Contacts of the strand formed by residues 467 - 478 (chain B) in PDB entry 4U7C


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 467 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    459B  LYS*     3.8    32.3    -      -       +      -
    460B  LEU      3.4     7.0    -      -       -      +
    461B  LYS*     3.6    31.9    -      -       +      +
    465B  PHE      3.5     6.7    +      -       -      +
    466B  GLU*     1.3    76.3    -      -       -      +
    468B  LYS*     1.3    69.8    +      -       -      +
    469B  THR*     4.9     4.7    -      -       +      -
      8P    G      4.7     7.8    +      -       -      +
      9P    A      5.1     6.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 468 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    458B  ILE      4.1     0.2    -      -       -      +
    459B  LYS*     3.7     1.4    -      -       -      +
    460B  LEU*     2.9    52.8    +      -       +      +
    462B  ASN*     6.1     3.6    -      -       -      +
    466B  GLU*     5.2     4.3    -      -       -      +
    467B  VAL*     1.3    78.9    -      -       -      +
    469B  THR*     1.3    64.9    +      -       -      +
    470B  ARG*     3.7    26.9    -      -       +      +
    495B  GLU*     4.0    16.7    +      -       -      +
    499B  ASP*     4.9     9.9    +      -       -      -
    504B  LEU*     6.2     2.0    -      -       -      +
      8P    G      3.5    21.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 469 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    457B  THR*     3.8    15.2    -      -       +      +
    458B  ILE      3.2    11.9    -      -       -      +
    459B  LYS*     4.2    22.0    -      -       +      -
    467B  VAL*     4.9     5.4    -      -       +      -
    468B  LYS*     1.3    78.4    -      -       -      +
    470B  ARG*     1.3    86.5    +      -       -      +
      7P    G      3.5    20.1    +      -       -      +
      8P    G      3.1    21.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 470 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    457B  THR*     3.2     2.7    -      -       -      -
    458B  ILE*     2.9    46.9    +      -       +      +
    460B  LEU*     5.4     2.7    -      -       +      -
    468B  LYS*     3.7    30.4    -      -       +      +
    469B  THR*     1.3    89.8    +      -       -      +
    471B  ALA*     1.3    61.9    +      -       -      +
    491B  LEU*     3.8    19.3    -      -       +      +
    495B  GLU*     3.0    42.1    +      -       +      +
      7P    G      3.3    41.1    +      -       -      +
      8P    G      3.4    11.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 471 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    455B  THR*     4.4     5.8    -      -       +      -
    456B  VAL      3.2     5.6    -      -       -      +
    457B  THR*     3.4    24.7    -      -       +      +
    470B  ARG*     1.3    75.1    -      -       -      +
    472B  SER*     1.3    69.6    +      -       -      +
    491B  LEU*     3.6     7.2    -      -       -      +
      6P    C      4.0    28.9    +      -       +      +
      7P    G      2.5    21.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 472 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454B  ARG      3.8     1.0    -      -       -      +
    455B  THR*     3.4     1.8    -      -       -      -
    456B  VAL*     2.9    31.5    +      -       -      +
    471B  ALA*     1.3    80.7    +      -       -      +
    473B  THR*     1.3    65.7    +      -       -      +
    474B  VAL*     4.1     6.5    +      -       -      +
    487B  ILE*     3.6    25.7    -      -       -      +
    490B  GLU*     5.6     2.6    -      -       -      +
    491B  LEU*     3.2    17.9    -      -       -      +
      6P    C      3.2     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 473 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454B  ARG*     3.2    37.9    -      -       -      +
    455B  THR*     2.8    24.5    +      -       -      +
    472B  SER*     1.3    74.1    -      -       -      +
    474B  VAL*     1.3    64.8    +      -       -      +
    515B  SER*     4.9     0.7    -      -       -      +
      5P    G      3.4    25.9    +      -       -      +
      6P    C      2.6    33.7    +      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
    454B  ARG*     2.8    43.2    +      -       +      +
    472B  SER*     4.6     6.3    -      -       -      +
    473B  THR*     1.3    80.8    -      -       -      +
    475B  SER*     1.3    67.3    +      -       -      +
    476B  SER      3.3    21.3    -      -       -      +
    478B  VAL*     4.4    15.0    -      -       +      -
    487B  ILE*     3.9    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 475 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454B  ARG*     3.8    13.1    +      -       -      +
    474B  VAL*     1.3    77.3    -      -       -      +
    476B  SER*     1.3    65.8    +      -       -      +
    477B  VAL      4.2     0.2    +      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
    454B  ARG*     3.8     3.1    -      -       -      +
    474B  VAL*     3.3    21.9    -      -       -      +
    475B  SER*     1.3    82.9    -      -       -      +
    477B  VAL*     1.3    71.3    +      -       -      +
    478B  VAL*     4.1     2.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 477 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    452B  LYS*     3.7    53.1    -      -       +      +
    453B  GLY*     3.5    14.8    -      -       -      +
    454B  ARG*     4.0    12.6    -      -       +      -
    475B  SER      4.2     0.6    +      -       -      -
    476B  SER*     1.3    82.1    -      -       -      +
    478B  VAL*     1.3    61.7    +      -       -      +
    483B  GLU*     5.4     0.9    -      -       -      +
    515B  SER      5.2     0.7    -      -       -      +
    517B  PRO*     4.4    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 478 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    452B  LYS*     3.6     3.0    -      -       -      -
    453B  GLY      2.7    34.4    +      -       -      +
    454B  ARG*     5.1     0.4    -      -       -      -
    456B  VAL*     4.9     2.5    -      -       +      -
    474B  VAL*     4.4    13.5    -      -       +      -
    476B  SER      4.1     7.6    -      -       -      +
    477B  VAL*     1.3    80.2    -      -       -      +
    479B  SER*     1.3    66.4    +      -       -      +
    483B  GLU*     3.4    36.3    -      -       +      +
    484B  ILE*     3.7    24.2    -      -       +      +
    487B  ILE*     4.5    13.5    -      -       +      -
    513B  ILE*     3.8    10.3    -      -       +      +
----------------------------------------------------------
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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