Contacts of the strand formed by residues 224 - 231 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220B  LEU*     3.5     4.4    -      -       -      -
    221B  TRP*     2.9    35.6    +      -       +      +
    222B  HIS      3.1     6.8    +      -       -      +
    223B  GLY*     1.3    77.6    -      -       -      +
    225B  SER*     1.3    65.3    +      -       -      +
    226B  VAL*     5.0     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 225 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218B  ARG*     4.4    11.8    +      -       -      -
    219B  GLY      3.4     6.5    -      -       -      -
    220B  LEU*     3.6    14.8    -      -       -      +
    223B  GLY      5.2     0.7    +      -       -      -
    224B  GLU*     1.3    75.6    -      -       -      +
    226B  VAL*     1.3    65.8    +      -       -      +
    278B  HIS*     5.0     1.2    -      -       -      -
    279B  TYR*     3.7    35.2    +      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
    202B  VAL*     4.1    16.8    -      -       +      -
    218B  ARG*     3.6     4.7    -      -       -      -
    219B  GLY*     2.7    50.5    +      -       -      +
    221B  TRP*     4.4    21.5    -      -       +      -
    224B  GLU*     4.7     4.7    -      -       +      +
    225B  SER*     1.3    79.4    -      -       -      +
    227B  ALA*     1.3    58.0    +      -       -      +
    228B  VAL*     4.2     5.4    -      -       +      -
    260B  ILE*     3.6    26.2    -      -       +      -
    276B  ILE*     3.9    18.6    -      -       +      -
    277B  THR      3.5     9.2    -      -       -      +
    278B  HIS*     5.5     0.2    -      -       -      -
    279B  TYR*     3.4    10.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 227 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    216B  VAL*     4.4    13.2    -      -       +      -
    217B  TRP      3.4     6.7    -      -       -      +
    226B  VAL*     1.3    73.2    -      -       -      +
    228B  VAL*     1.3    60.5    +      -       -      +
    229B  LYS      4.0     1.3    -      -       -      +
    257B  LEU*     6.1     0.2    -      -       +      -
    275B  LEU      3.7     1.0    -      -       -      +
    276B  ILE*     3.3     6.2    -      -       -      +
    277B  THR*     2.9    39.6    +      -       -      +
    278B  HIS      3.5    18.6    -      -       -      +
    279B  TYR*     3.6    16.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 228 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202B  VAL*     3.8    29.2    -      -       +      -
    204B  LEU*     4.1    13.2    -      -       +      -
    215B  GLU      3.8     0.2    -      -       -      +
    216B  VAL*     3.5     2.7    -      -       -      -
    217B  TRP*     2.9    44.1    +      -       +      +
    219B  GLY*     4.8     3.4    -      -       -      -
    226B  VAL*     4.2     7.9    -      -       +      -
    227B  ALA*     1.3    76.8    -      -       -      +
    229B  LYS*     1.3    61.1    +      -       -      +
    230B  ILE*     3.6    11.8    +      -       +      -
    274B  TRP*     3.7    39.3    -      -       +      -
    275B  LEU      3.5     3.6    -      -       -      +
    276B  ILE*     4.0    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 229 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213B  TYR*     3.7    37.0    -      -       +      +
    215B  GLU      3.4    10.8    -      -       -      +
    216B  VAL*     3.9    18.6    -      -       +      +
    227B  ALA*     4.0     1.6    -      -       -      +
    228B  VAL*     1.3    70.3    -      -       -      +
    230B  ILE*     1.3    64.9    +      -       -      +
    231B  PHE*     3.6    46.0    -      -       +      -
    235B  ASP*     5.0     1.6    +      -       -      -
    242B  GLU*     4.7     3.9    +      -       -      +
    274B  TRP*     3.5     2.8    -      -       -      -
    275B  LEU*     2.8    43.6    +      -       +      +
    277B  THR*     6.3     0.9    -      -       +      -
    348B  ASP*     4.4    24.2    +      -       -      +
    369B  ARG*     5.6     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 230 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204B  LEU*     4.1    17.5    -      -       +      -
    214B  GLY*     3.4     1.0    -      -       -      -
    215B  GLU*     2.8    44.0    +      -       +      +
    217B  TRP*     3.8    29.6    -      -       +      +
    228B  VAL*     4.3     9.6    -      -       +      +
    229B  LYS*     1.3    74.4    -      -       -      +
    231B  PHE*     1.3    68.6    +      -       -      +
    272B  GLN*     3.7    36.6    -      -       +      +
    273B  LEU      3.6     3.4    -      -       -      -
    274B  TRP*     3.6    29.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 231 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213B  TYR      3.6     7.4    -      -       -      -
    214B  GLY*     4.2     0.4    -      -       -      -
    229B  LYS*     3.6    45.5    -      -       +      -
    230B  ILE*     1.3    82.1    -      -       -      +
    232B  SER*     1.3    67.6    +      -       -      +
    233B  SER      4.1     0.2    +      -       -      -
    235B  ASP*     3.6    26.9    -      -       -      +
    238B  SER*     3.9    11.2    -      -       -      -
    239B  TRP*     3.5    38.8    -      +       +      -
    242B  GLU*     3.7    18.6    -      -       -      -
    272B  GLN*     5.4     3.8    -      -       -      +
    273B  LEU*     3.1    34.4    +      -       +      +
    275B  LEU*     3.8    24.9    -      -       +      -
----------------------------------------------------------
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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