Contacts of the strand formed by residues 2 - 14 (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 ASP 2 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1C  VAL*     1.3    77.4    +      -       -      +
      3C  PHE*     1.3    58.3    +      -       -      +
      4C  HIS*     4.0    20.2    +      -       +      +
     45C  LYS      3.5     1.0    -      -       -      +
     46C  LEU*     3.3     6.6    -      -       -      -
     47C  GLY      2.7    36.4    +      -       -      +
     48C  GLN*     4.2     3.3    -      -       -      -
     49C  GLU*     4.5     1.9    +      -       -      +
     59C  TYR*     2.6    41.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 3 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  VAL*     3.3    42.6    -      -       +      -
     46B  LEU*     3.7    41.5    -      -       +      -
     47B  GLY      4.5     3.8    -      -       -      -
     48B  GLN*     4.3    18.1    +      -       +      +
     60B  PHE*     4.2    12.8    -      +       -      -
     62B  THR*     5.0     0.7    -      -       -      -
      1C  VAL      3.9     1.6    +      -       -      +
      2C  ASP*     1.3    72.0    -      -       -      +
      4C  HIS*     1.3    73.5    +      -       -      +
     44C  LEU*     4.5    17.0    -      -       +      -
     45C  LYS      3.4    12.1    -      -       -      -
     46C  LEU*     4.0    13.5    -      -       +      -
    421C  TRP*     3.2    51.5    -      +       -      +
----------------------------------------------------------
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Residues in contact with HIS 4 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2C  ASP*     4.0    27.3    -      -       +      +
      3C  PHE*     1.3    78.6    +      -       -      +
      5C  GLY*     1.3    58.3    +      -       -      +
     45C  LYS*     2.7    51.9    +      -       +      +
     47C  GLY      6.2     0.2    -      -       -      -
     59C  TYR*     4.8     4.9    -      -       -      -
     61C  ASP*     6.2     0.4    -      -       -      -
    421C  TRP*     2.5    49.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 5 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  HIS*     1.3    77.9    -      -       -      +
      6C  TYR*     1.3    60.7    +      -       -      -
     43C  GLU*     3.1    13.2    -      -       -      -
     45C  LYS*     4.2    13.4    -      -       -      +
    420C  TRP*     3.2     6.6    -      -       -      +
    421C  TRP*     2.9    40.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 6 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  GLY*     1.3    75.7    -      -       -      +
      7C  ALA*     1.3    78.5    +      -       -      +
      8C  ARG*     3.0    42.0    +      -       -      +
     33C  ARG*     3.1     7.5    +      -       -      -
     41C  TYR*     3.8    24.5    -      +       -      -
     42C  ALA*     3.3     1.9    -      -       -      +
     43C  GLU*     2.7    45.8    +      -       +      +
    113C  HIS*     5.6     0.2    -      +       -      -
    418C  GLU*     2.6    39.8    +      -       +      -
    419C  ILE      3.4    12.8    -      -       -      -
    420C  TRP*     3.9    22.7    -      +       +      -
    421C  TRP*     3.3     3.7    -      -       -      -
      1F  GLC      4.9     9.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 7 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  PHE*     4.1    17.5    -      -       +      -
     84B  ALA*     5.1     3.4    -      -       +      -
      6C  TYR*     1.3    81.2    -      -       -      +
      8C  ARG*     1.3    62.1    +      -       -      +
     41C  TYR      3.2    10.3    -      -       -      +
     42C  ALA*     4.0    12.6    -      -       +      -
    417C  MET*     3.9    10.7    -      -       +      +
    418C  GLU*     3.4     4.0    -      -       -      +
    419C  ILE*     2.8    55.5    +      -       +      +
    421C  TRP*     3.8     0.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 8 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  TYR*     3.0    36.1    +      -       -      +
      7C  ALA*     1.3    76.1    -      -       -      +
      9C  SER*     1.3    64.9    +      -       -      +
     33C  ARG*     3.4     7.1    -      -       -      +
     37C  GLU*     3.5    33.0    +      -       -      +
     39C  GLU*     2.9    44.5    +      -       -      +
     40C  THR*     3.3     4.2    -      -       -      +
     41C  TYR*     2.9    45.5    +      -       -      +
    116C  ASP*     4.3     3.0    +      -       -      -
    416C  GLN*     3.9    10.3    -      -       -      +
    417C  MET*     3.4    14.8    -      -       -      +
    418C  GLU*     4.5     4.0    -      -       +      -
      1F  GLC      2.8    40.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 9 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  ALA*     3.4    21.1    -      -       -      -
    103B  GLY*     3.4     5.2    -      -       -      -
    104B  LYS*     3.2    25.1    +      -       -      +
      8C  ARG*     1.3    77.5    -      -       -      +
     10C  GLY*     1.3    59.2    +      -       -      +
     39C  GLU      4.7     0.9    -      -       -      -
     40C  THR*     2.7    26.8    +      -       -      -
     70C  GLN*     3.6     3.0    +      -       -      +
    416C  GLN*     3.5     5.7    -      -       -      +
    417C  MET*     2.8    40.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 10 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  GLY*     4.6     7.9    -      -       -      -
    125B  PRO*     3.9    15.0    -      -       -      +
    126B  GLY      4.9     3.1    -      -       -      -
      9C  SER*     1.3    76.9    +      -       -      +
     11C  ILE*     1.3    63.5    +      -       -      +
     20C  GLN*     5.9     0.4    -      -       -      -
     70C  GLN*     3.0    32.1    +      -       -      +
    415C  ALA      3.3    12.8    -      -       -      -
    416C  GLN*     3.9     6.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 11 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125B  PRO*     4.1     4.3    -      -       +      +
    126B  GLY*     3.7    28.5    -      -       -      +
    127B  ALA*     4.1    12.3    -      -       +      +
    143B  ALA*     4.0    10.1    -      -       +      +
    144B  THR      4.0    15.9    -      -       -      +
    145B  ARG*     3.8    41.5    -      -       +      +
    170B  ASP*     5.1     0.2    -      -       -      +
     10C  GLY*     1.3    74.9    -      -       -      +
     12C  GLY*     1.3    62.3    +      -       -      +
     13C  TRP*     3.9    32.5    -      -       +      -
     20C  GLN*     4.4     4.5    -      -       -      +
     70C  GLN*     5.0     1.3    -      -       -      -
    366C  PHE*     4.8     0.9    -      -       -      -
    414C  GLY*     3.3     1.7    -      -       -      -
    415C  ALA*     2.9    35.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 12 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145B  ARG*     3.0    24.6    +      -       -      +
     11C  ILE*     1.3    79.2    -      -       -      +
     13C  TRP*     1.3    65.5    +      -       -      -
     20C  GLN*     3.1    37.5    +      -       -      +
     70C  GLN*     5.7     0.4    +      -       -      -
    413C  PHE      3.3    11.0    -      -       -      -
    414C  GLY*     4.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 13 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143B  ALA*     4.2    21.1    -      -       +      -
    144B  THR      6.0     0.2    -      -       -      -
    145B  ARG*     3.3    10.2    -      -       -      +
    170B  ASP*     2.7    34.8    +      -       +      -
    172B  PHE*     4.3    17.2    -      +       -      -
    197B  ASN*     3.4    16.8    -      -       -      +
     11C  ILE*     3.9    37.5    -      -       +      -
     12C  GLY*     1.3    76.2    -      -       -      -
     14C  THR*     1.3    62.5    +      -       -      +
     18C  GLY      3.7     3.1    -      -       -      -
     20C  GLN*     3.7     6.2    -      -       -      +
    412C  THR*     3.2     6.9    -      -       -      -
    413C  PHE*     2.8    76.9    +      +       +      -
    414C  GLY*     4.1    15.5    -      -       -      -
    415C  ALA*     6.1     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 14 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197B  ASN*     5.8     0.3    +      -       -      -
     13C  TRP*     1.3    77.1    -      -       -      +
     15C  GLY*     1.3    61.7    +      -       -      +
     16C  SER*     3.7     8.5    -      -       -      +
     17C  GLY*     2.9    38.0    +      -       -      +
     18C  GLY      2.9     8.6    +      -       -      +
     19C  GLU      2.7    20.7    +      -       -      -
     21C  GLN*     3.0    33.6    +      -       -      +
    410C  GLU*     3.4    36.6    -      -       +      +
    411C  TRP      3.8     3.8    -      -       -      +
    412C  THR*     3.9     1.8    -      -       +      +
    413C  PHE*     4.9     1.0    -      -       -      -
----------------------------------------------------------
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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