Contacts of the strand formed by residues 22 - 29 (chain V) 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 ARG 22 (chain V).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10V  GLU*     2.8    34.5    +      -       -      +
     11V  VAL      3.4     7.4    -      -       -      +
     12V  ILE*     3.6    24.0    -      -       +      -
     13V  VAL*     5.8     0.4    -      -       -      -
     20V  GLY      4.2     2.7    -      -       -      +
     21V  LYS*     1.3    76.7    -      -       -      +
     23V  GLY*     1.3    58.5    +      -       -      +
     37V  GLU      4.7     1.6    -      -       -      +
     39V  ILE*     4.0    15.1    -      -       -      +
     73V  PHE*     3.6    33.9    -      -       +      -
     75V  ALA*     5.7     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 23 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10V  GLU*     3.2    12.9    +      -       -      +
     11V  VAL*     2.9    34.4    +      -       -      +
     22V  ARG*     1.3    76.0    -      -       -      +
     24V  LYS*     1.3    61.1    +      -       -      -
     36V  VAL*     4.0    15.4    -      -       -      +
     37V  GLU      4.2     8.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 24 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8V  ASP*     3.8    46.2    +      -       -      +
      9V  ASP      3.5     4.3    -      -       -      +
     10V  GLU*     4.6     4.0    -      -       +      +
     23V  GLY*     1.3    74.1    -      -       -      -
     25V  VAL*     1.3    67.8    +      -       -      +
     26V  LYS*     3.4     2.4    +      -       -      +
     36V  VAL*     4.1     1.9    -      -       -      +
     37V  GLU*     3.1    46.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 25 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5V  ILE*     4.3    11.9    -      -       +      -
      6V  ARG      4.1    13.5    -      -       -      +
      7V  ARG*     4.1     4.9    -      -       -      +
      8V  ASP*     3.1    30.3    +      -       -      +
      9V  ASP      3.1    15.3    +      -       -      +
     11V  VAL*     3.8    33.9    -      -       +      -
     24V  LYS*     1.3    73.8    -      -       -      +
     26V  LYS*     1.3    63.1    +      -       -      +
     27V  ASN*     3.9    21.3    -      -       -      +
     28V  VAL*     4.9     1.6    -      -       +      +
     34V  VAL*     4.5    14.4    -      -       +      -
     35V  ILE      3.9     8.1    -      -       -      +
     36V  VAL*     4.5     8.5    -      -       +      +
     70V  VAL*     6.2     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 26 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7V  ARG*     2.9    36.3    +      -       -      +
     24V  LYS      4.0     8.5    -      -       -      +
     25V  VAL*     1.3    73.1    -      -       -      +
     27V  ASN*     1.3    73.5    +      -       -      +
     35V  ILE*     2.8    22.7    +      -       +      +
     37V  GLU*     3.2    46.4    +      -       +      +
     62V  GLU*     4.1    16.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 27 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A    G      5.3     1.6    -      -       -      +
      7V  ARG*     4.6     8.1    -      -       -      +
     25V  VAL*     3.7     6.6    -      -       -      +
     26V  LYS*     1.3    92.5    +      -       -      +
     28V  VAL*     1.3    66.9    +      -       -      +
     29V  LEU*     3.5    22.0    -      -       -      +
     34V  VAL*     3.6     2.1    -      -       -      +
     35V  ILE*     2.8    46.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 28 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A    G      3.4    54.2    +      -       -      +
     86A    G      5.1     5.7    +      -       -      +
      5V  ILE      5.2     7.0    -      -       -      +
      6V  ARG      5.1     2.0    -      -       -      -
      7V  ARG*     4.7     6.1    -      -       -      +
     25V  VAL*     5.1     2.5    -      -       +      -
     27V  ASN*     1.3    81.4    -      -       -      +
     29V  LEU*     1.3    83.9    +      -       -      +
     30V  SER*     5.3     0.7    -      -       -      -
     32V  GLY*     6.3     0.2    -      -       -      -
     33V  LYS      3.6     5.4    -      -       -      +
     34V  VAL*     4.0    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 29 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A    G      5.9     0.4    -      -       -      -
     27V  ASN*     3.5    18.8    -      -       -      +
     28V  VAL*     1.3    95.1    -      -       -      +
     30V  SER*     1.3    60.8    +      -       -      +
     31V  SER*     2.9    24.3    +      -       -      +
     32V  GLY*     3.2    10.4    +      -       -      -
     33V  LYS*     2.8    20.6    +      -       +      +
     35V  ILE*     4.5    14.1    -      -       +      -
     64V  ALA*     4.4    21.3    -      -       +      -
----------------------------------------------------------
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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