Contacts of the strand formed by residues 108 - 113 (chain Z) 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 GLY 108 (chain Z).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7Z  ALA*     3.6    14.3    -      -       -      +
      8Z  GLY      3.3     6.6    +      -       -      +
      9Z  GLU      3.2    11.3    +      -       -      -
     11Z  PHE      3.2    28.7    -      -       -      +
    103Z  GLY      3.6     6.3    -      -       -      -
    104Z  LEU*     4.2     2.7    -      -       -      -
    106Z  GLY      3.8     1.2    -      -       -      -
    107Z  LYS*     1.3    73.6    -      -       -      +
    109Z  ALA*     1.3    57.0    +      -       -      -
    121Z  ARG*     3.0    15.4    +      -       -      -
    123Z  GLN*     5.5     1.6    +      -       -      +
    145Z  TYR*     6.0     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 109 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7Z  ALA*     3.8     4.0    -      -       -      +
     12Z  ALA*     3.9     1.5    -      -       -      +
     76Z  ILE*     4.0    25.5    -      -       +      +
    102Z  ALA*     3.1     7.8    -      -       -      +
    103Z  GLY      2.8    38.0    +      -       -      +
    105Z  ASP      4.2     4.5    -      -       -      +
    108Z  GLY*     1.3    74.3    -      -       -      -
    110Z  VAL*     1.3    64.6    +      -       -      +
    111Z  TYR*     4.3     6.3    -      -       +      -
    121Z  ARG*     3.4    27.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 110 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5Z  GLY*     3.9    12.6    -      -       -      +
      6Z  ILE      3.9    15.7    -      -       -      +
      7Z  ALA*     3.9    25.1    -      -       +      +
     12Z  ALA*     4.7     0.4    -      -       +      -
    100Z  ILE*     3.9    22.7    -      -       +      -
    101Z  ILE      3.3     2.7    -      -       -      -
    102Z  ALA*     4.3    12.3    -      -       +      -
    109Z  ALA*     1.3    80.5    -      -       -      +
    111Z  TYR*     1.3    64.1    +      -       -      +
    121Z  ARG*     3.3     6.8    -      -       -      +
    122Z  GLU*     2.8    49.1    +      -       +      +
    123Z  GLN      4.7     0.9    -      -       -      +
    124Z  CYS      4.8     1.1    -      -       -      -
    125Z  ARG*     4.3    14.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 111 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76Z  ILE*     4.0    41.2    -      -       +      +
     77Z  ASN*     3.6    25.7    -      -       +      +
     80Z  ALA*     3.6    20.2    -      -       +      -
    100Z  ILE*     3.4     3.8    -      -       -      +
    101Z  ILE*     2.9    45.4    +      -       +      +
    105Z  ASP*     5.9     0.3    -      -       -      +
    109Z  ALA*     4.3     4.0    -      -       +      -
    110Z  VAL*     1.3    80.4    -      -       -      +
    112Z  SER*     1.3    62.0    +      -       -      +
    113Z  PHE*     3.9    10.5    -      -       +      -
    119Z  TYR*     3.8    20.0    -      +       +      -
    120Z  GLU      3.4     4.7    -      -       -      +
    121Z  ARG*     3.6    48.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 112 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302Y  3SD      3.4    13.4    -      -       -      +
     99Z  THR      3.3    10.5    -      -       -      -
    100Z  ILE*     3.9     4.0    -      -       -      -
    111Z  TYR*     1.3    74.4    -      -       -      +
    113Z  PHE*     1.3    65.2    +      -       -      +
    119Z  TYR*     3.2    22.2    -      -       -      +
    120Z  GLU      3.1    10.4    +      -       -      -
    122Z  GLU*     2.7    27.5    +      -       -      -
    125Z  ARG*     3.2    32.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 113 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302Y  3SD      4.5     5.9    -      -       -      +
     80Z  ALA*     3.3    43.5    -      -       +      -
     83Z  ILE*     3.4    28.7    -      -       +      -
     84Z  GLN      3.9     5.2    -      -       -      -
     87Z  LEU*     3.7    16.4    -      -       +      -
     98Z  HIS*     4.1     8.5    +      -       -      +
     99Z  THR*     2.8    43.3    +      -       +      +
    101Z  ILE*     4.2    17.5    -      -       +      -
    111Z  TYR*     3.9    18.2    -      -       +      -
    112Z  SER*     1.3    76.5    -      -       -      +
    114Z  ASP*     1.3    71.2    +      -       -      +
    117Z  GLY      4.4     2.9    -      -       -      -
    118Z  SER      3.1     7.4    -      -       -      +
    119Z  TYR*     3.2    27.8    -      +       +      -
----------------------------------------------------------
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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