Contacts of the strand formed by residues 224 - 228 (chain D) in PDB entry 1C2O


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 ARG 224 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195D  MET      5.6     0.6    +      -       -      -
    196D  SER*     3.5    29.9    -      -       -      +
    197D  VAL      3.2     4.4    +      -       -      -
    198D  THR*     2.9    23.9    +      -       -      +
    199D  LEU      3.1    19.8    +      -       -      -
    222D  PHE*     3.5    11.6    -      -       -      -
    223D  HIS*     1.3    93.4    -      -       -      +
    225D  ALA*     1.3    59.7    +      -       -      +
    324D  LEU*     5.0     0.4    -      -       -      -
    325D  GLN*     3.1    45.1    +      -       +      +
    483D  PHE*     3.1    25.4    +      -       +      -
    484D  ALA      2.6    30.7    +      -       -      -
    485D  ARG      3.5    14.5    +      -       -      -
    486D  THR      4.8     1.8    +      -       -      -
    487D  GLY*     3.4     8.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 225 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199D  LEU*     3.4     7.6    -      -       +      +
    209D  VAL*     3.7    21.8    -      -       +      -
    213D  ILE*     3.9    20.6    -      -       +      -
    222D  PHE*     4.4     8.3    -      -       +      -
    224D  ARG*     1.3    77.0    -      -       -      +
    226D  VAL*     1.3    64.0    +      -       -      +
    227D  LEU*     4.3     3.8    -      -       +      -
    324D  LEU*     4.5     2.2    -      -       +      -
    325D  GLN      3.4     9.8    +      -       -      +
    326D  VAL*     3.2     6.5    -      -       +      +
    327D  LEU      2.9    23.2    +      -       -      +
    483D  PHE*     3.4     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 226 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198D  THR*     4.3     6.7    -      -       +      -
    199D  LEU      2.9     6.2    +      -       -      +
    200D  PHE*     3.5    22.7    -      -       +      -
    201D  GLY      3.7     5.1    +      -       -      -
    209D  VAL*     3.6    19.4    -      -       -      +
    225D  ALA*     1.3    77.4    -      -       -      +
    227D  LEU*     1.3    71.8    +      -       -      +
    228D  GLN*     3.9    17.7    -      -       +      +
    327D  LEU*     3.3    20.6    -      -       +      +
    428D  TYR*     5.4     0.2    -      -       +      -
    480D  TRP*     3.2    39.3    -      -       +      +
    483D  PHE*     4.0    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 227 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201D  GLY      3.8     4.5    -      -       -      -
    206D  ALA*     3.8    23.8    -      -       +      +
    209D  VAL*     4.1    11.4    -      -       +      -
    210D  GLY*     3.9    16.4    -      -       -      -
    213D  ILE*     4.6     6.7    -      -       +      -
    225D  ALA*     4.3     3.4    -      -       +      -
    226D  VAL*     1.3    86.1    -      -       -      +
    228D  GLN*     1.3    62.5    +      -       -      +
    229D  SER      3.9     0.5    +      -       -      -
    230D  GLY      3.8    16.7    +      -       -      +
    231D  THR*     5.8     0.2    -      -       +      -
    232D  PRO*     4.3     3.4    -      -       +      -
    326D  VAL*     3.5    30.1    -      -       +      -
    327D  LEU      3.0     8.0    +      -       -      +
    328D  VAL*     3.6    12.3    -      -       +      +
    329D  GLY      3.4    21.0    +      -       -      +
    414D  LEU*     3.7    26.2    -      -       +      -
    418D  LEU*     5.9     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 228 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117D  TRP*     4.0    10.9    -      -       -      -
    200D  PHE*     3.6    19.4    -      -       -      -
    201D  GLY      2.9    17.7    +      -       -      +
    202D  GLU*     3.1    25.0    -      -       +      +
    203D  SER      3.1     1.0    +      -       -      -
    206D  ALA*     3.4     0.9    -      -       -      +
    226D  VAL*     3.9    13.4    -      -       +      +
    227D  LEU*     1.3    72.2    -      -       -      +
    229D  SER*     1.3    71.4    +      -       -      +
    230D  GLY      3.0     2.6    +      -       -      -
    428D  TYR*     3.4    18.2    +      -       -      +
    450D  GLU*     2.7    41.2    +      -       -      +
    451D  ILE*     5.0     3.2    -      -       -      +
    454D  ILE*     4.0    10.3    -      -       -      +
    480D  TRP*     3.5    24.2    +      -       +      -
----------------------------------------------------------
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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