Contacts of the strand formed by residues 140 - 148 (chain F) in PDB entry 1I3R


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 LEU 140 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129F  PRO*     3.2     5.5    -      -       -      +
    130F  THR*     3.0    49.1    +      -       -      +
    131F  LYS*     5.0    16.6    -      -       +      +
    138F  HIS      4.5     2.9    -      -       -      +
    139F  ASN*     1.3    78.5    -      -       -      +
    141F  LEU*     1.3    61.3    +      -       -      +
    142F  VAL*     3.9     0.4    -      -       +      -
    169F  VAL*     5.6     0.7    -      -       +      -
    186F  MET*     3.7    41.7    -      -       +      -
    187F  LEU      3.0    33.7    -      -       -      +
    188F  GLU*     3.4    25.4    -      -       +      +
    189F  THR      4.4     1.6    -      -       -      -
    191F  PRO*     5.8     1.6    -      -       -      -
    313G  NAG      5.7     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 141 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127F  VAL*     4.2     3.4    -      -       +      -
    128F  TYR      3.8    21.1    -      -       -      +
    129F  PRO*     4.0     8.5    -      -       +      -
    140F  LEU*     1.3    72.6    -      -       -      +
    142F  VAL*     1.3    59.3    +      -       -      +
    157F  TRP*     3.4    28.5    -      -       +      -
    186F  MET*     3.3     3.0    -      -       -      -
    187F  LEU*     2.8    46.5    +      -       +      +
    189F  THR*     4.7     6.8    +      -       -      +
    191F  PRO*     5.0     5.8    -      -       +      +
    197F  TYR*     3.3    53.6    -      -       +      -
    214F  TRP*     3.8    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 142 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126F  THR      3.7     0.9    -      -       -      +
    127F  VAL*     3.3     6.9    -      -       -      +
    128F  TYR*     2.6    78.4    +      -       +      +
    130F  THR*     3.7    22.0    -      -       +      +
    140F  LEU*     4.6     1.6    -      -       +      +
    141F  LEU*     1.3    73.0    -      -       -      +
    143F  CYS*     1.3    63.6    +      -       -      +
    144F  SER      4.1     1.1    -      -       -      +
    157F  TRP*     3.8     2.5    -      -       -      -
    184F  LEU*     3.8    21.5    -      -       +      -
    186F  MET*     3.4    40.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 143 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125F  VAL*     3.8    20.0    -      -       -      -
    126F  THR      3.7     3.4    -      -       -      -
    127F  VAL*     4.5     1.1    -      -       -      -
    142F  VAL*     1.3    75.3    -      -       -      +
    144F  SER*     1.3    57.7    +      -       -      +
    145F  VAL*     3.7    10.4    +      -       -      +
    155F  VAL*     4.0     7.6    -      -       +      -
    157F  TRP*     3.3    17.2    -      -       +      +
    183F  THR      4.0     0.3    -      -       -      +
    184F  LEU*     3.8     0.5    -      -       -      -
    185F  VAL*     3.1    36.8    +      -       -      +
    199F  CYS*     2.0    50.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 144 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96E  PRO*     3.2    29.8    -      -       -      +
    124F  THR      3.3     2.4    -      -       -      +
    125F  VAL*     3.3     5.2    -      -       -      +
    126F  THR*     2.8    44.9    +      -       -      -
    128F  TYR*     4.0    18.2    -      -       -      -
    142F  VAL*     3.7     1.8    +      -       -      +
    143F  CYS*     1.3    70.6    -      -       -      +
    145F  VAL*     1.3    63.6    +      -       -      +
    146F  SER*     4.6     1.4    +      -       -      -
    183F  THR      4.4     0.3    +      -       -      -
    184F  LEU*     3.6    24.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 145 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123F  PRO*     3.5    18.4    -      -       +      -
    124F  THR      3.7     2.7    -      -       -      -
    125F  VAL*     4.5     4.7    -      -       +      -
    143F  CYS*     4.0    13.5    -      -       -      +
    144F  SER*     1.3    76.7    +      -       -      +
    146F  SER*     1.3    59.6    +      -       -      +
    148F  PHE*     3.0    12.8    -      -       +      -
    153F  ILE*     3.4    29.8    -      -       +      -
    155F  VAL*     4.0    14.1    -      -       +      -
    183F  THR*     3.0    43.5    +      -       +      -
    185F  VAL*     5.4     0.2    -      -       +      -
    201F  VAL*     3.8    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 146 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94E  ARG      4.8     0.9    -      -       -      -
     95E  SER*     4.1    11.6    -      -       -      -
     96E  PRO*     3.4    32.5    -      -       -      +
    123F  PRO*     3.7     0.5    -      -       -      +
    124F  THR*     3.0    41.0    +      -       -      +
    144F  SER*     4.0     1.8    -      -       -      -
    145F  VAL*     1.3    76.5    -      -       -      +
    147F  ASP*     1.3    71.0    +      -       -      +
    148F  PHE*     3.6     2.7    -      -       -      -
    181F  PHE      3.8     3.1    -      -       -      -
    182F  GLN*     4.1    14.4    -      -       -      +
    183F  THR      5.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 147 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94E  ARG*     2.9    43.6    +      -       -      +
     95E  SER*     5.0     5.9    -      -       -      -
    121F  VAL*     3.3    25.2    -      -       -      +
    122F  GLU      3.4    10.2    -      -       -      +
    124F  THR*     4.7     7.9    -      -       -      +
    146F  SER*     1.3    80.0    -      -       -      +
    148F  PHE*     1.3    56.9    +      -       -      +
    176F  ASN*     5.2     0.9    +      -       -      +
    180F  THR*     4.1    18.2    +      -       -      +
    181F  PHE      2.9    14.8    +      -       -      -
    182F  GLN*     4.7     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 148 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121F  VAL*     3.0    10.8    -      -       -      +
    123F  PRO*     3.4    27.1    -      -       +      -
    145F  VAL*     3.0    47.3    -      -       +      -
    146F  SER      3.9     2.7    -      -       -      -
    147F  ASP*     1.3    73.6    -      -       -      +
    149F  TYR*     1.3    63.6    +      -       -      +
    150F  PRO      3.6    11.4    -      -       -      -
    151F  GLY      3.7    19.3    -      -       -      -
    153F  ILE*     3.7    16.2    -      -       +      -
    173F  LEU*     3.9     7.2    -      -       +      -
    180F  THR*     3.8     1.6    -      -       -      -
    181F  PHE*     3.1    55.3    +      -       +      +
    182F  GLN*     4.0     1.3    -      -       -      -
    183F  THR*     3.8    16.2    -      -       +      -
    203F  HIS*     3.6    11.4    -      +       -      +
----------------------------------------------------------
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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