Contacts of the strand formed by residues 18 - 25 (chain Q) in PDB entry 4R2G


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 LEU 18 (chain Q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9Q  PRO*     5.1     0.9    -      -       +      -
     12Q  VAL*     4.2    19.1    -      -       +      -
     17Q  THR*     1.3    79.9    -      -       -      +
     19Q  SER*     1.3    66.3    +      -       -      +
     20Q  VAL*     3.5    33.0    -      -       +      +
     80Q  LEU*     4.2     4.7    -      -       +      +
     81Q  GLN*     3.2     4.0    -      -       -      -
     82Q  LEU*     2.9    61.6    +      -       +      +
     86Q  ASP*     4.6     4.9    -      -       +      +
     90Q  TYR*     4.1    25.6    -      -       +      +
    109Q  VAL*     3.5    34.3    -      -       +      -
    111Q  VAL*     6.0     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 19 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200K  VAL*     4.0     7.8    -      -       -      +
    202K  THR*     4.1    17.5    -      -       -      -
      8Q  GLY*     4.3     1.4    -      -       -      -
      9Q  PRO*     3.4    23.6    -      -       -      +
     17Q  THR      3.9     1.4    +      -       -      -
     18Q  LEU*     1.3    77.2    -      -       -      +
     20Q  VAL*     1.3    65.8    +      -       -      +
     21Q  THR*     5.1     3.1    -      -       -      +
     79Q  SER*     4.8     1.4    -      -       -      -
     80Q  LEU      3.4     4.3    -      -       -      -
     81Q  GLN*     3.0    29.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 20 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7Q  SER      3.5     7.2    -      -       -      +
      8Q  GLY*     4.0    11.2    -      -       -      -
      9Q  PRO*     4.2     0.9    -      -       +      -
     18Q  LEU*     3.5    20.8    -      -       +      +
     19Q  SER*     1.3    79.9    -      -       -      +
     21Q  THR*     1.3    64.9    +      -       -      +
     36Q  TRP*     3.6    26.2    -      -       +      -
     79Q  SER*     3.1     3.6    -      -       -      -
     80Q  LEU*     2.7    53.9    +      -       +      +
     90Q  TYR*     4.3     8.1    -      -       +      -
    107Q  THR*     4.3     9.4    -      -       +      -
    109Q  VAL*     3.9    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 21 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200K  VAL*     6.0     1.3    -      -       +      -
      6Q  GLU*     3.1     7.8    -      -       -      +
      7Q  SER*     2.9    47.2    +      -       -      -
      8Q  GLY*     5.4     0.2    -      -       -      -
     19Q  SER*     5.1     4.5    -      -       -      +
     20Q  VAL*     1.3    74.1    -      -       -      +
     22Q  CYS*     1.3    61.8    +      -       -      +
     23Q  ILE*     5.8     2.7    -      -       -      -
     36Q  TRP*     3.6     4.6    -      -       -      -
     77Q  GLN*     3.8    25.4    -      -       -      +
     78Q  LEU      3.1     7.6    -      -       -      +
     79Q  SER*     3.3    27.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 22 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4Q  LEU*     3.9    20.4    -      -       -      -
      5Q  GLN      3.5     7.2    -      -       -      -
      6Q  GLU*     4.0     5.8    -      -       +      -
     21Q  THR*     1.3    77.0    -      -       -      +
     23Q  ILE*     1.3    68.9    +      -       -      +
     24Q  VAL*     4.0     4.4    +      -       -      -
     34Q  TRP*     5.5     0.2    -      -       -      -
     36Q  TRP*     3.9     6.3    -      -       +      -
     77Q  GLN*     3.2     8.1    -      -       -      +
     78Q  LEU*     2.7    42.2    +      -       +      +
     92Q  CYS*     2.0    49.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 23 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3Q  GLN      3.6     3.5    -      -       -      +
      4Q  LEU*     3.6     0.2    -      -       -      -
      5Q  GLN*     2.9    40.6    +      -       +      +
      7Q  SER*     5.7     3.8    -      -       -      +
     21Q  THR*     5.8     2.2    -      -       -      -
     22Q  CYS*     1.3    74.3    -      -       -      +
     24Q  VAL*     1.3    72.1    +      -       -      +
     25Q  SER*     3.9     5.9    +      -       -      +
     75Q  LYS*     4.2    13.2    -      -       +      +
     76Q  ASN*     4.0     4.7    -      -       +      +
     77Q  GLN*     3.8    31.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 24 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2Q  VAL*     4.2    11.2    -      -       +      -
      3Q  GLN      3.2     7.6    -      -       -      +
      4Q  LEU*     4.7     1.3    -      -       +      +
     22Q  CYS*     4.7     3.6    -      -       -      +
     23Q  ILE*     1.3    81.3    -      -       -      +
     25Q  SER*     1.3    65.6    +      -       -      +
     27Q  GLY      3.3    20.9    -      -       -      +
     29Q  ILE*     3.9    15.9    -      -       +      +
     34Q  TRP*     3.7    37.2    -      -       +      -
     76Q  ASN*     2.8    43.0    +      -       -      +
     78Q  LEU*     4.0    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 25 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2Q  VAL*     3.2     7.6    -      -       -      +
      3Q  GLN*     2.9    51.2    +      -       -      +
      4Q  LEU      5.5     0.5    -      -       -      -
      5Q  GLN*     6.0     0.5    -      -       -      +
     23Q  ILE*     3.9     8.2    +      -       -      +
     24Q  VAL*     1.3    78.6    +      -       -      +
     26Q  GLY*     1.3    60.7    +      -       -      +
     27Q  GLY      3.3     4.4    +      -       -      -
----------------------------------------------------------
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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