Contacts of the strand formed by residues 25 - 31 (chain W) 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 LYS 25 (chain W).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7W  GLU*     4.3     6.3    +      -       -      -
     20W  LEU*     2.9    38.7    +      -       +      +
     21W  ARG*     3.2    12.5    -      -       -      +
     23W  ALA*     3.7    17.9    -      -       +      +
     24W  ASN*     1.3    78.8    -      -       -      +
     26W  PHE*     1.3    65.8    +      -       -      +
     41W  GLU*     3.6    30.8    +      -       +      +
     42W  LEU      3.2    18.3    +      -       -      +
     43W  ASP*     4.2    25.4    -      -       -      +
     44W  HIS*     4.1     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 26 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20W  LEU*     4.3     6.3    -      -       -      -
     21W  ARG*     4.3     5.8    -      -       +      -
     25W  LYS*     1.3    76.5    -      -       -      +
     27W  PRO*     1.3    84.8    -      -       +      +
     28W  ALA*     4.5     0.2    -      -       +      -
     42W  LEU*     2.9    57.0    +      -       +      -
     44W  HIS*     3.7    37.7    -      +       +      -
     47W  VAL*     3.9    17.9    -      -       +      -
     86W  LEU*     3.7    30.5    -      -       +      +
     87W  GLN      4.1     9.0    -      -       -      +
     88W  HIS*     4.2     1.6    -      -       -      -
     89W  ILE*     3.5    40.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 27 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75B    G      5.2     0.2    -      -       -      +
     76B    G      4.2    13.7    -      -       -      -
      9W  ARG*     3.5    33.4    -      -       -      +
     17W  SER*     4.4    12.1    -      -       -      +
     20W  LEU*     4.5     6.3    -      -       +      -
     21W  ARG*     4.0    27.4    -      -       +      +
     26W  PHE*     1.3   103.8    -      -       +      +
     28W  ALA*     1.3    60.3    +      -       -      +
     40W  ILE      3.4     7.0    -      -       -      +
     41W  GLU*     4.3     2.0    -      -       +      -
     87W  GLN      3.9     6.3    -      -       -      +
     88W  HIS*     3.5    19.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 28 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75B    G      4.6     2.6    +      -       -      -
      9W  ARG*     4.8     1.6    +      -       -      -
     26W  PHE*     3.9     0.8    +      -       +      -
     27W  PRO*     1.3    76.5    -      -       -      +
     29W  ILE*     1.3    64.4    +      -       -      +
     39W  ALA*     3.8     3.5    -      -       -      +
     40W  ILE*     2.9    38.4    +      -       +      +
     42W  LEU*     4.0    26.7    -      -       +      -
     88W  HIS*     4.0     6.3    -      -       -      -
     89W  ILE*     3.3    20.4    -      -       +      +
     91W  PHE*     4.0    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 29 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74B    U      3.8    26.2    -      -       -      +
     75B    G      3.3    40.2    -      -       -      +
     28W  ALA*     1.3    75.3    -      -       -      +
     30W  ILE*     1.3    74.2    +      -       -      +
     31W  TYR*     3.8    18.2    -      -       +      -
     37W  PRO*     4.6     3.4    -      -       +      -
     38W  LEU      3.5    18.6    -      -       -      +
     39W  ALA*     3.7    15.7    -      -       +      +
     88W  HIS*     4.1     3.8    +      -       +      -
     89W  ILE      3.0     5.6    +      -       -      +
     90W  ASP*     3.4    26.9    -      -       -      +
     91W  PHE*     2.9    27.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 30 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29W  ILE*     1.3    81.0    -      -       -      +
     31W  TYR*     1.3    59.2    +      -       -      +
     37W  PRO*     3.4     2.4    -      -       -      +
     38W  LEU*     2.9    43.9    +      -       +      +
     40W  ILE*     3.7    31.6    -      -       +      -
     63W  ILE*     3.6    29.8    -      -       +      -
     65W  VAL*     4.8     0.2    -      -       +      -
     70W  ILE*     3.7    25.8    -      -       +      -
     72W  VAL*     3.7    24.0    -      -       +      -
     91W  PHE*     3.4    10.3    -      -       +      +
     93W  ARG*     3.5    27.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 31 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73B    A      3.8    20.9    -      -       -      +
     74B    U      3.9     9.6    -      -       -      +
    103B    U      2.7    28.9    +      -       -      +
    104B    A      3.2    39.0    -      -       -      -
     29W  ILE*     3.8    16.2    -      -       +      -
     30W  ILE*     1.3    75.8    -      -       -      +
     32W  GLY*     1.3    67.7    +      -       -      +
     37W  PRO*     4.0    20.4    -      -       +      -
     75W  GLN*     3.7    12.6    -      -       +      +
     90W  ASP*     3.3    39.4    +      -       +      -
     91W  PHE      2.9    13.4    +      -       -      -
     92W  VAL*     3.2    12.9    -      -       +      -
     93W  ARG*     2.9    31.8    +      -       -      +
----------------------------------------------------------
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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