Contacts of the strand formed by residues 68 - 76 (chain N) in PDB entry 5U0A


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 68 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    472C  ARG*     4.6     7.0    -      -       -      +
    476C  LYS*     4.6    19.7    -      -       +      +
     29D  VAL*     3.5    39.5    -      -       +      -
     67N  GLY*     1.3    77.1    -      -       -      -
     69N  ARG*     1.3    67.4    +      -       -      +
     70N  LEU*     3.8     9.5    +      -       +      -
    108N  LEU*     3.6     2.2    -      -       -      -
    109N  ALA*     2.7    39.0    +      -       -      +
    110N  ASP*     5.0     4.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 69 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334C  ILE*     2.6    53.7    +      -       -      +
    471C  SER*     4.4     9.8    +      -       -      -
    472C  ARG*     4.5     7.6    +      -       -      -
    475C  ALA*     4.0    30.0    -      -       +      +
     25N  ASP*     2.3    31.3    +      -       -      -
     26N  THR*     2.7    32.0    +      -       -      +
     28N  PRO*     4.9    11.9    -      -       -      +
     67N  GLY      3.9     2.2    +      -       -      +
     68N  VAL*     1.3    76.7    -      -       -      +
     70N  LEU*     1.3    72.9    -      -       -      +
     71N  VAL*     6.6     0.2    -      -       -      -
    106N  SER*     4.5     7.9    -      -       -      -
    107N  TYR      3.6     9.0    -      -       -      +
    108N  LEU*     4.3    14.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 70 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    471C  SER*     6.0     0.7    -      -       -      -
    472C  ARG*     2.7    36.6    -      -       -      +
     27D  THR*     4.0     9.4    -      -       -      +
     29D  VAL*     3.6    39.9    -      -       +      +
     34D  GLU*     6.1     0.4    -      -       -      +
     68N  VAL*     4.4     8.3    -      -       +      +
     69N  ARG*     1.3    80.4    -      -       -      +
     71N  VAL*     1.3    61.2    +      -       -      +
    106N  SER*     3.5     2.4    -      -       -      -
    107N  TYR*     2.9    66.8    +      -       +      +
    109N  ALA*     4.0     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 71 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    467C  GLN*     5.5     4.3    -      -       +      +
    468C  HIS*     3.4    37.6    -      -       +      +
    471C  SER*     4.7    18.1    +      -       -      +
     23N  GLU*     5.7     2.2    -      -       -      +
     69N  ARG*     6.6     0.2    -      -       -      -
     70N  LEU*     1.3    73.3    -      -       -      +
     72N  ASP*     1.3    61.1    +      -       -      +
     73N  PHE*     3.7     2.5    +      -       -      +
    104N  SER*     3.0    40.6    -      -       -      +
    105N  ARG      3.8     2.9    -      -       -      +
    106N  SER*     4.2    11.4    -      -       -      +
    107N  TYR*     4.2     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 72 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26D  LYS*     3.3    12.5    -      -       -      -
     37D  ARG*     2.8    41.4    +      -       -      +
     39D  SER*     4.2     3.1    +      -       -      -
     41D  GLN*     4.5     1.6    +      -       -      -
    190D  HIS*     4.9     6.8    -      -       -      -
     71N  VAL*     1.3    70.5    -      -       -      +
     73N  PHE*     1.3    91.0    +      -       -      +
     74N  HIS*     3.7    14.9    +      -       -      +
    105N  ARG*     2.8    39.9    +      -       +      +
    107N  TYR*     3.5    17.9    -      -       +      -
    143N  PHE*     6.4     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 73 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    468C  HIS*     6.5     0.4    -      +       -      -
     19D  ARG      4.7     0.2    -      -       -      -
     20D  ASP*     4.3     8.4    +      -       +      +
     21D  ASP*     3.3    45.5    -      -       +      +
     26D  LYS*     4.4    12.9    -      -       -      +
      9K    C      3.7    49.8    +      +       -      -
     54M    G      5.9     0.2    -      +       -      -
     71N  VAL*     3.7     4.6    +      -       -      +
     72N  ASP*     1.3   101.5    +      -       -      +
     74N  HIS*     1.3    62.2    +      -       -      +
     75N  THR*     3.6    23.3    -      -       +      -
    102N  VAL*     3.6    28.5    -      -       +      -
    103N  THR      3.9     4.9    -      -       -      -
    104N  SER*     4.6    12.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 74 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41D  GLN*     3.1    40.8    +      -       +      +
      7K    C      3.0    51.8    +      +       +      -
      9K    C      3.8     6.1    -      -       -      -
     72N  ASP*     3.7    11.2    +      -       -      +
     73N  PHE*     1.3    80.7    -      -       -      +
     75N  THR*     1.3    60.4    +      -       -      +
     76N  ILE*     4.3     2.0    -      -       +      +
    103N  THR*     2.3    65.3    +      -       -      +
    105N  ARG*     3.4    32.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 75 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7K    C      2.8    12.1    +      -       -      -
      8K    G      2.7    63.4    +      -       -      +
      9K    C      3.4    19.2    +      -       +      +
     73N  PHE*     3.6    29.4    -      -       +      -
     74N  HIS*     1.3    74.9    -      -       -      +
     76N  ILE*     1.3    59.8    +      -       -      +
     78N  GLY      5.4     0.2    -      -       -      -
    100N  THR*     4.0     6.5    -      -       +      -
    101N  ILE      3.0    13.5    -      -       -      +
    102N  VAL*     4.2    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 76 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163C  TRP*     3.0    58.8    -      -       +      +
    174D  LEU*     5.6     2.5    -      -       +      -
      7K    C      3.2    29.6    -      -       -      +
      8K    G      3.8     3.8    -      -       -      +
     74N  HIS*     4.3     1.3    -      -       +      -
     75N  THR*     1.3    81.0    -      -       -      +
     77N  GLY*     1.3    62.9    +      -       -      +
     78N  GLY      3.4     1.6    -      -       -      -
     86N  VAL*     3.9    15.6    -      -       +      +
     99N  ALA      4.1     1.7    -      -       -      +
    100N  THR*     3.8     1.2    -      -       -      -
    101N  ILE*     2.9    47.4    +      -       +      +
    103N  THR*     4.0    30.1    -      -       +      +
    105N  ARG*     4.5     0.9    -      -       -      +
----------------------------------------------------------
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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