Contacts of the strand formed by residues 226 - 230 (chain E) in PDB entry 1C9T


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 226 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182E  CYS*     3.4     3.8    -      -       -      -
    183E  ALA      3.0    34.4    +      -       -      -
    189E  ASP*     3.4    28.0    +      -       -      -
    215E  TRP      4.0     4.7    -      -       -      -
    216E  GLY*     5.0     1.1    -      -       -      -
    225E  PRO*     1.3    72.9    -      -       -      +
    227E  VAL*     1.3    57.9    +      -       -      -
    228E  TYR*     3.1    16.3    -      -       -      -
     34K  LYS*     4.2     6.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 227 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172E  TYR*     3.7    36.3    -      -       +      -
    176E  ILE*     3.9    11.4    -      -       +      -
    180E  MET*     3.8    24.9    -      -       +      -
    181E  PHE      3.6     6.5    -      -       -      +
    182E  CYS*     4.0     4.9    -      -       -      +
    214E  SER*     3.3    19.8    +      -       -      -
    215E  TRP*     2.8    59.8    +      -       +      +
    225E  PRO      4.0     0.2    -      -       -      +
    226E  GLY*     1.3    71.0    -      -       -      -
    228E  TYR*     1.3    71.2    +      -       -      +
     34K  LYS*     4.9     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 228 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138E  ILE*     3.2    23.9    -      -       +      +
    180E  MET*     3.3     6.5    -      -       -      +
    181E  PHE*     2.8    57.6    +      +       +      +
    183E  ALA*     3.7    25.0    +      -       +      -
    189E  ASP*     3.8     7.4    +      -       -      -
    190E  SER*     2.7    26.0    +      -       -      -
    199E  VAL*     3.2    29.8    -      -       +      -
    212E  ILE      3.3     8.5    -      -       -      +
    213E  VAL*     3.3    37.9    -      -       +      -
    214E  SER*     4.3     3.4    -      -       -      +
    226E  GLY*     3.1    27.8    -      -       -      -
    227E  VAL*     1.3    76.8    -      -       -      +
    229E  THR*     1.3    63.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 229 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101E  ASN      5.5     0.2    -      -       -      +
    102E  ASP*     2.9    49.3    +      -       -      +
    103E  ILE*     4.6     3.6    -      -       +      -
    179E  ASN      3.6     8.7    -      -       -      +
    180E  MET*     4.8     1.1    -      -       -      +
    181E  PHE*     4.2     0.9    -      -       -      -
    211E  GLY*     2.9    21.5    -      -       -      -
    212E  ILE*     2.9    26.9    +      -       +      +
    214E  SER*     3.9     3.5    -      -       -      -
    228E  TYR*     1.3    70.7    -      -       -      +
    230E  LYS*     1.3    55.2    +      -       -      +
    231E  VAL*     2.8    16.2    +      -       -      +
    234E  TYR*     3.7    28.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 230 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128E  CYS*     4.1    11.5    -      -       -      -
    129E  ALA      5.9     2.0    -      -       -      -
    178E  SER*     3.3    21.8    +      -       -      +
    179E  ASN*     3.0    24.9    +      -       -      +
    180E  MET      4.2    10.2    +      -       -      +
    181E  PHE*     4.0    20.2    -      -       +      -
    210E  GLN*     4.0     4.9    -      -       -      +
    228E  TYR      3.6     2.2    +      -       -      -
    229E  THR*     1.3    67.2    -      -       -      +
    231E  VAL*     1.3    66.4    +      -       -      +
    232E  CYS*     2.9    29.4    +      -       -      -
    233E  ASN*     3.0    21.6    +      -       -      +
    234E  TYR*     3.2    14.7    -      -       -      -
     12J  PRO*     4.4    15.7    +      -       -      +
----------------------------------------------------------
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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