Contacts of the strand formed by residues 11 - 17 (chain W) 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 CYS 11 (chain W).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8W  GLY*     3.0    41.5    +      -       -      +
      9W  LYS      3.0    14.7    +      -       -      +
     10W  ASP*     1.3    79.3    -      -       -      +
     12W  VAL*     1.3    71.6    +      -       -      +
    104W  ILE*     3.8     4.8    -      -       -      +
    108W  PRO*     3.7     4.0    -      -       -      +
    146W  LEU      3.8     6.5    -      -       -      -
    148W  PRO*     3.9    26.7    -      -       +      -
    151W  LEU*     3.6    17.3    -      -       +      -
    177W  ILE*     5.2     1.3    -      -       +      -
    178W  ILE      3.2    15.5    -      -       -      +
    179W  LYS*     4.2     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 12 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6W  MET      3.4     9.2    -      -       -      +
      7W  THR*     4.2    10.1    -      -       +      -
     11W  CYS*     1.3    78.7    -      -       -      +
     13W  ALA*     1.3    61.1    +      -       -      +
    102W  ALA*     4.3     4.3    -      -       +      -
    103W  GLY*     3.7    26.9    -      -       -      +
    104W  ILE*     4.4     2.0    -      -       +      +
    108W  PRO*     3.4    24.2    -      -       +      -
    109W  PHE      3.8    16.6    -      -       -      +
    110W  ILE*     4.5     6.1    -      -       +      -
    151W  LEU*     4.0     4.9    -      -       -      +
    177W  ILE*     3.9     0.9    -      -       -      +
    178W  ILE*     2.8    60.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 13 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5W  ALA*     3.1     5.7    -      -       -      +
      6W  MET      2.8    32.3    +      -       -      +
     12W  VAL*     1.3    77.1    -      -       -      +
     14W  ILE*     1.3    61.4    -      -       -      +
    102W  ALA*     4.7     2.1    -      -       -      +
    151W  LEU*     3.5    22.2    -      -       +      -
    155W  ILE*     3.6    22.2    -      -       +      -
    175W  VAL*     5.0     0.4    -      -       +      -
    176W  TYR      3.2    11.0    -      -       -      +
    177W  ILE*     3.8    14.8    -      -       +      -
    178W  ILE*     5.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 14 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3W  VAL*     4.0     8.3    -      -       +      -
      4W  VAL      3.4    12.3    -      -       -      +
      5W  ALA*     3.9     4.0    -      -       +      -
     13W  ALA*     1.3    74.3    -      -       -      +
     15W  ALA*     1.3    63.4    +      -       -      +
     34W  ILE*     3.5    23.0    -      -       +      +
     42W  PHE*     4.2    13.2    -      -       +      +
     43W  LEU      4.5     1.8    -      -       -      -
     44W  GLY*     3.7    32.1    -      -       -      +
    100W  VAL*     4.0    14.6    -      -       +      +
    102W  ALA*     4.0    19.3    -      -       +      -
    155W  ILE*     4.6     0.4    -      -       -      -
    175W  VAL*     4.8     0.7    -      -       -      -
    176W  TYR*     2.9    42.9    +      -       +      -
    178W  ILE*     4.0    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 15 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3W  VAL*     3.3     5.2    -      -       -      +
      4W  VAL*     2.8    44.0    +      -       +      +
     14W  ILE*     1.3    74.6    -      -       -      +
     16W  CYS*     1.3    64.8    +      -       -      +
     34W  ILE*     3.6     2.5    -      -       -      -
    155W  ILE*     4.2     9.2    -      -       +      +
    159W  LEU*     4.1    11.4    -      -       +      -
    174W  VAL      3.2    13.2    -      -       -      +
    175W  VAL*     3.8    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 16 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2W  ILE      3.3    14.1    -      -       -      +
      3W  VAL*     3.8     8.3    -      -       +      -
     15W  ALA*     1.3    77.1    -      -       -      +
     17W  ASP*     1.3    72.3    +      -       -      +
     32W  GLU*     4.4     1.6    -      -       -      -
     33W  LYS*     3.5    26.9    -      -       +      -
     34W  ILE*     3.8    17.7    -      -       +      -
    159W  LEU*     4.1     8.3    -      -       -      +
    173W  ALA*     3.2     4.0    -      -       -      +
    174W  VAL*     2.9    53.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 17 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1W  GLY*     3.2     9.4    -      -       -      -
      2W  ILE*     2.7    50.0    +      -       +      +
     16W  CYS*     1.3    89.5    -      -       -      +
     18W  LEU*     1.3    60.4    +      -       -      +
     19W  ARG*     3.5     9.9    +      -       -      +
     31W  PHE      3.8     1.0    -      -       -      +
     33W  LYS*     3.0    20.3    +      -       -      -
    159W  LEU*     4.4     1.8    -      -       +      +
    163W  ALA*     5.6     0.9    -      -       +      -
    169W  SER*     3.5     8.0    -      -       -      -
    170W  GLY*     3.0    32.3    +      -       -      +
    172W  GLY      3.2    15.0    -      -       -      +
    173W  ALA*     4.1     2.2    -      -       +      +
    191W  MET*     5.7     0.4    -      -       -      -
----------------------------------------------------------
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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