Contacts of the strand formed by residues 467 - 478 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    459A  LYS*     3.9    20.9    -      -       +      -
    460A  LEU      3.3     7.2    -      -       -      +
    461A  LYS*     3.6    33.4    -      -       +      -
    465A  PHE      3.5     6.7    +      -       -      +
    466A  GLU*     1.3    74.9    -      -       -      +
    468A  LYS*     1.3    72.1    +      -       -      +
    469A  THR*     4.8     3.8    -      -       +      -
    603A  PEG      3.6    45.5    -      -       -      +
      8C    G      4.6     7.8    +      -       -      +
      9C    A      5.1     6.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 468 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    458A  ILE      4.1     0.3    -      -       -      +
    459A  LYS*     3.7     1.2    -      -       -      -
    460A  LEU*     2.9    51.6    +      -       +      +
    462A  ASN*     6.1     2.5    -      -       -      +
    466A  GLU*     5.3     3.6    -      -       -      +
    467A  VAL*     1.3    78.9    -      -       -      +
    469A  THR*     1.3    65.1    +      -       -      +
    470A  ARG*     3.6    25.4    -      -       +      +
    495A  GLU*     3.8    21.0    +      -       +      +
    504A  LEU*     6.2     2.0    -      -       -      +
      8C    G      3.6    20.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 469 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    457A  THR*     3.8    14.6    -      -       +      +
    458A  ILE      3.2    12.6    -      -       -      +
    459A  LYS*     4.1    22.7    -      -       +      -
    467A  VAL*     4.8     4.9    -      -       +      -
    468A  LYS*     1.3    78.3    -      -       -      +
    470A  ARG*     1.3    84.9    +      -       -      +
    603A  PEG      5.9     2.0    -      -       -      +
      7C    G      3.7    21.2    +      -       -      +
      8C    G      3.1    21.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 470 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    457A  THR*     3.3     1.9    -      -       -      -
    458A  ILE*     2.9    41.4    +      -       +      -
    460A  LEU*     5.6     1.3    -      -       +      -
    468A  LYS*     3.6    33.3    -      -       +      +
    469A  THR*     1.3    89.2    +      -       -      +
    471A  ALA*     1.3    61.0    +      -       -      +
    491A  LEU*     3.6    24.8    -      -       +      +
    495A  GLU*     2.9    42.6    +      -       +      +
      7C    G      3.4    32.4    +      -       -      +
      8C    G      3.3    22.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 471 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    455A  THR*     4.3     5.8    -      -       +      -
    456A  VAL      3.2     5.4    -      -       -      +
    457A  THR*     3.5    23.1    -      -       +      +
    470A  ARG*     1.3    75.0    -      -       -      +
    472A  SER*     1.3    70.0    +      -       -      +
    491A  LEU*     3.6     6.7    -      -       -      +
      6C    C      3.9    28.4    +      -       +      +
      7C    G      2.7    22.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 472 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454A  ARG      3.6     1.0    -      -       -      +
    455A  THR*     3.3     2.1    -      -       -      -
    456A  VAL*     2.9    31.7    +      -       -      +
    471A  ALA*     1.3    81.1    +      -       -      +
    473A  THR*     1.3    63.8    +      -       -      +
    474A  VAL*     4.5     7.0    -      -       -      +
    487A  ILE*     3.6    26.3    -      -       -      +
    490A  GLU*     5.9     1.4    -      -       -      +
    491A  LEU*     3.3    17.7    -      -       -      +
      6C    C      3.4     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 473 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454A  ARG*     3.2    37.0    -      -       -      +
    455A  THR*     2.8    22.5    +      -       -      +
    472A  SER*     1.3    75.5    -      -       -      +
    474A  VAL*     1.3    65.9    +      -       -      +
    515A  SER*     4.9     0.4    -      -       -      +
      5C    G      3.4    24.3    +      -       -      +
      6C    C      2.7    29.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 474 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454A  ARG*     2.8    40.4    +      -       +      +
    472A  SER*     4.5     8.7    -      -       -      +
    473A  THR*     1.3    81.3    -      -       -      +
    475A  SER*     1.3    66.7    +      -       -      +
    476A  SER      3.2    22.0    -      -       -      +
    478A  VAL*     4.4    14.6    -      -       +      -
    487A  ILE*     3.8    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 475 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454A  ARG*     3.9    11.7    +      -       -      +
    474A  VAL*     1.3    77.3    -      -       -      +
    476A  SER*     1.3    66.7    +      -       -      +
    477A  VAL*     5.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 476 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    454A  ARG*     3.8     2.6    -      -       -      +
    474A  VAL*     3.2    23.3    -      -       -      +
    475A  SER*     1.3    82.7    -      -       -      +
    477A  VAL*     1.3    71.1    +      -       -      +
    478A  VAL*     4.1     1.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 477 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    452A  LYS*     3.7    51.9    -      -       +      +
    453A  GLY*     3.5     9.6    -      -       -      +
    454A  ARG*     4.0    19.3    -      -       +      -
    476A  SER*     1.3    82.2    -      -       -      +
    478A  VAL*     1.3    63.3    +      -       -      +
    483A  GLU*     5.4     1.2    -      -       -      +
    515A  SER      5.1     0.2    -      -       -      +
    517A  PRO*     4.7    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 478 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    451A  LEU      4.6     0.2    -      -       -      +
    452A  LYS*     3.6     2.9    -      -       -      -
    453A  GLY      2.6    36.2    +      -       -      +
    454A  ARG*     5.1     0.4    -      -       -      -
    456A  VAL*     4.9     3.1    -      -       +      -
    474A  VAL*     4.4    13.5    -      -       +      -
    476A  SER      4.1     7.9    -      -       -      +
    477A  VAL*     1.3    78.9    -      -       -      +
    479A  SER*     1.3    66.0    +      -       -      +
    483A  GLU*     3.5    36.1    -      -       +      +
    484A  ILE*     3.6    25.6    -      -       +      +
    487A  ILE*     4.6    13.7    -      -       +      -
    513A  ILE*     3.8     9.3    -      -       +      +
----------------------------------------------------------
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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