Contacts of the strand formed by residues 470 - 477 (chain B) in PDB entry 3CB4


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 TYR 470 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81B  HIS*     4.7    14.1    -      +       -      -
     82B  VAL*     3.3    25.9    -      -       +      +
     83B  ASP*     3.7    14.1    +      -       -      +
    294B  GLN*     4.0    10.4    +      -       -      -
    345B  LEU*     3.7    37.9    +      -       +      +
    346B  LEU*     4.8     3.7    -      -       +      +
    404B  ALA*     4.3     5.2    -      -       +      -
    405B  GLU      3.3    10.3    -      -       -      +
    406B  CYS*     4.0    12.1    -      -       -      -
    447B  MET*     3.7    32.5    -      -       +      -
    450B  VAL*     4.1    21.5    -      -       +      -
    451B  VAL*     5.5     2.3    -      -       +      +
    455B  PHE*     6.1     2.5    -      +       +      -
    468B  LEU*     3.7    26.9    -      -       +      -
    469B  ASP*     1.3    79.9    -      -       -      +
    471B  ASN*     1.3    63.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 471 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82B  VAL*     5.4    10.0    -      -       +      +
     85B  SER*     5.7     4.3    -      -       -      +
    404B  ALA*     3.4     7.2    -      -       -      -
    405B  GLU*     3.0    38.7    +      -       -      +
    407B  HIS*     3.3    27.0    +      -       -      -
    447B  MET*     4.6     2.0    -      -       -      -
    469B  ASP*     4.7     3.3    -      -       -      +
    470B  TYR*     1.3    76.7    -      -       -      +
    472B  PHE*     1.3    79.7    +      -       -      +
    473B  LYS*     4.6     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 472 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294B  GLN*     5.4     6.9    +      -       +      +
    402B  PRO*     4.1    15.9    -      -       +      -
    403B  ILE      4.0     5.6    -      -       -      -
    447B  MET*     4.2    17.7    -      -       +      +
    471B  ASN*     1.3    86.1    +      -       -      +
    473B  LYS*     1.3    63.4    +      -       -      +
    474B  ARG*     3.7    30.7    -      -       -      -
    475B  PHE*     3.7    43.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with LYS 473 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    403B  ILE*     3.0    16.6    +      -       +      +
    404B  ALA      4.4     0.4    -      -       -      -
    405B  GLU*     3.2    53.0    +      -       +      +
    444B  GLU*     3.5    26.9    -      -       -      +
    471B  ASN*     4.8     3.1    -      -       -      +
    472B  PHE*     1.3    82.9    -      -       -      +
    474B  ARG*     1.3    73.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 474 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402B  PRO*     3.4     4.0    -      -       -      +
    403B  ILE*     2.7    54.0    +      -       +      +
    444B  GLU*     2.6    42.0    +      -       -      -
    472B  PHE*     3.7    15.7    -      -       -      -
    473B  LYS*     1.3    88.2    -      -       +      +
    475B  PHE*     1.3    78.4    -      -       -      +
    476B  GLN*     2.9    42.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 475 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    371B  VAL*     3.4    29.8    -      -       +      -
    373B  GLU*     3.5    50.7    -      -       +      +
    383B  TYR*     4.0    23.3    -      +       -      -
    400B  ARG*     3.7    23.2    -      -       +      -
    401B  GLU      3.5     1.1    -      -       -      -
    402B  PRO*     3.8    18.6    -      -       +      -
    472B  PHE*     3.7    25.8    -      +       -      -
    474B  ARG*     1.3    87.9    -      -       -      +
    476B  GLN*     1.3    61.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 476 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    400B  ARG*     3.4     7.5    -      -       -      +
    401B  GLU*     3.0    29.6    +      -       -      +
    403B  ILE*     4.1    15.0    -      -       +      +
    474B  ARG*     2.9    40.5    +      -       -      +
    475B  PHE*     1.3    76.0    -      -       -      +
    477B  ALA*     1.3    74.4    +      -       +      +
    478B  SER*     3.5     4.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 477 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    398B  GLU*     3.7    37.0    -      -       +      +
    399B  LEU      3.8     3.1    -      -       -      -
    400B  ARG*     3.3    12.6    -      -       -      +
    476B  GLN*     1.3    84.0    -      -       +      +
    478B  SER*     1.3    61.4    +      -       -      +
----------------------------------------------------------
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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