Contacts of the strand formed by residues 229 - 235 (chain C) in PDB entry 5IYB


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 PHE 229 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  ILE*     3.2     5.9    -      -       -      -
     23C  ILE*     2.9    43.3    +      -       +      +
     26C  THR*     3.4    39.9    -      -       +      -
     27C  ASP      3.7     2.9    -      -       -      -
     28C  LEU*     3.4    48.7    -      -       +      -
     31C  ALA*     3.7     7.4    -      -       +      -
    184C  PHE*     3.7    16.6    -      +       +      -
    185C  GLU      3.6     2.7    -      -       -      -
    186C  TYR*     3.4    24.2    -      +       +      -
    226C  PRO*     4.1    15.0    -      -       +      -
    227C  GLU*     4.6     3.1    -      -       -      -
    228C  ARG*     1.3    78.8    -      -       -      +
    230C  TYR*     1.3    61.5    +      -       -      +
    231C  TYR*     3.8    20.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 230 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21C  PHE      3.6     3.6    -      -       -      +
     22C  ILE*     3.7    30.1    -      -       +      +
    183C  ALA      4.4     0.5    -      -       -      -
    184C  PHE*     3.5     5.0    -      -       -      -
    185C  GLU*     2.8    50.5    +      -       +      +
    187C  ASP      4.6     0.2    -      -       -      -
    188C  PRO*     3.7    35.6    -      -       +      +
    208C  TYR*     3.3    68.8    +      +       +      +
    228C  ARG*     3.3    42.5    +      -       +      -
    229C  PHE*     1.3    72.5    -      -       -      +
    231C  TYR*     1.3    61.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 231 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20C  LYS*     3.6     5.4    -      -       -      +
     21C  PHE*     2.7    67.5    +      +       +      +
     23C  ILE*     3.8    26.2    -      -       +      +
     31C  ALA*     3.0    38.0    +      -       -      +
     34C  ILE*     4.3     6.0    -      -       +      +
     35C  ARG*     4.4     5.2    -      -       +      -
     38C  PHE*     3.8    26.9    -      +       -      -
    182C  VAL*     4.8     4.9    -      -       +      -
    183C  ALA*     3.6     8.1    -      -       -      -
    184C  PHE*     3.8    18.2    -      +       -      -
    208C  TYR*     4.4     3.4    +      -       -      -
    229C  PHE*     3.8    25.8    -      -       +      -
    230C  TYR*     1.3    79.4    -      -       -      +
    232C  ASN*     1.3    64.3    +      -       -      +
    233C  VAL*     4.9     1.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 232 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18C  ASN*     3.2    28.4    +      -       -      +
     19C  VAL      3.3    15.6    -      -       -      +
     20C  LYS*     3.6    33.6    -      -       +      +
    182C  VAL*     3.9     0.5    -      -       -      -
    183C  ALA*     3.1    42.8    +      -       +      +
    207C  GLU*     5.7     1.4    +      -       -      +
    208C  TYR*     5.1     2.7    -      -       -      +
    231C  TYR*     1.3    77.7    -      -       -      +
    233C  VAL*     1.3    61.7    +      -       -      +
    234C  GLU*     3.7     4.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 233 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17C  GLU      3.9     0.5    -      -       -      +
     18C  ASN*     3.6     1.7    -      -       -      -
     19C  VAL*     2.9    51.3    +      -       +      +
     21C  PHE*     4.5     7.9    -      -       +      -
     38C  PHE*     4.1    23.3    -      -       +      -
    179C  THR*     3.8    25.4    -      -       +      -
    181C  GLY      4.2     3.8    -      -       -      +
    182C  VAL*     3.9    20.9    -      -       +      +
    231C  TYR*     4.2     2.4    -      -       +      -
    232C  ASN*     1.3    74.5    -      -       -      +
    234C  GLU*     1.3    66.9    +      -       -      +
    235C  SER      4.2     1.3    +      -       -      +
    241C  PRO*     4.7     3.5    -      -       +      +
    244C  ILE*     5.0    11.9    -      -       +      -
    245C  VAL*     4.4    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 234 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    959B  GLU*     4.7     8.7    -      -       -      +
     17C  GLU*     3.3    12.9    -      -       +      +
     18C  ASN*     3.9    19.1    +      -       -      +
    179C  THR*     3.7     3.5    -      -       -      -
    180C  ALA*     3.1    41.2    +      -       +      +
    181C  GLY*     3.3    24.5    +      -       -      +
    232C  ASN      3.7     3.3    +      -       -      +
    233C  VAL*     1.3    79.7    -      -       -      +
    235C  SER*     1.3    63.1    +      -       -      +
     10J  CYS*     6.0     0.7    -      -       -      +
     12J  LYS*     3.2    34.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 235 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16C  ASP      3.9     5.0    +      -       -      -
     17C  GLU*     2.9    39.5    +      -       -      +
    178C  PRO      3.9     6.7    -      -       -      -
    180C  ALA*     3.6     8.1    -      -       -      +
    233C  VAL*     4.2     0.8    +      -       -      +
    234C  GLU*     1.3    79.3    -      -       -      +
    236C  CYS*     1.3    60.6    +      -       -      +
    237C  GLY*     3.2    12.2    +      -       -      -
    239C  LEU      3.2    27.2    +      -       -      -
    241C  PRO*     4.1    10.0    -      -       -      +
    244C  ILE*     4.1     7.6    -      -       -      -
     12J  LYS*     5.9     0.2    +      -       -      -
----------------------------------------------------------
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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