Contacts of the strand formed by residues 147 - 151 (chain A) in PDB entry 6S1M


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 TYR 147 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  PHE*     4.9     4.7    -      +       -      -
    145A  ALA      3.8    14.1    -      -       -      -
    146A  PRO*     1.3    77.2    -      -       +      +
    148A  PHE*     1.3    74.0    +      -       -      +
    149A  TYR*     3.5    33.1    +      +       -      -
    211A  ARG*     3.6    39.2    +      -       -      +
    212A  ILE      3.3    17.3    -      -       -      +
    213A  THR*     3.7    13.7    -      -       +      +
    214A  VAL*     4.4     2.0    -      -       -      +
    220A  VAL*     5.5     2.4    -      -       -      +
    246A  ALA      4.4     4.5    -      -       -      +
    247A  ASN*     5.8     0.2    -      -       -      -
    253A  ARG*     3.8    39.5    +      -       +      +
    257A  ASP*     3.6    31.4    +      -       -      -
    564A  MET*     4.7     5.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  TYR*     1.3    82.3    -      -       -      +
    149A  TYR*     1.3    88.9    +      -       -      +
    150A  THR*     3.4    18.4    -      -       -      -
    211A  ARG*     3.7     5.5    -      -       -      +
    212A  ILE*     2.9    53.1    +      -       +      +
    214A  VAL*     4.5    14.4    -      -       +      -
    220A  VAL*     3.8    31.6    -      -       +      -
    223A  ALA*     5.2    12.6    -      -       +      -
    224A  ARG*     5.7     6.7    -      -       +      -
    227A  LEU*     5.2    11.4    -      -       +      -
    228A  GLU*     5.5     1.8    -      -       -      -
    244A  TYR*     4.1    20.0    -      -       +      -
    245A  GLU      3.6    13.0    -      -       -      +
    246A  ALA      3.7    12.8    -      -       -      +
    247A  ASN*     4.8     5.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  TYR*     3.5    25.3    +      +       -      -
    148A  PHE*     1.3    85.6    -      -       -      +
    150A  THR*     1.3    69.6    +      -       -      +
    193A  CYS*     3.6    23.1    -      -       -      -
    195A  ARG*     3.4    38.6    +      -       -      -
    209A  PHE*     4.6     4.0    -      -       +      -
    210A  LEU      3.3    12.1    -      -       -      +
    211A  ARG*     3.4    35.1    +      -       +      -
    212A  ILE*     5.5     0.7    -      -       -      -
    245A  GLU*     3.2    28.9    +      -       +      +
    246A  ALA*     5.0     2.7    -      -       +      -
    253A  ARG*     5.3     5.2    -      -       -      -
    569A  LEU*     3.6    46.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  PHE*     3.4    18.0    -      -       -      -
    149A  TYR*     1.3    83.1    +      -       -      +
    151A  PRO*     1.3    83.0    -      -       +      +
    209A  PHE*     4.1     4.4    -      -       -      -
    210A  LEU*     2.8    33.4    +      -       +      +
    212A  ILE*     4.3    13.4    -      -       -      +
    227A  LEU*     4.7     4.8    -      -       +      +
    232A  ARG*     4.0    17.3    -      -       -      +
    242A  ALA*     3.7    18.6    -      -       +      +
    243A  PRO      3.5    16.5    +      -       -      +
    244A  TYR*     4.0     1.4    -      -       -      -
    245A  GLU      5.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  THR*     1.3    97.5    -      -       +      +
    152A  ALA*     1.3    62.6    +      -       -      +
    153A  PRO*     3.3    13.1    -      -       +      +
    208A  PRO      4.4     3.1    -      -       -      +
    209A  PHE*     3.8    32.5    -      -       +      -
    210A  LEU*     4.7     2.2    -      -       -      +
    232A  ARG*     5.2     0.3    +      -       -      -
    242A  ALA*     3.8     7.1    -      -       +      +
    243A  PRO*     3.6    28.7    -      -       +      +
    245A  GLU*     4.4    12.8    -      -       +      +
----------------------------------------------------------
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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