Contacts of the strand formed by residues 237 - 241 (chain A) in PDB entry 6TD3


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 ILE 237 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  ILE*     3.4    28.3    -      -       +      -
    231A  ILE      3.4     3.6    -      -       -      -
    232A  ILE*     3.8    21.5    -      -       +      -
    236A  SER*     1.3    76.8    -      -       -      +
    238A  THR*     1.3    59.9    +      -       -      +
    247A  ALA*     3.8     0.2    -      -       -      -
    248A  ILE*     3.1    39.9    +      -       +      +
    253A  ILE*     4.2    20.2    -      -       +      -
    258A  ILE*     4.7     1.3    -      -       +      -
    273A  LEU*     3.8    23.6    -      -       +      -
    283A  LEU*     3.9    15.3    -      -       +      -
    300A  LEU*     4.2    11.5    -      -       +      +
    302A  VAL*     3.8    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 238 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212A  VAL*     5.1     4.0    -      -       -      +
    213A  GLU*     6.5     0.2    -      -       +      -
    230A  ILE*     3.3     6.4    -      -       -      -
    231A  ILE*     2.9    46.2    +      -       -      +
    236A  SER*     4.2    17.5    -      -       -      +
    237A  ILE*     1.3    79.1    -      -       -      +
    239A  TYR*     1.3    59.9    +      -       -      +
    240A  HIS*     3.4    23.2    +      -       -      +
    245A  TYR*     4.3     8.3    -      -       +      +
    246A  LEU      3.3     7.4    -      -       -      -
    247A  ALA*     3.6    22.9    -      -       +      -
    300A  LEU*     4.6     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 239 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222A  VAL*     4.1     9.6    -      -       +      -
    226A  PHE*     3.1    23.6    +      -       +      +
    227A  GLY      2.9    27.9    +      -       -      -
    229A  ALA      3.4    23.3    -      -       -      -
    230A  ILE*     4.1    12.1    -      -       +      +
    238A  THR*     1.3    70.4    -      -       -      +
    240A  HIS*     1.3    66.6    +      -       -      +
    241A  ASN*     3.2    27.8    +      -       +      -
    244A  LYS*     4.3    22.2    -      -       +      -
    245A  TYR*     3.3     8.5    -      -       -      -
    246A  LEU*     2.9    37.5    +      -       +      +
    297A  LEU*     3.7    34.7    -      -       +      +
    300A  LEU*     4.1    18.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190A  VAL*     3.6    21.4    -      -       +      +
    207A  TRP*     3.6    25.6    -      -       +      -
    210A  GLU*     3.7    31.0    -      -       +      +
    211A  ASN      5.4     1.6    -      -       -      -
    212A  VAL*     3.9    12.7    -      -       +      +
    228A  GLY*     3.4     1.0    -      -       -      -
    229A  ALA      2.9    33.5    +      -       -      +
    231A  ILE*     4.3    10.3    -      -       +      -
    238A  THR*     3.4    28.8    +      -       -      +
    239A  TYR*     1.3    84.6    -      -       -      +
    241A  ASN*     1.3    63.0    +      -       -      +
    244A  LYS      3.9     4.0    -      -       -      -
    245A  TYR*     3.7    25.5    -      +       -      -
----------------------------------------------------------
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Residues in contact with ASN 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207A  TRP*     4.3    13.4    +      -       -      +
    226A  PHE      3.0    24.2    +      -       -      -
    227A  GLY*     4.9     0.2    -      -       -      -
    228A  GLY*     3.6    18.1    +      -       -      -
    239A  TYR*     3.2    24.6    +      -       +      +
    240A  HIS*     1.3    75.1    -      -       -      +
    242A  GLY*     1.3    64.3    +      -       -      +
    243A  ASP*     3.3    13.3    +      -       -      +
    244A  LYS*     3.2    18.7    +      -       +      +
----------------------------------------------------------
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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