Contacts of the strand formed by residues 188 - 193 (chain D) in PDB entry 3CMT


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 LEU 188 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40D  ILE*     4.9     9.4    -      -       +      -
     56D  LEU*     4.0    19.7    -      -       +      +
     57D  PRO      3.3    24.0    -      -       -      +
     58D  MET*     4.0    17.0    -      -       -      -
     59D  GLY      3.6     3.4    -      -       -      +
     60D  ARG      3.5    15.3    -      -       -      +
     62D  VAL*     3.8    24.0    -      -       +      -
     79D  VAL*     4.9     3.6    -      -       +      -
    139D  ASP      2.9    12.5    +      -       -      +
    140D  VAL*     3.3    13.9    -      -       +      -
    141D  ILE      2.8    26.9    +      -       -      +
    186D  ASN      3.9     0.8    +      -       -      -
    187D  THR*     1.3    76.0    -      -       -      +
    189D  LEU*     1.3    64.1    +      -       -      +
    190D  ILE*     3.9    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 189 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60D  ARG      3.1     9.5    +      -       -      +
     61D  ILE*     3.4     6.0    -      -       +      +
     62D  VAL*     2.9    26.3    +      -       -      +
    129D  CYS*     4.7     7.2    -      -       +      -
    141D  ILE*     3.2    22.2    -      -       +      +
    143D  VAL*     3.8    17.3    -      -       +      -
    178D  LEU*     3.8    17.9    -      -       +      -
    182D  LEU*     3.7    36.6    -      -       +      -
    187D  THR      3.8     0.4    +      -       -      -
    188D  LEU*     1.3    74.3    -      -       -      +
    190D  ILE*     1.3    75.8    -      -       -      +
    191D  PHE*     3.6    34.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 190 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56D  LEU*     3.8    23.6    -      -       +      -
     62D  VAL*     3.3    18.8    -      -       +      +
     64D  ILE*     3.6    28.5    -      -       +      -
     76D  THR*     4.0    13.0    -      -       -      +
     79D  VAL*     3.9    26.2    -      -       +      -
    140D  VAL*     4.8     6.3    -      -       +      -
    141D  ILE      2.8     9.8    +      -       -      +
    142D  VAL*     3.2    13.3    -      -       +      +
    143D  VAL      2.8    27.9    +      -       -      +
    188D  LEU*     3.9    18.2    -      -       +      -
    189D  LEU*     1.3    79.7    -      -       -      +
    191D  PHE*     1.3    68.8    +      -       -      +
    192D  ILE*     4.7     0.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 191 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61D  ILE*     3.7    25.4    -      -       +      -
     62D  VAL      2.7    12.2    +      -       -      +
     63D  GLU*     3.3     3.6    -      -       -      +
     64D  ILE      2.9    26.0    +      -       -      -
    126D  LEU*     4.2    21.1    -      -       +      -
    129D  CYS*     5.7     0.2    -      -       -      -
    143D  VAL*     3.8    31.4    -      -       +      -
    146D  VAL*     3.8    18.8    -      -       +      -
    149D  LEU*     4.5     4.7    -      -       +      -
    171D  MET*     4.8     3.4    -      -       +      -
    175D  MET*     3.8    29.6    -      -       +      -
    178D  LEU*     4.3     1.8    -      -       +      -
    189D  LEU*     3.6    33.2    -      -       +      -
    190D  ILE*     1.3    75.0    -      -       -      +
    192D  ILE*     1.3    60.9    +      -       -      +
    215D  LEU*     3.7    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 192 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64D  ILE*     3.4     7.6    -      -       +      +
     72D  LYS*     3.6    50.5    -      -       +      +
     73D  THR*     3.9     7.0    -      -       -      -
     76D  THR*     3.4    33.9    -      -       +      +
    142D  VAL*     4.4     2.9    -      -       +      -
    143D  VAL      2.9    11.2    +      -       -      +
    144D  ASP*     3.3    36.3    -      -       +      +
    145D  SER*     3.0    17.1    -      -       -      +
    146D  VAL*     2.8    28.5    +      -       -      +
    190D  ILE*     4.8     3.1    -      -       +      -
    191D  PHE*     1.3    74.5    -      -       -      +
    193D  ASN*     1.3    63.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 193 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63D  GLU*     3.1    21.4    -      -       -      +
     64D  ILE      2.8     8.4    +      -       -      +
     65D  TYR*     3.3    29.8    -      -       +      -
     66D  GLY      3.7     0.3    +      -       -      -
     72D  LYS*     3.4    12.8    -      -       -      +
    145D  SER*     4.9     0.2    -      -       -      +
    146D  VAL*     3.3    22.0    -      -       +      +
    147D  ALA      3.9     3.2    -      -       -      +
    191D  PHE      3.8     0.2    +      -       -      -
    192D  ILE*     1.3    76.4    -      -       -      +
    194D  GLN*     1.3    79.6    +      -       -      +
    209D  THR*     2.9    14.9    -      -       -      +
    210D  THR*     2.9    53.5    +      -       -      +
    215D  LEU*     4.5     1.7    -      -       -      +
----------------------------------------------------------
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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