Contacts of the strand formed by residues 134 - 142 (chain P) in PDB entry 3SDI


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 134 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31P  ILE*     3.7     6.5    -      -       -      +
     78P  VAL*     4.6     2.0    -      -       +      -
     79P  ALA      3.5     4.9    -      -       -      +
     80P  GLY*     4.4     2.5    -      -       -      -
     81P  LEU      3.3    26.0    -      -       -      +
     84P  ASP*     3.9     6.7    -      -       +      -
     85P  ALA*     3.7    19.5    -      -       +      +
     88P  LEU*     4.6     2.9    -      -       +      -
    120P  LYS*     3.7    10.2    +      -       -      +
    132P  PHE*     3.0    12.7    +      -       +      +
    133P  GLY*     1.3    81.8    -      -       -      +
    135P  SER*     1.3    67.6    +      -       -      +
    136P  PHE*     3.5    43.3    -      -       +      -
    153P  PRO*     3.3    21.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 135 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28P  LEU*     4.7     2.8    -      -       -      +
     31P  ILE*     3.6    25.3    -      -       -      +
     77P  ALA      3.7     0.3    -      -       -      +
     78P  VAL*     3.7     3.3    -      -       -      -
     79P  ALA*     2.7    39.5    +      -       -      +
    134P  VAL*     1.3    73.3    -      -       -      +
    136P  PHE*     1.3    62.5    +      -       -      +
    151P  SER      3.1     8.3    -      -       -      -
    152P  ASN*     3.4    24.3    -      -       -      +
    165P  VAL*     4.4    21.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 136 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76P  VAL*     4.0    17.5    -      -       +      -
     77P  ALA      3.3     4.3    -      -       -      -
     78P  VAL*     3.4    33.4    -      -       +      -
     85P  ALA*     4.2    10.3    -      -       +      -
     88P  LEU*     4.0    30.1    -      -       +      -
     89P  ILE*     4.4     7.9    -      -       +      -
    116P  LEU*     4.2     8.5    -      -       +      -
    120P  LYS*     3.4    20.0    -      -       -      -
    134P  VAL*     3.5    22.7    -      -       +      -
    135P  SER*     1.3    75.5    -      -       -      +
    137P  ILE*     1.3    63.1    +      -       -      +
    138P  TYR*     3.3    39.9    -      +       +      -
    150P  THR*     3.2    10.1    +      -       -      -
    151P  SER*     2.8    31.1    +      -       -      +
    165P  VAL*     4.8     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 137 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37P  ALA*     3.4    38.6    -      -       +      +
     38P  ILE      3.9     1.3    -      -       -      +
     39P  GLY*     3.8    16.2    -      -       -      +
     48P  LEU*     4.0    11.9    -      -       +      +
     76P  VAL*     3.0     6.6    -      -       -      +
     77P  ALA*     2.8    43.0    +      -       +      +
    136P  PHE*     1.3    76.5    -      -       -      +
    138P  TYR*     1.3    62.4    +      -       -      +
    139P  ALA      4.0     0.5    +      -       -      -
    148P  LEU*     3.8    25.4    -      -       +      -
    149P  TYR      3.2     9.6    -      -       -      +
    150P  THR*     4.2     4.0    -      -       -      +
    163P  ILE*     4.2    13.5    -      -       +      +
    164P  SER*     4.4     0.4    -      -       -      -
    165P  VAL*     3.6    28.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 138 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70P  LEU*     4.5     2.2    -      -       +      -
     74P  ILE*     5.0     4.0    -      -       +      -
     75P  ALA      3.6     3.8    -      -       -      +
     76P  VAL*     3.1    29.4    -      -       +      -
    109P  VAL*     5.0     4.0    -      -       +      -
    112P  LEU*     4.3    11.2    -      -       +      -
    113P  VAL*     3.5    36.7    +      -       +      -
    116P  LEU*     3.3    40.3    -      -       +      +
    120P  LYS*     4.4     0.2    +      -       -      -
    136P  PHE*     3.3    17.8    -      +       +      -
    137P  ILE*     1.3    72.6    -      -       -      +
    139P  ALA*     1.3    60.8    +      -       -      +
    140P  GLY      4.1     0.2    -      -       -      -
    147P  GLN      3.5     1.4    -      -       -      +
    148P  LEU*     3.2    11.4    -      -       -      +
    149P  TYR*     2.6    60.8    +      -       +      -
    150P  THR      4.2     0.2    -      -       -      -
    151P  SER*     3.0    37.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 139 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46P  ILE*     3.7    26.7    -      -       +      -
     48P  LEU*     3.9    27.8    -      -       +      +
     74P  ILE*     3.3     3.8    -      -       -      +
     75P  ALA      2.8    38.0    +      -       -      +
    137P  ILE      4.0     1.2    +      -       -      -
    138P  TYR*     1.3    72.8    -      -       -      +
    140P  GLY*     1.3    58.6    +      -       -      +
    147P  GLN      3.7     4.5    -      -       -      -
    148P  LEU*     4.3     0.9    -      -       +      -
    215P  ILE*     3.2    19.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 140 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46P  ILE*     3.5     6.7    -      -       -      +
     73P  LYS      3.1    12.1    -      -       -      -
     74P  ILE*     4.2     3.4    -      -       -      -
    109P  VAL*     3.8    20.9    -      -       -      +
    138P  TYR      4.1     0.4    -      -       -      -
    139P  ALA*     1.3    75.6    -      -       -      +
    141P  TYR*     1.3    60.8    +      -       -      -
    145P  GLY      3.7     0.2    -      -       -      +
    146P  TYR*     3.5     3.8    -      -       -      -
    147P  GLN*     2.9    34.7    +      -       -      -
    215P  ILE*     4.2     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 141 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73P  LYS*     3.0    39.8    +      -       +      +
     74P  ILE*     5.1     0.5    -      -       -      +
    107P  ILE      5.5     1.0    -      -       -      +
    109P  VAL*     3.8     6.4    -      -       -      +
    140P  GLY*     1.3    75.4    -      -       -      -
    142P  ASP*     1.3    80.6    +      -       -      +
    143P  ASP*     4.3     7.4    -      -       +      -
    145P  GLY*     3.5    28.6    -      -       -      -
    146P  TYR*     3.8    33.2    -      +       +      -
    215P  ILE*     4.6     1.6    -      -       +      -
    216P  LYS*     3.4    36.3    +      -       -      -
    219P  VAL*     3.5    38.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 142 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73P  LYS*     5.3     3.6    -      -       +      -
    106P  ASP      6.0     0.4    -      -       -      +
    107P  ILE      4.9     2.5    -      -       -      +
    108P  PRO*     3.6    20.1    -      -       +      +
    109P  VAL*     3.2    23.4    +      -       +      +
    110P  GLU      4.7     0.3    +      -       -      -
    141P  TYR*     1.3    89.3    -      -       -      +
    143P  ASP*     1.3    61.7    +      -       -      +
    144P  ARG*     2.7    37.2    +      -       -      +
    145P  GLY*     2.9    32.0    +      -       -      -
    147P  GLN*     3.1    19.9    +      -       -      +
----------------------------------------------------------
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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