Contacts of the strand formed by residues 459 - 469 (chain B) in PDB entry 1F6A


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 LYS 459 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    452B  GLU*     5.5     2.3    -      -       -      -
    453B  TRP      5.8     0.2    +      -       -      -
    456B  SER*     3.6    33.9    +      -       -      +
    457B  ARG      3.7     1.6    -      -       -      -
    458B  ASP*     1.3    86.8    -      -       +      +
    460B  ARG*     1.3    68.8    +      -       -      +
    461B  THR*     5.6     0.4    -      -       -      -
    511B  VAL      3.8    10.1    -      -       -      +
    512B  THR*     5.8     2.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 460 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    450B  THR*     3.6    22.8    +      -       -      +
    451B  PRO*     4.2     4.6    -      -       -      +
    452B  GLU*     3.0    60.3    +      -       +      +
    457B  ARG      5.6     3.1    +      -       -      +
    458B  ASP      4.3     0.2    -      -       -      -
    459B  LYS*     1.3    81.2    -      -       -      +
    461B  THR*     1.3    62.5    +      -       -      +
    462B  LEU*     5.2     3.7    -      -       +      +
    510B  GLU*     5.1     0.4    -      -       -      -
    511B  VAL*     3.1    36.8    +      -       +      +
    516B  TRP*     4.4    30.8    -      -       +      -
    543B  VAL*     2.9    40.7    -      -       +      +
    544B  ASN*     4.6     7.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 461 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    449B  ALA*     3.8     0.3    -      -       -      -
    450B  THR*     3.1    45.5    +      -       -      +
    459B  LYS      5.4     0.5    +      -       -      -
    460B  ARG*     1.3    74.2    -      -       -      +
    462B  LEU*     1.3    76.3    +      -       -      +
    508B  ARG*     3.7    23.4    +      -       +      +
    510B  GLU*     4.6    12.1    -      -       +      +
    465D  LEU*     4.3     7.4    -      -       +      -
    467D  GLN*     3.1    39.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 462 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    448B  PHE      3.4    17.7    -      -       -      +
    449B  ALA*     3.6    18.2    -      -       +      -
    460B  ARG*     5.2     4.0    -      -       +      +
    461B  THR*     1.3    86.2    -      -       -      +
    463B  ALA*     1.3    61.6    +      -       -      +
    478B  TRP*     3.8    28.9    -      -       +      -
    508B  ARG*     3.4     5.5    -      -       -      +
    509B  LEU*     3.1    40.3    +      -       +      +
    511B  VAL*     4.2    10.8    -      -       +      -
    522B  PHE*     3.4    39.0    -      -       +      -
    541B  VAL*     4.0     9.4    -      -       +      -
    542B  SER*     5.9     1.1    -      -       -      +
    543B  VAL*     5.5     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 463 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    447B  ALA*     3.7     1.9    -      -       -      +
    448B  PHE*     2.9    44.2    +      -       +      +
    461B  THR      4.4     0.2    +      -       -      -
    462B  LEU*     1.3    76.5    -      -       -      +
    464B  CYS*     1.3    63.0    +      -       -      +
    465B  LEU      4.3     0.2    -      -       -      -
    478B  TRP*     4.3     3.1    -      -       -      -
    506B  PHE*     6.1     1.8    -      -       +      -
    507B  SER      3.2     6.7    -      -       -      -
    448D  PHE*     5.8     6.1    -      -       +      -
    465D  LEU*     4.5     8.1    -      -       +      -
    506D  PHE*     3.7    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 464 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    445B  VAL*     3.5    24.7    -      -       -      -
    446B  TYR      3.8     5.6    -      -       -      -
    447B  ALA*     4.4     4.5    -      -       -      +
    463B  ALA*     1.3    77.0    -      -       -      +
    465B  LEU*     1.3    57.9    +      -       -      +
    466B  ILE*     4.0     7.4    +      -       -      +
    478B  TRP*     3.8    15.0    -      -       +      -
    505B  VAL      3.9     1.2    -      -       -      +
    506B  PHE*     3.7     5.4    -      -       -      -
    507B  SER*     3.0    33.2    +      -       -      +
    524B  CYS*     2.0    49.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 465 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    444B  GLU      3.4     1.6    -      -       -      +
    445B  VAL*     3.2     3.6    -      -       -      -
    446B  TYR*     3.1    40.7    +      -       +      +
    448B  PHE*     5.0     9.1    -      -       +      -
    463B  ALA      4.3     0.2    -      -       -      -
    464B  CYS*     1.3    70.7    -      -       -      +
    466B  ILE*     1.3    87.7    +      -       -      +
    467B  GLN*     3.9    29.6    -      -       +      +
    504B  PHE*     4.4    11.0    -      -       +      -
    505B  VAL      3.8     5.2    -      -       -      +
    506B  PHE*     3.1    38.8    -      -       +      -
    450D  THR*     5.1     7.0    -      -       -      +
    461D  THR*     4.3    14.8    -      -       +      -
    463D  ALA*     4.5    11.2    -      -       +      -
    508D  ARG*     4.6     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 466 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    443B  PRO*     3.6    31.2    -      -       +      -
    444B  GLU      3.2     6.7    -      -       -      +
    445B  VAL*     4.2    13.0    -      -       +      -
    464B  CYS*     4.3    13.2    -      -       -      +
    465B  LEU*     1.3    81.2    -      -       -      +
    467B  GLN*     1.3    61.4    +      -       -      +
    469B  PHE*     3.3     5.2    -      -       +      -
    474B  ILE*     3.6    14.4    -      -       +      -
    476B  VAL*     3.5    37.9    -      -       +      -
    504B  PHE*     3.2     2.4    -      -       -      -
    505B  VAL*     2.9    40.7    +      -       +      +
    507B  SER*     6.2     0.2    -      -       -      -
    524B  CYS*     4.6     0.7    -      -       -      -
    525B  ARG      4.5     2.2    -      -       -      +
    526B  ALA*     3.7    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 467 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    443B  PRO*     3.7     0.5    -      -       -      +
    444B  GLU*     2.8    47.6    +      -       +      +
    446B  TYR*     4.1    13.3    +      -       +      -
    465B  LEU*     3.9    11.3    -      -       +      +
    466B  ILE*     1.3    74.6    -      -       -      +
    468B  ASN*     1.3    95.4    +      -       -      +
    469B  PHE*     3.2     6.8    +      -       -      -
    503B  PHE      3.3     7.6    -      -       -      -
    504B  PHE*     3.7    14.4    -      -       +      -
    450D  THR*     5.8     0.2    -      -       -      +
    461D  THR*     3.0    32.8    +      -       -      +
    508D  ARG*     2.9    35.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 468 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    441B  ALA*     4.0     8.8    -      -       -      +
    442B  ALA      2.8    16.5    -      -       -      +
    444B  GLU*     2.6    42.0    +      -       -      +
    467B  GLN*     1.3    98.7    -      -       -      +
    469B  PHE*     1.3    56.8    +      -       -      +
    470B  MET*     5.9     0.2    -      -       -      -
    498B  THR*     4.2     9.1    +      -       -      -
    500B  GLY*     5.4     7.1    -      -       -      +
    502B  GLY*     4.3    12.5    -      -       -      -
    503B  PHE      2.9     9.5    +      -       -      +
    508D  ARG*     4.1    14.6    +      -       -      -
    510D  GLU*     4.5     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 469 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    441B  ALA      3.0    12.8    -      -       -      +
    442B  ALA      3.8     5.4    -      -       -      +
    443B  PRO*     3.8     9.2    -      -       +      -
    466B  ILE*     3.3    22.0    -      -       +      -
    467B  GLN*     3.5    11.2    -      -       -      -
    468B  ASN*     1.3    77.7    -      -       -      +
    470B  MET*     1.3    69.2    +      -       -      +
    471B  PRO      3.4    12.8    -      -       -      -
    472B  GLU      4.0     8.7    -      -       -      -
    474B  ILE*     3.8    36.8    -      -       +      -
    495B  PRO*     4.9     3.1    -      -       +      -
    502B  GLY*     3.4     1.6    -      -       -      -
    503B  PHE*     2.8    73.2    +      -       +      -
    504B  PHE*     3.6     4.5    -      -       -      -
    505B  VAL*     4.4     7.2    -      -       +      -
    528B  HIS*     3.2    31.2    -      +       +      +
----------------------------------------------------------
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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