Contacts of the strand formed by residues 147 - 153 (chain C) in PDB entry 3I5D


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 VAL 147 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  ILE*     3.6     4.0    -      -       +      +
     75A  ALA      6.4     0.2    -      -       -      -
     76A  LEU*     4.8    12.3    -      -       +      -
     86A  ILE*     3.4    10.2    -      -       +      +
    138C  GLY*     5.5     2.7    -      -       -      -
    141C  ASP*     3.0    14.6    -      -       +      -
    146C  GLY*     1.3    71.7    -      -       -      -
    148C  ARG*     1.3    63.0    +      -       -      +
    164C  VAL*     3.7     1.1    -      -       -      -
    165C  LEU*     2.6    62.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 148 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    401A  NAG      6.0     1.9    -      -       -      +
    135C  CYS*     5.8     0.2    -      -       +      -
    136C  LYS      3.8     8.3    -      -       -      +
    137C  ARG*     3.3     1.6    -      -       -      +
    138C  GLY*     2.8    27.5    +      -       -      -
    140C  ASN*     3.6    20.4    -      -       +      -
    141C  ASP*     2.9    28.6    -      -       -      +
    146C  GLY      3.7     0.4    +      -       -      -
    147C  VAL*     1.3    71.4    -      -       -      +
    149C  THR*     1.3    63.9    +      -       -      +
    162C  CYS*     4.9     5.6    -      -       +      -
    163C  GLU      3.3    13.2    -      -       -      +
    164C  VAL*     3.6     8.1    -      -       +      -
    165C  LEU*     5.7     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 149 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    401A  NAG      6.2     4.5    -      -       -      -
    118C  LYS*     4.9     3.6    -      -       +      -
    135C  CYS*     4.1     5.4    -      -       -      +
    136C  LYS      4.9     0.2    -      -       -      -
    137C  ARG*     4.2     4.5    -      -       -      -
    147C  VAL      3.5     2.4    +      -       -      -
    148C  ARG*     1.3    76.6    -      -       -      +
    150C  GLY*     1.3    66.6    +      -       -      +
    151C  ARG*     2.8    20.2    +      -       -      +
    163C  GLU*     2.9    52.0    +      -       +      +
    164C  VAL*     4.4     2.7    -      -       -      +
    165C  LEU*     4.8    14.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 150 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132C  HIS*     3.6    12.1    -      -       -      +
    135C  CYS*     2.9    38.5    -      -       -      +
    137C  ARG*     3.6    22.6    -      -       -      +
    149C  THR*     1.3    74.5    +      -       -      +
    151C  ARG*     1.3    56.8    +      -       -      +
    152C  CYS      3.6     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 151 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132C  HIS*     4.6    10.8    -      -       +      -
    135C  CYS*     3.3     3.6    -      -       -      -
    149C  THR*     2.8    18.5    +      -       -      +
    150C  GLY*     1.3    77.7    -      -       -      +
    152C  CYS*     1.3    60.2    +      -       -      +
    153C  VAL*     4.2     3.6    -      -       +      -
    163C  GLU*     3.1    43.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 152 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129C  CYS*     2.0    46.0    -      -       -      -
    130C  THR      4.6     1.3    -      -       -      -
    131C  SER*     3.6    35.9    -      -       -      +
    132C  HIS*     3.8    20.2    +      -       +      +
    135C  CYS*     3.7     8.1    -      -       -      -
    150C  GLY      3.6     1.0    +      -       -      -
    151C  ARG*     1.3    73.7    -      -       -      +
    153C  VAL*     1.3    71.2    +      -       -      +
    160C  LYS*     4.5     6.3    -      -       -      -
    161C  THR      4.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 153 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119C  CYS*     4.6     0.7    -      -       -      -
    120C  ALA*     4.0    21.3    -      -       +      +
    151C  ARG*     5.1     2.9    -      -       +      -
    152C  CYS*     1.3    81.4    -      -       -      +
    154C  SER*     1.3    57.1    +      -       -      +
    160C  LYS*     3.5     6.1    -      -       -      +
    161C  THR      2.5    47.9    +      -       -      +
    163C  GLU*     3.5    42.8    -      -       +      +
----------------------------------------------------------
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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