Contacts of the strand formed by residues 56 - 68 (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 LYS 56 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  ILE*     3.8    28.0    -      -       +      -
     51C  TRP*     3.8    18.7    -      -       +      -
     52C  LYS*     3.3     3.7    -      -       -      +
     53C  GLU*     2.9    37.5    +      -       +      +
     55C  ASP*     1.3    84.6    -      -       +      +
     57C  SER*     1.3    64.3    +      -       -      +
     89C  LYS      3.4     4.5    -      -       -      -
     90C  ASN*     3.1    26.3    +      -       +      +
     91C  LEU*     4.0    10.0    -      -       +      +
     93C  GLU*     5.2    13.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 57 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49C  GLU*     3.9    23.3    +      -       -      -
     51C  TRP*     3.2    17.2    -      -       -      -
     52C  LYS*     4.0    12.0    +      -       -      -
     55C  ASP      4.0     1.8    +      -       -      -
     56C  LYS*     1.3    76.7    -      -       -      +
     58C  PHE*     1.3    65.0    +      -       -      +
     59C  TYR*     5.8     0.3    -      -       -      +
     88C  GLY*     3.5     3.1    -      -       -      -
     89C  LYS*     2.8    55.2    +      -       -      +
     91C  LEU*     4.3     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 58 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  ILE*     5.3     1.3    -      -       +      -
    351A  TRP      4.1    11.2    -      -       -      -
    352A  GLN*     3.6    24.9    -      -       -      -
    353A  ALA*     3.6    24.5    -      -       +      -
    361A  PRO*     3.8    26.2    -      -       +      -
    363A  ILE*     4.3    10.1    -      -       +      -
     49C  GLU*     3.6     5.1    -      -       -      +
     50C  VAL*     3.0    30.4    +      -       +      -
     51C  TRP*     3.0    36.4    +      +       +      +
     57C  SER*     1.3    75.4    -      -       -      +
     59C  TYR*     1.3    60.5    -      -       -      +
     86C  VAL*     3.7    20.6    -      -       +      -
     87C  GLN      3.3     4.0    -      -       -      -
     88C  GLY*     4.0     8.5    -      -       -      -
     91C  LEU*     3.5    33.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 59 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2C  ASP*     2.6    41.3    +      -       -      +
      4C  HIS*     4.8     5.7    -      -       -      -
     47C  GLY*     3.6     5.8    -      -       -      -
     48C  GLN      3.6     5.6    -      -       -      -
     49C  GLU*     3.5    32.3    -      -       +      -
     50C  VAL*     5.2     0.7    -      -       -      -
     57C  SER*     4.3     1.1    -      -       -      +
     58C  PHE*     1.3    75.6    -      -       -      +
     60C  PHE*     1.3    73.1    +      -       -      +
     61C  ASP*     4.0    22.0    +      -       +      -
     85C  ASN*     3.8     0.7    -      -       -      +
     86C  VAL*     3.3     6.6    -      -       -      +
     87C  GLN*     2.9    43.7    +      -       +      +
     89C  LYS*     3.8    25.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 60 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  PHE*     4.2    12.6    -      +       -      -
      7A  ALA*     4.1     8.1    -      -       +      -
     44A  LEU*     4.9     0.4    -      -       +      -
    417A  MET*     4.1    13.7    -      -       +      -
    419A  ILE*     3.6    39.9    -      -       +      -
    421A  TRP*     3.3    55.2    -      +       -      -
     46C  LEU      5.1     0.4    -      -       -      -
     47C  GLY*     3.0     3.6    -      -       -      -
     48C  GLN*     2.8    39.6    +      -       +      +
     50C  VAL*     4.3     4.7    -      -       +      -
     58C  PHE      4.3     0.4    -      -       -      -
     59C  TYR*     1.3    76.4    -      -       -      +
     61C  ASP*     1.3    75.5    +      -       -      +
     62C  THR*     3.4    25.8    -      -       +      -
     84C  ALA*     4.8     2.0    -      -       +      -
     85C  ASN      3.6     9.6    -      -       -      -
     86C  VAL*     4.1     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 61 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  HIS*     6.2     0.2    -      -       -      -
     45C  LYS*     2.6    40.0    +      -       -      +
     46C  LEU      4.0     3.3    -      -       -      +
     47C  GLY*     4.0    11.6    +      -       -      -
     59C  TYR*     4.0    18.8    +      -       +      -
     60C  PHE*     1.3    77.3    -      -       -      +
     62C  THR*     1.3    70.4    +      -       -      +
     83C  GLU*     4.4     6.5    -      -       -      +
     84C  ALA*     3.3     5.2    +      -       -      -
     85C  ASN*     3.1    49.2    +      -       -      +
     87C  GLN*     4.7     5.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 62 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  PHE*     5.0     0.4    -      -       +      -
     44A  LEU*     4.1    27.8    -      -       +      +
     44C  LEU      4.8     1.6    +      -       -      -
     45C  LYS*     3.2    29.2    +      -       -      +
     46C  LEU*     2.7    34.7    +      -       -      +
     60C  PHE*     3.4    35.4    -      -       +      -
     61C  ASP*     1.3    77.0    +      -       -      +
     63C  ASN*     1.3    62.1    +      -       -      +
     64C  VAL*     5.6     0.8    -      -       -      +
     81C  PHE*     4.8     7.9    -      -       +      -
     83C  GLU*     3.1    14.1    -      -       -      +
     84C  ALA*     4.8     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 63 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43C  GLU*     3.3    34.6    -      -       -      +
     44C  LEU      3.7     6.9    -      -       -      +
     45C  LYS*     3.7    12.5    -      -       -      +
     62C  THR*     1.3    76.7    -      -       -      +
     64C  VAL*     1.3    71.4    +      -       -      +
     65C  ALA*     4.1     2.2    -      -       -      +
     81C  PHE*     3.8     3.3    -      -       -      -
     82C  ARG*     2.9    29.5    +      -       -      +
     83C  GLU*     2.9    47.4    +      -       +      +
    106C  PHE*     3.2    24.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 64 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  LEU*     4.3    12.3    -      -       +      -
     66A  TYR*     3.8    26.5    -      -       +      +
     43C  GLU*     3.6     0.5    -      -       -      -
     44C  LEU*     2.9    37.4    +      -       +      +
     62C  THR*     5.6     0.7    -      -       -      +
     63C  ASN*     1.3    77.8    -      -       -      +
     65C  ALA*     1.3    61.8    +      -       -      +
     66C  TYR*     3.5    39.1    -      -       +      +
     79C  PRO*     3.8    14.4    -      -       +      -
     80C  ALA      3.5     6.1    -      -       -      +
     81C  PHE*     3.8    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 65 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  TRP*     4.1    10.9    -      -       +      -
     41C  TYR*     3.6    24.5    -      -       +      +
     42C  ALA      3.2     7.6    -      -       -      +
     43C  GLU*     3.9     7.0    -      -       +      +
     63C  ASN*     4.1     0.8    -      -       -      +
     64C  VAL*     1.3    74.1    -      -       -      +
     66C  TYR*     1.3    60.9    +      -       -      +
     78C  ASP      4.6     0.3    -      -       -      +
     79C  PRO*     3.2     8.5    -      -       -      +
     80C  ALA*     2.8    33.0    +      -       +      +
     82C  ARG*     3.7    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 66 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  TYR*     4.0     4.3    +      -       -      -
     74A  TRP*     5.2     0.2    -      -       -      -
     64B  VAL*     3.8    34.5    -      -       +      +
     66B  TYR*     4.0     8.1    +      -       -      -
     79B  PRO*     4.3     7.7    -      -       +      +
     81B  PHE*     3.8    42.3    -      +       +      -
     40C  THR      3.8     0.9    -      -       -      +
     41C  TYR*     3.3     8.4    -      -       -      -
     42C  ALA      2.8    38.4    +      -       -      +
     44C  LEU*     4.3    19.1    -      -       +      +
     64C  VAL*     3.5    38.7    -      -       +      +
     65C  ALA*     1.3    74.4    -      -       -      +
     67C  SER*     1.3    61.7    +      -       -      +
     68C  VAL      4.2     0.4    -      -       -      -
     77C  THR*     4.0    17.9    -      -       +      -
     78C  ASP      5.6     0.7    -      -       -      -
     79C  PRO*     3.6    24.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 67 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  TRP*     4.4    18.6    -      -       -      -
     39C  GLU*     4.1    16.3    -      -       -      +
     40C  THR      3.4     7.6    +      -       -      -
     41C  TYR*     3.9    14.0    -      -       -      -
     66C  TYR*     1.3    76.6    -      -       -      +
     68C  VAL*     1.3    66.2    +      -       -      +
     77C  THR*     3.5    14.3    +      -       -      -
     78C  ASP      5.7     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 68 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81B  PHE*     4.2    20.0    -      -       +      +
    104B  LYS*     4.4     5.6    -      -       -      -
     39C  GLU*     3.5     6.5    -      -       -      +
     40C  THR*     2.9    57.8    +      -       +      +
     67C  SER*     1.3    80.3    -      -       -      +
     69C  ALA*     1.3    59.8    +      -       -      +
     70C  GLN      3.2     0.4    +      -       -      +
     75C  GLU*     3.5    38.8    -      -       +      +
     76C  ALA      5.0     0.4    -      -       -      +
     77C  THR*     3.7    29.6    -      -       +      -
----------------------------------------------------------
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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