Contacts of the strand formed by residues 224 - 228 (chain B) in PDB entry 5DTI


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 ARG 224 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195B  MET      4.9     1.0    +      -       -      -
    196B  SER*     2.9    38.6    +      -       -      +
    197B  VAL      3.3     2.6    +      -       -      -
    198B  THR*     3.3    15.7    +      -       -      +
    199B  LEU      2.9    21.8    +      -       -      -
    222B  PHE*     3.5     9.8    -      -       -      -
    223B  HIS*     1.3    94.6    +      -       -      +
    225B  ALA*     1.3    63.4    +      -       -      +
    324B  LEU*     4.6     1.8    -      -       -      -
    325B  GLN*     3.1    46.5    +      -       +      +
    483B  PHE*     3.4    15.0    +      -       +      -
    484B  ALA      3.0    20.1    +      -       -      -
    485B  ARG      4.2     7.1    +      -       -      -
    486B  THR      4.8     2.4    -      -       -      -
    487B  GLY*     3.4    27.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 225 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198B  THR*     4.5     0.2    -      -       -      -
    199B  LEU      3.2     5.4    -      -       -      -
    209B  VAL*     3.5    25.1    -      -       +      -
    213B  ILE*     3.8    24.7    -      -       +      -
    222B  PHE*     4.3     5.4    -      -       +      -
    224B  ARG*     1.3    80.1    -      -       -      +
    226B  VAL*     1.3    63.5    +      -       -      +
    227B  LEU*     4.2     3.4    -      -       +      -
    324B  LEU*     5.0     1.1    -      -       +      +
    325B  GLN      3.3     7.6    +      -       -      +
    326B  VAL*     3.3     8.0    -      -       +      +
    327B  LEU      2.9    23.7    +      -       -      +
    483B  PHE*     3.5     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 226 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115B  LEU*     5.8     0.9    -      -       +      -
    198B  THR*     4.1     5.6    -      -       +      -
    199B  LEU      2.7    11.1    +      -       -      +
    200B  PHE*     3.4    21.4    -      -       +      -
    201B  GLY      3.3    21.3    +      -       -      -
    209B  VAL*     4.1     5.0    -      -       -      +
    225B  ALA*     1.3    77.0    -      -       -      +
    227B  LEU*     1.3    64.7    +      -       -      +
    228B  GLN*     3.9    16.8    -      -       +      +
    327B  LEU*     3.1    29.2    -      -       +      +
    428B  TYR*     5.2     1.1    -      -       +      -
    480B  TRP*     3.6    29.4    -      -       +      +
    483B  PHE*     3.7    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 227 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206B  ALA*     3.4    29.4    -      -       +      +
    209B  VAL*     4.0    15.0    -      -       +      -
    210B  GLY*     3.9    14.1    -      -       -      -
    213B  ILE*     4.1    12.1    -      -       +      -
    225B  ALA*     4.2     2.2    -      -       +      -
    226B  VAL*     1.3    77.7    -      -       -      +
    228B  GLN*     1.3    62.7    +      -       -      +
    229B  SER      3.7     1.1    +      -       -      -
    230B  GLY      3.6    20.6    -      -       -      +
    231B  THR*     5.7     0.4    -      -       +      -
    232B  PRO*     4.0     4.3    -      -       +      -
    326B  VAL*     3.9    24.0    -      -       +      -
    327B  LEU      2.8    10.2    +      -       -      -
    328B  VAL*     3.3    11.9    -      -       +      +
    329B  GLY      3.2    23.7    +      -       -      +
    411B  VAL*     5.5     1.5    -      -       +      +
    414B  LEU*     3.7    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 228 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117B  TRP*     4.1     8.2    -      -       -      -
    200B  PHE*     4.0    15.6    -      -       -      -
    201B  GLY      3.0    18.3    +      -       -      +
    202B  GLU*     3.1    13.1    -      -       -      +
    203B  SER      2.8    32.1    +      -       -      -
    206B  ALA*     3.4     1.3    -      -       -      +
    226B  VAL*     3.9    13.1    -      -       +      +
    227B  LEU*     1.3    71.2    -      -       -      +
    229B  SER*     1.3    59.6    +      -       -      +
    230B  GLY      3.2     1.6    +      -       -      -
    428B  TYR*     3.3    23.1    -      -       -      +
    450B  GLU*     3.1    30.2    +      -       -      +
    451B  ILE*     4.3     5.3    -      -       -      +
    454B  ILE*     4.4     8.0    -      -       -      +
    480B  TRP*     3.0    29.8    +      -       +      -
----------------------------------------------------------
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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