Contacts of the strand formed by residues 68 - 75 (chain Q) in PDB entry 5GAG


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 GLU 68 (chain Q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9L  ASN*     5.6     1.4    +      -       -      +
     64L  ARG*     3.2    38.6    +      -       -      +
     79L  PHE*     3.6     7.8    -      -       -      +
     80L  ASP*     5.2     1.6    -      -       +      -
     81L  GLY*     3.0    39.4    +      -       -      +
    101L  GLY*     5.5     0.4    -      -       -      -
    102L  PRO*     3.9    15.2    -      -       +      +
     64Q  ILE*     4.1     3.3    -      -       -      +
     65Q  SER      2.9    36.3    +      -       -      +
     66Q  ASN      3.0     5.1    +      -       -      +
     67Q  GLY*     1.3    80.3    -      -       -      +
     69Q  GLY*     1.3    76.6    +      -       -      +
     70Q  VAL*     3.5     4.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 69 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79L  PHE*     3.4     7.6    -      -       -      -
     80L  ASP*     3.2    47.9    +      -       -      +
     62Q  ARG*     4.6     2.5    -      -       -      -
     63Q  LYS      3.7     5.8    -      -       -      -
     64Q  ILE*     3.8    14.0    -      -       -      +
     67Q  GLY      4.2     1.0    +      -       -      -
     68Q  GLU*     1.3    78.1    -      -       -      +
     70Q  VAL*     1.3    64.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 70 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77L  ILE*     4.6     3.4    -      -       +      -
     78L  ARG      3.7     2.2    -      -       -      -
     79L  PHE*     3.7    27.6    -      -       +      -
    102L  PRO*     3.9    18.6    -      -       +      -
    123L  LEU*     4.2     9.0    -      -       +      -
     43Q  PHE*     3.6    29.4    -      -       +      -
     61Q  VAL      3.9     0.3    -      -       -      +
     62Q  ARG*     3.3     4.0    -      -       -      +
     63Q  LYS*     2.9    47.0    +      -       +      +
     65Q  SER*     4.5     8.1    -      -       -      +
     68Q  GLU*     3.8     9.9    -      -       -      +
     69Q  GLY*     1.3    79.7    -      -       -      +
     71Q  GLU*     1.3    68.5    +      -       -      +
     72Q  ARG      4.0     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 71 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76L  VAL      3.9     0.4    -      -       -      +
     77L  ILE*     3.6     4.5    -      -       -      +
     78L  ARG*     3.0    75.4    +      -       +      +
     80L  ASP*     4.5     5.7    -      -       -      +
     48Q  ILE*     4.2     7.5    -      -       +      +
     60Q  THR*     4.3     9.0    -      -       +      +
     61Q  VAL      3.3     7.6    -      -       -      +
     62Q  ARG*     3.7    26.2    +      -       +      +
     69Q  GLY      4.2     0.2    -      -       -      -
     70Q  VAL*     1.3    75.0    -      -       -      +
     72Q  ARG*     1.3    61.9    +      -       -      +
     73Q  VAL*     4.2     1.3    -      -       +      +
    101Q  ARG*     2.7    48.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 72 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71L  ARG*     4.1    29.1    -      -       -      +
     75L  SER*     4.6     8.7    +      -       -      -
     76L  VAL      3.3    13.9    -      -       -      +
     77L  ILE*     3.6    30.3    -      -       +      +
    123L  LEU*     4.0    15.9    +      -       -      +
     30Q  VAL*     4.4    22.4    -      -       -      +
     32Q  VAL*     5.4     2.6    -      -       -      +
     41Q  GLN*     4.5    12.1    -      -       -      +
     43Q  PHE*     3.7    33.1    -      -       +      +
     59Q  PHE      3.9     0.2    -      -       -      +
     60Q  THR*     4.6     0.7    -      -       -      -
     61Q  VAL*     2.9    32.6    +      -       -      +
     70Q  VAL*     4.0     1.5    +      -       +      -
     71Q  GLU*     1.3    75.6    -      -       -      +
     73Q  VAL*     1.3    64.7    +      -       -      +
     74Q  PHE*     3.2    43.6    +      -       +      -
     80Q  VAL*     5.3     4.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 73 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2684A    U      4.2    25.4    -      -       -      +
   2685A    G      3.9     8.7    -      -       -      +
     74L  GLY      5.7     1.1    -      -       -      +
     75L  SER*     3.4    10.2    +      -       -      -
     76L  VAL*     2.8    46.6    +      -       +      +
     78L  ARG*     3.8    24.0    -      -       +      +
     58Q  ALA*     4.7     3.6    -      -       +      -
     59Q  PHE      3.6    10.8    -      -       -      +
     60Q  THR*     3.4    22.4    -      -       +      +
     71Q  GLU*     5.7     1.3    -      -       +      -
     72Q  ARG*     1.3    76.3    -      -       -      +
     74Q  PHE*     1.3    70.8    +      -       -      +
     75Q  GLN*     5.5     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 74 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75L  SER*     4.0     7.4    -      -       -      -
     28Q  VAL*     4.2    14.8    -      -       +      -
     30Q  VAL*     4.1    11.9    -      -       +      -
     43Q  PHE*     3.6    36.3    -      +       +      -
     58Q  ALA*     3.4     5.5    -      -       -      +
     59Q  PHE*     2.9    69.2    +      +       +      -
     61Q  VAL*     4.2     4.5    -      -       +      -
     72Q  ARG*     3.2    58.8    -      -       -      -
     73Q  VAL*     1.3    79.5    -      -       -      +
     75Q  GLN*     1.3    64.8    +      -       -      +
     76Q  THR      3.7     0.3    +      -       -      -
     80Q  VAL*     6.2     0.9    -      -       +      -
     81Q  VAL*     4.0    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 75 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2683A    C      3.0    31.6    +      -       -      -
   2684A    U      4.0     2.3    +      -       -      -
     13D  ARG*     3.1    30.8    +      -       -      +
     15D  PHE*     4.6     6.3    -      -       +      -
     73L  ASP*     3.5    25.3    +      -       -      +
     74L  GLY*     3.7    13.3    -      -       -      +
     75L  SER*     4.0     5.2    +      -       -      +
     56Q  HIS      4.3     0.8    +      -       -      -
     57Q  SER      4.1     3.8    +      -       -      +
     58Q  ALA*     3.5    23.2    -      -       -      +
     73Q  VAL*     5.5     1.9    -      -       +      +
     74Q  PHE*     1.3    73.2    +      -       -      +
     76Q  THR*     1.3    68.1    +      -       -      +
     77Q  HIS      3.5     0.9    -      -       -      -
     78Q  SER*     3.2    29.3    -      -       -      +
     81Q  VAL*     3.9    12.1    -      -       -      +
----------------------------------------------------------
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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