Contacts of the strand formed by residues 65 - 72 (chain X) 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 GLY 65 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30X  SER*     3.3     1.0    -      -       -      -
     31X  VAL*     2.9    40.0    +      -       -      +
     63X  ALA      3.8     1.6    +      -       -      -
     64X  ASP*     1.3    75.5    -      -       -      +
     66X  LYS*     1.3    62.1    +      -       -      -
     82X  ILE*     4.0     6.2    -      -       -      +
     83X  GLU      3.1    10.3    -      -       -      -
     85X  GLU*     3.2    25.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 66 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28X  GLY*     4.3    13.6    +      -       -      +
     29X  GLU      3.1     7.6    -      -       -      +
     30X  SER*     3.7    20.4    -      -       -      +
     65X  GLY*     1.3    73.1    -      -       -      -
     67X  VAL*     1.3    65.6    +      -       -      +
     68X  LYS      3.7     0.2    +      -       -      -
     82X  ILE*     3.5     4.5    -      -       -      +
     83X  GLU*     2.9    48.0    +      -       +      +
     85X  GLU*     3.9    28.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 67 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25X  ARG*     4.6     6.7    -      -       +      +
     26X  PHE      3.6    17.0    -      -       -      +
     27X  GLY*     3.8     2.6    -      -       -      -
     28X  GLY*     3.3    19.8    +      -       -      -
     29X  GLU*     3.0    14.7    +      -       +      +
     31X  VAL*     4.1    23.8    -      -       +      -
     37X  ILE*     4.3    13.0    -      -       +      -
     66X  LYS*     1.3    74.8    -      -       -      +
     68X  LYS*     1.3    65.2    +      -       -      +
     69X  PHE*     3.9    28.7    -      -       +      -
     80X  ILE*     4.3    17.7    -      -       +      -
     81X  SER      4.4     0.4    -      -       -      +
     82X  ILE*     3.6    17.5    -      -       +      -
     83X  GLU*     5.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 68 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27X  GLY*     5.4     0.2    -      -       -      -
     67X  VAL*     1.3    78.1    -      -       -      +
     69X  PHE*     1.3    76.8    +      -       -      +
     70X  GLU*     3.4    27.7    +      -       -      +
     79X  PHE      3.6     0.3    -      -       -      +
     80X  ILE*     3.4     5.2    -      -       -      +
     81X  SER*     2.9    48.8    +      -       -      +
     83X  GLU*     3.3    35.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 69 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    856A    G      3.3    33.5    +      -       -      +
    857A    G      3.6    43.5    -      -       -      +
     23X  VAL*     4.1    13.0    -      -       +      -
     25X  ARG      4.0    15.3    -      -       -      -
     26X  PHE*     3.8     4.3    -      -       -      -
     27X  GLY*     3.4    21.5    -      -       -      -
     45X  PHE*     3.9    15.7    -      +       -      -
     67X  VAL*     3.9    10.3    -      -       +      -
     68X  LYS*     1.3    91.2    +      -       -      +
     70X  GLU*     1.3    64.4    +      -       -      +
     78X  LYS*     6.1     0.9    -      -       +      -
     79X  PHE      3.6     2.7    -      -       -      -
     80X  ILE*     3.5    34.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 70 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48X  GLY*     5.3     1.2    -      -       -      -
     68X  LYS*     3.4    25.9    +      -       -      +
     69X  PHE*     1.3    75.9    -      -       -      +
     71X  VAL*     1.3    62.5    +      -       -      +
     72X  LYS*     3.7    33.6    -      -       +      +
     78X  LYS*     3.4     7.2    -      -       -      +
     79X  PHE*     2.8    48.6    +      -       +      +
     81X  SER*     3.4    28.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 71 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B    C      3.9    21.6    +      -       -      +
     70X  GLU*     1.3    75.8    -      -       -      +
     72X  LYS*     1.3    67.2    +      -       -      +
     73X  GLY      5.7     0.2    -      -       -      +
     76X  ASN*     3.7    35.9    -      -       +      +
     77X  ARG      3.3     7.2    -      -       -      +
     78X  LYS*     4.2    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 72 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B    C      2.8    42.4    +      -       -      +
     12B    C      4.7     5.2    +      -       -      -
     70X  GLU*     3.7    34.9    -      -       +      +
     71X  VAL*     1.3    80.6    +      -       -      +
     73X  GLY*     1.3    65.5    +      -       -      +
     76X  ASN*     3.5     1.5    -      -       -      -
     77X  ARG*     3.0    35.6    +      -       -      +
     79X  PHE*     4.1    24.9    -      -       +      -
----------------------------------------------------------
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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