Contacts of the strand formed by residues 173 - 179 (chain X) 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 173 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2X  ILE*     4.6     9.9    -      -       +      -
      4X  LEU*     5.5     0.2    -      -       +      -
     15X  ALA*     4.1     8.1    -      -       +      -
     16X  SER*     3.1    27.6    -      -       -      +
     17X  SER*     4.0     2.2    -      -       -      +
     18X  LYS*     4.0    11.3    -      -       -      +
    159X  VAL*     3.6    35.0    -      -       +      +
    170X  PHE*     4.1    12.1    -      -       +      -
    172X  GLY*     1.3    76.4    -      -       -      +
    174X  ILE*     1.3    62.2    +      -       -      +
    175X  VAL*     3.9    12.7    +      -       +      +
    190X  PHE*     3.8    32.7    -      -       +      +
    191X  GLN*     5.5     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 174 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14X  LEU      3.4     1.7    -      -       -      +
     15X  ALA*     3.2     4.5    -      -       -      -
     16X  SER*     2.8    37.0    +      -       -      +
     18X  LYS*     3.7    23.8    -      -       +      +
     30X  SER      4.4     5.8    -      -       -      +
     31X  ASP      3.6    24.9    -      -       -      +
     32X  ASP*     4.1    22.2    -      -       +      +
    173X  VAL*     1.3    73.2    -      -       -      +
    175X  VAL*     1.3    62.8    +      -       -      +
    176X  LYS*     4.0    30.7    -      -       +      -
    186X  GLN*     4.2    20.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 175 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13X  ILE*     3.3    28.9    -      -       +      -
     14X  LEU      3.2     4.0    -      -       -      +
     15X  ALA*     4.0     1.1    -      -       +      -
    152X  LEU*     4.0    16.6    -      -       +      -
    155X  LEU*     4.0    12.3    -      -       +      -
    173X  VAL*     3.9    15.2    +      -       +      +
    174X  ILE*     1.3    77.1    -      -       -      +
    176X  LYS*     1.3    71.2    +      -       -      +
    186X  GLN*     3.6     5.4    -      -       -      +
    187X  VAL*     3.1    41.2    +      -       +      +
    190X  PHE*     3.7    37.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 176 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12X  VAL      3.7     1.0    -      -       -      +
     13X  ILE*     3.4     4.0    -      -       -      -
     14X  LEU*     2.9    36.6    +      -       +      +
     32X  ASP*     2.9    30.4    +      -       -      -
     34X  THR*     3.1    22.9    -      -       +      +
     42X  LEU*     3.7    33.6    -      -       +      +
    174X  ILE*     4.0    10.3    -      -       +      -
    175X  VAL*     1.3    80.6    -      -       -      +
    177X  ILE*     1.3    64.9    +      -       -      +
    178X  VAL*     4.9     1.0    -      -       -      +
    184X  ILE*     4.6    10.0    -      -       +      +
    185X  ARG      3.3    10.8    -      -       -      +
    186X  GLN*     3.7    25.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 177 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11X  SER*     3.5    31.0    -      -       -      +
     12X  VAL      3.5     4.9    -      -       -      +
     13X  ILE*     4.5    12.6    -      -       +      -
    148X  THR*     3.7    19.1    -      -       +      -
    152X  LEU*     4.4     8.7    -      -       +      -
    176X  LYS*     1.3    76.4    -      -       -      +
    178X  VAL*     1.3    63.7    +      -       -      +
    179X  ASP*     4.0    12.3    -      -       -      +
    183X  GLY      3.4     1.2    -      -       -      +
    184X  ILE*     3.2     7.3    -      -       -      +
    185X  ARG*     2.9    67.0    +      -       +      +
    187X  VAL*     3.5    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 178 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11X  SER*     3.2     4.9    -      -       -      -
     12X  VAL*     2.9    45.1    +      -       +      +
     14X  LEU*     5.5     2.5    -      -       +      -
     40X  HIS*     3.3    33.9    -      -       -      +
     42X  LEU*     4.0    18.4    -      -       +      -
    102X  GLY*     3.8    17.5    -      -       -      +
    103X  GLY*     3.8     3.4    -      -       -      -
    104X  TYR*     3.6    17.3    -      -       +      +
    176X  LYS      4.9     1.3    -      -       -      +
    177X  ILE*     1.3    77.3    -      -       -      +
    179X  ASP*     1.3    61.4    +      -       -      +
    183X  GLY      3.2     7.6    -      -       -      +
    184X  ILE*     3.9    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 179 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10X  ASP*     3.5    16.4    -      -       +      +
     11X  SER*     3.8     6.6    -      -       -      -
     40X  HIS*     3.7     3.1    -      -       -      -
    104X  TYR*     3.6    22.8    -      -       -      +
    148X  THR*     5.3     2.0    +      -       -      +
    177X  ILE*     4.1     6.0    -      -       -      +
    178X  VAL*     1.3    74.0    -      -       -      +
    180X  LYS*     1.3    67.6    -      -       +      +
    181X  ASP*     2.9    35.3    +      -       -      +
    183X  GLY*     2.9    22.2    +      -       -      +
    185X  ARG*     2.8    31.6    +      -       -      -
----------------------------------------------------------
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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