Contacts of the strand formed by residues 121 - 128 (chain C) in PDB entry 3DC6


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 121 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117C  VAL*     3.9     8.2    -      -       -      +
    119C  GLY      3.9     1.6    +      -       -      -
    120C  SER*     1.3    77.5    -      -       -      +
    122C  TRP*     1.3    69.9    +      -       -      -
    139C  CYS      3.2    12.3    -      -       -      -
    141C  ASN      3.7    10.5    -      -       -      -
    159C  VAL*     2.8    31.3    +      -       -      +
    160C  TRP*     3.4    10.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 122 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73C  ASN*     3.4    41.2    -      -       +      +
     74C  HIS*     3.8    15.9    -      +       -      -
     77C  PHE*     3.6    32.1    -      +       +      -
    117C  VAL*     4.2     5.6    -      -       -      +
    121C  GLY*     1.3    76.5    -      -       -      -
    123C  GLY*     1.3    59.1    +      -       -      +
    124C  TRP*     3.4    38.5    -      +       -      +
    138C  THR*     3.2     7.9    -      -       -      -
    139C  CYS*     2.9    37.4    +      -       +      +
    141C  ASN      3.3    22.3    +      -       -      -
    142C  GLN*     3.0    20.0    +      -       -      -
    157C  ILE      3.4    12.6    -      -       -      -
    158C  ASP*     3.5    52.9    +      -       +      -
    159C  VAL*     4.4     0.9    -      -       -      -
    160C  TRP*     4.0     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 123 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110C  LEU*     3.9     7.2    -      -       -      +
    114C  THR*     3.3    26.9    +      -       -      +
    122C  TRP*     1.3    73.5    -      -       -      +
    124C  TRP*     1.3    61.4    +      -       -      -
    137C  ALA      3.6     5.6    -      -       -      -
    138C  THR*     4.2     5.2    -      -       -      -
    155C  PHE      3.9     0.2    -      -       -      +
    156C  GLY*     3.2     4.0    -      -       -      -
    157C  ILE*     2.9    35.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 124 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73C  ASN*     4.0    23.6    +      -       -      -
     76C  ILE*     3.6    39.0    -      -       +      -
     77C  PHE      5.1     0.7    -      -       -      -
     80C  ASN*     4.7     0.2    -      -       -      -
    110C  LEU*     3.5    10.6    -      -       -      +
    122C  TRP*     3.4    44.8    -      +       +      +
    123C  GLY*     1.3    75.5    -      -       -      -
    125C  LEU*     1.3    59.0    +      -       -      +
    135C  LYS      3.7     0.2    -      -       -      +
    136C  VAL*     3.4     5.7    -      -       -      -
    137C  ALA*     2.7    39.5    +      -       +      +
    139C  CYS*     3.8    28.2    -      -       -      +
    143C  ASP      5.1     0.4    +      -       -      -
    145C  LEU*     3.7    35.4    -      -       +      +
    153C  PRO*     3.7    21.3    -      -       +      -
    155C  PHE      3.3    12.6    -      -       -      -
    156C  GLY*     3.2    32.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 125 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92C  LEU*     5.1     4.3    -      -       +      -
     96C  ILE*     5.1     0.2    -      -       +      -
    100C  PHE*     4.1    16.8    -      -       +      -
    106C  LEU*     3.9    36.1    -      -       +      -
    110C  LEU*     4.0    15.3    -      -       +      +
    124C  TRP*     1.3    74.0    -      -       -      +
    126C  GLY*     1.3    59.6    +      -       -      +
    134C  LEU*     4.4    16.6    -      -       +      -
    135C  LYS      3.6     8.5    -      -       -      +
    136C  VAL*     4.8     2.5    -      -       +      +
    153C  PRO*     4.0     2.1    -      -       -      +
    154C  LEU*     3.0    46.9    +      -       +      -
    155C  PHE*     2.8    22.7    +      -       +      +
    180C  TRP*     6.3     0.2    -      -       +      -
    185C  TRP*     4.9     7.9    -      -       +      -
    188C  VAL*     4.3    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 126 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124C  TRP*     3.8     1.2    -      -       -      +
    125C  LEU*     1.3    73.2    -      -       -      +
    127C  TYR*     1.3    60.8    +      -       -      -
    134C  LEU*     3.5    10.1    -      -       -      +
    135C  LYS      2.7    40.0    +      -       -      -
    137C  ALA*     6.2     0.2    -      -       -      +
    145C  LEU*     4.3    10.8    -      -       -      -
    151C  LEU*     4.5     9.4    -      -       -      -
    152C  VAL      3.2    12.8    -      -       -      -
    154C  LEU*     4.4     2.5    -      -       -      -
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Residues in contact with TYR 127 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95C  ALA*     6.3     0.4    -      -       +      -
    126C  GLY*     1.3    74.3    -      -       -      +
    128C  CYS*     1.3    70.6    +      -       -      +
    129C  PRO*     3.3    21.0    +      -       +      +
    132C  LYS*     3.4    44.1    -      -       -      +
    133C  ILE      3.8     9.6    -      -       -      -
    134C  LEU*     3.8    10.5    -      -       +      -
    151C  LEU*     3.6     3.4    -      -       -      -
    152C  VAL*     2.8    36.5    +      -       +      +
    154C  LEU*     4.2     7.4    -      -       +      -
    192C  PHE*     3.8    26.2    -      +       +      -
    195C  ALA*     3.5    47.6    -      -       +      -
    196C  GLN*     3.9    23.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 128 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127C  TYR*     1.3    74.0    -      -       -      +
    129C  PRO*     1.3    66.9    -      -       -      +
    130C  LYS*     3.9     7.9    -      -       -      -
    131C  GLY*     3.4    22.9    -      -       -      -
    132C  LYS*     2.9    29.5    +      -       -      -
    133C  ILE*     2.9    30.4    +      -       +      +
    135C  LYS*     3.7    20.6    -      -       +      +
    150C  GLY      6.4     0.2    -      -       -      -
    151C  LEU*     3.5    19.4    -      -       +      +
----------------------------------------------------------
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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