Contacts of the strand formed by residues 223 - 227 (chain B) in PDB entry 3COG


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 GLY 223 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86B  ALA*     3.4     2.3    -      -       -      -
     87B  PHE*     2.8    41.0    +      -       -      +
     89B  SER      3.3    21.8    -      -       -      -
     90B  GLY*     4.0     0.4    -      -       -      -
     93B  ALA*     4.4     1.6    -      -       -      -
    208B  TYR      3.3    12.1    -      -       -      -
    222B  MET*     1.3    73.8    -      -       -      +
    224B  LEU*     1.3    71.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 224 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71B  LEU*     4.4     6.1    -      -       +      -
     72B  GLU*     5.6     0.7    -      -       +      -
     75B  VAL*     3.8    29.8    -      -       +      -
     84B  CYS*     4.2    16.6    -      -       -      -
     85B  LEU      3.4     2.2    -      -       -      -
     86B  ALA*     3.7    22.9    -      -       +      -
     93B  ALA*     4.5     0.6    -      -       -      +
    207B  MET*     3.4     3.1    -      -       -      +
    208B  TYR*     2.8    45.8    +      -       +      +
    210B  ALA*     3.7    25.4    -      -       +      -
    214B  MET*     4.3    16.6    -      -       +      -
    222B  MET*     4.1     9.9    -      -       +      -
    223B  GLY*     1.3    82.3    -      -       -      +
    225B  VAL*     1.3    66.9    +      -       -      +
    226B  SER      4.3     0.4    -      -       -      -
    255B  CYS*     4.4     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 225 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  CYS*     3.2     3.3    -      -       -      -
     85B  LEU*     2.8    45.6    +      -       +      +
     87B  PHE*     3.6    24.9    -      -       +      -
     93B  ALA*     3.8    16.8    -      -       +      -
     97B  ILE*     3.9    20.4    -      -       +      -
    205B  ILE*     3.6    23.8    -      -       +      -
    206B  SER      3.7     3.8    -      -       -      -
    207B  MET*     4.5     2.5    -      -       +      +
    224B  LEU*     1.3    81.0    -      -       -      +
    226B  SER*     1.3    62.4    +      -       -      +
    236B  LEU*     4.0    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 226 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75B  VAL*     3.8     4.7    +      -       -      +
     76B  ALA*     4.2     0.5    -      -       -      -
     79B  ASP*     2.6    44.4    +      -       -      +
     81B  ALA*     3.9     4.0    -      -       -      -
     83B  TYR      3.2     8.3    -      -       -      -
     84B  CYS*     3.6    20.3    -      -       -      +
    199B  LEU*     3.8     6.1    -      -       -      +
    205B  ILE*     3.4     8.1    -      -       -      +
    206B  SER*     2.9    32.8    +      -       -      -
    208B  TYR*     4.7     0.9    -      -       -      -
    224B  LEU      4.3     0.2    -      -       -      -
    225B  VAL*     1.3    70.9    +      -       -      +
    227B  VAL*     1.3    61.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 227 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81B  ALA*     3.8     2.7    -      -       -      +
     82B  LYS      3.5     2.9    +      -       -      -
     83B  TYR*     2.9    52.5    +      -       +      +
     85B  LEU*     4.2    12.1    -      -       +      -
    199B  LEU*     4.3     1.8    -      -       -      -
    204B  ASP      3.6    16.6    -      -       -      +
    205B  ILE*     4.6     2.5    -      -       +      -
    225B  VAL*     5.1     0.2    -      -       +      -
    226B  SER*     1.3    75.6    -      -       -      +
    228B  ASN*     1.3    65.8    +      -       -      +
    229B  CYS      3.8    11.0    -      -       -      +
    232B  LEU*     3.7    30.5    -      -       +      -
    233B  HIS*     3.8    23.1    -      -       +      +
    236B  LEU*     4.3     8.3    -      -       +      -
----------------------------------------------------------
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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