Contacts of the strand formed by residues 196 - 204 (chain M) 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 196 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38M  ASP      4.6     8.7    -      -       -      -
    190M  ILE      3.6     1.6    -      -       -      +
    191M  ILE*     3.5     3.1    -      -       -      -
    192M  ASP*     2.7    45.1    +      -       -      +
    194M  ASN      3.2     3.8    +      -       -      -
    195M  THR*     1.3    79.1    -      -       -      +
    197M  LEU*     1.3    59.3    +      -       -      -
    198M  THR*     4.0     1.0    +      -       -      -
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Residues in contact with LEU 197 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35M  PRO*     4.2    15.0    -      -       +      -
     37M  GLY      4.4     4.7    -      -       -      +
     38M  ASP*     3.8    31.2    +      -       +      +
     39M  ASN      4.5     0.7    -      -       -      +
     40M  THR      4.2    10.1    -      -       -      +
     41M  VAL*     4.0    26.2    -      -       +      -
    189M  ALA*     5.7     0.7    -      -       +      -
    190M  ILE      3.5     7.2    -      -       -      +
    191M  ILE*     4.5     9.2    -      -       +      +
    195M  THR      3.6     3.7    +      -       -      +
    196M  GLY*     1.3    72.9    -      -       -      -
    198M  THR*     1.3    64.3    +      -       -      +
    199M  PHE*     4.2    20.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 198 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189M  ALA*     3.3     3.6    -      -       -      +
    190M  ILE*     2.9    54.1    +      -       +      +
    192M  ASP*     6.1     0.2    -      -       -      +
    195M  THR*     4.7    17.0    +      -       -      +
    196M  GLY      4.7     2.3    +      -       -      -
    197M  LEU*     1.3    74.8    -      -       -      +
    199M  PHE*     1.3    62.6    +      -       -      +
    200M  LYS*     4.0    23.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 199 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31M  GLU*     3.5    41.5    -      -       +      -
     33M  LEU*     3.7    29.4    -      -       +      -
     35M  PRO*     4.0    29.4    -      -       +      -
     41M  VAL*     4.9     3.1    -      -       +      -
    187M  SER*     4.5     4.9    -      -       -      -
    188M  LEU      3.8     2.0    -      -       -      -
    189M  ALA*     3.9    17.5    -      -       +      -
    197M  LEU*     4.1    14.8    +      -       +      +
    198M  THR*     1.3    75.7    -      -       -      +
    200M  LYS*     1.3    62.5    +      -       -      +
    201M  LYS*     3.6    30.5    +      -       +      +
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Residues in contact with LYS 200 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165M  GLU*     2.6    39.1    +      -       -      +
    187M  SER*     3.4     6.9    -      -       -      -
    188M  LEU*     2.7    46.0    +      -       +      +
    190M  ILE*     4.2    18.2    -      -       -      +
    198M  THR*     4.5    20.2    -      -       +      +
    199M  PHE*     1.3    75.3    -      -       -      +
    201M  LYS*     1.3    60.7    +      -       -      +
    203M  LEU*     3.8    27.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 201 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31M  GLU*     3.3    32.0    +      -       -      +
    186M  PHE      4.5     0.2    -      -       -      -
    187M  SER*     4.4     4.0    -      -       -      +
    199M  PHE*     3.6    31.8    +      -       +      +
    200M  LYS*     1.3    73.0    -      -       -      +
    202M  ASN*     1.3    83.5    +      -       -      +
    203M  LEU*     3.2    13.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 202 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17M  ASN*     4.9    13.1    -      -       -      +
    185M  ASN*     5.0     5.4    -      -       -      +
    186M  PHE      3.9     6.1    +      -       -      -
    187M  SER*     4.8     2.4    +      -       -      -
    201M  LYS*     1.3    85.0    -      -       -      +
    203M  LEU*     1.3    63.4    +      -       -      +
    204M  GLN*     3.9     6.4    +      -       -      +
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Residues in contact with LEU 203 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165M  GLU*     5.3     2.2    -      -       -      +
    169M  VAL*     5.5     2.9    -      -       +      -
    185M  ASN*     3.1     8.1    -      -       -      +
    186M  PHE*     3.0    56.8    +      -       +      +
    188M  LEU*     3.8    33.0    -      -       +      +
    200M  LYS*     3.8    34.5    -      -       +      +
    201M  LYS      3.2    17.9    +      -       -      +
    202M  ASN*     1.3    77.9    -      -       -      +
    204M  GLN*     1.3    60.6    +      -       -      +
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Residues in contact with GLN 204 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1872  GLN*     5.6     2.7    +      -       -      -
    169M  VAL*     5.6     3.6    -      -       -      +
    184M  ARG*     3.7    28.9    +      -       +      +
    185M  ASN*     3.6    27.2    +      -       +      +
    186M  PHE*     3.9     9.5    -      -       -      -
    202M  ASN      3.9     6.9    +      -       -      +
    203M  LEU*     1.3    79.1    -      -       -      +
    205M  VAL*     1.3    64.4    +      -       -      +
    206M  GLU*     3.2    33.9    +      -       +      +
----------------------------------------------------------
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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