Contacts of the strand formed by residues 221 - 226 (chain G) in PDB entry 5U0A


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 221 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21F  ASP*     4.3     2.0    -      -       -      +
    203G  PHE*     3.3    32.3    -      -       +      -
    204G  PHE      3.7     6.1    -      -       -      -
    205G  THR*     4.3     7.4    -      -       +      -
    220G  HIS*     1.3    86.9    +      -       -      +
    222G  ASN*     1.3    77.9    +      -       -      +
     27K    C      3.7    23.6    -      -       +      +
     36M    G      3.3    42.2    -      -       +      +
     37M    C      3.4    61.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 222 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203G  PHE*     3.4    15.1    -      -       -      -
    204G  PHE*     2.8    51.1    +      -       +      +
    220G  HIS*     2.5    28.2    +      -       -      -
    221G  MET*     1.3    89.2    +      -       -      +
    223G  ALA*     1.3    63.4    +      -       -      +
     32J  ARG*     3.0    27.4    -      -       -      +
     33J  ARG*     3.8    19.4    -      -       -      +
     37M    C      4.9     0.4    +      -       -      -
     38M    A      3.2    20.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 223 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201G  VAL*     3.8    24.7    -      -       +      -
    202G  ASP      3.3     9.0    -      -       -      +
    203G  PHE*     4.3     9.4    -      -       +      -
    204G  PHE*     3.9     0.9    -      -       -      -
    222G  ASN*     1.3    81.9    -      -       -      +
    224G  GLY*     1.3    60.1    +      -       -      +
    225G  GLN*     3.5    12.2    -      -       -      +
     33J  ARG*     4.0    28.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 224 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202G  ASP*     2.9    36.9    +      -       -      +
    204G  PHE*     3.2    18.7    -      -       -      -
    223G  ALA*     1.3    73.4    -      -       -      +
    225G  GLN*     1.3    63.4    +      -       -      -
    226G  PHE*     4.2    12.8    -      -       -      -
    271G  LYS*     6.5     0.2    -      -       -      -
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Residues in contact with GLN 225 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16G  ASN*     2.5    30.1    +      -       -      -
     22G  LEU*     3.8    10.7    +      -       -      +
     23G  GLY*     3.4     7.6    +      -       -      +
     24G  SER*     3.3    41.0    -      -       -      +
     25G  PRO*     3.5     3.7    -      -       -      +
    199G  VAL*     3.4    21.5    -      -       +      -
    200G  GLU      3.4     7.6    -      -       -      +
    201G  VAL*     4.2     9.7    -      -       -      +
    223G  ALA      3.5    15.0    -      -       -      +
    224G  GLY*     1.3    71.0    -      -       -      -
    226G  PHE*     1.3    56.8    +      -       -      +
     43J  ARG*     3.6    28.1    +      -       -      +
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Residues in contact with PHE 226 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41F  GLN*     5.7     1.3    -      -       -      -
    190F  HIS*     3.8    18.4    -      +       -      -
     14G  TYR*     3.3    42.2    -      +       +      -
     15G  SER      4.8     0.4    -      -       -      -
     16G  ASN*     3.1    27.1    -      -       +      +
     25G  PRO*     4.6     2.9    -      -       -      -
    199G  VAL*     4.0     1.4    -      -       -      +
    200G  GLU*     2.9    35.9    +      -       -      +
    202G  ASP*     4.4    16.6    -      -       +      -
    204G  PHE*     6.2     2.2    -      +       -      -
    224G  GLY*     4.3    15.9    -      -       -      -
    225G  GLN*     1.3    82.1    -      -       -      +
    227G  SER*     1.3    64.3    +      -       -      +
    271G  LYS*     3.4    37.7    -      -       +      -
    274G  ALA*     5.3     4.0    -      -       +      -
    275G  THR*     3.9    10.3    -      -       +      -
----------------------------------------------------------
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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