Contacts of the strand formed by residues 470 - 477 (chain E) in PDB entry 5IIO


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 GLN 470 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    465E  GLU      3.5     2.1    -      -       -      +
    466E  GLU*     3.6     3.5    -      -       -      +
    467E  ASN*     2.8    44.6    +      -       +      +
    468E  GLY      4.3     0.9    -      -       -      +
    469E  GLN*     1.3    79.6    -      -       -      +
    471E  GLN*     1.3    61.4    +      -       -      +
    472E  LYS*     5.6     1.6    -      -       +      -
    492E  ILE*     4.1     5.7    -      -       +      +
    493E  VAL      3.5     4.3    -      -       -      -
    494E  VAL*     3.4    32.2    -      -       +      +
    495E  PRO*     4.3     0.2    -      -       +      -
    498E  GLU*     2.9    30.5    +      -       -      +
    502E  ALA*     4.2     2.2    -      -       -      +
    506E  PHE*     4.0    12.1    -      -       -      -
    529E  GLU*     2.9    41.6    +      -       -      +
    530E  HIS*     3.5    10.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 471 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    440E  HIS*     4.6     8.9    +      -       -      -
    441E  ARG*     5.3     2.8    -      -       -      +
    442E  GLY*     5.2     8.2    +      -       -      +
    444E  PHE*     3.5    46.0    -      -       +      +
    445E  SER*     5.2     1.2    +      -       -      -
    464E  GLN*     3.8    15.1    +      -       +      +
    465E  GLU      3.5     4.0    -      -       -      +
    466E  GLU*     3.4    23.6    -      -       -      +
    469E  GLN      4.7     6.7    +      -       -      +
    470E  GLN*     1.3    74.8    -      -       -      +
    472E  LYS*     1.3    60.8    +      -       -      +
    492E  ILE*     3.3     6.2    -      -       -      +
    493E  VAL*     2.9    52.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 472 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    444E  PHE*     3.5     5.1    -      -       -      -
    462E  VAL*     4.3     1.4    -      -       -      +
    464E  GLN*     3.5     4.9    -      -       -      -
    465E  GLU*     2.8    76.8    +      -       +      +
    467E  ASN*     6.1     0.2    -      -       -      +
    470E  GLN*     5.6     1.8    -      -       +      +
    471E  GLN*     1.3    74.5    -      -       -      +
    473E  TYR*     1.3    62.6    +      -       -      +
    474E  LEU*     3.7    27.3    +      -       +      +
    490E  ASP*     5.3     1.1    -      -       +      -
    491E  ILE      3.4     2.7    -      -       -      +
    492E  ILE*     3.9    27.4    -      -       +      -
    505E  TYR*     5.4     3.0    -      -       -      -
    506E  PHE*     4.2    13.2    -      -       +      -
    529E  GLU*     5.6     3.4    +      -       -      -
      6G    C      2.8    42.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 473 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    444E  PHE*     3.6    17.7    -      -       +      -
    448E  LEU*     3.5    31.9    -      -       +      -
    452E  ARG*     4.5     0.2    -      -       -      -
    457E  LEU*     3.8    31.7    -      -       +      +
    459E  ASP      3.0    15.2    +      -       -      -
    460E  ASP*     2.7    39.7    +      -       +      -
    462E  VAL      3.7     7.0    -      -       -      -
    463E  SER*     3.6     7.9    -      -       -      -
    472E  LYS*     1.3    72.9    -      -       -      +
    474E  LEU*     1.3    66.8    +      -       -      +
    475E  GLY*     3.4    23.1    -      -       -      -
    476E  VAL      3.7     2.1    +      -       -      -
    489E  LEU*     3.8    11.0    -      -       +      -
    490E  ASP*     3.2     7.6    -      -       -      +
    491E  ILE*     2.7    51.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 474 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342E  TRP*     4.2    13.9    -      -       +      -
    460E  ASP      3.9     0.5    -      -       -      -
    461E  LEU*     2.9    12.4    +      -       +      -
    462E  VAL*     2.8    65.5    +      -       +      +
    465E  GLU*     5.4     5.2    -      -       +      +
    472E  LYS*     3.7    27.1    +      -       +      +
    473E  TYR*     1.3    82.5    -      -       -      +
    475E  GLY*     1.3    58.3    +      -       -      +
    488E  ARG*     4.4     4.3    -      -       -      +
    490E  ASP*     3.2    34.1    -      -       -      +
      5G    A      5.8     0.7    -      -       -      +
      6G    C      3.8    26.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 475 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    459E  ASP      3.5     5.2    -      -       -      -
    461E  LEU*     3.8     9.0    -      -       -      -
    473E  TYR*     3.4    17.3    -      -       -      -
    474E  LEU*     1.3    75.4    -      -       -      +
    476E  VAL*     1.3    67.0    +      -       -      +
    488E  ARG*     3.0    23.2    +      -       -      +
    489E  LEU*     3.0    24.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 476 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    375E  ILE*     4.0    12.1    -      -       +      -
    379E  HIS*     3.9     5.2    -      -       +      -
    383E  PHE*     3.6    27.4    -      -       +      -
    457E  LEU*     3.4     8.9    -      -       -      +
    458E  THR*     2.9    39.2    +      -       -      +
    459E  ASP*     2.8    29.4    +      -       +      +
    461E  LEU*     4.2     8.5    -      -       +      -
    473E  TYR*     3.7     2.3    +      -       -      -
    475E  GLY*     1.3    79.0    -      -       -      +
    477E  CYS*     1.3    64.0    +      -       -      +
    486E  HIS*     3.7    26.2    -      -       +      -
    487E  ARG      3.4     8.1    -      -       -      +
    489E  LEU*     5.2     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 477 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    395E  ILE*     3.5    32.3    -      -       -      -
    456E  PHE*     3.2    42.2    -      -       +      +
    457E  LEU*     4.6     1.6    -      -       +      -
    458E  THR*     4.3     3.8    -      -       -      +
    476E  VAL*     1.3    75.4    -      -       -      +
    478E  ARG*     1.3    64.0    +      -       -      +
    486E  HIS*     3.4     2.4    -      -       -      -
    487E  ARG*     2.7    46.1    +      -       -      +
    489E  LEU*     3.9    22.4    -      -       +      +
----------------------------------------------------------
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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