4.3    17.3    -      -       +      +
    211S  SER*     4.3     7.4    -      -       -      +
    212S  ILE      3.4     8.7    -      -       -      +
    213S  ALA*     4.4     0.2    -      -       -      +
    221S  PHE*     4.0     9.0    -      -       +      -
    222S  THR*     1.3    75.8    -      -       -      +
    224S  TYR*     1.3    71.4    +      -       -      +
    225S  ASP*     3.9    23.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 224 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190S  ILE*     5.1     9.6    -      -       +      -
    211S  SER*     3.7     0.5    +      -       -      -
    212S  ILE*     2.6    49.6    +      -       +      +
    214S  ILE*     3.9    25.1    -      -       +      +
    219S  THR*     5.6     3.1    -      -       -      +
    222S  THR*     3.9    22.0    +      -       -      +
    223S  ILE*     1.3    78.7    -      -       -      +
    225S  ASP*     1.3    65.7    +      -       -      +
    228S  ALA*     4.1    23.6    -      -       +      +
    229S  VAL*     3.3    23.3    -      -       +      +
    232S  TYR*     5.5     7.2    -      +       +      -
----------------------------------------------------------
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Residues in contact with ASP 225 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52S  LYS*     3.5    19.1    +      -       -      +
     65S  LYS*     5.7     4.2    -      -       -      +
    210S  LEU      3.5     6.7    -      -       -      +
    211S  SER*     2.5    32.7    +      -       -      -
    223S  ILE*     3.9    13.8    +      -       +      +
    224S  TYR*     1.3    75.7    -      -       -      +
    226S  GLY*     1.3    62.5    +      -       -      +
    227S  GLU*     3.1    19.7    -      -       -      +
    228S  ALA*     3.8     7.9    +      -       -      +
    229S  VAL*     4.2     2.7    -      -       -      -
----------------------------------------------------------
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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