Contacts of the strand formed by residues 408 - 421 (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 SER 408 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    371C  LYS*     3.3    11.6    +      -       -      +
    372C  TRP*     2.9    61.2    +      -       -      +
    405C  ARG      5.0     2.5    -      -       -      -
    407C  ASP*     1.3    80.5    +      -       -      +
    409C  ASP*     1.3    73.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 409 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    369C  TYR*     2.4    43.4    +      -       -      -
    370C  ALA      3.5     4.2    -      -       -      +
    371C  LYS*     3.0    19.4    -      -       -      +
    372C  TRP*     3.8     5.9    -      -       -      -
    408C  SER*     1.3    82.6    +      -       -      +
    410C  GLU*     1.3    70.9    +      -       -      +
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Residues in contact with GLU 410 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14C  THR*     3.4    20.0    -      -       +      +
     15C  GLY      3.9     0.2    +      -       -      -
     16C  SER*     2.5    41.4    +      -       -      -
     21C  GLN*     4.7     7.4    +      -       -      +
     23C  PHE*     3.8    28.7    -      -       +      -
    369C  TYR*     3.6     6.4    -      -       -      -
    370C  ALA*     3.0    32.7    +      -       -      +
    372C  TRP*     3.8    11.2    -      -       +      -
    409C  ASP*     1.3    81.5    -      -       -      +
    411C  TRP*     1.3    89.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 411 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14C  THR*     3.7     0.5    -      -       -      +
     15C  GLY*     2.8    51.5    +      -       -      -
     16C  SER      5.1     0.2    -      -       -      -
     23C  PHE*     5.2     0.4    -      -       -      -
    367C  ALA*     5.5     5.8    -      -       +      -
    368C  THR      3.0    12.8    -      -       -      +
    369C  TYR*     4.3    14.8    -      +       +      -
    410C  GLU*     1.3    91.4    +      -       -      +
    412C  THR*     1.3    69.1    +      -       -      +
    413C  PHE*     3.4    41.7    -      +       +      -
----------------------------------------------------------
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Residues in contact with THR 412 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13C  TRP      3.2    15.3    -      -       -      +
     14C  THR*     3.9     6.1    -      -       +      +
     15C  GLY      4.4     0.9    -      -       -      +
     20C  GLN*     4.1     9.6    +      -       -      +
     21C  GLN      3.5    32.9    +      -       -      +
     23C  PHE*     3.7    16.9    -      -       +      -
     35C  GLY      3.9     8.3    +      -       -      -
    366C  PHE*     4.0     3.5    -      -       -      -
    367C  ALA*     3.3     4.0    -      -       -      +
    368C  THR*     2.7    54.6    +      -       -      +
    411C  TRP*     1.3    83.0    -      -       -      +
    413C  PHE*     1.3    65.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 413 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12C  GLY*     3.3     2.6    -      -       -      -
     13C  TRP*     2.8    75.0    +      +       +      +
     14C  THR      4.9     0.9    -      -       -      -
     15C  GLY*     4.7     8.3    -      -       -      -
    366C  PHE*     3.2    23.4    -      -       -      +
    367C  ALA*     4.2     7.6    -      -       +      -
    411C  TRP*     3.4    36.6    -      +       +      -
    412C  THR*     1.3    78.2    -      -       -      +
    414C  GLY*     1.3    60.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 414 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11C  ILE      3.3    11.2    -      -       -      -
     13C  TRP*     4.1    14.4    -      -       -      -
    365C  VAL*     3.4     8.5    -      -       -      +
    366C  PHE*     2.9    41.9    +      -       -      +
    413C  PHE*     1.3    78.8    -      -       -      +
    415C  ALA*     1.3    60.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 415 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102B  ALA*     4.5     5.4    -      -       +      -
    127B  ALA*     3.7    29.8    -      -       +      -
     10C  GLY*     3.3     1.7    -      -       -      -
     11C  ILE*     2.9    35.4    +      -       +      +
     13C  TRP*     5.1     0.9    -      -       +      -
    363C  ILE*     5.9     1.3    -      -       +      -
    364C  ARG      3.1    11.4    -      -       -      +
    365C  VAL*     4.4    12.1    -      -       +      -
    366C  PHE*     4.4     2.3    -      -       -      -
    414C  GLY*     1.3    74.1    -      -       -      +
    416C  GLN*     1.3    65.2    +      -       -      +
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Residues in contact with GLN 416 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102B  ALA*     4.0     7.7    -      -       -      +
      8C  ARG*     3.9    15.5    -      -       -      +
      9C  SER      3.5    16.8    -      -       -      +
     10C  GLY*     3.9     3.1    -      -       -      +
     35C  GLY*     5.1     8.1    +      -       -      +
     37C  GLU*     2.8    41.6    +      -       -      +
     39C  GLU      5.7     0.8    +      -       -      -
    362C  ALA      3.8     0.5    -      -       -      +
    363C  ILE*     3.5     2.1    -      -       -      +
    364C  ARG*     2.8    69.5    +      -       -      +
    366C  PHE*     4.4    15.2    -      -       +      -
    415C  ALA*     1.3    78.1    -      -       -      +
    417C  MET*     1.3    73.7    +      -       -      +
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Residues in contact with MET 417 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  PHE*     4.0    18.4    -      -       +      -
     84B  ALA*     3.6    30.7    -      -       +      +
     85B  ASN*     3.9     5.2    -      -       -      +
     86B  VAL*     3.7    27.6    -      -       +      +
    102B  ALA*     3.4    27.5    -      -       +      +
      7C  ALA*     3.9    19.3    -      -       +      +
      8C  ARG*     3.4     3.1    -      -       -      +
      9C  SER*     2.8    45.9    +      -       -      +
    362C  ALA      3.2    10.3    -      -       -      +
    363C  ILE*     4.5     4.0    -      -       +      -
    364C  ARG*     5.1     0.2    -      -       -      -
    416C  GLN*     1.3    82.5    -      -       -      +
    418C  GLU*     1.3    69.4    +      -       -      +
    419C  ILE*     4.0     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 418 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  TYR*     2.6    39.9    +      -       +      +
      7C  ALA      3.4     5.6    -      -       -      +
      8C  ARG*     4.5     2.7    -      -       +      -
     33C  ARG*     3.3    19.6    +      -       -      -
     37C  GLU*     4.4     3.2    -      -       -      +
    113C  HIS*     3.6     8.7    +      -       -      -
    360C  ARG*     2.9    36.3    +      -       -      +
    361C  PRO*     3.3     4.0    -      -       -      +
    362C  ALA      3.0    30.7    +      -       -      +
    364C  ARG*     2.9    36.3    +      -       -      +
    416C  GLN*     4.8     0.4    -      -       -      +
    417C  MET*     1.3    76.3    -      -       -      +
    419C  ILE*     1.3    65.2    +      -       -      +
    420C  TRP*     4.1     1.3    -      -       +      -
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Residues in contact with ILE 419 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  VAL*     4.1    15.3    -      -       +      -
     60B  PHE*     3.7    53.4    -      -       +      -
     86B  VAL*     4.4     1.8    -      -       +      -
      6C  TYR*     3.4     7.9    -      -       -      -
      7C  ALA*     2.8    43.1    +      -       +      +
    360C  ARG*     4.0     6.3    -      -       -      -
    361C  PRO*     3.8    33.2    -      -       +      -
    417C  MET*     4.0     6.3    -      -       -      -
    418C  GLU*     1.3    78.8    -      -       -      +
    420C  TRP*     1.3    75.5    +      -       -      +
    421C  TRP*     4.0    13.7    -      -       +      -
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Residues in contact with TRP 420 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  GLY      3.2    14.4    -      -       -      +
      6C  TYR*     3.9    26.0    -      +       +      -
    113C  HIS*     3.5    30.1    -      +       -      -
    358C  TRP*     3.5    46.1    +      +       +      -
    360C  ARG*     3.5    53.7    -      -       +      +
    361C  PRO*     5.4     0.2    -      -       -      +
    418C  GLU*     4.0     4.7    -      -       -      -
    419C  ILE*     1.3    80.0    -      -       -      +
    421C  TRP*     1.3    64.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 421 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  GLN*     4.1    16.7    +      -       +      +
     50B  VAL*     4.3    22.9    -      -       +      -
     60B  PHE*     3.3    42.6    -      +       -      -
      3C  PHE*     3.2    49.0    +      +       -      +
      4C  HIS*     2.5    58.6    +      -       -      +
      5C  GLY      2.9    33.7    +      -       -      +
      6C  TYR      3.3    35.4    -      -       -      -
      7C  ALA*     3.8     2.9    -      -       +      -
     43C  GLU      3.6     9.4    -      -       -      -
     44C  LEU*     4.1     5.8    -      -       +      -
    419C  ILE*     4.0    12.3    -      -       +      -
    420C  TRP*     1.3    84.0    -      -       -      +
----------------------------------------------------------
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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