Contacts of the strand formed by residues 224 - 231 (chain C) in PDB entry 3MY0


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 224 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220C  LEU*     3.5     5.4    -      -       -      -
    221C  TRP*     3.0    39.9    +      -       +      +
    222C  HIS      3.1     5.5    +      -       -      +
    223C  GLY*     1.3    77.5    -      -       -      +
    225C  SER*     1.3    67.6    +      -       -      +
    226C  VAL*     5.0     4.9    -      -       +      -
    278C  HIS*     5.8     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 225 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218C  ARG*     4.4    14.5    +      -       -      -
    219C  GLY      3.4     7.8    +      -       -      -
    220C  LEU*     4.7     7.9    -      -       -      +
    223C  GLY      5.3     0.5    +      -       -      -
    224C  GLU*     1.3    80.0    -      -       -      +
    226C  VAL*     1.3    65.7    +      -       -      +
    278C  HIS*     5.0     1.2    -      -       -      -
    279C  TYR*     3.7    36.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 226 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202C  VAL*     4.0    23.1    -      -       +      -
    218C  ARG*     3.6     3.5    -      -       -      -
    219C  GLY*     2.7    53.9    +      -       -      +
    220C  LEU      4.5     0.2    -      -       -      +
    221C  TRP*     4.4    22.0    -      -       +      -
    224C  GLU*     4.7     5.8    -      -       +      +
    225C  SER*     1.3    79.3    -      -       -      +
    227C  ALA*     1.3    58.2    +      -       -      +
    228C  VAL*     4.3     2.9    -      -       +      -
    260C  ILE*     3.6    25.6    -      -       +      -
    276C  ILE*     4.0    16.4    -      -       +      -
    277C  THR      3.5     9.6    -      -       -      +
    278C  HIS*     5.5     0.2    -      -       -      -
    279C  TYR*     3.5     8.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 227 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216C  VAL*     4.5    13.0    -      -       +      -
    217C  TRP      3.5     6.7    -      -       -      +
    226C  VAL*     1.3    73.2    -      -       -      +
    228C  VAL*     1.3    59.7    +      -       -      +
    229C  LYS      4.0     1.1    -      -       -      +
    257C  LEU*     6.0     0.4    -      -       +      -
    275C  LEU      3.7     0.7    -      -       -      +
    276C  ILE*     3.2     7.1    -      -       -      +
    277C  THR*     2.9    49.4    +      -       -      +
    278C  HIS      3.5     8.7    -      -       -      +
    279C  TYR*     3.7    16.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 228 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202C  VAL*     3.9    20.6    -      -       +      -
    204C  LEU*     3.7    31.0    -      -       +      -
    215C  GLU      3.8     0.3    -      -       -      +
    216C  VAL*     3.6     2.4    -      -       -      -
    217C  TRP*     2.9    37.4    +      -       -      +
    219C  GLY*     4.8     1.1    -      -       -      -
    226C  VAL*     4.3     7.9    -      -       +      +
    227C  ALA*     1.3    75.9    -      -       -      +
    229C  LYS*     1.3    60.2    -      -       -      +
    230C  ILE*     3.6    13.4    +      -       +      +
    274C  TRP*     3.7    36.1    -      -       +      -
    275C  LEU      3.5     3.4    -      -       -      +
    276C  ILE*     4.0    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 229 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213C  TYR*     3.7    36.6    -      -       +      +
    215C  GLU      3.4    11.2    -      -       -      +
    216C  VAL*     3.9    18.1    -      -       +      +
    227C  ALA*     4.0     1.8    -      -       +      +
    228C  VAL*     1.3    71.0    -      -       -      +
    230C  ILE*     1.3    64.6    +      -       -      +
    231C  PHE*     3.6    46.6    -      -       +      -
    235C  ASP*     5.0     1.8    +      -       -      -
    238C  SER*     5.9     0.4    -      -       -      -
    242C  GLU*     4.5     2.8    +      -       -      -
    274C  TRP*     3.5     3.6    -      -       -      -
    275C  LEU*     2.8    47.3    +      -       +      +
    277C  THR*     6.4     0.2    -      -       +      -
    348C  ASP*     4.4    23.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 230 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204C  LEU*     4.2    15.5    -      -       +      -
    214C  GLY*     3.4     1.2    -      -       -      -
    215C  GLU*     2.8    47.0    +      -       +      +
    217C  TRP*     3.6    31.0    -      -       +      +
    228C  VAL*     4.2     9.2    -      -       +      +
    229C  LYS*     1.3    73.8    -      -       -      +
    231C  PHE*     1.3    66.8    +      -       -      +
    268C  ASN*     6.2     1.3    -      -       +      -
    272C  GLN*     3.9    39.9    -      -       +      +
    273C  LEU      3.6     3.1    -      -       -      -
    274C  TRP*     3.6    22.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 231 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213C  TYR      3.6     7.4    -      -       -      -
    214C  GLY*     4.2     0.2    -      -       -      -
    229C  LYS*     3.6    48.5    -      -       +      -
    230C  ILE*     1.3    81.2    -      -       -      +
    232C  SER*     1.3    68.2    +      -       -      +
    235C  ASP*     3.7    27.6    -      -       -      +
    236C  GLU*     5.2     1.1    -      -       -      +
    238C  SER*     3.9    10.8    -      -       -      -
    239C  TRP*     3.5    42.4    -      +       +      -
    242C  GLU*     3.7    18.4    -      -       -      -
    272C  GLN*     5.3     1.7    -      -       -      +
    273C  LEU*     3.1    31.6    +      -       +      +
    275C  LEU*     3.7    24.2    -      -       +      -
----------------------------------------------------------
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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