Contacts of the strand formed by residues 206 - 210 (chain B) in PDB entry 4P22


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 MET 206 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185B  LYS*     3.2    31.9    -      -       +      +
    202B  PHE*     3.3    36.3    -      -       +      +
    203B  GLY      3.3    12.5    +      -       -      +
    204B  GLU      3.3     4.4    -      -       -      -
    205B  GLU*     1.3    96.3    -      -       -      +
    207B  ILE*     1.3    68.3    +      -       +      +
    208B  LEU*     3.9    20.2    -      -       +      -
    300B  LYS*     3.4     4.1    -      -       -      +
    301B  ILE*     2.7    35.7    +      -       -      +
    303B  PHE*     3.8    15.5    -      -       +      -
    411B  LYS      5.5     0.4    -      -       -      +
    415B  GLY      3.7    22.9    -      -       -      +
    417B  PHE      5.4     1.8    -      -       -      +
    419B  PRO*     4.7     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 207 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205B  GLU      4.1     9.2    -      -       -      +
    206B  MET*     1.3    83.7    -      -       -      +
    208B  LEU*     1.3    69.2    +      -       -      +
    298B  PRO*     4.8     4.7    -      -       +      -
    299B  LYS      3.1     5.4    -      -       -      +
    300B  LYS*     3.0    41.5    -      -       +      +
    415B  GLY      4.1     0.2    -      -       -      +
    416B  LYS*     2.8    60.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 208 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206B  MET*     3.9    13.0    -      -       +      -
    207B  ILE*     1.3    72.5    -      -       -      +
    209B  THR*     1.3    64.2    +      -       -      +
    210B  ASP*     3.8    15.7    -      -       -      +
    297B  VAL      3.7     0.3    -      -       -      +
    298B  PRO*     4.2     1.1    -      -       -      -
    299B  LYS*     2.8    33.5    +      -       +      +
    301B  ILE*     3.5    31.4    -      -       +      -
    416B  LYS*     2.6    24.9    -      -       -      +
    417B  PHE      3.9     7.0    -      -       -      +
    418B  MET*     3.7    25.8    -      -       +      +
    419B  PRO*     3.6    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 209 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  TYR*     4.4     5.2    +      -       -      -
    208B  LEU*     1.3    78.4    -      -       -      +
    210B  ASP*     1.3    64.2    +      -       -      +
    245B  GLY      4.3     1.3    -      -       -      +
    247B  PHE*     4.3    24.2    -      -       +      -
    296B  LYS*     3.6    26.2    +      -       +      +
    297B  VAL      3.5     4.0    -      -       -      +
    298B  PRO*     3.8    30.7    -      -       +      -
    416B  LYS*     2.8    24.5    +      -       +      +
    417B  PHE*     4.3    17.8    -      -       -      -
    418B  MET*     5.1     7.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 210 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208B  LEU*     3.8    14.7    -      -       +      +
    209B  THR*     1.3    76.7    -      -       -      +
    211B  SER*     1.3    67.3    +      -       -      +
    296B  LYS*     3.6    15.4    -      -       -      +
    297B  VAL*     2.8    43.1    +      -       -      +
    299B  LYS*     3.7    28.1    -      -       -      +
    418B  MET*     5.7     4.0    -      -       +      -
----------------------------------------------------------
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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