Contacts of the strand formed by residues 124 - 132 (chain C) in PDB entry 1AF6


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 124 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  ASP*     4.0    15.0    -      -       -      -
     82C  ARG      5.7     1.3    -      -       -      -
    101C  TRP*     5.1     0.9    -      -       -      -
    103C  GLY      3.7     0.2    -      -       -      +
    104C  LYS*     4.0     7.9    -      -       -      -
    105C  ARG*     3.1    25.3    +      -       -      +
    122C  ILE      3.5     1.8    +      -       -      -
    123C  SER*     1.3    77.7    -      -       -      +
    125C  PRO*     1.3    79.5    -      -       -      +
    126C  GLY*     3.4     2.1    +      -       -      -
    144C  THR*     4.7     4.2    -      -       -      +
    145C  ARG      4.3     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 125 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  GLY      3.9    16.4    -      -       -      +
     11A  ILE*     4.0     4.8    -      -       +      +
     70A  GLN*     3.2    44.4    -      -       +      +
     71A  GLN*     4.1     1.6    -      -       -      -
     72A  ASN      3.7    20.0    -      -       -      +
    103C  GLY      3.9     6.1    -      -       -      +
    104C  LYS*     4.0    11.6    -      -       +      -
    124C  GLY*     1.3    86.0    -      -       -      +
    126C  GLY*     1.3    58.7    +      -       -      +
    144C  THR*     3.2     2.8    -      -       -      -
    145C  ARG*     2.9    51.3    +      -       +      +
----------------------------------------------------------
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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
----------------------------------------------------------
     10A  GLY      4.8     1.0    +      -       -      -
     11A  ILE*     3.8    17.5    +      -       -      +
    101C  TRP*     3.5    12.3    -      -       -      -
    102C  ALA*     3.3     1.0    -      -       -      +
    103C  GLY      2.9    34.2    +      -       -      -
    124C  GLY      3.4     0.6    +      -       -      -
    125C  PRO*     1.3    75.7    -      -       -      +
    127C  ALA*     1.3    63.0    +      -       -      +
    143C  ALA      3.1    13.9    -      -       -      -
    144C  THR*     4.1     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 127 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  ILE*     4.0     6.6    -      -       +      +
    415A  ALA*     3.6    30.5    -      -       +      -
    101C  TRP*     3.2    25.1    -      -       -      +
    102C  ALA*     4.0     2.5    -      -       +      -
    126C  GLY*     1.3    75.7    -      -       -      +
    128C  GLY*     1.3    60.3    +      -       -      +
    142C  ALA*     3.5     2.9    -      -       -      +
    143C  ALA*     3.0    31.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 128 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100C  ILE*     3.5     5.4    -      -       -      +
    101C  TRP*     3.0    45.7    +      -       -      +
    127C  ALA*     1.3    77.0    -      -       -      +
    129C  LEU*     1.3    61.5    +      -       -      +
    141C  LEU      3.2    13.2    -      -       -      -
    142C  ALA*     4.1     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 129 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92C  ILE*     4.5     9.2    -      -       +      -
     95C  LEU*     3.9    16.6    -      -       +      -
     98C  SER*     3.6    27.6    -      -       -      +
     99C  THR      3.4    11.0    -      -       -      +
    100C  ILE*     3.9    18.6    -      -       +      -
    101C  TRP*     4.3     0.4    -      -       -      +
    128C  GLY*     1.3    73.4    -      -       -      +
    130C  GLU*     1.3    58.9    +      -       -      +
    132C  ILE*     3.7    25.3    -      -       +      +
    140C  SER*     3.6     2.1    -      -       -      -
    141C  LEU*     2.9    45.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 130 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87C  GLN*     5.2     0.7    -      -       -      +
     98C  SER*     3.2     3.7    -      -       -      -
     99C  THR*     2.8    54.3    +      -       -      +
    101C  TRP*     4.1     8.6    -      -       +      +
    105C  ARG*     2.8    43.1    +      -       -      -
    107C  TYR*     4.0     6.7    -      -       -      +
    108C  GLN*     2.8    36.0    +      -       -      +
    129C  LEU*     1.3    74.0    -      -       -      +
    131C  ASN*     1.3    84.5    +      -       +      +
    132C  ILE      3.4     2.0    -      -       -      -
    140C  SER*     3.6     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 131 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96C  PRO      4.6     0.3    -      -       -      +
     97C  GLY      3.9    14.1    -      -       -      +
     98C  SER*     3.4    14.0    +      -       -      -
     99C  THR*     4.9     2.0    -      -       -      +
    108C  GLN*     4.6     3.1    +      -       -      -
    130C  GLU*     1.3    94.3    -      -       +      +
    132C  ILE*     1.3    64.9    +      -       -      +
    133C  ASP      3.4     2.9    +      -       -      -
    138C  LYS*     3.6    42.9    +      -       -      +
    139C  LEU      3.3     2.6    +      -       -      -
    140C  SER*     3.0    16.5    +      -       -      -
    178C  GLN*     5.2     1.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 132 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95C  LEU*     3.8    29.2    -      -       +      -
     98C  SER*     4.3    10.8    -      -       -      -
    129C  LEU*     3.7    43.3    -      -       +      +
    130C  GLU      4.7     1.1    -      -       -      -
    131C  ASN*     1.3    73.5    -      -       -      +
    133C  ASP*     1.3    72.0    +      -       -      +
    134C  VAL*     3.2    12.2    +      -       +      -
    138C  LYS*     3.4     3.5    -      -       -      -
    139C  LEU*     2.7    63.7    +      -       +      +
    141C  LEU*     4.5    11.9    -      -       +      -
----------------------------------------------------------
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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