Contacts of the strand formed by residues 221 - 225 (chain O) in PDB entry 2V10


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 CYS 221 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204O  GLN*     3.4    14.1    +      -       -      +
    205O  MET*     2.8    29.5    +      -       -      -
    217O  CYS*     2.0    47.1    -      -       +      -
    220O  GLY*     1.3    75.5    -      -       -      +
    222O  LEU*     1.3    72.9    +      -       -      +
    313O  TRP*     3.7    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 222 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196O  ILE*     3.0    37.9    -      -       +      -
    197O  LYS*     6.2     0.2    -      -       +      -
    202O  GLN*     3.0    28.0    -      -       +      +
    203O  ILE      3.6     3.4    -      -       -      +
    204O  GLN*     4.8     2.5    -      -       -      +
    205O  MET*     5.0     1.8    -      -       -      -
    221O  CYS*     1.3    89.2    -      -       -      +
    223O  ALA*     1.3    63.5    +      -       -      +
    308O  PRO      5.2     3.4    -      -       -      +
    309O  THR      4.5     3.1    -      -       -      +
    311O  PRO*     4.0    18.1    +      -       +      +
    312O  THR*     3.4    12.1    -      -       -      +
    313O  TRP*     2.9    30.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 223 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202O  GLN*     3.1     2.9    -      -       -      -
    203O  ILE*     2.7    49.0    +      -       +      +
    205O  MET*     4.0    24.9    -      -       +      -
    222O  LEU*     1.3    79.0    -      -       -      +
    224O  LEU*     1.3    60.4    +      -       -      +
    312O  THR*     3.7     1.1    -      -       -      -
    313O  TRP*     3.0     8.1    -      -       +      +
    315O  LEU*     4.0    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 224 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39O  THR      4.8     7.9    -      -       -      +
     40O  GLY*     5.0     4.7    -      -       -      -
    135O  GLN*     6.0     0.7    -      -       -      +
    200O  VAL*     4.5    16.4    -      -       +      -
    201O  TRP*     3.1    20.2    -      -       -      +
    202O  GLN*     3.9     9.9    -      -       +      +
    223O  ALA*     1.3    76.1    -      -       -      +
    225O  VAL*     1.3    74.6    +      -       -      +
    226O  ASP*     3.8     8.5    -      -       +      +
    305O  ILE*     5.2     0.7    -      -       +      -
    309O  THR*     5.4     6.3    -      -       +      +
    312O  THR*     3.3    18.8    +      -       +      +
    313O  TRP      2.5    13.9    +      -       -      +
    314O  ALA*     3.8    16.2    -      -       +      -
    315O  LEU*     2.7    31.4    +      -       -      +
   1341O  C61      3.8    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 225 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39O  THR*     2.6    26.5    +      -       -      -
    201O  TRP      2.8    18.7    +      -       -      +
    203O  ILE*     4.5    12.6    -      -       +      -
    224O  LEU*     1.3    74.8    -      -       -      +
    226O  ASP*     1.3    50.0    +      -       -      +
    227O  THR      3.9     0.2    +      -       -      -
    315O  LEU*     3.7    25.6    -      -       +      +
    319O  PHE*     6.2     0.4    -      -       +      -
    320O  ILE*     4.9     8.5    -      -       +      -
    325O  THR*     4.4    11.0    -      -       +      -
    327O  PHE*     3.6    25.7    -      -       +      -
    334O  ILE*     3.6    25.4    -      -       +      -
    336O  PHE*     4.0    19.5    -      -       +      -
----------------------------------------------------------
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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