Contacts of the strand formed by residues 413 - 419 (chain B) in PDB entry 3FO5


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 VAL 413 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    409B  GLU*     3.2     4.2    -      -       -      -
    410B  ILE      2.9    34.6    +      -       -      +
    411B  SER*     3.0    16.7    -      -       -      +
    412B  GLN*     1.3    80.8    -      -       -      +
    414B  ARG*     1.3    63.8    +      -       -      +
    428B  MET*     3.4    29.6    -      -       +      -
    429B  GLU      3.4    11.0    -      -       -      +
    430B  MET*     4.2    15.9    -      -       +      -
    570B  TYR*     3.4    12.0    -      -       +      +
    573B  PHE*     3.8    16.4    -      -       +      -
    574B  LYS*     6.3     1.6    -      -       -      +
    577B  GLU*     6.1     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 414 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    406B  LEU*     3.8    15.4    -      -       +      +
    408B  SER      3.6     3.1    -      -       -      -
    409B  GLU*     3.4    39.8    +      -       -      +
    412B  GLN      4.9     2.5    -      -       -      +
    413B  VAL*     1.3    73.8    -      -       -      +
    415B  LEU*     1.3    61.3    +      -       -      +
    416B  TYR*     3.3    37.7    +      -       +      -
    427B  HIS      3.8     0.9    -      -       -      +
    428B  MET*     3.2     9.1    -      -       -      +
    429B  GLU*     2.9    50.1    +      -       +      +
    543B  LYS*     5.6     1.8    -      -       -      +
    570B  TYR*     4.2     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 415 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    406B  LEU*     3.7     2.8    -      -       -      +
    407B  SER*     2.8    31.3    +      -       -      -
    408B  SER*     3.0    24.4    +      -       -      +
    414B  ARG*     1.3    72.9    -      -       -      +
    416B  TYR*     1.3    66.1    +      -       -      +
    426B  PHE*     4.1    12.6    -      -       +      -
    427B  HIS      3.5     6.7    -      -       -      +
    428B  MET*     3.5    24.2    -      -       +      -
    561B  ASN      4.1    21.8    -      -       -      +
    562B  VAL*     4.1    19.1    -      -       +      +
    569B  PHE*     4.0    21.3    -      -       +      -
    570B  TYR*     3.4    26.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 416 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    404B  TRP*     3.8    12.3    -      -       +      -
    405B  VAL*     3.2    11.9    -      -       -      -
    406B  LEU*     3.6    36.1    -      -       +      +
    414B  ARG*     3.3    47.3    +      -       +      -
    415B  LEU*     1.3    76.4    -      -       -      +
    417B  THR*     1.3    64.8    +      -       -      +
    426B  PHE*     3.2     8.0    -      -       -      +
    427B  HIS*     2.8    68.3    +      +       +      +
    429B  GLU*     3.4    29.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 417 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    403B  ASN      3.7     1.4    -      -       -      +
    404B  TRP*     3.4     5.9    -      -       -      -
    405B  VAL*     2.8    41.6    +      -       -      +
    407B  SER*     3.2    23.9    +      -       -      +
    415B  LEU*     5.1     1.1    -      -       +      -
    416B  TYR*     1.3    78.8    -      -       -      +
    418B  LEU*     1.3    60.8    +      -       -      +
    419B  GLU*     4.1    15.6    +      -       -      +
    424B  LEU*     4.2    10.9    -      -       +      +
    425B  SER      3.2    12.3    -      -       -      +
    426B  PHE*     4.4     1.1    -      -       +      -
    562B  VAL*     3.6    36.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 418 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    398B  LEU*     4.1    10.5    -      -       +      -
    401B  LYS*     3.6    28.0    -      -       +      -
    403B  ASN*     3.1    56.8    -      -       -      +
    404B  TRP*     3.5    31.2    -      -       +      +
    417B  THR*     1.3    74.0    -      -       -      +
    419B  GLU*     1.3    61.9    +      -       -      +
    420B  ASP*     3.3    18.5    +      -       -      +
    423B  PHE      3.3     0.7    -      -       -      +
    424B  LEU      3.7     1.0    -      -       -      -
    425B  SER*     2.8    50.3    +      -       -      +
    549B  GLN*     5.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 419 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356B  LYS*     5.6     3.5    -      -       -      -
    359B  ARG*     3.8    17.5    +      -       -      -
    360B  LEU*     3.7    26.0    -      -       -      +
    363B  LYS*     3.7    22.2    +      -       -      +
    364B  TYR*     2.9    17.6    +      -       -      +
    403B  ASN*     4.8     8.4    +      -       -      +
    417B  THR*     4.3    12.6    +      -       -      +
    418B  LEU*     1.3    72.7    -      -       -      +
    420B  ASP*     1.3    64.6    +      -       -      +
    423B  PHE      3.9     0.7    -      -       -      -
    424B  LEU*     4.0    14.1    -      -       +      +
----------------------------------------------------------
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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