Contacts of the strand formed by residues 469 - 476 (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 ASP 469 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    388B  SER*     2.6    33.8    +      -       -      -
    464B  GLN*     3.4     2.0    +      -       -      +
    465B  VAL*     2.9    35.5    +      -       +      -
    466B  ASP*     2.5    45.8    +      -       -      +
    467B  GLU      3.7     0.4    +      -       -      -
    468B  ASP*     1.3    82.6    -      -       -      +
    470B  ALA*     1.3    64.1    +      -       -      +
    491B  LEU*     4.7     5.8    -      -       +      -
    492B  ALA      3.2     6.3    -      -       -      +
    493B  SER*     2.7    24.3    +      -       -      +
    495B  ARG*     3.5     8.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 470 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461B  LEU*     3.7    17.3    -      -       +      -
    463B  GLN      3.4     7.2    -      -       -      +
    464B  GLN*     4.1    12.1    -      -       -      +
    465B  VAL*     4.1     1.8    -      -       -      +
    469B  ASP*     1.3    76.7    -      -       -      +
    471B  ILE*     1.3    62.1    +      -       -      +
    472B  TYR*     3.6    26.7    -      -       +      +
    490B  ILE      3.6     0.9    -      -       -      +
    491B  LEU*     3.5     4.1    -      -       -      +
    492B  ALA*     2.7    40.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 471 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    379B  TRP*     3.6    41.7    -      -       +      +
    461B  LEU*     3.3     6.2    -      -       -      +
    462B  VAL*     2.8    38.4    +      -       +      -
    463B  GLN*     2.9    36.4    +      -       +      +
    465B  VAL*     4.1     4.9    -      -       +      -
    470B  ALA*     1.3    75.9    -      -       -      +
    472B  TYR*     1.3    58.9    +      -       -      +
    489B  VAL*     3.8    27.8    -      -       +      -
    490B  ILE      3.2     6.7    -      -       -      +
    491B  LEU*     4.0    16.4    -      -       +      -
    511B  VAL*     4.1     8.5    -      -       +      -
    513B  LEU*     4.2    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 472 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    444B  SER      4.1     7.8    +      -       -      -
    445B  ASP*     4.4     5.5    +      -       -      -
    446B  LEU*     3.8    37.2    +      -       +      -
    447B  ARG*     4.1    16.3    +      -       +      +
    459B  VAL*     3.4    26.7    -      -       +      -
    460B  GLU      3.2    10.5    -      -       -      +
    461B  LEU*     4.0    17.9    -      -       +      +
    462B  VAL*     4.0     4.7    -      -       -      -
    464B  GLN*     5.5     1.0    +      -       -      -
    470B  ALA*     3.6    32.5    -      -       +      +
    471B  ILE*     1.3    75.8    -      -       -      +
    473B  HIS*     1.3    59.5    +      -       -      +
    474B  VAL*     3.9    17.0    +      -       +      -
    488B  PHE      3.7     0.5    -      -       -      +
    489B  VAL*     3.4     4.9    -      -       -      +
    490B  ILE*     2.8    35.9    +      -       +      +
    492B  ALA*     3.8    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 473 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    458B  SER*     4.0     1.0    +      -       -      +
    459B  VAL*     3.5     2.8    -      -       -      -
    460B  GLU*     2.7    62.2    +      -       -      +
    462B  VAL*     3.7    16.8    -      -       +      +
    472B  TYR*     1.3    72.9    -      -       -      +
    474B  VAL*     1.3    61.1    +      -       -      +
    475B  THR*     4.1    18.9    +      -       +      +
    487B  ASP*     2.7    34.0    +      -       +      +
    488B  PHE      3.3    15.5    -      -       -      -
    489B  VAL*     4.1    15.0    -      -       +      +
    516B  HIS*     4.9    11.2    -      +       +      -
    522B  TYR*     4.6     9.9    -      +       -      -
    524B  ARG*     4.0     2.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 474 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  1PE      5.5     2.2    -      -       -      +
    446B  LEU*     5.2     2.0    -      -       +      -
    455B  HIS      5.4     0.7    -      -       -      +
    456B  TYR*     3.7    41.1    -      -       +      +
    458B  SER      3.4    10.5    -      -       -      +
    459B  VAL*     4.2     5.4    -      -       +      -
    472B  TYR*     4.1    17.9    -      -       +      +
    473B  HIS*     1.3    77.7    -      -       -      +
    475B  THR*     1.3    73.7    +      -       -      +
    476B  SER*     5.4     0.9    -      -       -      -
    487B  ASP*     3.1     4.9    -      -       -      +
    488B  PHE*     2.7    56.6    +      -       +      +
    490B  ILE*     4.0    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 475 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    456B  TYR*     3.8     0.3    -      -       -      -
    457B  ARG*     2.9    47.0    +      -       -      -
    458B  SER*     2.4    37.9    +      -       -      +
    473B  HIS*     4.1    13.0    -      -       +      +
    474B  VAL*     1.3    84.5    -      -       -      +
    476B  SER*     1.3    61.4    +      -       -      +
    486B  GLN      3.3     8.1    -      -       -      -
    487B  ASP*     4.0     8.7    -      -       +      -
    522B  TYR*     3.7    30.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 476 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  1PE      4.2    11.1    +      -       -      -
    455B  HIS*     2.8    22.6    +      -       -      +
    457B  ARG*     4.3     2.7    -      -       -      -
    474B  VAL*     5.4     0.4    -      -       -      -
    475B  THR*     1.3    76.1    -      -       -      +
    477B  PRO*     1.4    74.9    +      -       -      +
    479B  LEU*     5.5     3.3    -      -       -      +
    485B  PRO*     3.2     7.5    -      -       -      +
    486B  GLN*     2.8    38.1    +      -       -      -
    488B  PHE*     3.9    24.7    -      -       -      -
----------------------------------------------------------
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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