Contacts of the strand formed by residues 387 - 393 (chain C) in PDB entry 5U07


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 ASP 387 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153C  TRP*     3.2    24.1    -      -       +      -
    379C  PHE*     4.0    15.9    -      -       +      -
    381C  GLN*     3.3    13.0    -      -       +      +
    382C  ASP      4.7     0.4    -      -       -      +
    385C  ALA      4.4     5.6    -      -       -      +
    386C  ARG*     1.3    79.3    -      -       -      +
    388C  LYS*     1.3    61.4    +      -       -      +
     21N  PHE*     3.1    47.4    -      -       +      +
     22N  GLY      4.5     2.1    +      -       -      -
     23N  GLU*     4.4     1.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 388 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329C  GLU*     5.3     1.4    -      -       -      +
    330C  ALA*     3.8    18.2    -      -       -      +
    331C  GLU*     5.3     1.8    -      -       -      +
    380C  ASP*     3.0    49.4    +      -       +      +
    381C  GLN*     4.1     7.9    -      -       -      -
    382C  ASP      5.3     1.6    -      -       -      +
    387C  ASP*     1.3    76.1    -      -       -      +
    389C  GLN*     1.3    74.7    +      -       +      +
     19N  SER*     4.6     0.3    +      -       -      -
     21N  PHE*     3.7    17.7    -      -       -      +
     23N  GLU*     3.1    45.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 389 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330C  ALA*     3.8    25.6    -      -       +      +
    379C  PHE*     3.5     9.2    -      -       -      -
    380C  ASP*     2.5    50.1    +      -       -      +
    388C  LYS*     1.3    82.6    +      -       +      +
    390C  TRP*     1.3    72.1    +      -       -      +
    391C  PHE*     5.0     3.1    -      -       +      -
     18N  HIS*     3.5     6.5    -      -       -      +
     19N  SER*     2.9    39.2    +      -       -      -
     20N  MET      4.6     1.0    +      -       -      -
     21N  PHE*     4.8     4.0    -      -       -      -
     23N  GLU*     3.6    15.5    +      -       +      +
     25N  ASP*     2.9    32.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 390 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60C  PRO      4.6     4.7    +      -       -      -
     61C  LEU*     4.5    20.6    -      -       +      -
     62C  PRO*     3.1    38.4    -      -       +      +
     63C  PRO*     4.6     6.1    -      -       +      -
    153C  TRP*     4.8    12.6    -      -       +      -
    378C  GLY      3.2     8.7    -      -       -      +
    379C  PHE*     3.2    42.2    -      +       +      -
    389C  GLN*     1.3    77.8    +      -       -      +
    391C  PHE*     1.3    69.8    +      -       -      +
    392C  THR      5.4     0.2    -      -       -      -
     18N  HIS*     2.9    53.2    +      -       +      +
     20N  MET*     3.6    48.2    -      -       +      -
     21N  PHE*     3.5    25.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with PHE 391 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62C  PRO*     4.2     6.5    -      -       -      +
    219C  VAL*     4.6    11.4    -      -       +      -
    221C  TYR*     5.9     0.4    -      -       -      -
    328C  ALA*     4.1    18.4    -      -       +      -
    329C  GLU      4.2    19.3    -      -       -      -
    330C  ALA*     4.6     7.0    -      -       -      -
    332C  ARG*     5.7     5.4    -      -       -      -
    334C  ILE*     5.5     9.6    -      -       +      -
    376C  ALA*     3.6     3.2    -      -       +      +
    377C  PHE*     3.6     1.2    -      -       -      -
    378C  GLY*     2.9    68.6    +      -       -      -
    380C  ASP*     4.3    10.5    -      -       -      -
    389C  GLN*     4.9     3.4    -      -       +      -
    390C  TRP*     1.3    87.3    -      -       -      +
    392C  THR*     1.3    69.9    +      -       -      +
    393C  ALA*     4.8     9.6    -      -       +      -
     18N  HIS*     4.4    15.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 392 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62C  PRO*     4.9     4.1    -      -       -      +
    375C  ARG*     3.8    14.5    +      -       -      +
    376C  ALA      3.1     9.6    +      -       -      -
    377C  PHE*     3.6    25.5    -      -       -      -
    390C  TRP*     5.4     0.4    -      -       -      -
    391C  PHE*     1.3    80.2    -      -       -      +
    393C  ALA*     1.3    71.0    +      -       -      +
    394C  THR*     4.4     3.3    -      -       -      +
     18N  HIS*     6.1     0.4    -      -       -      +
    199N  VAL*     4.6    22.7    -      -       +      +
    200N  LEU*     6.0     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 393 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334C  ILE*     3.3    34.5    -      -       +      -
    375C  ARG*     3.5     1.6    -      -       -      -
    376C  ALA*     2.9    34.5    +      -       +      +
    391C  PHE*     4.8     7.9    -      -       +      -
    392C  THR*     1.3    81.4    +      -       -      +
    394C  THR*     1.3    61.1    +      -       -      +
    395C  THR*     3.0    14.0    +      -       +      +
----------------------------------------------------------
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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