Contacts of the strand formed by residues 145 - 151 (chain A) in PDB entry 2MIB


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 ASP 145 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  ASP*     3.5     3.8    -      -       -      -
     13A  GLU*     2.9    49.3    +      -       +      +
    106A  VAL*     3.7     6.4    -      -       -      +
    109A  LYS*     3.6    26.2    -      -       +      +
    110A  VAL      3.6     1.3    -      -       -      -
    111A  GLU*     2.6    34.9    -      -       -      +
    143A  ILE*     3.6     3.8    -      -       -      +
    144A  ILE*     1.3    89.1    +      -       -      +
    146A  PHE*     1.3    62.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  LEU*     4.0    21.5    -      -       +      -
     11A  ARG      3.6     6.7    -      -       -      +
     12A  ASP*     3.7    30.1    -      -       +      -
     18A  LEU*     4.2    21.5    -      -       +      -
    108A  SER      4.0     0.2    -      -       -      +
    109A  LYS*     3.1    10.9    -      -       -      -
    110A  VAL*     2.7    52.8    +      -       +      +
    112A  PHE*     4.5    10.1    -      +       +      -
    122A  ILE*     3.4    43.3    -      -       +      -
    123A  SER*     4.5     1.6    -      -       -      -
    124A  THR*     4.0    22.0    -      -       +      -
    143A  ILE      4.5     0.9    -      -       -      -
    144A  ILE*     3.5    16.8    -      -       -      -
    145A  ASP*     1.3    78.5    -      -       -      +
    147A  THR*     1.3    64.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  ARG      3.7     0.3    -      -       -      +
     10A  LEU*     3.4     9.2    -      -       -      +
     11A  ARG*     3.0    43.3    +      -       +      +
     12A  ASP      4.9     1.2    +      -       -      -
     15A  GLN*     5.2     6.6    +      -       -      +
    108A  SER      4.4     8.5    +      -       -      +
    109A  LYS*     3.5    22.9    +      -       -      +
    146A  PHE*     1.3    72.8    -      -       -      +
    148A  MET*     1.3    74.3    +      -       -      +
    149A  GLU*     4.6     5.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  TYR*     3.9    35.6    -      -       +      +
      9A  ARG      3.6     4.3    -      -       -      +
     10A  LEU*     4.1    13.5    -      -       +      -
     44A  MET*     4.2    17.3    -      -       -      -
    103A  LYS*     4.4     9.2    -      -       +      +
    105A  GLU*     4.4    10.3    -      -       -      +
    108A  SER      4.9     4.6    +      -       -      -
    110A  VAL*     3.7    42.2    -      -       +      -
    112A  PHE*     4.2    11.0    -      -       -      -
    147A  THR*     1.3    80.7    -      -       -      +
    149A  GLU*     1.3    59.1    +      -       -      +
    150A  SER      3.8     1.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  TYR*     3.1     5.7    -      -       -      -
      9A  ARG*     2.8    72.3    +      -       +      +
     11A  ARG*     3.0    31.7    +      -       -      +
     36A  ILE*     5.8     3.5    -      -       -      +
    147A  THR*     4.1     6.6    -      -       +      +
    148A  MET*     1.3    72.8    -      -       -      +
    150A  SER*     1.3    70.7    +      -       -      +
    151A  VAL*     3.8     1.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  HIS      3.8     4.5    +      -       -      -
      8A  TYR*     3.6    22.9    +      -       -      -
      9A  ARG*     5.7     0.2    +      -       -      -
    148A  MET      3.8     3.2    +      -       -      -
    149A  GLU*     1.3    81.7    -      -       -      +
    151A  VAL*     1.3    69.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  HIS      2.9    17.5    +      -       -      +
      8A  TYR      3.6    26.9    -      -       -      -
      9A  ARG*     3.7    42.4    -      -       -      +
     41A  ILE*     3.8    29.2    -      -       +      -
     63A  LYS*     5.7     2.2    -      -       -      +
    149A  GLU*     3.8     2.0    -      -       -      +
    150A  SER*     1.3    87.8    +      -       -      +
    152A  SER*     1.3    78.0    +      -       -      +
----------------------------------------------------------
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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