Contacts of the strand formed by residues 138 - 143 (chain C) in PDB entry 6MOL


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 138 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129C  ALA*     4.2     2.5    -      -       +      -
    130C  ARG      3.4    17.3    -      -       -      +
    131C  LEU*     4.7     5.6    -      -       +      +
    137C  HIS*     1.3    79.7    -      -       -      +
    139C  VAL*     1.3    68.9    +      -       -      +
    140C  LEU*     4.9     2.2    -      -       +      -
    182C  VAL*     3.7     2.8    -      -       -      +
    183C  LEU*     3.1    48.5    +      -       +      +
    186C  LEU*     3.7    17.5    -      -       +      -
    194C  PHE*     3.8    30.7    -      -       +      -
    218C  LEU*     3.8    22.0    -      -       +      -
    220C  THR*     5.3     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 139 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128C  VAL      3.6     1.7    -      -       -      +
    129C  ALA*     3.6     2.1    -      -       -      -
    130C  ARG*     2.7    52.5    +      -       +      +
    132C  ALA*     3.7    28.3    -      -       +      -
    134C  GLU*     5.0     4.0    -      -       -      +
    138C  VAL*     1.3    72.8    -      -       -      +
    140C  LEU*     1.3    61.2    +      -       -      +
    141C  ARG*     4.1    32.3    +      -       +      +
    180C  GLU*     5.1     2.5    -      -       +      +
    181C  CYS      3.6     8.7    -      -       -      +
    182C  VAL*     4.1    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 140 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127C  LEU*     3.9    22.0    -      -       +      -
    128C  VAL      3.5    13.9    -      -       -      +
    129C  ALA*     3.7    20.2    -      -       +      -
    138C  VAL*     3.9     3.9    +      -       +      -
    139C  VAL*     1.3    75.1    -      -       -      +
    141C  ARG*     1.3    61.6    +      -       -      +
    142C  TRP*     4.0    13.2    -      -       +      -
    158C  VAL*     4.2    20.9    -      -       +      -
    180C  GLU*     3.2     6.9    -      -       -      +
    181C  CYS      3.0    34.6    +      -       -      +
    183C  LEU*     3.8    22.2    -      -       +      -
    194C  PHE*     3.8    41.1    -      -       +      -
    216C  VAL*     5.6     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 141 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126C  GLY      3.0     4.9    -      -       -      +
    127C  LEU*     3.5     0.6    -      -       -      -
    128C  VAL*     2.8    47.0    +      -       +      +
    130C  ARG*     5.2    10.5    -      -       -      +
    139C  VAL*     4.1    20.1    -      -       +      +
    140C  LEU*     1.3    79.9    -      -       -      +
    142C  TRP*     1.3    59.7    +      -       -      +
    143C  LEU*     5.7     0.4    -      -       -      -
    179C  THR      3.8     4.5    -      -       -      +
    180C  GLU*     2.9    32.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 142 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124C  PRO*     4.4     0.9    -      -       +      -
    125C  VAL      4.1     5.6    -      -       -      +
    126C  GLY      3.4     6.7    -      -       -      -
    127C  LEU*     3.7    22.9    -      -       +      -
    140C  LEU*     3.6    31.0    -      -       +      -
    141C  ARG*     1.3    80.5    -      -       -      +
    143C  LEU*     1.3    76.4    +      -       -      +
    156C  TYR*     3.2    58.0    -      +       +      -
    158C  VAL*     4.0    10.1    -      -       +      -
    174C  ILE*     3.8    27.8    -      -       +      -
    179C  THR*     3.1    46.3    +      -       -      +
    180C  GLU*     3.7    16.8    -      -       -      -
    181C  CYS*     3.9     3.6    -      -       +      -
    196C  VAL*     3.8    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 143 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124C  PRO*     3.3    16.8    -      -       -      +
    125C  VAL*     2.8    28.5    +      -       +      +
    126C  GLY*     3.8    24.9    -      -       -      +
    141C  ARG      5.7     0.4    -      -       -      -
    142C  TRP*     1.3    79.7    -      -       -      +
    144C  PRO*     1.3    80.3    -      -       +      +
----------------------------------------------------------
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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