Contacts of the strand formed by residues 362 - 373 (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 ALA 362 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    350C  GLN*     3.8    31.0    -      -       -      +
    351C  TRP      3.3     5.8    -      -       -      -
    352C  GLN*     4.0     5.4    -      -       +      -
    359C  SER      4.4     0.9    -      -       -      +
    360C  ARG*     4.1    15.9    -      -       -      -
    361C  PRO*     1.3    75.7    -      -       -      +
    363C  ILE*     1.3    64.1    +      -       -      +
    364C  ARG*     4.1    12.9    -      -       -      +
    416C  GLN      3.8     0.3    -      -       -      +
    417C  MET*     3.2     8.3    -      -       -      +
    418C  GLU      3.0    29.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 363 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58B  PHE*     4.3     9.2    -      -       +      -
     86B  VAL*     3.9    33.2    -      -       +      +
     88B  GLY      3.9     9.9    -      -       -      +
    100B  ILE*     3.6    50.7    -      -       +      +
    101B  TRP*     4.4     5.4    -      -       -      +
    102B  ALA*     4.4    13.9    -      -       +      +
    350C  GLN*     3.3     4.0    -      -       -      -
    351C  TRP*     2.8    44.6    +      -       +      +
    362C  ALA*     1.3    76.2    -      -       -      +
    364C  ARG*     1.3    66.1    +      -       -      +
    365C  VAL*     5.6     2.7    -      -       +      -
    415C  ALA*     5.9     0.9    -      -       +      -
    416C  GLN      3.5     5.6    -      -       -      +
    417C  MET*     4.5     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 364 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33C  ARG*     6.1     1.6    -      -       -      +
     34C  LEU*     3.8    26.6    -      -       +      +
     37C  GLU*     4.4     4.6    +      -       -      -
    311C  ARG*     4.0    10.3    -      -       -      +
    348C  ALA*     4.6    11.4    -      -       +      -
    349C  GLN      3.4     5.8    -      -       -      +
    350C  GLN*     3.3    31.6    +      -       +      +
    360C  ARG*     3.3    22.2    -      -       -      +
    362C  ALA*     4.1     7.5    -      -       +      +
    363C  ILE*     1.3    78.8    -      -       -      +
    365C  VAL*     1.3    63.6    +      -       -      +
    366C  PHE*     4.6     6.7    -      -       +      -
    415C  ALA*     3.1     8.3    -      -       -      +
    416C  GLN*     2.8    71.5    +      -       +      +
    418C  GLU*     2.9    42.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 365 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348C  ALA*     3.1     3.1    -      -       -      -
    349C  GLN*     2.8    40.7    +      -       +      +
    351C  TRP*     4.3    19.3    -      -       +      -
    363C  ILE*     5.6     3.8    -      -       +      -
    364C  ARG*     1.3    78.6    -      -       -      +
    366C  PHE*     1.3    64.1    +      -       -      +
    414C  GLY      3.4    10.3    -      -       -      +
    415C  ALA*     4.4    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 366 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11C  ILE      4.8     0.2    -      -       -      -
     20C  GLN*     3.5    30.5    -      -       -      -
     34C  LEU*     6.1     1.1    -      -       +      -
     35C  GLY*     3.5    36.8    -      -       -      +
    346C  THR*     4.2     7.4    -      -       +      -
    347C  LEU      3.2    10.5    -      -       -      +
    348C  ALA*     3.9    11.9    -      -       +      -
    364C  ARG*     4.6     7.9    -      -       +      -
    365C  VAL*     1.3    79.8    -      -       -      +
    367C  ALA*     1.3    64.1    +      -       -      +
    368C  THR*     3.8     7.4    -      -       -      -
    412C  THR*     4.0     6.1    -      -       -      -
    413C  PHE*     3.2    15.5    -      -       -      +
    414C  GLY*     2.9    69.7    +      -       -      +
    415C  ALA*     3.9    13.5    -      -       -      -
    416C  GLN*     4.4    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 367 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345C  ILE      4.0     0.3    -      -       -      +
    346C  THR*     3.4     4.2    -      -       -      +
    347C  LEU*     2.9    38.6    +      -       +      +
    366C  PHE*     1.3    76.4    -      -       -      +
    368C  THR*     1.3    62.8    +      -       -      +
    411C  TRP*     5.5     7.0    -      -       +      -
    412C  THR      3.3     9.0    -      -       -      +
    413C  PHE*     4.5     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 368 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  PHE*     4.2    15.5    -      -       +      -
     35C  GLY*     2.9    22.8    +      -       -      +
     36C  ASN*     5.2     0.2    -      -       +      -
    344C  LYS*     3.9    21.5    -      -       +      -
    345C  ILE      3.4     3.4    -      -       -      -
    346C  THR*     2.7    31.2    +      -       -      +
    366C  PHE*     3.8     1.0    -      -       -      -
    367C  ALA*     1.3    73.5    +      -       -      +
    369C  TYR*     1.3    66.4    +      -       -      +
    411C  TRP*     3.0     8.0    -      -       -      +
    412C  THR*     2.7    54.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 369 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343C  TYR*     4.0    16.8    +      +       -      +
    344C  LYS*     3.4     2.4    -      -       -      +
    345C  ILE*     2.7    62.4    +      -       +      +
    368C  THR*     1.3    75.9    -      -       -      +
    370C  ALA*     1.3    61.4    +      -       -      +
    371C  LYS*     3.8    20.1    -      -       +      +
    409C  ASP*     2.4    46.8    +      -       -      -
    410C  GLU*     3.6    15.5    -      -       -      -
    411C  TRP*     4.3    13.5    -      +       +      -
----------------------------------------------------------
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Residues in contact with ALA 370 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  PHE*     3.6    41.1    -      -       +      -
    342C  GLN*     4.4     4.5    -      -       -      -
    343C  TYR      3.4     9.2    -      -       -      +
    344C  LYS*     4.3     7.2    -      -       +      -
    368C  THR*     4.6     0.4    -      -       -      +
    369C  TYR*     1.3    79.9    -      -       -      +
    371C  LYS*     1.3    60.7    +      -       -      +
    372C  TRP*     3.8    10.6    -      -       +      -
    409C  ASP*     3.5     4.3    -      -       -      +
    410C  GLU      3.0    31.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 371 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341C  ASN*     4.9     3.1    +      -       -      +
    342C  GLN*     3.3     3.0    -      -       -      +
    343C  TYR*     3.0    68.5    +      -       +      +
    369C  TYR*     3.8     7.6    -      -       +      +
    370C  ALA*     1.3    73.1    -      -       -      +
    372C  TRP*     1.3    87.0    +      -       -      +
    373C  ASP*     4.5     7.0    -      -       -      -
    407C  ASP*     2.9    26.1    +      -       -      -
    408C  SER*     3.3    12.6    +      -       -      +
    409C  ASP*     3.0    22.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 372 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21C  GLN*     6.1     0.2    -      -       -      -
     23C  PHE*     3.9    17.7    -      +       -      -
    341C  ASN*     3.3    13.5    -      -       -      +
    342C  GLN*     3.8    18.4    -      -       +      +
    370C  ALA*     3.8    20.9    -      -       +      -
    371C  LYS*     1.3    87.1    +      -       -      +
    373C  ASP*     1.3    62.0    +      -       -      +
    374C  GLU*     4.3     5.4    -      -       +      -
    405C  ARG*     3.1    65.2    +      -       +      +
    406C  GLY      3.4    13.9    -      -       -      -
    407C  ASP*     3.5     0.2    -      -       -      -
    408C  SER*     2.9    58.1    +      -       -      +
    409C  ASP      3.8    20.2    -      -       -      -
    410C  GLU*     3.8    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 373 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339C  LYS      4.1     2.4    -      -       -      +
    340C  ASN*     3.6     2.6    -      -       -      -
    341C  ASN*     2.9    47.6    +      -       -      +
    371C  LYS*     4.5     6.2    -      -       -      -
    372C  TRP*     1.3    77.6    -      -       -      +
    374C  GLU*     1.3    63.2    +      -       -      +
    375C  LYS*     3.7    34.5    +      -       -      +
    406C  GLY      3.5     2.9    -      -       -      -
    407C  ASP*     4.1    24.1    -      -       -      +
----------------------------------------------------------
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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