Contacts of the strand formed by residues 668 - 672 (chain B) in PDB entry 3UO8


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 LEU 668 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    614B  ILE      3.8     0.2    -      -       -      +
    615B  TYR*     3.0     5.0    -      -       -      -
    616B  THR*     2.9    41.0    +      -       -      +
    629B  ASP*     6.1     1.6    -      -       +      +
    630B  ALA      3.6    24.0    -      -       -      +
    631B  TYR*     4.9     2.2    -      -       +      -
    647B  ASN*     3.9    35.9    -      -       +      +
    648B  LYS      3.2    15.3    -      -       -      +
    649B  GLY*     4.1     6.3    -      -       -      +
    667B  CYS*     1.3    80.2    -      -       -      +
    669B  TYR*     1.3    61.9    +      -       -      +
    670B  THR*     5.3     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 669 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    613B  ILE*     4.2     7.6    -      -       +      -
    614B  ILE      3.3     6.1    -      -       -      +
    615B  TYR*     3.4    30.5    -      +       +      -
    647B  ASN      3.2     4.0    +      -       -      -
    648B  LYS      2.8    37.3    +      -       -      +
    649B  GLY      3.3    14.8    +      -       -      -
    650B  THR      3.7     0.9    -      -       -      -
    651B  PRO*     3.6    50.2    -      -       +      +
    654B  THR*     3.4    12.7    -      -       +      +
    660B  SER*     5.6     2.8    +      -       -      -
    663B  LEU*     4.2    13.2    -      -       +      -
    664B  PRO      2.8    27.8    +      -       -      -
    665B  LYS*     3.6     1.7    -      -       -      -
    666B  HIS      3.5     6.6    +      -       -      -
    667B  CYS*     3.2    35.0    +      -       +      -
    668B  LEU*     1.3    73.2    -      -       -      +
    670B  THR*     1.3    63.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 670 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    613B  ILE*     3.5     6.0    -      -       -      +
    614B  ILE*     2.9    38.6    +      -       -      +
    632B  VAL*     3.4    19.7    -      -       -      +
    635B  PHE*     4.1    14.8    -      -       +      -
    641B  ILE*     4.9     4.0    -      -       +      -
    645B  ASP      5.4     0.2    -      -       -      +
    646B  ALA*     3.7    19.2    -      -       +      +
    647B  ASN*     3.0    23.4    +      -       -      +
    654B  THR*     4.2     3.6    -      -       -      -
    668B  LEU      5.3     0.3    +      -       -      -
    669B  TYR*     1.3    72.2    +      -       -      +
    671B  ARG*     1.3    63.5    +      -       -      +
    672B  LEU*     3.6    23.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 671 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363B  LEU*     3.8    19.8    -      -       -      +
    384B  LEU*     4.1    12.5    -      -       -      +
    607B  GLU*     3.1    32.3    +      -       -      -
    611B  VAL*     3.6    21.6    -      -       +      +
    613B  ILE*     3.5    13.9    -      -       +      -
    641B  ILE*     4.2    10.6    -      -       -      +
    645B  ASP      5.1     2.4    +      -       -      -
    654B  THR*     3.5    40.5    +      -       -      +
    655B  GLY      3.5    12.9    +      -       -      -
    656B  SER*     3.5    14.5    -      -       -      +
    670B  THR*     1.3    74.3    -      -       -      +
    672B  LEU*     1.3    67.7    +      -       -      +
    673B  SER*     3.7    24.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 672 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    611B  VAL*     3.4     3.5    -      -       -      -
    612B  MET*     2.8    45.5    +      -       +      +
    614B  ILE*     3.2    33.2    -      -       +      -
    635B  PHE*     4.0    15.3    -      -       +      -
    639B  LEU*     4.7     4.3    -      -       +      -
    641B  ILE*     4.0    24.5    -      -       +      -
    670B  THR*     3.6    22.9    -      -       +      +
    671B  ARG*     1.3    80.3    -      -       -      +
    673B  SER*     1.3    63.0    +      -       -      +
    675B  LEU*     3.8    17.2    -      -       +      +
    682B  LEU*     4.0    25.6    -      -       +      -
----------------------------------------------------------
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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